This article reviews the different technical aspects and pitfalls of gadolinium (Gd)-ethoxibenzyl (EOB)-diethylenetriamine pentaacetic acid (DTPA) and the advantages of the hepatocellular phase (HCP) and defines its specific imaging features of liver lesions.Gd-EOB-DTPA is a contrast agent with combined properties of a conventional non-specific extracellular and a hepatocyte-specific contrast agent. Benign cirrhosis-associated nodules are characterised by isointensity in dynamic imaging and the HCP. Hepatocellular carcinomas (HCCs) usually show hyperenhancement in the arterial phase, with washout in the portal vein pressure (PVP) and hypointensity in the HCP. Among other characteristic findings, we have the mosaic pattern, a capsule, the “nodule-in-nodule” appearance and the satellite nodules. The fibrolamellar HCC is a large enhancing heterogeneous lesion, on a non-cirrhotic liver, with a hypointense scar in every sequence. THIDs (transient hepatic intensity differences) are perfusional alterations, characterised by hyperintensity in the arterial phase, with no alterations in the rest of the sequences including the HCP. Adenoma and focal nodular hyperplasia (FNH) are lesions, occurring more frequently in young women, with brisk arterial enhancement, differentiated by the scar and the uptake of Gd-EOB-DTPA in the HCP. Focal eosinophilic infiltration is a difficult diagnosis, with characteristics such as a non-spherical shape and irregular borders suggesting it. Besides these lesions, in which Gd-EOB-DTPA has a clear advantage, there are a few where the specificities of this agent can be troublesome: haemangiomas, focal fat/sparing, foreign body reaction, cholangiocarcinoma and metastases.Gd-EOB-DTPA is comparable to extracellular agents, and uptake by functioning hepatocytes in the delayed phase provides additional information that further improves detection and characterisation of many hepatic lesions.Gd-EOB-DTPA offers advantages for the imaging of many liver lesions including HCC, fibrolamellar HCC, FNH and adenoma.The properties of Gd-EOB-DTPA can pose problems when dealing with haemangiomas, cholangiocarcinoma and metastases among others.The uptake of Gd-EOB-DTPA by functioning hepatocytes in the delayed phase provides additional information that further improves detection and characterisation of many hepatic lesions. Hepatocyte-specific magnetic resonance (MR) imaging contrast agents were developed for detection and characterisation of focal liver lesions. Currently, there are two hepatocyte-specific agents available: gadolinium (Gd)-ethoxibenzyl (EOB)-diethylenetriamine pentaacetic acid (DTPA) and gadobenate dimeglumine (Gd-BOPTA). Gd-EOB-DTPA has greater hepatocellular uptake and biliary excretion than Gd-BOTPA and is the focus of this review.Gd-EOB-DTPA—known generically as gadoxetic acid and commercially as Eovist (United States) or Primovist (most parts of the World) —is a highly water-soluble contrast agent in which a lipophilic EOB group is attached to gadolinium (Gd)-DTPA Fig. . The resGd-EOB-DTPA has been shown to be comparable to non-specific extracellular agents for lesion detection and characterisation in the vascular imaging phases. Moreover, uptake by functioning hepatocytes in the delayed phase provides additional information that further improves detection and characterisation of many hepatic lesions, reported in recent articles , 8. The Arterial phase enhancement of vessels and lesions with Gd-EOB-DTPA tends to be less intense than with extracellular agents due to the following factors. Gd-EOB-DTPA is administered in a smaller dose than extracellular agents (0.025 mmol/kg), providing a shorter temporal window to acquire images during peak arterial enhancement. Additionally, there is a higher frequency of imaging artefacts in the arterial phase when compared with extracellular agents. The cause of these artefacts is not well understood. These “truncation” artefacts may occur due to abrupt concentration changes during high spatial k-space filling, and may alter the intensity, shape and anatomical detail of the structures.Hepatocellular uptake begins almost immediately, leading to rapidly progressive liver enhancement. Consequently, there is no pure venous or equilibrium phase. Because the liver enhances sooner and more intensely than with extracellular agents, the intensity of the lesions relative to the liver may appear different. For example, blood vessels and blood-pool lesions, such as haemangiomas, which remain hyperintense in comparison to the liver during all vascular phases with extracellular agents, appear to “wash out” with Gd-EOB-DTPA and, after 5-10 min, become hypointense.The degree of hepatocellular enhancement depends on liver function, which roughly correlates with serum bilirubin levels, which is not a perfect predictor. In livers with good hepatic function, intense enhancement occurs. In livers without good function, due to cholestasis or hepatocellular dysfunction, enhancement of liver parenchyma may be weak. In such cases, blood vessels and blood pool lesions become isointense rather than hypointense in comparison to the liver.The vascular imaging phases using Gd-EOB-DTPA are similar to those using extracellular agents with a few caveats:Regenerative and dysplastic nodulesOverview: Cirrhosis is pathologically defined by extensive fibrosis, nodular regeneration and architectural distortion of the parenchyma. The vast majority of cirrhosis-related nodules exhibit regenerative changes without cellular atypia and are known as regenerative nodules (RNs). A minority have dysplastic features and are known as dysplastic nodules (DNs). The differentiation between RN and DN is unreliable when attempted non-invasively, difficult with histopathology, and is of minor, if any, clinical relevance. For these reasons, these two entities are discussed together as benign cirrhosis-associated nodules.Unenhanced MRI features: Typically, benign cirrhosis-associated nodules are <2 cm and isointense to hyperintense on T1-weighted images, isointense to hypointense on T2-weighted images and isointense on diffusion-weighted (DW) images. Lipid-containing nodules or steatotic nodules display signal loss on out-of-phase gradient echo (GRE) images in comparison with in-phase images. Iron-containing nodules or siderotic nodules appear markedly hypointense on T2-weighted and T2*-weighted images  ). In some 2.5-8.5%), uptake of the contrast agent can paradoxically occur  shunt, atypical haemangioma and hepatic adenoma are possible diagnosis. The usual occurrence in a cirrhotic liver, in addition to the dynamic and hepatocelullar phase imaging, usually permit the differential diagnosis.Some HCCs will uptake Gd-EOB-DTPA in the hepatobiliary phase. These can usually be differentiated from RN, DN and FNH-like lesions because of their heterogeneity or mosaic pattern, the nodule-in-nodule appearance, the presence of a hypoenhancing rim (capsule) or the absence of a scar.Infiltrative HCC may manifest as subtle heterogeneity and mild ill-defined hypointensity in the HCP. This may mimic background cirrhotic parenchyma and escape detection.Fibrolamellar HCC is an uncommon type of HCC affecting young adults.It is usually seen as a large, well-circumscribed focal lesion with low signal intensity on T1-weighted MR images and high signal intensity on T2-weighted images. A central radiating scar is seen in 80% of cases and has low signal intensity on T1- and T2-weighted images. Areas of liquefactive necrosis may occur centrally and appear markedly hyperintense on T2-weighted images.There is usually early heterogeneous contrast enhancement, which fades on subsequent images. The scar has minimal or no enhancement on contrast-enhanced images, being usually hypointense relative to the remainder of the tumour Fig. .Fig. 9FiIn hepatocellular phase some viable areas of the tumour may show some uptake of Gd-EOB-DTPA. The scar remains hypointense .Hypointensity of the scar on T2-weighted images and the hypointensity in the HCP distinguish fibrolamellar HCC from a FNH. It can be distinguished from HCC due to the presence of a scar, calcifications, larger size and occurrence in younger patients with no cirrhosis.The absence of a scar and the uptake of Gd-EOB-DTPA in the HCP may be confounders.These perfusional alterations are phenomenon characterised by a patchy wedge-shaped area of enhancement involving a hepatic subsegment or by an arterial enhancing focal lesion that fades in the venous phase.Generally, there are no alterations in morphology or signal intensity.This finding is seen immediately after contrast material administration, with fading on subsequent images. They are thought to represent an imbalance between the hepatic arterial and portal venous supply, caused by increased hepatic arterial blood flow in the presence of portal vein obstruction Figs.  and 11. No alterations in the hepatobiliary phase, due to intact hepatocyte function of these lesions, make it possible to differentiate from small HCCs , 23.Small HCCs and hypervascular metastases are possible diagnosis. Usually the absence of a defect in the HCP makes the diagnosis of THID.Rarely, vascular alterations are associated with dysfunction of the hepatocytes, which reveal a defect in the HCP, complicating the diagnosis.FNH is the second most common benign tumour of the liver, after hepatic haemangiomas. FNH typically occurs as a solitary lesion in young female patients. It consists of aggregates of hepatocytes and is thought to be secondary to a proliferative response of hepatocytes, secondary to an underlying vascular malformation. Biliary structures proliferate without connection to the adjacent biliary tree. Kupffer cells are present, often in greater amounts than in the surrounding normal liver parenchyma. The central scar in FNH is not a true scar, but represents a congeries of blood vessels, bile ducts and sometimes a focal area of cirrhosis. About 20% of FNH cases are classified as non-classic. These non-classic FNH subtypes lack the findings of nodular architecture or malformed vessels but always have bile duct proliferation.The lesion varies from mildly hypointense to isointense on T1-weighted MR images and from mildly hyperintense to isointense on T2-weighted images. The “central scar” is characteristically hyperintense on T2-weighted images. The hyperintensity of the lesion on T2-weighted images may be related to the presence of vascular channels or oedema throughout the lesion.FNH is perfused by the hepatic arterial system and shows marked, nearly uniform arterial-phase enhancement. The degree of lesion enhancement lessens on subsequent contrast-enhanced images, with lesion signal intensity approaching that of the surrounding liver parenchyma. The central scar has low signal intensity on early phase contrast-enhanced images but gradually enhances to become hyperintense relative to the rest of the lesion on delayed phase images , 25. TheWith hepatobiliary-specific agents, it shows homogenous or heterogeneous enhancement in the hepatocellular phase, as it lacks a well-formed bile canalicular system for normal excretion. It becomes isointense to hyperintense to the normal liver, allowing the differential diagnosis , 26. MorAdenoma and fibrolamellar HCC. The isointensity to hyperintensity in the HCP and the imaging features of the central scar of FNH are usually helpful in the differential diagnosis. The adenoma does not present a central scar and is hypointense in the HCP. The F-HCC is usually larger, more heterogeneous and its scar is hypointense in every sequence.Also, the non-classic forms often present a diagnostic challenge in imaging: e.g. telangiectatic FNH has been shown to demonstrate atypical imaging features, including lack of a central scar, high signal intensity on T1- and T2-weighted images and persistent enhancement on delayed phase images .About 12% of FNH can show atypical imaging features on Gd-EOB-DTPA enhanced MRI, such as the absence of a scar or an eccentric one, or washout in the venous phase.Hepatic adenomas are rare benign tumours of the liver. On histopathological analysis, hepatic adenomas contain well-differentiated hepatocytes lacking bile ducts or portal tracts. The majority of adenomas are solitary (80%) and typically occur in female patients (90%). Predisposing factors to adenoma formation include oral contraceptive use in female patients, anabolic steroid use in male patients and glycogen storage disease .They are generally well circumscribed, without contour lobulation and have variable degrees of haemorrhage, necrosis, fat and, rarely, calcification. At MR imaging, adenomas are typically hyperintense to isointense on T1-weighted images and slightly hyperintense on T2-weighted images.After administration of contrast material, adenomas typically demonstrate moderate enhancement on arterial phase images; they may show washout and enhancement similar to that of surrounding liver parenchyma on portal venous and delayed phase images .Usually no enhancement of hepatic adenoma is seen in the hepatocellular phase because of absent or strongly reduced hepatocellular uptake of Gd-EOB-DTPA Fig. . HoweverFNH and HCC.The age and gender of the patient, occurring in a non-cirrhotic liver (as opposed to HCC), the absence of a scar or the enhancement pattern, usually helps in the diagnosis, since FNH is isointense to hyperintense in the HCP, while the adenoma is typically hypointense.The adenoma may show faint enhancement in the HCP, which is a confounder, but the other imaging characteristics usually permit the diagnosis.FEI of the liver is a focal hepatic lesion caused by eosinophil-related tissue damage. It is associated with various eosinophilia-related conditions such as parasitic infections, allergic reactions, hypereosinophilic syndrome and tumours.They have an indistinct margin and a non-spherical shape , 30. On The dynamic imaging is characterised by poor enhancement on the arterial phase with homogeneous enhancement on portal venous phase images.They show mixed hypointensity, irregular margins and non-spherical shapes in hepatocellular phase Fig. .Fig. 14FMetastases and abscesses. The non-spherical shape and irregular margins favour FEI.The differential diagnosis from metastases in a patient with known primary malignancy is still challenging.Focal fibrosis occurs in the process of hepatic parenchyma collapse and its replacement with focal fibrotic masses, in the context of cirrhosis. It is usually located in the anterior and medial segments of the liver and has a wedge-shaped appearance. In some patients the entire segment is involved.Fibrosis can appear as an area of low signal intensity on T1-weighted MR images and high signal intensity on T2-weighted images. It shows a typical geographic pattern of involvement, associated to retraction of the liver capsule.It usually demonstrates delayed enhancement on contrast-enhanced images.It shows low signal intensity due to decreased hepatic function from fibrosis Fig. .Fig. 15CInfiltrative HCC and cholangiocarcinoma. Confluent fibrosis can be differentiated from infiltrative tumours on the basis of typical geographic appearance, location, no adjacent vascular invasion and no surrounding ductal dilatation.Contrary to delayed enhancement of fibrosis on gadolinium-enhanced MRI, confluent hepatic fibrosis demonstrates hypointense areas due to decreased or absent hepatocellular uptake of Gd-EOB-DTPA.Cavernous haemangiomas represent the most common primary liver tumour and consist of multiple large, blood-filled vascular channels. Typically, haemangiomas are solitary, although multiplicity is not uncommon. Although they are typically small, giant cavernous haemangiomas may range in size (greater than 20 cm). Haemangiomas are associated with several clinical syndromes including Klippel-Trenaunay-Weber syndrome, Osler-Rendu-Weber disease, and von Hippel–Lindau disease.On MR imaging, hepatic haemangiomas typically demonstrate low signal intensity on T1-weighted images and marked high signal intensity on T2-weighted images.On enhanced MRI, there is a typical peripheral nodular enhancement with centripetal progression, resulting in diffuse high signal intensity on delayed phase images. Less commonly, flash filling of an entire small haemangioma or enhancement of small portions of the lesion, on arterial phase images, may be seen. Larger lesions may not demonstrate uniform enhancement on delayed phase images, probably due to areas of thrombosis or insufficient delay time. Central scars may be seen in hepatic haemangiomas.With this contrast, the enhancement of a haemangioma tends to follow the blood vessels. Hepatic haemangiomas will “pseudo washout” to become darker than the liver because of rapid uptake of the contrast agent by the surrounding normal liver during equilibrium phase Fig. . HoweverSmall haemangioma may mimic hypervascular metastasis. In these cases, the bright signal of haemangiomas in heavily T2-weighted sequences is helpful. Furthermore, in the dynamic phases, the intralesional degree of enhancement is similar to that of the adjacent vessels, pointing to a lesion filling with less enhanced blood due to the uptake of the hepatocytes.In patients with prolonged intravascular dwell time due to hepatic or renal insufficiency, haemangiomas may appear isointense to the liver in the hepatocellular phase rather than hypointense. The key is parallelism to the blood pool.Focal fatty deposition and focal fatty sparing may manifest as a “pseudolesion”. Clues to this diagnosis are its more common occurrence in the following areas of the liver: the medial aspect of the left lobe, along the falciform ligament, round the gallbladder fossa and within the central aspect of segment IV, adjacent to the porta hepatis. In addition, focal fatty infiltration is not seen to exert mass effect and vessels are seen to pass through these areas unimpeded.MR imaging provides a useful method for characterising suspected geographic fatty infiltration by using in-phase and opposed-phase gradient-echo T1-weighted sequences. The relative increase in intravoxel fat in areas of focal fatty infiltration demonstrates decreased signal intensity on the opposed-phase images in comparison to the in-phase images. On MR imaging, areas of fatty sparing may be identified due to the lack of decrease in signal intensity on opposed-phase gradient-echo T1-weighted images and appear hyperintense relative to surrounding steatosis. Focal fat often appears dark on opposed-phase images, while focal sparing often appears bright .Focal fat deposition and fat sparing areas show similar degree of enhancement to surrounding hepatic parenchyma.Areas of focal fat sparing area can be shown as mildly increased signal intensity on the hepatobiliary phase because the signal intensity of the focal fat sparing area is already higher on the unenhanced fat saturated sequence Fig. .Fig. 17FFocal hepatic lesion and lipoma. The typical locations and the T2 findings usually permit the diagnosis, since these pseudo-lesions are invisible on that sequence.Areas of focal fat sparing are enhanced because they have functional hepatocytes and these can appear as real focal lesions in the dynamic phases. However, the other imaging findings described permit the diagnosis.Cholangiocarcinoma is the most common biliary tumour and the second most common primary malignant hepatic tumour in adults. Risk factors for the development of cholangiocarcinoma include primary sclerosing cholangitis (PSC), familial polyposis, choledochal cyst, biliary papillomatosis and clonorchiasis.Intrahepatic cholangiocarcinoma may be mass forming or peribiliar infiltrative. They are usually hypointense on T1-weighted MR images and hyperintense on T2-weighted images. Associated findings may include adjacent biliary ductal dilatation, capsular retraction, satellite nodules, vascular encasement and hepatolithiasis –34.On contrast-enhanced images, it demonstrates initial peripheral enhancement with concentric internal filling on delayed-phase images.Usually no enhancement is seen in the hepatocellular phase due to lack of hepatocytes Fig. .Fig. 18CHCC and cholangitis. The delayed enhancement and the typical hilar location point to cholangiocarcinoma.Delayed enhancement of cholangiocarcinoma is one of the characteristic findings when using extracellular agents, due to its abundant fibrosis. However, the tumour shows low signal intensity on delayed and hepatobiliary phases of Gd-EOB-DTPA, due to strong enhancement of the surrounding liver parenchyma.Islet cell tumours, breast cancer, melanoma, thyroid cancer and carcinoid tumour are among the most common primary tumours that lead to hypervascular hepatic metastases.These metastatic lesions usually demonstrate low signal intensity on T1-weighted MR images and are iso to hyperintense on T2-weighted images.Hypervascular metastases are best seen during the arterial phase of enhancement. Small hypervascular metastases usually present with homogeneous enhancement, whereas larger lesions appear heterogeneous or show an enhancing peripheral rim surrounding the necrosis. Frequently, centripetal contrast enhancement is observed, as well as irregular or peripheral washout. Hypervascular metastatic lesions may show a target appearance on delayed phase, with the rim appearing hypointense relative to the centre. This centripetal progression of enhancement, with simultaneous peripheral washout, is specific for malignancy.Generally no enhancement is seen in the hepatocellular phase.HCC, THID, adenoma and FNH. The presence of multiple lesions in a non-cirrhotic liver, in a patient with a known malignancy and a defect on the HCP point to metastases.In the centre of metastatic lesions, there may be pooling of Gd-EOB-DTPA in the extracellular matrix of the lesion, giving the misguiding appearance of uptake in the hepatobiliary phase Fig. .Fig. 19MColon, lung, prostate, gastric and transitional cell carcinomas are the most common primary tumours with hypovascular metastases to the liver.These metastatic lesions usually demonstrate low signal intensity on T1-weighted MR images and are iso to hyperintense on T2-weighted images.The ring-like enhancement surrounding liver metastases is typically seen during the hepatic arterial phase. In the portal and delayed phase, the metastases often show washout in the outer parts and a progressive enhancement toward the centre of the lesions Fig. .Fig. 20MNo enhancement is seen in the hepatocellular phase.HCC, cholangiocarcinoma and focal eosinophilic infiltration. Multiple lesions, a known primary malignant tumour and a non-cirrhotic liver, point to the diagnosis. The pattern of enhancement and the spherical shape are other helpful findings.As mentioned earlier, with Gd-EOB-DTPA, the differential diagnosis can be difficult.Various foreign bodies introduced into the human organism during surgery or trauma, as well as exposure to some chemical substances, may cause a granulomatous reaction.Imaging features are usually hypointensity in T1-weighted images and hyperintensity in T2-weighted images, with possible hypointense bands within the cystic cavity.It shows peripheral enhancement of the mass on arterial or portal venous phase.No enhancement is seen in the hepatocellular phase Fig. .Fig. 21FMetastatic disease. It could be considered in patients with a perihepatic lesion with previous history of trauma or surgery.A foreign body can gradually move from a subcapsular to an intraparenchymal position.Focal hepatic lesions that show similar behaviour with ECF contrast agent and Gd-EOB-DTPA include hepatic cysts Fig. , biliaryThe following lesions were never studied with Gd-EOB-DTPA-enhanced MRI: hematoma, peliosis, paranglioma and angiosarcoma.For a summary, see Tables


In 2005 the American Thoracic Society and Infectious Diseases Society of America (ATS/IDSA) published guidelines for managing hospital-acquired pneumonia (HAP), ventilator-associated pneumonia (VAP), and healthcare-associated pneumonia (HCAP). Although recommendations were evidence based, collective guidelines had not been validated in clinical practice and did not provide specific tools for local implementation. We initiated a performance improvement project designated Improving Medicine Through Pathway Assessment of Critical Therapy in Hospital-Acquired Pneumonia (IMPACT-HAP) at four academic centers in the United States. Our objectives were to develop and implement the project, and to assess compliance with quality indicators in adults admitted to intensive care units (ICUs) with HAP, VAP, or HCAP.The project was conducted in three phases over 18 consecutive months beginning 1 February 2006: 1) a three-month planning period for literature review to create the consensus pathway for managing nosocomial pneumonia in these ICUs, a data collection form, quality performance indicators, and internet-based repository; 2) a six-month implementation period for customizing ATS/IDSA guidelines into center-specific guidelines via educational forums; and 3) a nine-month post-implementation period for continuing education and data collection. Data from the first two phases were combined (pre-implementation period) and compared with data from the post-implementation period.P = 0.06). Similarly, empiric antibiotics were more likely to be compliant with ATS/IDSA guidelines during post-implementation (79/257 (30.7%) vs 66/151 (43.7%); P = 0.01), an effect that was sustained over quarterly intervals (P = 0.0008). Between-period differences in compliance with obtaining cultures and use of de-escalation were not statistically significant.We developed a consensus pathway based on ATS/IDSA guidelines and customized it at the local level to accommodate formulary and microbiologic considerations. We implemented multimodal educational activities to teach ICU staff about the guidelines and continued education throughout post-implementation. We registered 432 patients . Diagnostic criteria for nosocomial pneumonia were more likely to be met during post-implementation (247/257 (96.1%) vs 150/151 (99.3%); Developing a multi-center performance improvement project to operationalize ATS/IDSA guidelines for HAP, VAP, and HCAP is feasible with local consensus pathway directives for implementation and with quality indicators for monitoring compliance with guidelines. The American Thoracic Society and Infectious Diseases Society of America (ATS/IDSA) published guidelines for the management of hospital-acquired pneumonia (HAP), ventilator-associated pneumonia (VAP), and healthcare-associated pneumonia (HCAP) in 2005 . The guiThe goal of the ATS/IDSA guidelines is to provide an organizational framework for initial evaluation and management of adults with bacterial HAP, VAP, or HCAP; however, the authors acknowledged that the guidelines had several limitations . For exaInspired by the ATS/IDSA guidelines  and the We conducted a multicenter performance improvement project at four academic tertiary care centers in the United States. Participating centers were The Ohio State University Medical Center, Columbus, Ohio; Henry Ford Health System, Detroit, Michigan; University of Miami Miller School of Medicine/Jackson Memorial Hospital, Miami, Florida; and University of Louisville, Louisville, Kentucky. The project was conducted in selected adult medical ICUs at two centers  on the basis of local staffing to conduct the project; and in all adult ICUs at two centers . The project was approved by the institutional review board at each participating center; each waived the need for informed consent.We conducted a prospective performance improvement project in three phases over 18 consecutive months from 1 February 2006 through 31 July 2007. The first phase was a three-month pre-implementation period. Representatives from each center planned the project. The IMPACT-HAP investigators evaluated the ATS/IDSA guidelines [The second phase was a six-month implementation period. Principal investigators at each center formed multidisciplinary teams to customize ATS/IDSA guidelines and create a local consensus pathway based on their respective order sets, hospital formulary, and local epidemiology (unit-specific antibiograms), including consideration of center-specific resistance patterns. Educational efforts were initiated during implementation. The third phase was a nine-month post-implementation period with continued education and data collection.Adults in participating ICUs were eligible for inclusion in the database if they met ATS/IDSA definitions for HAP, VAP, or HCAP , includiComorbid conditions were prospectively defined and extracted from patient records. Respiratory disease was defined as a history of chronic obstructive pulmonary disease. Renal disease was defined as a history of chronic renal disease, or abnormal blood urea nitrogen and creatinine. Cardiac disease was defined as systolic or diastolic ventricular dysfunction by history, physical examination, chest radiogram, or echocardiogram. Immunosuppression was defined as active malignancy; AIDS; end-stage renal, liver, or lung disease; steroids (prednisone ≥10 mg for >7 days); or active chemotherapy or radiotherapy within 30 days. Severe sepsis was determined by calculation of the sepsis criteria and organ dysfunction criteria , which wInvestigators completed a data collection form for each patient. Principal investigators at each site reviewed each form, added any missing data, and internally validated the information before transferring it via the Internet to the repository. Validation of data quality was also performed at the IMPACT-HAP study center. Initial empiric therapy was classified as appropriate if the isolated pathogen was susceptible to at least one prescribed antibiotic. For the purpose of this analysis, data from the first two phases were combined into one nine-month period ) and compared with data from the third nine-month phase .Staphylococcus aureus (MRSA). Reasons for noncompliance were recorded. Clinical outcome was categorized on Day 14 as cure (complete resolution of signs and symptoms of pneumonia), improvement , or failure (deterioration of signs and symptoms of pneumonia). Clinical success was defined as cure or improvement.Selection of empiric antibiotics was based on ATS/IDSA guidelines  and the t-test for normally distributed variables and the Wilcoxon rank sum test for non-normally distributed variables. P-values of ≤0.05 were considered to be statistically significant. All data analyses were performed using SAS software, version 9.2 .Descriptive statistics were calculated for baseline demographics and severity-of-illness scores, compliance with guidelines, and reasons for noncompliance in patients enrolled during the pre-implementation and post-implementation periods. Compliance with each quality performance indicator was calculated as the percentage of patients who met the criteria for each indicator based on the total number evaluable for each quality indicator. Between-implementation differences were compared using the Chi-square test or, if applicable, Fisher's exact test for categorical variables and, for continuous variables, the Student's A consensus pathway was developed based on the principles of the ATS/IDSA guidelines  for the On Day 0, patients with suspected nosocomial pneumonia (on the basis of the recognition of the presenting signs and symptoms) were stratified by the presence or absence of risk factors for MDROs. Patients without risk factors for MDROs were to receive limited-spectrum monotherapy, which included the following options: ceftriaxone, fluoroquinolone, ampicillin/sulbactam, or ertapenem. Most centers chose ceftriaxone or moxifloxacin, except one center chose ampicillin/sulbactam or ceftriaxone plus azithromycin or moxifloxacin.Patients with risk factors for MDROs were to receive expanded-spectrum combination therapy with dual gram-negative coverage and either linezolid or vancomycin as anti-MRSA therapy. Of the ATS/IDSA options for primary gram-negative coverage , centers chose the following three options: cefepime, imipenem or piperacillin-tazobactam. Of the ATS/IDSA options for secondary gram-negative coverage , most centers chose tobramycin or amikacin.Acinetobacter was of concern, as was the case in one ICU.The intent of the IMPACT-HAP pathway Figure  was to aPseudomonas aeruginosa or Acinetobacter spp. The total duration of antibiotics was not to exceed 14 days.On Day 3, antibiotic therapy was to be discontinued in patients who met the criteria for short-course therapy as described by Singh and colleagues . CriteriWe developed a data collection form to collect patient demographics, comorbidities, physical examination, laboratory, and chest radiograph findings; risk factors for MDROs; and six quality performance indicators. We tested the data collection form and data repository in the first 30 patients, adjusted the form, and then used the revised form for subsequent patients.before antibiotics were initiated. The numerator for QI-3 was the number who received antibiotics compliant with ATS/IDSA guidelines [Quality performance indicators were expressed as percentages and calculated by dividing the number of patients who met the criteria for the quality indicator by the total number of patients in whom antibiotics for HAP, VAP, or HCAP were started, unless otherwise stated. The numerator for the first quality indicator QI-1) was the number of patients who met diagnostic criteria for HAP, VAP, or HCAP and whose physicians recognized and appropriately documented the risk factors for HAP, VAP, or HCAP. The numerator for QI-2 was the number of patients in whom respiratory (QI-2a) and blood cultures (QI-2b) were obtained  was the Educational efforts were started during the implementation phase. The principal investigators led a variety of didactic forums including grand rounds, internal medicine house staff lectures, infectious diseases and pulmonary and critical care divisional conferences, ICU-specific physician and nursing staff unit meetings, and pharmacy and respiratory therapy conferences -- all emphasizing the ATS/IDSA guidelines  with theP = 0.04 for race). Distribution of comorbidities was similar, except that fewer patients had renal disease during pre-implementation . CPIS at baseline and presence of severe sepsis were similar during the two periods, but Acute Physiology and Chronic Health Evaluation (APACHE) II score was lower during pre-implementation . Patients were also less likely to have a risk factor for an MDRO during pre-implementation .A total of 449 patients were captured in the Internet-based repository; 17 were excluded because of missing data. Of the remaining 432 patients, 274 were registered during pre-implementation (1 February through 31 October 2006), and 158 during post-implementation (1 November 2006 through 31 July 2007). Some differences existed in patient profiles when grouped by time of registry (Table P = 0.01) and with center-specific guidelines . Analysis of QI-3 at quarterly intervals revealed improved compliance with ATS/IDSA guidelines over time  and only a small number of patients (n = 37) were eligible for short-course therapy during the project. Other between-period differences in compliance with quality indicators were not statistically significant.Evaluation of compliance with quality performance indicators revealed some differences between periods Table . SpecifiThe IMPACT-HAP project demonstrated the feasibility of developing a performance improvement project for HAP, VAP, and HCAP based on the ATS/IDSA guidelines , while oWe had initially planned to complete our educational series at the end of the implementation period in order to assess the impact of our initiative. Upon implementation, however, we recognized the need for continual education to accommodate monthly rotations by house staff, some of whom had not attended the formal grand rounds or lectures. This is not unexpected, as recurrent education is yet another feature of other successful interventions ,9,15,16.Compliance with the quality performance indicators related to making the clinical and microbiologic diagnosis of HAP, VAP, and HCAP (QI-1 and QI-2) exceeded 80%. Compliance was high before implementation of our project and remained high during post-implementation. These findings are consistent with the aggressive management of critically ill patients, the high quality of care generally practiced in ICUs, and the knowledge base at these four academic centers.P = 0.01). Notably, improvement became evident during implementation and, importantly, was sustained throughout post-implementation. The most common reason for noncompliance was failure to administer a secondary gram-negative agent, which is consistent with the selective implementation of the consensus pathway at participating centers in the IMPACT-HAP study. Specifically, two centers did not use the secondary gram-negative agent because their local antibiograms indicated adequate coverage with the primary gram-negative agent or reserved the secondary gram-negative agent for patients with VAP. Therefore, initial empiric therapy could be compliant with center-specific guidelines but not with ATS/IDSA guidelines. Others have also questioned the need for dual gram-negative coverage in patients with risk factors for MDROs because of concerns regarding potential renal toxicity associated with aminoglycoside use and lack of an additional benefit based on the local microbiology [We found a statistically significant improvement in administration of initial empiric therapy compliant with ATS/IDSA guidelines ; however, this difference was not statistically significant and less than 10% of our patients met the criteria for short-course therapy. Antibiotics were de-escalated on Day 3 based on microbiologic findings only in about one-third of candidates for de-escalation during both periods (QI-5b: 32.4% vs 37.5%). We did not capture reasons for failure to de-escalate, which merits further evaluation as this is an additional area for potential improvement. The last quality performance indicator, clinical success at Day 14, remained unchanged . Potential reasons for the inability to show changes in clinical outcomes despite improvement in compliance with empiric therapy include early adoption of the protocol during the implementation phase and the decision to continue educational efforts throughout the study despite our initial plans to complete our educational series at the end of the implementation phase, as previously discussed. Another consideration is the high clinical success rate observed during the pre-implementation period , making it difficult to demonstrate further improvement.et al. evaluated 819 patients [et al. [While the compliance rates for certain quality performance indicators including compliance with empiric antibiotics appear low, our collective compliance rates were generally consistent with those in studies comparing outcomes before and after implementation of guidelines for severe HAP and VAP ,13,19 orpatients -22 did npatients  or cente [et al.  evaluate [et al.  and 58%  [et al. . In the  [et al. ,13,19.Further studies are needed to validate the ATS/IDSA guidelines for patients with HAP, HCAP, and VAP. Some studies have shown that compliance with guidelines shortens the duration of mechanical ventilation and ICU stay  or is asOur project had several limitations. Most importantly, the participants were adults in multiple ICUs, an inherently complex group with many comorbidities. This was a non-randomized, observational study with the natural limitations of real-world academic medical center practices. However, data from IMPACT-HAP were for the most part prospectively collected and validated before entry into the data repository. Another limitation was the inability to capture all patients admitted to these ICUs during the study period. Specifically, we enrolled as many patients as possible but missed some, especially those admitted on weekends or discharged from the ICU before we could learn of them. Furthermore, patient enrollment was not evenly distributed among centers. For these reasons, our findings may not be generalizable to other ICU populations or patients treated outside the ICU setting. Finally, feedback was not provided to investigators until after the post-implementation period was completed. Real-time feedback might have improved compliance with ATS/IDSA guidelines and other quality indicators.Developing a multi-center performance improvement project for implementation of the ATS/IDSA guidelines for HAP, HCAP, and VAP is feasible. Important features of IMPACT-HAP included flexibility to accommodate expected differences in unit-specific epidemiologic data and hospital formularies, ongoing education, and benchmarking. Diagnostic work-ups were performed according to ATS/IDSA guidelines for most patients. Empiric antibiotics were compliant with the guidelines in less than half of the patients; however, improvement in compliance during post-implementation was statistically significant and was sustained. Similarly, short-course therapy and de-escalation were performed in no more than half of eligible patients. The low overall performance in these areas despite educational interventions suggests the need for additional studies to better understand how to influence physician behavior. Additional studies are also needed to validate ATS/IDSA guidelines for HAP, HCAP, and VAP.• A performance improvement project for implementing ATS/IDSA guidelines for HAP, VAP, and HCAP should be flexible enough to accommodate local epidemiology and hospital formulary considerations.• The project should include leaders who can champion the initiative and should engage relevant stakeholders.• Educational efforts should be repeated routinely and continued indefinitely in training centers.• Benchmarking should be performed to provide feedback to participating centers.Staphylococcus aureus; QI: quality indicator; SOPs: standard operating procedures; VAP: ventilator-associated pneumonia.APACHE: Acute Physiology and Chronic Health Evaluation; ATS: American Thoracic Society; CPIS: clinical pulmonary infection score; HAP: hospital-acquired pneumonia; HCAP: healthcare-associated pneumonia; IDSA: Infectious Diseases Society of America; IMPACT-HAP: Improving Medicine Through Pathway Assessment of Critical Therapy in Hospital-Acquired Pneumonia; MDRO: multidrug resistant organisms; MIC: minimal inhibitory concentration; MRSA: methicillin-resistant Funding for this study was provided by Pfizer Inc., US Medical. The University of Louisville Foundation was responsible for project oversight and distribution of funds to participating institutions. JEM has served on advisory boards for Madcat Healthcare, Pfizer, Astellas, and Merck; and received educational grants from Fallon Medica. DHK has received research support from Pfizer, and has served as a consultant to and is on the speakers' bureaus of Astellas, Cubist, Glaxo Smith Kline, and Pfizer. MJZ has received honoraria for lectures from Pfizer, Cubist, and Astellas, as well as grant support from Henry Ford Hospital, Pfizer, Johnson and Johnson, and Cubist. JAR has received research support from Pfizer, is a consultant for Pfizer, and has received honoraria from Pfizer, Merck, and Wyeth for lectures. PP has no conflicts of interest to disclose. VLW, KDF and EGS are employees of Pfizer, Inc.JEM, DHK, MJZ, JAR, PP, EGS and KDF contributed to project development and implementation. JAR, PP and VLW had full access to all data and take responsibility for the integrity of data and accuracy of data analysis. All authors contributed to analysis and interpretation of data, and to drafting of the manuscript and critical revision for important intellectual content. All authors read and approved the final manuscript.Center-specific algorithm.Click here for file


Motivation: Recent transcriptome studies have revealed that total transcript numbers vary by cell type and condition; therefore, the statistical assumptions for single-cell transcriptome studies must be revisited. SAMstrt is an extension code for SAMseq, which is a statistical method for differential expression, to enable spike-in normalization and statistical testing based on the estimated absolute number of transcripts per cell for single-cell RNA-seq methods.Availability and Implementation: SAMstrt is implemented on R and available in github (https://github.com/shka/R-SAMstrt).Contact:shintaro.katayama@ki.seSupplementary Information:Supplementary data are available at Bioinformatics online. Unbiased molecular measurements are required to form precise hypotheses on molecular mechanisms, and measurements at single-cell resolution can give detailed snapshots of heterogeneous cell cultures or tissues. Recently described single-cell mRNA sequencing technology is one promising method for such purposes  and fibroblasts (MEF) in the earlier study A. In ourThe second issue to consider is the process and underlying hypothesis for normalization. Normalization is required to correct bias coming from technical sources. For statistical tests of differential expression in sequencing-based profiles, the most recent proposed normalization procedures include rescaling by estimated sequencing depth , and thoTo handle these two issues, we have developed a method for robust statistics that has tolerance for large sequencing depth variations and that can also perform normalization that considers differences of total transcript counts per cell.P = 0.2394 by Welch’s two sample t-test for the distributions) and both methods kept a few false discovery in the trials  other genes that were overexpressed in cell B.R CMD install with a downloaded file from https://github.com/shka/R-SAMstrt/archive/0.99.0.tar.gz followed by installation of samr. However, this package will be in the future bioconductor releases (submitted), and the bug-fix and new features will be released at github and bioconductor. This package is released under the GNU Lesser General Public License (LGPL) version 3. Although the help documents of the package contain basic usages, Supplementary Data file of this article includes more concrete sample codes and the input data for The proof-of-concept was implemented in R (version 3.0) with the samr package (version 2.0). Presently, users need to install this package by RNA_SPIKE_’ (e.g. RNA_SPIKE_1). Those are read counts, which aligned to the spike-in sequences. Therefore, users can apply this package to any RNA-seq libraries using not only 8 ArrayControl spike-in molecules but also, for example, 92 ERCC spike-ins.It is necessary to prepare a SAMseq-compatible feature matrix as input, and the matrix must contain several rows beginning with ‘library(SAMstrt)] overwrites the sequencing-depth estimation of SAMseq for the spike-in normalization. Therefore, users can use all problem types  and the other optimization parameters also for the spike-in-based statistical tests via function SAMseq after loading of the SAMstrt package.This implementation contains two functions; one is a statistical test for differential expression, and the other one is calculation of the normalized values. Loading of the SAMstrt package [SAMstrt.normalization calculates the spike-in-based normalized values with conversion to estimated transcripts/sample values based on the initial concentration of spike-in RNAs. Those estimations would be transcripts/cell in single-cell experiments and would be transcripts/1 ng-totalRNA in case of 1-ng experiment; however, users should count number of cells before RNA extraction for the latter case. This function would be useful for visualization of the expression changes, or the other type of statistics, e.g. principal component analysis. However, this package does not normalize mRNA length bias (neither does SAMseq), as theoretically STRT synthesizes only one first-strand cDNA from one poly(A)+ RNA ; and the Strategic Research Programme in Diabetes at Karolinska Institutet. The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project b2010037.Conflict of Interest: none declared.


MCAD-deficiency is the most common inborn error of fatty acid oxidation now included in many newborn screening programms using MS/MS. During prolonged catabolic episodes, patients may suffer from metabolic decompensation with dysfunction of liver, skeletal- and heart muscle as well as brain. In anabolism, neither clinical symptoms nor biochemical signs of organ dysfunction occur.We report a female patient with MCAD-deficiency in whom at the age of 11 years isolated AST-elevation was found without any clinical or biochemical signs of organ dysfunction. We showed by polyethylene glycol precipitation that macro-AST formation was responsible for this biochemical finding. AST was probably complexed with immunoglobulins possibly related to an allergic disposition. Macro-AST formation is not a special feature of MCAD-deficiency but rather a non-specific, coincidental finding which also occurs in healthy individuals. The general practitioner consulted by the patient before coming to our outpatient clinic for inborn errors of metabolism was worried that isolated AST-elevation indicated cell damage in MCAD-deficiency. He ordered further diagnostic tests like ultrasound, ECG and echocardiography without any pathology.In isolated AST-elevation, macro-AST has to be considered in order to avoid unnecessary, costly and invasive evaluation. This is not only true for healthy persons but for patients with chronic diseases like MCAD as well. Medium chain acyl CoA-dehydrogenase (MCAD)-deficiency OMIM #201450) is the most common inborn error of mitochondrial fatty acid oxidation. It is inherited as an autosomal-recessive trait and leads to compromised breakdown of C4-C12 acyl-CoAs. The incidence in Northern Europe is 1:9,000 to 1:11,000  was first noticed. AST-levels remained elevated ever since (500–700 U/l) without any other laboratory abnormalities. Ultrasound of the abdomen, ECG and echocardiography were repeatedly normal, infection with hepatotropic viruses and autoimmune processes were excluded. The general practitioner concluded that isolated AST-elevation was related to MCAD-deficiency and indicates some organ dysfunction though the organ affected could not be specified yet.The girl first presented at our outpatient clinic for inborn errors of metabolism at the age of 15 years. Psychomotor development was normal, physical examination was unrevealing. In line with MCAD-deficiency, the acylcarnitine profile in a dried blood spot showed elevations of C6, C8, C10 and C10:1 acylcarnitines, free carnitine concentration was normal. Analyses of amino acids in plasma and organic acids in urine were unrevealing. Concentrations of creatine kinase, ALT, alkaline phosphatase, gamma-glutamyltransferase, lipase and lactate dehydrogenase were not elevated there were no signs of hemolysis. Blood count was normal except for eosinophilia indicating an allergic disposition. AST was elevated . In the absence of clinical and biochemical organ dysfunction, we considered macro-AST. More than 95% of AST-activity could be precipitated by polyethylene glycol indeed, thus confirming the presence of macro-AST. Macro-AST is supposed to result from complex formation with immunoglobulins which prompted us to determine immunoglobulin concentrations in blood. IgE-levels were above normal , probably related to birch allergy already diagnosed during childhood, while all other immunoglobulins were not elevated.Informed consent for publishing this case was obtained from the parents and the patient.MCAD-deficiency can lead to organ damage  as a result of cellular energy deficiency and/or accumulation of endogenous toxic intermediates. Hypoketotic hypoglycaemia based (amongst other factors) on compromised hepatic ketogenesis from fatty acids is another pathophysiological mechanism leading to encephalopathy during prolonged fasting or intercurrent illness. Organ dysfunction is triggered by longer episodes of catabolism (febrile infection/prolonged fasting) and can usually be prevented by administering carbohydrates. Cell damage leads to spill-over of intracellular enzymes like AST, ALT, creatine kinase, lactic dehydrogenase into the blood circulation. Usually, this does not occur when the patient is well nor does it lead to isolated leakage of intracellular AST. However, metabolites accumulating in MCAD-deficiency are known to be toxic and may lead to organ dysfunction in the long run. There are no large prospective studies describing the outcome of patients diagnosed by neonatal mass screening in adulthood. Therefore, the assumption by the general practitioner that sustained, isolated AST-elevation indicated organ damage in our patient was reasonable. We could show that isolated AST-elevation in this MCAD-patient was caused by macro-AST. This was not a congenital condition as AST-levels were normal initially.Macro-AST has been described in the literature as a benign condition due to binding of AST to macromolecules like immunoglobulins e.g.-6). Thes. Thes6])Macro-AST has not only been described in healthy persons but also in patients with hepatic diseases like hepatitis C or maligIn summary, we describe a girl with MCAD-deficiency developing isolated AST-elevation without any clinical or biochemical signs for organ dysfunction. We could detect macro-AST as the cause of AST-elevation.Macro-AST has to be considered in any healthy individual or patient with a chronic disease displaying an isolated AST-elevation. This goes for patients with chronic metabolic diseases like MCAD-deficiency as well. Thus, unnecessary costly and invasive evaluation can be avoided. In our opinion, MCAD-patients should be regularly followed. Apart from dealing with acute health problems this will allow us to study the long-term biochemical and clinical outcome in patients with this rare disease diagnosed by neonatal mass screening.ALT: Alanine aminotransferase; AST: Aspartate aminotransferase; ECG: Electrocardiogram; MCAD: Medium chain acyl-CoA dehydrogenase; MS/MS: Tandem-mass spectrometry.The authors declare that they have no competing interests.AMD treated the patient in the metabolic outpatient clinic, drafted and approved the manuscript. NJ and SD performed the analysis for macro-AST and advised regarding interpretation of results. NJ assisted in drafting the manuscript. AF performed ultrasound, ECG, echocardiography and various blood tests in the patient. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-230X/12/119/prepub


One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function.Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA , which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM.Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins. Protein loops correspond to all residues not assigned to regular secondary structures. Unlike α-helices and β-strands, protein loops were initially seen as random coils because their sequences and structures are highly variable. But the ever-increasing availability of protein structures in the Protein Data Bank (PDB) allowed extensive analyzes of protein loops, which suggested a more complex view. For example, Panchenko et al.  XXXXGK[TS] [Figure XXGK[TS] .YUOD and UODO correspond to the nucleotide-binding site annotation with precision greater than 80%. YUOD and UODO are thus functional words with residues directly involved in ATP/GTP-binding sites, as shown in Figure YUOD word. In the initial data set, two YUOD-fragments and eleven UODO-fragments are unannotated. SitePredict indeed predicts ATP/GTP-binding sites for four of the eleven unannotated UODO-fragments (see Table S4). The sensitivity is equal to 35 and 38%, meaning that roughly one third of the ATP/GTP-binding sites adopt conformations described by these structural words.Structural words NAD(P)-binding sites Two structural words, OEIJ and EIJU are strongly over-represented in the "NAD(P)-binding Rossmann-fold domain" superfamily (SCOP id = 51735) grouping proteins with NAD(P)-binding sites. These words are often overlapping: in 95% of cases, OEIJ is followed by the letter U.OEIJ is associated with the NP_BIND annotation with precision equal to 86% and 47% respectively, they thus are functional words. One OEIJ-fragment and seven EIJU-fragments are unannotated. Two of the seven unannotated EIJU-fragments are predicted as NAD(P)-binding sites by SitePredict (see Table S5). The sensitivity is quite low, ranging from 14 to 20%, meaning that NAD(P)-binding sites probably adopt various conformations, and not only the ones encoded by OEIJ and EIJU.Word RUDO is strongly over-represented in the "S-adenosyl-L-methionine-dependent methyltransferase" superfamily (SCOP id = 53335), grouping proteins with SAH/SAM-binding sites. Figure RUDO and its amino-acid signature, with glycine residues preferred at positions 1, 3 and 5. Figure RUDO-fragment, showing the residues involved in the SAH/SAM-binding site. This word corresponds to the "binding" annotation with a precision equal to 50%, therefore it is a functional word. Three out of the five unannotated RUDO-fragments actually correspond to SAH/SAM-binding sites according to our analysis using LigPlot. The sensitivity is equal to 18%, suggesting that SAH/SAM-binding sites adopt other conformations than the one identified by the RUDO word.The superfamily-specific word QXUS, ZSGI, GSUS, GZDO, USLG, UZCI, UGRU, EGZD, GRUD and SLGS, indicated in italics in Table Ten superfamily-specific structural words The previous analysis was based on the Swiss-Prot annotations of the annotation data set. Since many proteins of the initial data set are lost in the UniProt/PDB mapping step, we complement our results using a data set specifically built to maximize the coverage by Swiss-Prot: the validation data set composed of 2 636 proteins. In the validation data set, 17% of seven-residue fragments in loops are covered by a Swiss-Prot annotation versus only 2% in the initial data set.For the functional words identified in the previous section, we compute the precision and sensitivity measures presented in Table In this work, we used a structural alphabet-based simplification of protein structures and applied an exact statistical approach to identify structural motifs over-represented in loops in SCOP superfamilies. Our underlying hypothesis was that structural words with unexpectedly high frequency are probably linked to structural or functional implication. We discovered two distinct trends: some words, termed ubiquitous words, are over-represented in several superfamilies, whereas others, termed superfamily-specific words, are over-represented in a small number of superfamilies. We then investigated the link between these structural motifs and known structural motifs and functional sites annotated in Swiss-Prot, on a subset of structural words with extreme over-representation scores.YUODO, ZDODQ, corresponding to eight-residue motifs or shorter motifs consensus as LGI common to SLGI, QLGI. These results suggest that this motif approach could be extended to motifs of different lengths.We focused on structural motifs formed by seven consecutive residues, i.e. four structural letters, since it is the optimal length to have a good description of the 3D conformations and enough data to allow statistical treatments . Howeverβ-turn, nest or niche motifs. Several studies have shown that turns, nest and niche motifs may play a functional role in determining the conformation of enzyme active sites and binding sites DOD) instead of "exact" word. This would certainly increase the ability to detect functional sites.To quantify the correspondence between extreme superfamily-specific words and Swiss-Prot annotations, we computed the precision and sensitivity of annotation detection by these words. We observed that sensitivity values depend on the functional sites and structural words. For example, two overlapping words YUOD and UGBB. This indicates each word can detect one part of the GTP-binding site, thus each word is expected to detect to 50% of the NP_BIND annotations at most. Thus, the weak sensitivity value of some functional words shows that these words can detect one part of the functional site. To identify the entire functional sites, we could couple the different functional words associated to the same annotation.In Figure Several approaches address the link between local structures and protein function. These methods can be clustered into three groups.The first group corresponds to the characterization of structural motifs specific to functional sites -28. SuchThe second group corresponds to the discovery of conserved structural motifs in proteins with the same function. These methods start from protein superfamilies and search for structural motifs specific to superfamilies ,21,68. Ta posteriori the association between fragment clusters and protein superfamilies or GO annotations. Our approach is based on the same philosophy as these methods.The third group corresponds to structural classification of local conformations, followed by an analysis of the association between clusters and functional sites ,17,18,69et al. [Compared to Espadaler et al. , Tendulket al.  makes thet al. [et al. [α-helices and β-strands. In these two studies, structural motifs were extracted by a systematic classification of eight-residue fragments based on geometric invariants [al. [al. [Two studies by Tendulkar et al.  and Mani [et al.  aimed atvariants  or dihedvariants . They thvariants  or GO tevariants . Tendulknts [al.  defined al. [al.  identifiet al. [et al. focused on DNA-binding sites by searching structural words present in DNA-binding proteins binding and absent in others, and considered long and degenerated structural words (26 residues) without secondary structure restriction. In the present study, we discarded helices and strands. In addition, our statistical treatment is radically different from theirs, and allows retrieving structural words shared by several superfamilies, even in superfamilies with few proteins. Even if based on a similar method of protein structure simplification, both these works thus pursue quite different objectives and consider different structural motifs.Recently, Wu et al.  have proet al.  is compoubiquitous structural motifs over-represented in several superfamilies, and superfamily-specific structural motifs over-represented in few superfamilies. Some ubiquitous words correlate with known 3D motifs such as β-turns, niches and nests. The link between the word over-representation and functionality was proved for some superfamily-specific words. Thus, some of these structural words allows the detection of calcium-binding sites, some part of nucleotide, SAH-binding sites, or active site. As in DNA sequence analysis, statistical over-representation can be related to functional features.In this study, we present a systematic extraction of 3D motifs from loops likely to be important for protein structure or function. This method is based on the structural alphabet HMM-SA and an advanced method for pattern statistics. We identified These results could be used for the prediction of functional sites in protein structures: the identification of these structural motifs in uncharacterized proteins could provide useful clues to protein function in complement to usual methods based on homologous proteins.As some functional annotations are supported by regular secondary structures, current perspectives include the consideration of regular secondary structures. Also, some functional words present sequence specificity, which opens the perspective to the prediction of these functional motifs from their amino-acid sequence.LR, JM, and ACC conceptualized the project. LR developed the software, performed the experiments and drafted the paper. JM extensively edited the manuscript. All authors analyzed the experimental results. All authors contributed to writing the paper and approved the final manuscript.Supplementary information. This file is a pdf file. It contains different information about the comparison between some over-represented words and biological annotations: • Table S1: Precision of annotation dectection by extreme ubiquitous words. • Table S2: Analysis of UQHS fragments. • Table S3: Analysis of DODQ fragments. • Table S4: Analysis of UODO-unannotated fragments. • Table S5: Analysis of EIJU fragments. • Table S6: Analysis of UGRU fragments. • Table S7: Analysis of ZCLH fragments. Table S8 present the results of the computation of a random sensitivity for each functional word.Click here for file


The relationship between subjective social status (SSS), a person's perception of his/her relative position in the social hierarchy, and the ability to achieve long-term smoking abstinence during a specific quit attempt is unknown. The purpose of this study was to examine the relationship between SSS and long-term smoking abstinence among 421 racially/ethnically diverse smokers undergoing a specific quit attempt, as well as the interactive effects of race/ethnicity and sex.The main effects and moderated relationships of SSS on biochemically-confirmed, continuous smoking abstinence through 26 weeks post-quit were examined using continuation ratio logit models adjusted for sociodemographics and smoking characteristics.p = 0.044). The statistical significance of this relationship, however, did not vary by race/ethnicity or sex.Even after adjusting for the influence of socioeconomic status and other covariates, smokers endorsing lower SSS were significantly less likely to maintain long-term smoking abstinence during a specific quit attempt than those with higher SSS (OR = 1.14, 95% CI: 1.00 - 1.28; SSS independently predicts long-term smoking abstinence during a specific quit attempt. SSS may be a useful screener to identify smokers at elevated risk of relapse who may require additional attention to facilitate long-term abstinence. More research is needed to understand the mechanisms underlying the relationship between SSS and long-term smoking abstinence in order to appropriately tailor treatment to facilitate abstinence among lower SSS smokers. Subjective Social Status (SSS) refers to the self-perception of one's status in the social hierarchy . In geneSSS may represent an incremental predictor of various health-related outcomes over traditional indicators of SES because it captures the nuances of SES that might affect social standing , taps into rarely assessed SES components , and captures the experience of societal inequalities and inequities ,2,9,10. The purpose of this study was to examine the independent effect of SSS on long-term smoking abstinence during a specific quit attempt, while controlling for race/ethnicity, sex, SES, age, partner status, pre-quit smoking rate, and the number of years smoked. A complementary aim was to explore whether the relationship between SSS and long-term abstinence differed by race/ethnicity and/or sex. This study represents an extension of our earlier work linking SSS with short-term smoking abstinence (through 2 weeks post-quit)  to examith largest city in the U.S. and the most populous of Texas' metropolitan statistical areas. The enrollment period for this study was from April 2005 - April 2007. Recruitment was via local print and radio advertisements. Inclusion criteria included: ≥21 years of age, daily smoker (≥5 cigarettes per day for the last year), motivated to quit in ≤30 days, and ≥6th grade English proficiency. Potential participants were excluded if the nicotine patch was contraindicated, they reported use of tobacco products other than cigarettes, or they reported participation in a smoking cessation program within the past 90 days. Data for the current study were collected one week before quitting (baseline) and post-quit weeks 1, 2, 4, and 26.Data for the current study were collected in Houston, Texas, as part of a longitudinal, cohort study designed to examine social disparities in smoking cessation ,which waTreating Tobacco Use and Dependence Clinical Practice Guideline, . In analyses controlling for race/ethnicity, sex, SES, age, partner status, pre-quit smoking rate, and the number of years smoked, SSS remained a significant predictor of long-term smoking abstinence  or adjusted  analyses.The relationship between SSS and long-term abstinence was not moderated by race/ethnicity or sex in unadjusted )This study examined whether SSS predicted long-term abstinence from smoking during a specific quit attempt, and assessed potential moderation by racial/ethnic group or sex. Our results indicated that smokers endorsing higher SSS were more likely to maintain long-term smoking abstinence during a specific quit attempt than smokers with lower social status ratings, regardless of their race/ethnicity or sex. Although a number of studies have supported inverse relationships between SES indicators  and smoking cessation (cf. ), the cuThe authors do not have any competing interests directly pertaining to this work; however, we would like to report that PM Cinciripini has served on the scientific advisory board of Pfizer Pharmaceuticals and has conducted educational talks for physicians on smoking cessation that were sponsored by Pfizer within the past five years.LRR, MSB, DEK, YCastro, and DWW conceptualized the research question and wrote the manuscript. YL and YCao conducted the data analysis, interpreted results, and reviewed the data analysis and results sections. DWW is the senior author of the paper, and the principal investigator on the supporting grant . CAM, LC-W, and PMC helped with the conceptualization of the overall project and methodology, and reviewed and edited manuscript drafts. PMC is a co-investigator on the supporting grant. All authors have read, contributed to, and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/11/135/prepub


Health information technology can enhance self-management and quality of life for patients with chronic disease and overcome healthcare barriers for patients with limited English proficiency. After a randomized controlled trial of a multilingual automated telephone self-management support program (ATSM) improved patient-centered dimensions of diabetes care in safety net clinics, we collaborated with a nonprofit Medicaid managed care plan to translate research into practice, offering ATSM as a covered benefit and augmenting ATSM to promote medication activation. This paper describes the protocol of the Self-Management Automated and Real-Time Telephonic Support Project (SMARTSteps).This controlled quasi-experimental trial used a wait-list variant of a stepped wedge design to enroll 362 adult health plan members with diabetes who speak English, Cantonese, or Spanish and receive care at 4 publicly-funded clinics. Through language-stratified randomization, participants were assigned to four intervention statuses: SMARTSteps-ONLY, SMARTSteps-PLUS, or wait-list for either intervention. In addition to usual primary care, intervention participants received 27 weekly calls in their preferred language with rotating queries and response-triggered education about self-care, medication adherence, safety concerns, psychological issues, and preventive services. Health coaches from the health plan called patients with out-of-range responses for collaborative goal setting and action planning. SMARTSteps-PLUS also included health coach calls to promote medication activation, adherence and intensification, if triggered by ATSM-reported non-adherence, refill non-adherence from pharmacy claims, or suboptimal cardiometabolic indicators. Wait-list patients crossed-over to SMARTSteps-ONLY or -PLUS at 6 months. For participants who agreed to structured telephone interviews at baseline and 6 months (n = 252), primary outcomes will be changes in quality of life and functional status with secondary outcomes of 6-month changes in self-management behaviors/efficacy and patient-centered processes of care. We will also evaluate 6-month changes in cardiometabolic  and utilization indicators for all participants.Outcomes will provide evidence regarding real-world implementation of ATSM within a Medicaid managed care plan serving safety net settings. The evaluation trial will provide insight into translating and scaling up health information technology interventions for linguistically and culturally diverse vulnerable populations with chronic disease.NCT00683020ClinicalTrials.gov:  As health systems and public health agencies grapple with the rising burden of diabetes, they face significant challenges with the persistent and widening disparities in the prevalence, quality of care, and clinical outcomes across such factors as race/ethnicity, language, health literacy, and socioeconomic status -3. PatieSelf-management support programs are a critical component of chronic disease care delivery that can improve outcomes by providing individualized assessment, collaborative goal-setting, skills enhancement, follow-up, and access to resources and continuity of care -16. DespPatient-facing health information technology (HIT) holds promise to increase access to self-management support and enhance health outcomes for vulnerable populations in safety net settings -34. AutoThe Improving Diabetes Efforts Across Language and Literacy (IDEALL) study - a randomized controlled trial of ATSM among English-, Spanish-, and Chinese-speaking patients with poorly controlled diabetes - demonstrated high engagement with ATSM, particularly among participants with limited health literacy and limited English proficiency . CompareThis paper presents a description of the study design and recruitment results for the Self-Management Automated and Real-Time Telephonic Support Study (SMARTSteps/Pasos Positivos/ 明智進步計劃), a controlled quasi-experimental evaluation study to improve diabetes quality of life, self-management, and clinical outcomes with two variants of language-concordant ATSM intervention implemented by a Medicaid managed care plan serving a low-income, ethnically diverse urban population. We hypothesized that intervention participants would demonstrate greater improvements in diabetes self-management, patient-centered outcomes, and cardiometabolic outcomes compared to wait-list controls and that improvements would be greatest for patients exposed to ATSM with an enhanced medication activation communication strategy triggered by pharmacy claims and self-reported medication non-adherence.Among ethnically and linguistically diverse persons with diabetes receiving care in a primary care safety net system:Primary Aim: To investigate differences in 6-month changes in patient-centered outcomes including quality of life and functional status (SF-12 and number of days spent in bed due to illness), comparing patients exposed to ATSM with wait-list controls and comparing patients exposed to ATSM (SMARTSteps-ONLY) with ATSM augmented by medication adherence and intensification (SMARTSteps-PLUS).Secondary Aims: To investigate differences in 6-month changes in diabetes self-management behaviors and self-efficacy, patient-centered processes of care, cardiometabolic outcomes , receipt of recommended health services, and healthcare utilization, comparing patients exposed to ATSM with wait-list controls and comparing patients exposed to ATSM (SMARTSteps-ONLY) with ATSM augmented by medication adherence and intensification (SMARTSteps-PLUS).The study was a controlled quasi-experimental evaluation trial with a wait-list variant of a stepped wedge design . SFHP is a non-profit Medicaid managed care plan created in 1994 to provide high quality medical care to the largest possible number of low-income San Francisco residents. In addition to managing Medicaid benefits, SFHP administers "Healthy Workers," an insurance program for people working as in-home support service providers for elderly or disabled people in San Francisco. At the time SFHP contacted the UCSF investigative team in 2008, it managed the care of approximately 50,000 enrollees and served an ethnically diverse population comprised of 48% Asian-Americans, 26% Latinos, 12% African-Americans; 60% of their membership were non-English speaking.http://familymedicine.medschool.ucsf.edu/research/research_programs/crn/crn.aspx). CHNSF is comprised of 12 community health centers and hospital-based clinics centers affiliated with the county's acute care facility, San Francisco General Hospital. CHNSF maintains a single electronic medical information system with unique patient identifiers across the clinical sites and a clinical registry that integrates patient data such as diagnoses, vital signs, and laboratory data.CHNSF is the integrated healthcare delivery system of the San Francisco Department of Public Health and part of the UCSF San Francisco Bay Area Collaborative Research Network, one of the longest standing U.S. practice-based research networks ; English-, Cantonese-, or Spanish-speaking; access to a touch-tone phone; and plans to remain in the region during the evaluation period (12 months). Patients who were pregnant or unable to provide verbal consent were excluded. The diagnosis of diabetes was assessed in two ways. First, we searched for SFHP members in the CHNSF electronic diabetes registry. Second, we searched for members with SFHP claims data consistent with diabetes . If members were identified through SFHP claims data but were not found in the registry, we validated the diabetes diagnosis by reviewing electronic health records for fasting glucose ≥ 126 mg/dl and/or clinician-documented diagnosis of diabetes based on HbA1c ≥ 7% . During SFHP mailed to potentially eligible members' homes and clinicians' offices SMARTSteps post cards describing this new benefit in English, Spanish, and Cantonese and offering an SFHP number to call for information. SFHP enrollment workers fluent in these three languages also actively recruited potentially eligible health plan members through scripted telephone calls. The enrollment workers confirmed eligibility for SMARTSteps by phone and offered $25 gift cards as incentives for participation. All eligible members who reported interest in SMARTSteps were then randomized by SFHP to one of four intervention statuses (described below) regardless of interest in the UCSF evaluation.SFHP workers also assessed participant willingness to complete evaluation interviews administered by UCSF staff. Those members willing to participate in the interviews were then telephoned by UCSF research assistants to obtain verbal consent for participation in the evaluation interviews and were offered $50 gift cards as incentives for each interview completed (up to $150).The Committee on Human Research at the University of California, San Francisco (H9894-32044-01) approved collection of interview data by UCSF from consenting participants after obtaining verbal consent. Because all recruitment and implementation was conducted by SFHP by phone, it was felt that requiring a separate visit to obtain written consent at UCSF or the primary care clinic sites reduce participation, leading to selection bias, and disrupt clinic workflow. Because the interviews offered minimal risk, the Committee approved verbal telephone consent for these interviews. In addition, ethics approval included waiver of informed consent to abstract and analyze CHNSF clinical data from the CHNSF electronic health record, CHNSF diabetes registry, SFHP claims data, and SFHP health coaching data for all SFHP members eligible for SMARTSteps.All eligible SFHP members interested in the SMARTSteps program were assigned by SFHP through language-stratified randomization to one of four intervention statuses: SMARTSteps-ONLY, SMARTSteps-PLUS, wait-list for SMARTSteps-ONLY, or wait-list for SMARTSteps-PLUS.Those randomized to the wait-list continued to receive usual care through their clinics, as well as all existing SFHP benefits  ,47. At tParticipants randomized to SMARTSteps-ONLY received the ATSM intervention within 2 weeks. Developed with extensive input from patients to be sensitive to literacy, language, and culture in the target populations , this ATPatients answering "out-of-range" on an item or selecting a "call back" option received a telephone call within 3 days from a language-concordant SFHP health coach. This system was designed to promote health coach efficiency and effectiveness by focusing outreach calls to patients needing further support based on ATSM responses. Health coaches provided education and engaged in collaborative goal-setting to form patient-centered action plans, a core process for self-management support by which patients set short-term goals to improve their self-management ,35.SFHP used a health coach for responding to ATSM triggers, rather than a nurse practitioner care manager as was done in the IDEALL trial . Health Health coaches documented the content of their phone interactions, including patient-generated action plans and whether they were achieved, using an SFHP care management database system. SFHP health coaches also contacted the designated clinic contact and/or the primary care provider (PCP) using standardized templates for patients with pre-specified safety issues  or access concerns (such as need for refills or appointments). Non-urgent issues were communicated by email or fax, while urgent issues were also conveyed by phone.Patients who indicated on their ATSM responses that they missed their diabetes, blood pressure, or cholesterol medications for 3-7 days in the previous week received calls from health coaches to troubleshoot barriers to adherence. These calls were only triggered by patient self-disclosure in response to ATSM queries, unlike adherence counseling calls triggered for SMARTSteps-PLUS participants described below.The goal of the SMARTSteps-PLUS intervention was to detect and intervene for participants whose medication treatment was suboptimal, either because of non-adherence or potential missed opportunities to intensify their regimens. Because SFHP does not have prescribing authorization for its members, the intervention focused on enhancing medication regimens and adherence through collaborative goal-setting with patients and feedback to PCPs. Participants randomized to SMARTSteps-PLUS immediately received the ATSM intervention described above, as well as medication activation and intensification coaching triggered by refill non-adherence or suboptimal achievement of cardiometabolic treatment goals. Based on review of evidence-based guidelines , SFHP anThe medication activation protocol targeted 3 groups of patients within the SMARTSteps-PLUS arm , cholesterol-lowering medications, or glucose testing strips (for patients receiving insulin or sulfonylureas), based on pharmacy claims data. We chose a lower limit of 15-days to account for potential delays in SFHP receipt of pharmacy claims and an upper limit of 6 months in case healthcare providers actively discontinued these medications.3. Patients with suboptimal achievement of cardiometabolic goals :• Systolic blood pressure ≥ 130 mmHg at last recorded check or no measurement in clinical registry within preceding 6 months• Diastolic blood pressure ≥ 80 mmHg at last recorded check or no measurement in clinical registry within preceding 6 months• Hemoglobin A1c (HbA1c) > 7.0% on last measurement or no measurement in clinical registry within preceding 6 months• Low-density lipoprotein (LDL) > 100 mg/dL on last measurement or no measurement in clinical registry within preceding 12 months• Urinary albumin/creatinine > 30 mcg/mg for patients who were not prescribed or late to refill an ACE inhibitor or angiotensin-receptor blockerAn individual SMARTSteps-PLUS participant could fall into none, one, or more than one of these groups at any given time. SFHP queried the pharmacy claims and clinical registry data monthly to provide health coaches with a list of SMARTSteps-PLUS participants to be called.For patients with evidence of non-adherence, SFHP health coaches were trained with specific written protocols and scripts to promote self-disclosure of medication non-adherence and troubleshoot barriers such as confusion about doses or frequency of medications, forgetfulness, concerns about side effects, or health beliefs  software or paper survey, with responses later entered into the CATI-created database. Consenting participants completed baseline interviews within 2 weeks of being randomized, prior to the first ATSM call. SMARTSteps-ONLY and SMARTSteps-PLUS participants completed the 6-month follow-up interviews after the conclusion of their ATSM intervention, and wait-list participants completed the 6-month follow-up interviews before the start of their ATSM calls. Wait-list groups received an additional 6-month follow-up interview (12 months after enrollment) after completion of intervention period. Participants received a $50 gift card for a pharmacy store at the completion of each interview.For all eligible SFHP members, we collected socio-demographic variables and cardiometabolic outcomes data using monthly downloads of SFHP claims data and CHNSF clinical registry data. At the conclusion of the project, we will obtain SFHP administrative and claims data for utilization outcomes.Self-reported socio-demographic variables included age, gender, race/ethnicity, language, English proficiency, years since immigration to the U.S., marital status, educational attainment, employment status, annual household income, self-reported health literacy ,50, and The primary outcome variables are physical and mental functional status (SF-12) and the number of days spent in bed due to illness . SecondaThese secondary outcomes will be analyzed on the larger set of SFHP participants randomized in the trial (N = 362), regardless of whether or not they participated in the evaluation interviews. Cardiometabolic outcomes include measures of HbA1C, LDL, and blood pressure obtained by clinical providers. Data will be derived from CHNSF electronic health record, the clinical registry database, and paper chart review. Values will be used at baseline only if obtained within one year before program enrollment. Follow-up laboratory and blood pressure values will be included only if obtained within 90 days before or after the 6-month and 12-month follow-up dates.Finally, for all eligible participants, we will use SFHP administrative claims data to examine measures of care delivery processes: proportion receiving blood pressure checks, laboratory testing, retinal examinations, influenza vaccination, and pneumococcal vaccination at guideline-concordant frequencies . We willUsing data from the ATSM system, we will assess patient engagement as measured by exposure intensity  and the proportion of weekly calls that are determined to be complete , partially complete , and incomplete  . In addiWe will assess the similarity of baseline characteristics between study arms using t-tests, chi-square tests, and Fisher's exact tests. We will control for any significant differences in baseline characteristics in analyses of all primary and secondary outcomes.For each outcome, we will compare differences between study arms in 6-month changes using intent-to-treat analyses. Because this study is a quasi-experimental evaluation trial with a wait-list variant of a stepped wedge design, analyses of outcome changes will be conducted with two distinct methodologies. The first method will involve analyzing the data as if the trial was a standard intervention versus control study, comparing all participants who were randomized to the ATSM intervention (either SMARTSteps-ONLY or SMARTSteps-PLUS) versus all participants randomized to the wait-list control groups. We will use linear regression for continuous variables, logistic regression for dichotomous variables, and negative binomial models for the outcome variable of number of bed days because of its non-parametric data distribution. We will include as model covariates the baseline value of outcome variables and any socio-demographic or medical variables that may have differed by chance among the groups.The second method will take advantage of the wait-list variant, stepped wedge design with study cross-over of participants from control to intervention . It willTo explore the added value of the medication activation arm, both the first and second methods above will also be used to compare SMARTSteps-ONLY versus SMARTSteps-PLUS in all primary and secondary outcomes.Sample size calculations were based on comparison of primary outcomes for the combined intervention groups (SMARTSteps-ONLY and SMARTSteps-PLUS) with the combined wait-list control groups. Based on an eligible population of approximately 500 SFHP members, we anticipated recruitment of 260 participants to intervention and control with a 10% drop-out or loss to follow-up rate at 6 months. Using a two-tailed test, we calculated that we would have 80% power to detect a standardized effect size (SE) of 0.35 in the primary outcome of SF-12 scores, comparing the combined intervention groups with the combined wait-list groups. In the prior RCT, we observed standardized effect sizes in this range .We estimated that over the course of the two-year observation period, approximately 20% of enrolled participants would have insufficient data for secondary cardiometabolic outcomes to be included in these analyses. Under this assumption, we would have 80% power to detect a difference in HbA1c of 0.51% (SE 0.28) when comparing wait-list vs. combined ATSM interventions participants. This effect size is intermediate between that estimated to be the effect on glycemic control of diabetes disease management programs that involve team changes (-0.3% HbA1c improvement) and those that involve medication intensification strategies (-0.6%) .Figure At close of evaluation trial, 362 patients were enrolled and randomized for the SMARTSteps program, with 278 completing baseline interviews for the evaluation trial. Table With SF-12 scores on 278 patients at baseline, assuming 10% loss to a 6-month follow-up sample of 250, we would have an 80% power to detect a mean difference of 2.85 in the SF-12 physical component score and 3.44 in the SF-12 mental component score.Clinical registry data included available baseline HbA1c values for 348 total patients. With an assumption of 20% loss to follow-up, our study would have 80% power to detect a HbA1c difference of 0.37%.The results of our recruitment process suggest that ATSM with health coach counseling may be a viable strategy for low-income managed care plans caring for linguistically and culturally diverse vulnerable persons with diabetes using population-based recruitment. In the IDEALL study, we found high levels of engagement, particularly with non-English speakers, and our early measures of reach suggest that this intervention model can be scaled up for larger populations ,33,37.The quasi-experimental design of the SMARTSteps evaluation trial offers a useful illustration of the advantages and challenges of a wait-list variant of a stepped wedge design. This design enabled all eligible SFHP members to receive ATSM as a benefit and increased the feasibility of scaling up the intervention through recruitment waves, while retaining elements of randomization that help minimize bias. However, this design requires careful evaluation of both intervention fidelity and potential confounders over time as well as investigation into the impact of extended follow-up time, potential time trends, and the impact of clustering in the data analysis strategy .Translational evidence from safety net settings is needed to understand whether HIT applications such as ATSM can be effective in real-world settings and to inform how to harness HIT to support chronic disease self-management among vulnerable populations and improve patient-centered outcomes. In response to Medicaid and Medicare incentives arising from the 2009 Health Information Technology for Economic and Clinical Health Act, safety net settings are required to integrate electronic health records (EHRs) into the care environment and meet "meaningful use" criteria, including patient education and tracking of quality indicators -60. In aThe results of this evaluation trial, when completed, must be interpreted within the following limitations. First, SFHP's phone-based population recruitment targeted different languages over time due to enrollment worker availability, with greater emphasis on Cantonese-speaking populations earlier. Thus, potential differences in intervention impact by language may relate to changes in project implementation over time. Second, because SFHP does not have medication prescribing authority for its members or authority to document within participants' medical records, the interventions will not be fully-integrated into care delivery in the context of participants' medical homes; this may limit the effectiveness of the intervention, particularly the SMARTSteps-PLUS medication intensification arm. Finally, because data for cardiometabolic outcomes relies on collection through routine medical care rather than scheduled study visits, we may not be powered to detect a modest impact of the intervention on glycemic or blood pressure control.Improving health communication through the use of tailored, proactive HIT is one scalable vehicle to improve chronic disease care for vulnerable populations ,33. FocuATSM: automated telephone self-management; CATI: computer-assisted telephone interview; CHNSF: Community Health Network of San Francisco; HbA1c: hemoglobin A1c; HIT: health information technology; IPC: Interpersonal Processes of Care instrument; LDL: low-density lipoprotein; PACIC: Patient Assessment of Care for Chronic Conditions instrument; PCP: primary care provider; SDSCA: Summary of Diabetes Self-Care Activities instrument; SE: standardized effect size; SFHP: San Francisco Health Plan; SMARTSteps: Self-Management Automated and Real-Time Telephonic Support; UCSF: University of California, San FranciscoThe salaries of the investigators  working on this study were partially funded by the McKesson Foundation. No funders had any role in the study design; collection, analysis, and interpretation of data; writing of the manuscript; or decision to submit the manuscript for publication.NR participated in the design and implementation of the study and drafted the manuscript. MH participated in the design and implementation of the study and helped to draft the manuscript. JQ participated in the implementation of the study, performed statistical analyses, and helped to draft the manuscript. US participated in the design and implementation of the study and helped to draft the manuscript. CS participated in the design and implementation of the study. KP participated in the design and implementation of the study. DS conceived of the study, oversaw the design and implementation of study, and helped to draft the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1472-6963/12/22/prepubSMARTSteps-PLUS medication intensification scripts. This document offers an example of SMARTSteps-PLUS medication intensification scripts for health coach phone calls in a quasi-experimental evaluation trial of a language-concordant automated telephone diabetes self-management health plan intervention.Click here for file