Adenosine deaminase (ADA) deficiency leads to an accumulation of toxic purine degradation by-products, most potently affecting lymphocytes, leading to adenosine deaminase-deficient severe combined immunodeficiency. Whilst most notable affects are on lymphocytes, other manifestations include skeletal abnormalities, neurodevelopmental affects and pulmonary manifestations associated with pulmonary-alveolar proteinosis. Affected patients present in early infancy, usually with persistent infection, or with pulmonary insufficiency. Three treatment options are currently available. Initial treatment with enzyme replacement therapy may alleviate acute symptoms and enable partial immunological reconstitution, but treatment is life-long, immune reconstitution is incomplete, and the reconstituted immune system may nullify the effects of the enzyme replacement. Hematopoietic stem cell transplant has long been established as the treatment of choice, particularly where a matched sibling or well matched unrelated donor is available. More recently, the use of gene addition techniques to correct the genetic defect in autologous haematopoietic stem cells treatment has demonstrated immunological and clinical efficacy. This article reviews the biology, clinical presentation, diagnosis and treatment of ADA-deficiency. ADA gene results in one of the more common causes of autosomal recessive severe combined immunodeficiency (SCID), accounting for approximately 10–15% of cases in outbred populations [Adenosine deaminase (ADA) is a key enzyme of the purine salvage pathways and deficiency caused by mutations in the ulations . Early d1, A2A, A2B and A3), which play different roles in regulating normal cellular physiology in a wide variety of tissues including the brain, cardiovascular system and lungs [ADA is a ubiquitously expressed metabolic enzyme, although level of enzyme activity varies, with highest levels observed in lymphoid tissues, particularly the thymus, the brain and gastrointestinal tract , and is nd lungs .ADA gene, located on chromosome 20q12-q13.11 and in which over 70 causative mutations have been identified.Diagnosis of ADA-deficiency is established by biochemical and molecular genetic testing. Biochemical testing demonstrates absent or greatly reduced ADA activity  and marked elevation of the metabolite dATP or total dAdo nucleotides  in erythrocytes. Reduced activity of SAH hydrolase in erythrocytes  is also characteristic . If a paSupportive laboratory findings include lymphocytopaenia, with absence of T- and B-lymphocytes and NK cells and low serum immunoglobulins, although in early infancy IgG may be normal due to materno-placental transfer. T-lymphocyte proliferative responses are low or absent, as are specific antibody responses. The level of metabolic substrates and the genotype have been shown to correlate with the severity of the clinical phenotype .The dominant consequences of ADA deficiency are on the immune system, causing severe depletion of T- and B-lymphocytes and NK cells, resulting in impaired cellular and humoral immunity. High levels of ADA are expressed in lymphoid tissues due to the high levels of cell turnover, particularly in the thymus, likely accounting for the resulting severe lymphocytotoxic effects of deficiency . The undThe B-lymphocyte compartment is also affected in ADA-deficiency with patients exhibiting severe B-lymphocytopaenia and hypogammaglobulinaemia, although, in contrast to T-lymphocytes, early B-lymphocyte development does not appear to be disturbed . AbnormaPneumocystis jiroveci, being characteristic. Physical findings include absent thymus gland on thoracic-radiographs and absence of lymphoid tissues.As a result of severely defected cellular and humoral immunity, the typical presentation of ADA-deficiency occurs early in life with severe infections and failure to thrive, and affected individuals will normally succumb within the first or second year of life without intervention. The clinical picture of ADA-deficient SCID is similar to other genetic forms of SCID, with persistent diarrhoea, dermatitis, and serious infections, often caused by opportunistic pathogens such as The ubiquitous nature of ADA also means that consequences of deficiency are not limited to lymphocytes, and many other systemic non-immunological features are also observed, with known impact on the nervous, auditory, skeletal, pulmonary, hepatic and renal systems as well as cognitive and behavioural abnormalities. Non-immunological manifestations have become more apparent in recent years as survival and immune reconstitution improves following stem cell transplantation, and awareness and identification of involvement of multiple organ systems is essential to allow timely optimal management.Children with ADA-deficiency have been shown to exhibit a range of behaviour abnormalities, including attention deficits, hyperactivity, aggression and social problems, which appear to develop independently of the influences associated with HSCT , 15. IQ Bilateral sensorineural hearing loss was first reported in two patients with ADA-deficiency who had been successfully treated with HSCT. Structural and infectious causes were excluded and both patients did not receive any conditioning prior to HSCT, precluding that as a potential cause and implicating the underlying metabolic defect . A high The metabolic role of adenosine deaminase and consequences of toxic substrate accumulation in the lungs has been demonstrated in experimental models, with ADA(−/−)mice displaying severe pulmonary inflammation, with accumulation of activated macrophages and eosinophils, and airway remodeling, reversible upon initiation of ERT . Mouse mSkeletal abnormalities such as involving the costochondral joints are widely reported, possibly related to an imbalance between nuclear factor-κB ligand (RANKL) and osteoprotegerin (OPG), disturbing the interaction between osteoblasts and osteoclasts and subsequent bone formation, although abnormalities are mainly only apparent on radiological imaging without dysmorphic consequences –24. The Hepatic involvement in ADA-deficiency appears to differ between mice and humans. Murine ADA(−/−) models display severe hepatocellular degeneration that is fatal in the perinatal period . In compWhile ADA-deficiency is widely accepted as a systemic metabolic disorder, it is important to consider that certain systemic manifestations have only been reported in a small number of patients. Other contributing factors such as infectious agents may be involved and further investigation into the underlying pathogenesis of these manifestations is needed. Nevertheless, awareness of multi-organ involvement is essential for optimal patient care.There is heterogeneity in the phenotype of ADA-deficiency, with approximately 15–20% of patients exhibiting a ‘delayed clinical onset’ presenting with less severe, but gradually worsening, combined immune deficiency later in life, usually within the first decade, but occasionally in adulthood , 30, 31.Unlike other forms of SCID, management of ADA-deficiency includes multiple options; ERT, allogeneic HSCT, and autologous GT, of which only the latter two are curative.ERT with polyethylene glycol-conjugated adenosine deaminase (PEG-ADA) is the one therapeutic option that is not definitive in terms of disease correction but allows systemic clearance or ‘detoxification’ of the toxic metabolic substrates. ERT is an option if there is not a suitable HSCT donor, or if there are contraindications to HSCT, however, long-term ERT is associated with sub-optimal immune reconstitution . Other lTraditionally, HSCT has been the treatment of choice for ADA-deficient SCID, usually performed as soon as possible following diagnosis to minimise the time exposed to high levels of toxic metabolites and before acquisition of infections. In the largest study to date examining the outcome of 106 patients with ADA-deficient SCID following HSCT, earlier HSCT was associated with a better overall survival but this did not reach statistical significance, possibly due to smaller patient numbers in the older groups . A superLess than 25% of patients with ADA-deficient SCID have a MSD or MFD available, and in such situations GT has become established as an accepted therapeutic option. Following initial development more than 20 years ago –43, GT fTransplantation using a MSD or MFD without conditioning early after diagnosis is associated with a good outcome in terms of survival and CD3+ recovery in the first year post HSCT , but litThe ubiquitous expression of ADA means that deficiency can lead to a complex systemic metabolic disorder with multiple organ involvement with potential to cause significant morbidity unrelated to the immunodeficiency. Further understanding of non-immune manifestations is required. Early definitive therapy with HSCT using a MSD or MFD results in a good overall outcome, and GT is now an accepted therapeutic option for those without a suitable donor. The long term outcome of patients regardless of the type of therapy given is unknown and further monitoring is needed.


Bacterial resistance to biocides used as antiseptics, dyes, and disinfectants is a growing concern in food preparation, agricultural, consumer manufacturing, and health care industries, particularly among Gram-negative Enterobacteriaceae, some of the most common community and healthcare-acquired bacterial pathogens. Biocide resistance is frequently associated with antimicrobial cross-resistance leading to reduced activity and efficacy of both antimicrobials and antiseptics. Multidrug resistant efflux pumps represent an important biocide resistance mechanism in Enterobacteriaceae. An assortment of structurally diverse efflux pumps frequently co-exist in these species and confer both unique and overlapping biocide and antimicrobial selectivity. TolC-dependent multicomponent systems that span both the plasma and outer membranes have been shown to confer clinically significant resistance to most antimicrobials including many biocides, however, a growing number of single component TolC-independent multidrug resistant efflux pumps are specifically associated with biocide resistance: small multidrug resistance (SMR), major facilitator superfamily (MFS), multidrug and toxin extruder (MATE), cation diffusion facilitator (CDF), and proteobacterial antimicrobial compound efflux (PACE) families. These efflux systems are a growing concern as they are rapidly spread between members of Enterobacteriaceae on conjugative plasmids and mobile genetic elements, emphasizing their importance to antimicrobial resistance. In this review, we will summarize the known biocide substrates of these efflux pumps, compare their structural relatedness, Enterobacteriaceae distribution, and significance. Knowledge gaps will be highlighted in an effort to unravel the role that these apparent “lone wolves” of the efflux-mediated resistome may offer. Biocides describe a chemically diverse range of antimicrobial compounds used as antiseptics, disinfectants, and preservatives. In an effort to eradicate potentially infectious bacteria from food preparation, healthcare, and veterinary facilities, biocides such as benzalkonium, chlorhexidine, and triclosan, are commonly used to disinfect exposed surfaces , periplasm, and plasma membrane (PM) through a protein complex between an outer membrane protein (OMP), a membrane fusion protein (MFP), and efflux pump protein(s)  family members such E. coli MacAB system (Poole Resistance-Nodulation-Cell Division (RND) efflux family members AcrAB  such as EmrAB  family , herbicides (methyl viologen), and dyes  that have one or more permanently charged cationic atoms, typically nitrogen, are referred to as quaternary ammonium compounds (QACs) . At only 110 amino acids in length (12 kDa), EmrE consists of four transmembrane α-helical TMH domains that arrange to form a minimal homodimeric functional unit  within the first TMH which participates in both H+ and drug binding during transport ; and paired SMR proteins (PSMR) based on phenotypic and phylogenetic sequence analysis  in comparison to QacE based on overexpression experiments , adenylyltransferase (aad), and dihydrofolate reductase (dfrA)  in E. coli that was later demonstrated to be a cloning artifact  related to the SMP subclass  and C- (7-12) terminal domains with a hydrophobic cleft connected by a cytoplasmic loop between TMH 6–7 similar to MFS members  superfamily   residue in the first TMH domain   due to its ability to relieve toxic concentrations of iron stress , and TM5 ; as well as a number of hydrophobic cleft forming residues located in TMH2, TMH3, and TMH5; along with salt bridge forming aspartate and lysine residues located in TMH3 and cytoplasmic domains   represent a family of transporters in all three kingdoms of life that confer metal tolerance/resistance by efflux of zinc and heavy metal ions , the type of growth media used, and the background genotype of the bacterial strain used to measure minimum inhibitory concentration values attributed to specific pump activity [as reviewed by , provide some hope that more responsible biocide regulations and stewardship may soon be on the global horizon. By reducing environmental biocide exposure, we may begin to reduce the selective pressure driving the spread and adaptation of these efflux systems towards biocides and antimicrobials.Single component efflux pump systems have been largely overlooked as compared to other well studied efflux families, such as multipartite RND pumps, however, their prevalence on mobile genetic elements, along with their frequent detection in healthcare and environmental Enterobacterial isolates, suggests that there is sufficient selective pressure to maintain and spread these efflux pumps to other systems. The selection for these single component efflux pumps may be perpetuated by the widespread overuse of antimicrobials, especially cationic antiseptics such as QACs, and the detection of these efflux pumps may be a marker for anthropogenic contamination of the environment with these antimicrobials; driving a shift towards decreased membrane permeability in Gram-negative bacilli. The recent ban of biocides from hand soaps by the US Food and Drug Administration (Sept. 2016), which includes triclosan, and many QAC antiseptics as well as even more stringent regulations imposed on the use and inclusion of biocides in commercial products by the European union over the last 10 years (Biocidal Products Regulation;


Performance-based incentives (PBIs) have garnered global attention as a promising strategy to improve healthcare delivery to vulnerable populations. However, literature gaps in the context in which an intervention is implemented and how the PBIs were developed exist. Therefore, we (1) characterized the barriers and promoters to prevention of vertical transmission of HIV (PVT) service delivery in rural Mozambique, where the vertical transmission rate is 12 %, and (2) assessed the appropriateness for a PBI’s intervention and application to PVT.n = 7, total participants N = 92) and elicited participant perspectives on PBIs. The ecological motivation-opportunity-ability framework guided our iterative data collection and thematic analysis processes.We conducted 24 semi-structured interviews with nurses, volunteers, community health workers, and traditional birth attendants about the barriers and promoters they experienced delivering PVT services. We then explored emergent themes in subsequent focus group discussions , high workload, stock-outs, poor infrastructure (facility environment), and delays in obtaining patient results and donor payment discrepancies (administrative). Community-based cadres’ opportunity challenges included lack of supplies, distance (work environment), lack of incorporation into the health system (administration), and ability challenges of incorrect knowledge . PBIs based on social recognition and that enable action on intrinsic motivation through training, supervision, and collaboration were thought to have the most potential for targeting improvements in record and referral systems and better integrating community-based health workers into the health system. Concerns about the implementation of incentives included neglect of non-incentivized tasks and distorted motivation among colleagues.We found that highly motivated health workers encountered severe opportunity challenges in their PVT mandate. PBIs have the potential to address key barriers that facility- and community-based health workers encounter when delivering PVT services, specifically by building upon existing intrinsic motivation and leveraging highly valued social recognition. We recommend a controlled intervention to monitor incentives’ effects on worker motivation and non-incentivized tasks to generate insights about the feasibility of PBIs to improve the delivery of PVT services.The online version of this article (doi:10.1186/s12960-016-0157-0) contains supplementary material, which is available to authorized users. The implementation of evidence-based biomedical practices and policies over the past decade has demonstrated potential to significantly reduce rates of vertical transmission of HIV to as low as 1–2 % . There, Mozambique experiences significant challenges to both uptake and delivery of PVT services. First, women of reproductive age experience a high prevalence of HIV (16 %), fifth-highest among women aged 15–24 globally . Second,Performance-based incentives (PBIs) have been effective in improving uptake and delivery of health services in low-resource settings. On the delivery side, PBIs are the distribution of money or material goods after a performance target has been achieved and aim to counteract weak health system incentives by aligning rewards with health outcomes . DeliverTherefore, we (1) characterized the barriers and promoters experienced by health workers delivering PVT services in rural Mozambique and (2) assessed the potential for PBIs to support delivery of PVT services.Two complimentary frameworks were applied to guide the study design and data analysis  Fig. 1)1). The ftécnicos de cirúrgia  have helped address the skilled labor shortage for surgical needs . Financial support could be used to help me as an individual, but it is not a way to improve the activities .All cadres were dissatisfied with the current form, amount, or timeliness of compensation. Nearly all community-based workers held another job, predominantly subsistence farming, to support themselves. While one activistas) and called for assistance in already-underway home births (to TBAs) challenged community-based cadres.For nurses, patients not presenting at the health facility, dropping out of care, and not adhering to treatment regimens challenged their ability to deliver PVT care. Patients who gave false addresses , expansion of services to treat adults (CHWs), and kits for attending “emergency” births (TBAs).All cadres reported lacking supplies or wanting additional ones to execute their responsibilities. Most problematic was medication stock-outs for PVT. Community-based cadres lamented that they lacked materials to assist in home care , two lacked electricity, and one did not have locks or running water. Both activistas and TBAs who traveled to patients’ homes and accompanied them to the health facility. For example, activistas were frustrated when they traveled long distances to find the patient was not home.Distance was a major challenge to activistas and TBAs into the health system resulted in missed opportunities to leverage their motivation and skills.Administrative-level challenges for nurses were tempered by the planned roll-out of new PVT programs, including the “one-stop” strategy to streamline PVT services in mid-2013 and Option B+ to initiate HIV-infected pregnant women on lifelong ART  in 2014. However, at the time of data collection, long waits for CD4 count and PCR infant HIV test results and referral of ART-eligible patients to large facilities were significant challenges to service delivery and retaining women in PVT care. In the community, lack of systematic incorporation of Discrepancy existed in raises and allowances between positions paid directly by the Ministry of Health and by donors. For example, HIV-specific facility-based workers whose positions were funded through the PEPFAR-implementing partner reported not receiving a raise when other facility-based colleagues did.All cadres were sensitive to their patients’ opportunity challenges. Nurses supported women in disclosing their HIV status to their partners and considered maternal finances when counseling on infant- and child-feeding options. Community-based workers were generally very sensitive to maternal poverty, food insecurity, and distance to the health facility.activistas and TBAs reported outdated and incorrect messages for HIV-infected women. One TBA reported just learning that attending home births without protection was a potential route of HIV exposure.Although this study was not designed to evaluate knowledge, health workers discussed the infant and young child feeding messages that they counseled women on. All nurses and some community-based health workers relayed the updated guidelines Mozambique had adopted , but somactivistas, and CHWs received refresher trainings on an annual basis. For nurses, these trainings were provided by the Ministry of Health often at the provincial level. For the activistas, training was provided by CARE International, and for CHWs, by the Ministry of Health at the district or facility level. Some TBAs had attended trainings over the decades they had served their communities, which had been provided by different organizations, including CARE, in partnership with the Ministry of Health. All groups reported wanting more training.Nurses, activistas, and CHWs welcomed additional supervision to help them learn and to provide on-the-job feedback. In addition, activistas wanted supervision from the health facility to increase recognition, tying back to extrinsic motivation.Nurses, Activistas met weekly, but TBAs reported interacting with other TBAs at irregularly held trainings.Nurse and CHW interactions within their respective cadres varied according to their health facility and community. All health workers were open to more collaboration to support mothers through the PVT cascade. Existing intra-cadre collaboration depended on the community leadership and cadre presence in the catchment area.Maternal and child health nurses and facility-based staff were interested in both personal incentives and reinvestment in service delivery. Suggested individual personal incentives included financial or material rewards such as paid work-related trips to the “best” performing health worker or group. Group incentives that built upon social recognition  were also of interest. Staff proposed reinvesting PBIs in collaborations , social support mechanisms , and infrastructural improvements  to help retain HIV-infected women and their HIV-exposed children in the cascade of PVT services.activistas were interested in directing incentives to support the sustainability of their associations. Activistas proposed using PBIs to build an office for meeting and storage space and to start income-generating activities. Similar to health facilities, activistas sought to use incentives  to support knowledge sharing and coordination of care with other community-based actors. Activistas saw opportunities to reinvest incentives in service delivery by repairing bicycles, community engagement , and facilitating community health worker collaborations.In addition to personal incentives and reinvestment in service delivery, TBAs were primarily interested in PBIs as means of individual financial incentives, materials to support their work , and collaboration with other community-based cadres.Suggested metrics for awarding incentives at health facilities included evaluation of staff performance through records and patient ratings of the quality of the care interaction. There was interest in both individual and group metrics; however, tracking metrics at the individual health worker level would be difficult with the record systems and reporting practices that were in place. In addition, health facility participants felt that all facility-based workers contributed to clinical PVT care, but tracking PVT indicators would primarily reflect nurse and midwife efforts.Activistas debated whether performance goals should be set at the individual or association level. While all cadres discussed effects on motivation, activistas were particularly concerned that awarding PBIs on an individual basis might demotivate their colleagues who did not receive the incentives. Activistas were concerned that incentives for particular indicators would detract from their other services.activistas, TBAs had no interest in setting group goals because they operated individually in their respective communities. TBAs also found individual goal setting problematic because of the variance in number of TBAs and pregnant women in their communities. Like activistas, TBAs were concerned with creating competition with their colleagues that would disrupt their collegial relationships.In contrast to the facility-based workers and This theoretically driven evaluation of barriers and promoters of PVT service delivery revealed that health workers were highly motivated but encountered severe opportunity challenges. Facility-based staff were challenged across the ecological motivation-opportunity-ability domains by late payment and uncompensated after-hours work (motivation) and patients circumventing care, poor referral and record systems, heavy workloads, stock-outs, poor infrastructure, and administrative factors (opportunity). We found community-based cadres were dissatisfied with compensation (motivation), challenged by lack of supplies, distance, lack of incorporation into the health system (opportunity), and incorrect and outdated knowledge on infant- and young child feeding (ability).Our findings reflect challenges encountered by facility-based workers in sub-Saharan Africa , 35. We One of the most striking challenges for community-based workers was the lack of integration into the health system, which threatens effective task shifting. Lack of integration and poor follow-up on their referrals prevents community-based providers’ efforts from translating into health impact , 43. In Our data suggest that PBIs would be appropriate for addressing the barriers that most cadres encounter across the ecological levels. PBIs are designed to target workers’ ability to act on intrinsic motivation  and external motivation  and are structured to address opportunity and ability challenges . FacilitOur participants’ concerns about the implementation of PBIs align with those in the literature. PBIs can introduce potential for neglect of non-incentivized tasks , gaming,We recognize that at the health system scale, incentives cannot overcome major structural barriers , includiWe employed a strong qualitative design that led to iterative analysis among the four cadres that deliver PVT services, including often-overlooked TBAs. The use of the ecological motivation-opportunity-ability framework addresses the dearth of multilevel theoretical frameworks that extend beyond an ecological approach to the advanced delivery of PVT care . FinallyThis study may not be generalizable to other regions of sub-Saharan Africa due to the history of Mozambique’s health system. However, given similarities in motivation and opportunity challenges across sub-Saharan Africa, this work contributes important perspectives to the appropriateness of a touted method to PVT services. The cross-sectional nature of the interviews may have precluded the building of relationships necessary to discuss grave challenges, particularly with the CHWs and TBAs who were not heavily engaged in participant observation. Participant responses may have been influenced by social desirability bias  as well Finally, this paper evaluates the appropriateness of PBIs in addressing barriers that health workers, but not HIV-infected pregnant women and mothers, experience. We recognize that multifaceted and community-engaged solutions are necessary to eliminate the vertical transmission of HIV , 63. HowWe found that highly motivated health workers encountered severe opportunity challenges in their mandate to prevent vertical transmission of HIV. PBIs have the potential to address key barriers that facility- and community-based health workers face in delivering care to HIV-infected women and their HIV-exposed children, specifically by building upon existing intrinsic motivation and leveraging highly valued social recognition. Therefore, a controlled intervention monitoring the effects of PBIs on health worker motivation could lead to important insights about the feasibility of PBIs to improve the delivery of PVT services.


Grass carp hemorrhagic disease, caused by grass carp reovirus (GCRV), is the most fatal causative agent in grass carp aquaculture. Protein-protein interactions between virus and host are one avenue through which GCRV can trigger infection and induce disease. Experimental approaches for the detection of host-virus interactome have many inherent limitations, and studies on protein-protein interactions between GCRV and its host remain rare.In this study, based on known motif-domain interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction pair searching strategy. These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. Differentially expressed genes during GCRV infection process were extracted and mapped to our predicted interactome, the overlapped genes displayed different tissue expression distributions on the whole, the overall expression level in intestinal is higher than that of other three tissues, which may suggest that the functions of these genes are more active in intestinal. Function annotation and pathway enrichment analysis revealed that the host targets were largely involved in signaling pathway and immune pathway, such as interferon-gamma signaling pathway, VEGF signaling pathway, EGF receptor signaling pathway, B cell activation, and T cell activation.Although the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. The findings of this work will contribute to the development of system biology for GCRV infectious diseases, and help guide the identification of novel receptors of GCRV in its host.The online version of this article (doi:10.1186/s12859-017-1500-8) contains supplementary material, which is available to authorized users. Ctenopharyngodon idellus) is an important aquaculture fish widely cultured in Asian countries, especially in China. However, disease outbreaks in this species are very frequent and leading to huge economic losses. Grass carp hemorrhagic disease that caused by grass carp reovirus (GCRV) is one of the most serious diseases, which mainly outbreak in young fingerling and yearling fish [Aquareovirus genus in the Reoviridae family. The genome of GCRV consists of 11 segments of dsRNA, and encodes eleven proteins, including seven structural proteins and four non-structural proteins [Orthoreoviruse than any other known species of Aquareovirus [Grass carp , the orthologous gene of JAM-A in human has been proved to be the only known receptor for mammalian reovirus (MRV). We further evaluated the influences of the interactions by analyzing expression data during different infection stages. Finally, functional annotations and pathway analysis were performed to explore the potential mechanisms associated with host targets. The present work provided the first system-based framework about the interactome of GCRV infection, the findings may complement and guide further experiments aiming to identify host hub genes that are necessary for GCRV survival and replication within the host cells.PPI is always driven by contact of essential residues around interface in DDIs (domain-domain interactions) and DMIs (domain-motif interactions) . CompareFirstly, we performed domain annotation against the grass carp protein sequences by the software InterProScan , here we3did database includes 549 motif patterns, 149 domains, and 651 domain-motif interactions, including inter-chain interactions and intra-chain interactions. However, iELM database includes 103 domains, 206 motif patterns, and 225 domain-motif interactions. There are only 48 domains appeared in both databases, suggesting the discrepancy in database construction. These overlapped domains are more likely to interact with motifs, such as SH3_1, PDZ, WW domains, which were once proved to be the most highly interactive domains, recognized by short peptides, in signaling pathways . The datThereafter, we linked the motifs to host proteins containing its domain partners. Previous studies proved that host proteins in virus-host PPIs expressed abundantly across multiple tissues . Thus weVarious types of motif patterns were detected among different proteins. We found that several virus proteins shared the same interacting domains by using different motifs in both databases, such as ARM, SH3-1, PDZ domains. In contrast, SspB domain was only predicted to interact with S8 protein. We also found that the number of occurrences differs greatly across domains, as shown in Fig. GCRV virus-host interaction network consists of 11 virus proteins and 1757 host proteins. The statistics information of GD108 and the number of predicted host proteins were listed in Table For GCRV, the outer capsid proteins, such as VP7, VP5, are always proved to play key roles in virus’s attachment and infection by interacting with proteins expressed on host cell surface , but theWe performed structure comparison aiming to illuminate the underlying interaction mode between JAM-A and Sigma1 proteins. For MRV, Sigma1 protein is a fibrous trimer, consisting of an elongated tail N-terminal domain and a globular head C-terminal domain. The N-terminal domain inserts into the virion, whereas the C-terminal domain projects away from the virion surface. Hence, Sigma1 protein attaches the virion to the host cell membrane , 35. We p-value < 0.05, |log2 (Fold_Change)| > 1.5) were present in our virus-host interactome. We listed the detailed information about these genes in Additional file CIS, STA31, STAT4, STAT1 and so on, are mainly involved in negative regulation of cytokines, and function in signaling through the JAK/STAT pathway. Likewise, RHOG, RAB20, DBNL, CTTN and FAM111A genes participate in pathways of micropinocytosis and phagosomes. FAM111A gene is proved to be targeted by virus to overcome host range restriction to promote virus DNA synthesis and play a key role in defense response to virus [When a pathogen infects its host, extensive PPIs happen along with related altered gene expression level. Thus, transcriptomic signatures may be useful in identifying genes that play crucial roles during infection process. We obtained RNA-seq data from four diseased grass carp tissues  with three replicates at four times after  GCRV challenge , and invto virus . Hence, p-value < 0.05, binomial test). The top 20 significantly overrepresented pathways were shown in Fig. In order to explore whether or not host proteins targeted by GCRV are involved in essential infection events, we carried out gene ontology analysis and pathway analysis against the total putative host targets. A total of 48 cellular components were annotated Fig. , includiCdc42 and Rac signaling, indicating that this signaling was also involved in the response to GCRV infection. These findings suggest those genes that expressed on the surface of cell are worthy of further studies and provide more chances for the development of vaccine.Reovirus infection is initiated by attachment of the virus component to different receptors expressed on the cell surface, and spur post binding signaling events, some lead to a cascade of apoptosis, others trigger immune response . HoweverProteins are the vehicles of immune response and of viral entry into cells, identification of virus-host PPIs is at the heart of virus research. Besides possessing smaller genome and fewer proteins, viruses always distinguish them from other pathogens for lacking of known domains and fast evolutionary rate. Due to high cost of traditional experiments and of transient nature of PPIs between virus and host, identification of virus-host PPIs is a challenge task. With the accumulation of fast-growing sequence and structural data, many computational approaches have been successfully applied to predict pathogen-host interactions , 15, 39.Aquareovirus, even Orthoreovirus, have been rarely seen. Grass carp hemorrhagic disease, caused by GCRV, has become the most fatal causative agent in grass carp aquaculture. The task of identifying host proteins targeted by GCRV is worthwhile because it may help decipher underlying disease mechanisms and vaccine design. In this study, we adopted a method that based on structural information of motif-domain interactions deposited in two existing data resource, and successfully predicted the PPIs between GCRV and its host grass carp, by using GD108 as the representative GCRV strain. Compared with other computational methods, using structural information as platform to predict PPIs can also provide the detailed information about interfaces that proteins interact through. Although we combined two motif databases to compile a more refined known motif-domain interaction information, the overlapped domain content is limited, suggesting the discrepancy in database construction.Despite that computational approaches have been successfully applied in prediction of PPIs in pathogen-host system, there are still few published reports about PPIs in non-model species conversely. To date, the reports of studies on PPIs of GCRV viruses of different subgroups have not only rather limited sequence identities due to fast evolution, but also the level of pathogenicity, subtype II strains are pathogenic higher and spreading more rapid than subtype I. The cause of this discrepancy may lie in the fact that diversities in protein sequences among different strains lead to different interactome in host. We found that various motifs were identified corresponding to different domains, indicating wide diversity of binding modes for components of GCRV. Motifs of Sigma1-like protein that maybe known as the counterpart of Sigma1 protein in MRV were also detected to interact with JAM proteins in grass carp. Function analysis showed that many proteins are involved in biological regulation and signaling pathways, suggesting that many interactions are transient and partially explain the virus targeted interface tend to be “date”-like , that isThe GCRV infection caused pathology and physiologic dysfunction in a wide range of organs and tissues. Previous study has suggested that reovirus spread from the intestine to sites of secondary infection through bloodstream dissemination , indicatOn the whole, it is still difficult to judge the accuracy of predictions for protein interactions in host-virus systems, especially for those viruses such as GCRV that have received less attention than their worldwide burden deserves. It is expected that the findings of our work will contribute to the development of system biology for GCRV infectious diseases, and help guide the identification of novel receptors that GCRV targeted by.In brief, we demonstrated the power of motif-based strategy to predict virus-host interactome in a non-model species. Our work provided a systems-based framework for the understanding of the GCRV infectome and diseasome. This is the first draft description of PPIs for GCRV virus-host system, and the results will complement and guide further experiments aiming to identify host hub genes that are necessary for GCRV survival and replication within the host cells. Although the predicted PPIs may contain some false positives, the computational methods provide reasonable amount of interactions which can be further validated by high throughput experiments. Our work will contribute to understanding the mechanism of pathogenesis associated with GCRV infection, and prioritize targets for a rational vaccine-design and disease-resistant breeding.Grass carp protein sequences were downloaded from our previous work . InterPrFor each motif set of GCRV based on the above two databases, If one GCRV protein was both predicted to interact with the same domain in the two datasets, we considered that this interaction pair was true. However, both databases have different domain contents, which may lead to loss of some important domains. Hence, for both databases, we collected the interactions between database-specific domains and motifs. Furthermore, we evaluated the occurrences of motif patterns, some motif patterns that can be frequently appeared in any protein were discarded (occurrences >4), thus the rarely appeared motifs were reserved and added to the previous interaction pairs. Finally, we linked the motifs to host proteins containing its domain partners.Previous studies proved that host proteins in virus-host PPIs expressed abundantly across multiple tissues , thus weWe downloaded the complex structure (PDB ID: 3eoy) between MRV Sigma1 protein and human JAM-A protein from Protein Data Bank (PDB) database . Structup-value < 0.05, |log2 (Fold_Change)| > 1.5). The four resulting DEGs sets were merged together, and mapped to our predicted host targets. Hence, the overlapping genes were not only host targets but also demonstrating different expression, we analyzed the expression profile of these genes.Transcriptome data were retrieved from our previous work to investigate the expression pattern of host proteins targeted by virus proteins during various stages of GCRV infection. RNA-seq data were obtained from four diseased grass carp tissues  with three replicates at four times after  GCRV challenge , 54. ExpGene functional annotation for host proteins targeted by GCRV GD108 was performed by using Blast2GO software . Pathway


The decision to implement an orders-based versus an encounters-based imaging workflow poses various implications to image capture and storage. The impacts include workflows before and after an imaging procedure, electronic health record build, technical infrastructure, analytics, resulting, and revenue. Orders-based workflows tend to favor some imaging specialties while others require an encounters-based approach. The intent of this HIMSS-SIIM white paper is to offer lessons learned from early adopting institutions to physician champions and informatics leadership developing strategic planning and operational rollouts for specialties capturing clinical multimedia. Images are being captured with increased frequency across specialties outside of radiology and cardiology throughout medical enterprises, including dermatology, ophthalmology, wound care, otolaryngology, and emergency departments . Secure,We define encounters-based imaging as being performed during a clinic visit or procedure when image content acquisition is not considered the purpose of the visit. There is usually no indication preceding the visit that imaging will be performed and imaging is at the sole discretion of the provider, as with dermatology photos. Often, encounters-based imaging compliments other clinical documentation, including progress notes, associated to the visit or procedure and may be referenced during follow up, surgery, or additional diagnostic exams.Orders-based imaging acknowledges a more traditional approach . An ordeFrom a technical perspective, encounters-based imaging may be considered unsolicited, whereas orders-based imaging is considered solicited. However, this differentiation depends upon the methods employed by an organization to handle encounters-based images . When anIdentify all images associated with the care event, through the assignment of a unique study identifier,Associate images with a patient encounter, usually through a modality worklist or patient schedule,Manipulate image data, if required by the image use case,View images within the electronic health record (EHR) or directly from the EHR through a link associated with the note or report describing the visit where the images were obtained,Easily identify the type of imaging performed and the anatomical region through an EHR imaging description,Associate report or note describing the visit where the images were obtained with images in enterprise viewer, andSearch necessary imaging metadata to serve business intelligence needs.Regardless of the enterprise imaging strategy or individual workflows used, orders-based and encounters-based image storage and management workflows utilizing standards-based methods should provide the ability to:Common clinical examples of orders-based image management workflows include procedures that are separately billable, having usually a technical and professional fee charged, such as MRI, CT, radiography, and echocardiography. There typically is a result separate from the originating clinical encounter; this result may or may not be necessary as part of reimbursement. Orders-based imaging workflows often require downstream system integrations for efficient resulting, such as to structured reports in echocardiography, electrocardiography, and obstetric ultrasound.By contrast, several use cases exist today which are often first defined as encounters-based workflows for image management. Encounters-based workflows usually do not require a separate result and instead findings would be found in an associated encounter, procedure, or progress note, regardless of the visit being ambulatory, inpatient, or acute care. Medical photography is the most common use case for encounters-based workflows today. Often, but not always, dermatology, plastic surgery, emergency services, pathology, and endoscopy providers prefer encounters-based approaches. Recently, ophthalmology clinics are repositioning toward orders-based workflows due to reimbursement, report needs, and EHR integrations.With respect to performing department user workflow, requiring an order for imaging performed ad hoc, acquired during clinic visits or associated with a procedure is not intuitive for clinicians and may be perceived as a responsibility not appropriate for a non-physician. For specialties like dermatology or wound care, multiple orders may be necessary to differentiate varied body parts and laterality. More specific localization information, like anatomical position, would require significant build within an EHR and may create system manageability issues. Difficulties in following moles, and other skin disorders/pathologies, without identifying more specific localization information may occur when several images of the same body part are acquired to document and follow multiple moles on the same patient. Placing orders for ad hoc imaging may require additional steps for the ordering clinician, such as opening an encounter only for imaging order placement. Multiple orders will also require clinicians to select a new modality worklist entry (DICOM MWL) for each order placed prior to acquisition and may inherently deter acceptance and compliance. For example, a patient on whom clinical photographs are taken in multiple anatomic locations, such as the right hand, upper back, and left ear, an orders-based workflow would require separate order placement for each set of images.While specialties such as radiology may be able to offer orders combining multiple body parts which are often imaged together, this is not feasible for other specialties such as dermatology. For example, a CT of the chest, abdomen, and pelvis is routinely performed on patients based upon diagnosis protocols, whereas in dermatology, the body parts imaged are rarely indicated prior to the clinical visit and may be one of thousands of possible combinations. Although the ability to automatically spawn orders from an order set, or upon scheduling a clinic visit, is possible, implementing this build with encounters-based imaging may require a more generic description as the clinic visit will usually not contain indicators of the imaging to be performed. Since encounters-based imaging follows an ad hoc workflow, implications to post-procedure workflows may be noted, including cleanup of unused orders.Encounters-based imaging workflows usually involve manually typing name and medical record number into the modality before images are taken. While this may take more time than entering the order and choosing the order at the modality, these steps are often done by non-providers in parallel with other patient care events by the provider. Limitations in resource availability to enter orders present administrative challenges. For example, staff may not be available or sufficiently trained to enter the order prior to acquisition and address subsequent order matching requirements and clean-up. Additionally, and perhaps of more significant concern, manual typing of patient demographics and exam information increases the probability of inaccurate identification and a higher incidence of data entry errors , 9.For encounters-based imaging methods to be viable, mechanisms enabling the delivery of consistent image-specific information should be available on the capture device, including body part identification, acquiring specialty or an associated procedure description, and delivered as part of the image metadata. EHRs today are typically very familiar with orders-based approaches in radiology and cardiology and have components to accommodate those workflows; encounters-based workflows vary considerably and are generally not as well integrated with EHRs. The most notable considerations and implications of orders-based and encounters-based approaches before imaging are outlined in Table Major benefits associated with using an orders-based workflow include EHR users often find it permits better searchability and content relevance and is widely supported by image management systems and EHRs. A user may know if a given line item entry in the EHR pertains to their information need, or not, based on the order description and without opening the hyperlinked images. For example, a knee surgeon searching for scope camera images may be interested in knee scope images EHR entries, and will happily bypass elbow scope images. In contrast, encounters-based workflows may result in non-standard or generic imaging descriptors in the EHR.Entirely orders-based workflows do have downsides after the procedure. Reconciliation workflows must be developed for cases where orders are not placed before imaging is performed, as occasionally happens during emergency department FAST exams. Likewise, when a procedure is performed and an imaging order is placed, but images are lost or never obtained, a cleanup process for the order is necessary. This cleanup may come at the expense of the user who placed the order or the institution health information management department.In encounters-based approaches, some image management archives can instantiate orders from the modality sending the images, such that images from a given modality are all assigned an identical procedure order. This workflow may have limitations with modalities that are shared between multiple clinical specialties , where a single order  may not be relevant or intuitive to EHR end users. Some organizations may instead employ ADT to orders transformation logic, generating the accession number within an interface engine and delivering a generic procedure description. This workflow may result in multiple instances of the same generated order or multiple body parts mixed within a single instance.Image display protocols and multidisciplinary relativity should also be considered. The body parts and procedure descriptions traditionally associated with orders-based imaging often drive the ability to identify priors of like content for automated viewing protocols. Encounters-based workflows may only provide a lengthy encounter number and generic study description, unusable for such purposes. When implementing encounters-based workflows and desiring multidisciplinary relativity, it is necessary to determine the capabilities available for associating body part and a detailed description with the acquired images. Generic descriptions such as clinical photo will not provide enough information for comparison internal to the department or external to other specialties. The most notable considerations and implications of orders-based and encounters-based approaches after imaging performance are outlined in Table EHR vendors today may have limited capability to index and tie metadata to medical images, perform image lifecycle management functions, or share images outside of the EHR system. Document management systems may be functionally limited in relating priors for comparison, may not offer multidisciplinary relativity capabilities, and may not support video and associated audio. Thus, EHRs and document management systems can not be the single location for storage of all medical images today; a separate vendor neutral archive or picture archiving and communication system (PACS) remains necessary. However, EHRs or document management systems may be the single storage location for a given specialty within a health system if the images are not DICOM, if metadata indexing is not critical to that specialty, comparison across acquisition dates is not desired, availability of a continuous image record across specialties is not essential, or if resulting workflows heavily favor having result text and images consumed together clinically on a given user interface.In EHRs, using an orders-based workflow requires orders creation and distribution to the lists of commonly requested or performed procedures of involved clinical staff. Providers may not want the extra responsibility of placing an order for the image-based workflow to support image storage. Most providers would prefer to encourage their staff to adopt the order placement similar to how they may encourage their in-clinic staff to populate an ultrasound modality with demographic metadata in preparation for image capture. Often, the non-provider staff that the provider would prefer place the order do not have clearance to place EHR orders because this level of system security would also provide them with access to order many unrelated procedures. Designing an imaging workflow must additionally consider the access securities of those who would use it.Automated methods of spawning an image order from appointments, operative case requests, and procedure encounters may not be technically available in all systems. Automated methods may present further challenges in specialties acquiring clinical photos such as dermatology and emergency services, as the visit does not specifically identify the body region where photos may be acquired. Confusion with compliance, IT, or operations staff may also be noted, believing that the order to store images actually represents an order to perform a procedure; for example, a scope camera image storage order may be misperceived as the order to perform an endoscopic procedure.The support for DICOM modality worklist capabilities, both on modalities and on image review software applications, among vendors outside of cardiology and radiology is inconsistent. Workgroups and development is ongoing in specialties such as ophthalmology and pathology . For botIn an encounters-based image archive model, solutions are expected to interpret and utilize a wide array of ADT events including A01s (Pt. Admit), A04s (Pt. Registration), A02s (Pt. Transfer), and A10s (Pt. Arrived) . Logic sIn contrast with EHRs, many PACS do not support non-DICOM image storage and distribution, leading organizations to look to VNAs for Cross-Enterprise Document Sharing (XDS) content support or requiring the purchase of vendor-specific systems to manage content and output DICOM formatted image files to the larger, centralized archive . AlthougDepending on the method of storage, images from encounters-based workflows may be more difficult to locate or share outside of the institution. Some EHR and ECM systems have imaging content storage that does not easily accommodate record sharing or transfer of images outward. A more extensive image exchange discussion is detailed in the HIMSS-SIIM Joint Workgroup white paper “Considerations for Exchanging and Sharing Medical Images” . The mosImage metadata applied from an order offers easily searchable terms for query and analysis. Although available image metadata may include patient- and order-specific information, often encounter information is not consumed or stored in a PACS or VNA and remains unavailable unless managing analytics through a third party data warehouse. Visit-specific information such as admitting diagnosis compared with resulting diagnosis may be desired for research, peer review processes, and quantifying value. Orders-based workflows may employ questions suggested or required during the order process that may capture additional relevant information for analytics.A compromise that sites employing encounters-based workflows may sustain is having inherently “dirty data” in exchange for fewer clicks. Currently, there is limited ability within encounters-based workflows for data/exam validation the way there is with orders validation. For example, user typos manually entered at the modality to associate images with a patient and encounter can result in downstream errors of image association within the chart. In this instance, images could be lost or be filed in the wrong patient’s imaging record. Metadata added during encounters-based workflows, which are isolated to the storage system, will also limit the ability to search using EHR level queries. The most notable metadata considerations and implications of orders-based and encounters-based approaches are outlined in Table Results may take several forms, and often differ based on a given provider or specialty’s use of orders or encounters-based imaging. Results may simply be an unstructured image description or a reference in the patient’s clinic note incorporated into other diagnostic test results. The image result may consist of a discrete description with a standard or frequently used template format. The result may be fully structured text, fully unstructured, or a mix of the two.It is important for some specialties to include textual descriptions of the findings on the image, and ideally have the two reference each other. For example, the description and the image of a rash are often very valuable together, and more difficult to understand separately. With a small number of images, the images and result may be easily linked in same categorical or tabular EHR location, and often consumed in the same graphic user interface at any moment.However, some order-based imaging specialties, such as cardiology and radiology, have many images per exam and require dedicated image manipulation tools for image review. All images from these specialties cannot be efficiently incorporated into an EHR note. Thus, resulting orders-based exams with images is best done through either a hyperlink to the full set of exam images that opens a dedicated viewer, or only the most critical images from the examination should be incorporated with the exam text.Encounters-based workflows can be supported if resulting is managed through the EHR/Information System. It is challenging to manage when using third party resulting products. Providing imaging results back to an EHR/Information System without an order is not currently supported, unless the archive is capable of storing and relaying the associated visit number. Although this can associate the result to the encounter, it may also create two unlinked records within the encounter; one for the image hyperlink and another for the result. Delivering the EHR result to an image archive may present additional challenges associating the result to the images acquired during that visit.When implementing a workflow requiring order placement in addition to the actual procedure order, as with scope video associated with a surgical procedure, the procedure notes and result may appear in a separate location from the imaging. Requiring the placement of multiple orders against a procedural encounter should be carefully considered when designing EHR and imaging workflows. Further noted, EHRs are often limited in their approach to intuitively display reports and notes with the associated images, frequently storing them as separate documents in the EHR, electronic content management system (ECM), or PACS/VNA. The most notable considerations and implications of orders-based and encounters-based approaches for resulting are outlined in Table Reimbursement usually drives how organizations design their imaging workflow rather than the imaging workflow determining how billing will occur. For example, if some insurers require a separate report for US exams, while others allow the result to be interpreted within a procedure note, an organization will most likely require that all US exam results be interpreted as separate reports. Usually, a third party product is used to dictate the US reports and an orders-based workflow would then be necessary. In some cases where a separate result is not required, a technical fee, if billable, can be added as charge and the pro fee wrapped into the clinic visit.Generally, the method of image storage and management does not impact billing and reimbursement, assuming the images are stored somewhere that can be accessed in the event of a billing audit. However, long-term image storage is often required by regulatory or accreditation agencies or by insurers for reimbursement. In some cases, insurers require submission of imaging performed prior to a procedure for reimbursement of the procedure, as with clinical photos required for reimbursement of a blepharoplasty. This storage may occur either with encounters-based or orders-based approaches.For specialties practicing purely visible light still imaging, handheld photography, or video, such as dermatology or plastics, translating clinical workflows into the EHR leaves for clumsy and click-heavy image management and exceptions workflows. The majority of high-resolution cameras used in hospitals today cannot accommodate a DICOM modality worklist or an EHR ADT feed to associate images with metadata or with a patient encounter. The smoothest workflow today for clinical staff in dermatology, wound care, plastics, and other specialties utilizing photos for clinical documentation and follow up lies in image capture and management without orders. Orders-based workflow in these specialties is simply time prohibitive, user-unfriendly, and should not be expected.To better support orders-based imaging workflow, EHR vendors should facilitate development of order securities that permit placement of order “containers” for images to live under in the EHR to document care, but do not permit placement of diagnostic test orders to dictate care. Application of searchable metadata to the orders should be simple and available at the point of care. Developing efficient processes for automated order or order set placement by non-providers during close encounter workflows could make metadata association with captured images easier. Finally, EHR vendors should better facilitate orders-based workflow image consumption alongside clinical text.To better support encounters-based imaging workflow device vendors of visible light technologies will need to establish standards-based methods to provide a patient schedule, pass constant values describing image content, and make associating the image metadata more user friendly and time efficient than non-provider clinic staff placing an order. Image management systems will also need to develop practical support for encounters-based workflows, which is scalable across service lines and includes storage and utilization of ADT and case scheduling (SIU) events, provides workflow management tools, and supports EHR integration in conjunction with order-based images.Whether an organization implements an orders-based, encounters-based, or combined workflow, developing methods to dynamically incorporate select archived images within progress notes, encounter notes, or distinct reports can eliminate the need to copy/paste or import specific images to provide a more complete result.Identify all images associated with the care event, through the assignment of a unique study identifier,Associate images with a patient encounter, usually through a modality worklist or patient schedule,Manipulate image data, if required by the image use case,View images within the EHR or directly from the EHR through a link associated with the note or report describing the visit where the images were obtained,Easily identify the type of imaging performed and the anatomical region through an EHR imaging description,Associate report or note describing the visit where the images were obtained with images in enterprise viewer, andSearch necessary imaging metadata to serve business intelligence needs.The goals of orders-based and encounters-based workflows are very similar, and ultimately amount to best patient care:It is anticipated that traditionally DICOM-based diagnostic image specialties such as cardiology, obstetrics, and radiology will stay orders-based for the foreseeable future. At least today, organizations prioritizing imaging analytics and searchability of images within the EHR may choose orders-based workflows in many clinical areas to capture necessary metadata to drive business intelligence and care after the initial image capture encounter. In environments with evolving and quickly advancing imaging use cases and technology, such as ophthalmology, operative suite, scope camera, and pathology, the choice of orders-based versus encounters-based workflow remains unclear. Future development and innovation is ongoing.Orders-based workflows, while more refined and technologically supported, may create clinical workflow challenges for certain specialties where the imaging is inherently encounters-based and unpredictable. Counter-intuitive image acquisition and storage methods may incur provider frustration and limited adoption.Currently, encounters-based imaging workflows are minimally developed by medical imaging device and system vendors, and are sub-optimally accommodated by EHRs. Many of the visible light modalities primarily associated with encounters-based imaging lack standards-based acquisition and storage methods resulting in limited associated metadata, generic descriptors, and prevalence for manual entry errors, EHR searchability issues, and analytic impact.When determining which workflow to implement, organizations should understand the benefits and impacts within their environment and be clear with industry partners on needed functionality, while accommodating the workflow that provides the best patient care for that use case. We recommend that the goals proposed within this paper additionally be considered to ensure content availability and value.


Rheumatoid arthritis (RA) is an autoimmune, inflammatory disorder associated with excess cardiovascular morbidity and mortality. A complex interplay between traditional risk factors  and chronic inflammation is implicated in the development of premature atherosclerosis and consequently in the higher incidence of cardiovascular events observed in RA patients. Despite the acknowledgment of elevated cardiovascular risk among RA individuals, its management remains suboptimal. While statin administration has a crucial role in primary and secondary cardiovascular disease prevention strategies as lipid modulating factors, there are limited data concerning the precise benefit of such therapy in patients with RA. Systemic inflammation and anti-inflammatory treatments influence lipid metabolism, leading to variable states of dyslipidemia in RA. Hence, the indications for statin therapy for cardiovascular prevention may differ between RA patients and the general population and the precise role of lipid lowering treatment in RA is yet to be established. Furthermore, some evidence supports a potential beneficial impact of statins on RA disease activity, attributable to their anti-inflammatory and immunomodulatory properties. This review discusses existing data on the efficacy of statins in reducing RA-related cardiovascular risk as well as their potential beneficial effects on disease activity. Rheumatoid arthritis (RA) imparts a significant risk for cardiovascular disease (CVD)-related morbidity and mortality , 2. It iDyslipidemia constitutes the leading factor for cardiovascular events in the general population, making it the key target of current primary and secondary CVD prevention strategies . In thisCardiovascular events remain the major cause of death in patients with RA, urging a reassessment of the current approach to CVD risk management. Although many lines investigating this topic have been written, the exact benefit from statin treatment in RA needs further clarification. The scope of this manuscript is to undertake a narrative review of existing literature on the efficacy of statins in CVD prevention in RA, to discuss existing and future therapeutic targets arising from their pleiotropic pharmacological properties while addressing knowledge gaps and future research.ClinicalTrials.gov to search for any recently completed or ongoing relevant pharmaceutical research. Conference proceedings, not accessible abstracts, case reports, or articles not in English, were excluded  test provides an ultrasonic assessment of nitric oxide-dependent vascular endothelial function, which is disturbed in atheromatous vessels . ArteriaIn a trial of 20 RA patients, administration of simvastatin 40 mg/day significantly improved FMD compared with placebo . NotablyThe effect of intensive lipid lowering treatment was evaluated in the ROsuvastatin in Rheumatoid Arthritis and Ankylosing Spondylitis study , 39. A rIn the context of biomarkers of endothelial activation, the Trial for Atorvastatin in Rheumatoid Arthritis (TARA) included 116 RA patients, randomized to receive 40 mg atorvastatin or placebo additionally to the existing disease-modifying therapy. A significant improvement in intercellular adhesion molecule 1 and fibrinogen levels was observed in the atorvastatin group after six months of treatment .Taking it all into account, statins seem to have a favorable effect on structural, morphological and biochemical parameters of vascular function in RA patients, particularly those with higher disease activity Table . HoweverSeveral factors seem to influence the lipid profile of RA patients, including inflammatory disease activity, antirheumatic drugs, and reduced physical activity . Despitepost hoc analysis of 4,655 patients included in tocilizumab trials found that postbaseline initiation of statins was related to a gradual decrease and stabilization of LDL-C after two years of treatment, in contrast to the patients not receiving statins, where a significant increase in lipid levels was observed  levels . Lipid lThe oxidized particles of LDL-C, known as oxidized LDL (oxLDL), are recognized as crucial factors in the pathogenesis of atherosclerosis, inducing endothelial dysfunction through stimulation of monocyte infiltration and smooth cell proliferation, impairment of endothelial signaling and generation of reactive oxygen species . AtherogControversial data were presented from a retrospective analysis, addressing an adverse relation between markers of inflammation and the likelihood οf achieving LDL therapeutic targets in RA subjects . The pren = 2,986, median follow-up of 2.53 years) indicates a 34% reduction of major cardiovascular events in the statin group compared to placebo .While several reports highlight the improvement of various CVD markers and effectiveness in dyslipidemia management after statin administration in RA, comprehensive assessments on the statins’ potentials on CVD prevention can be obtained through controlled trials with “hard” cardiovascular end points. Aimed at assessing the hypothesis of atorvastatin’s superiority to placebo, the TRACE-RA trial  without previous cardiovascular event, statins induced a 16% decrease in TC levels and were associated with a significant CVD risk reduction  and all-cause mortality  . ComparaCurrent guidelines encourage the early initiation of statins and the adoption of strict LDL-C treatment goals after the incidence of myocardial infarction (MI) , 62. As p = 0.70), while no difference was noted considering the lipid lowering effect of treatment, although lower baseline TC and LDL-C values were recorded in the RA group. In addition, a post hoc analysis of the IDEAL trial and data provided by the Treating to New Targets study, also examined the effect of intensive statin therapy on secondary composite cardiovascular outcomes. The study reported a 20% cardiovascular risk reduction with atorvastatin 80 mg in both patients with and those without inflammatory joint disease, compared to less intensive statin treatment  study . Cardiovreatment . HoweverThe general consensus is that statin treatment in RA is not inferior regarding both the achievement of lipid targets and cardiovascular risk management, compared to the general population. To provide additional support, poor compliance in RA patients already assigned to statin treatment was associated with 67% increased risk of acute MI , regardless of the timing of first statin prescription or prior CVD status . Last buIdeally, more prospective, large controlled trials investigating the impact of statins on hard cardiovascular outcomes in RA patients are needed. Ethical considerations, and the very large sample sizes and long follow-up periods required to reach statistical significance, make such trials extremely difficult. Therefore, a reevaluation and elaborate approach of existing data becomes more necessary in order to redefine the role of statins in CVD management in RA.Although in the general population the cardioprotective effect of statins is almost entirely attributed to their lipid-lowering properties, there is some evidence supporting that their therapeutic properties expand beyond these and may be particularly elevant in inflammatory states such as RA. Their so-called pleiotropic effects include anti-inflammatory, antiproliferative, antithrombotic, antioxidative, and immunomodulatory properties  Figure . Hence, p = 0.0002), with an I2 value of 68%, documenting the positive effect of statins on RA activity  and acute-phase reactants compared with placebo after 6 months of treatment . Greateractivity . InteresThe contribution of statins to the improvement of clinical aspects of RA could be attributed to their ability to affect multiple steps in the pathogenesis of the disease. Chronic joint inflammation results from the overexpression of several inflammatory mediators, including cytokines, growth factors, adhesion molecules and T lymphocytes . Given tOn the other hand, the reduction in CRP levels following statin treatment might not necessarily be accompanied by improvement in the overall disease status, as shown in a study evaluating the effects of 6-month rosuvastatin therapy in 50 RA patients . In contp = 0.007)  .Most of the observations concerning the anti-inflammatory effects of statins were made on study populations already receiving a multitude of disease suppressing drugs, so any impact on systemic inflammation cannot be attributed solely to a statin effect. Although some of the evidence points to a potential anti-inflammatory statin effect in RA, this “additional” effect has not been consistent or accurately quantified and its clinical significance (in the context of high-grade rheumatic inflammation) remains undetermined. However, the lack of significant adverse events in RA patient cohorts receiving several other potentially hepatotoxic medications is reassuring and their significant clinical effect at reducing cardiovascular risk make them an attractive choice in suitable patients.Optimal cardiovascular risk management remains a challenging theme in RA. Inflammation and primary atherosclerosis are highly associated and cannot be treated as independent factors. Statins have a beneficial impact on RA-related cardiovascular risk, due to their lipid lowering but also possibly angioprotective, antioxidative and anti-inflammatory effects. This, and their safety profile, makes them an ideal choice in the overall armamentarium aimed at complete control of RA disease and associated vascular morbidity. Despite this, the blanket use of statins on all RA patients cannot be supported by evidence, thus appropriate CV risk assessment tools for this population are necessary, which in addition to established risk factors could include non-invasive vascular assessments, particularly carotid IMT . WhetherSS: literature search and writing of the manuscript. EN: design and revision of the manuscript. TD: literature search, writing, and revision of the manuscript. GK: design and final revision of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Rapid Diagnosis of Chikungunya Virus Infection To the Editor: Chikungunya virus (CHIKV) has become a global health problem. Clinical manifestations are not specific and are difficult to differentiate from those of similar viral diseases . Diagnostic laboratories must be prepared to meet the changing epidemiology of viral diseases. CHIKV infection is currently identified by viral genome detection, using reverse transcription PCR (RT-PCR), viral culture, and serologic testing for IgG and IgM by indirect immunofluorescence (IFA) or ELISA. RT-PCR is most sensitive during the early phase of CHIKV infection (within 5–7 days of symptom onset), but its use is limited by the short viremic phase of the disease. After the acute phase, serologic testing for IgG and IgM is a more accurate indicator of disease. Molecular and serologic tests are complementary, reliable, and sensitive methods, but they require special equipment and a medium-to-high level of technical skill that may not be available in many laboratories, especially those in rural areas, where outbreaks usually occur.Accurate and rapid detection of CHIKV infection by reliable point-of-care (POC) assays has been recommended to facilitate outbreak control. To meet this need, rapid CHIKV IgM POC tests are now available, but little information exists regarding their performance. The sensitivity of these tests evaluated in settings with a high prevalence of CHIKV infection is poor (range 1.9%–50.8%) compared with that for reference assays, especially in the acute phase of disease  and real-time RT-PCR  for CHIKV diagnosis. In addition, we evaluated the OnSite Chikungunya IgM Combo Rapid Test CE  for CHIKV infection.The rapid test identified IgM in only 3 of 8 patients (sensitivity 37.5%). All patients were negative for viral RNA, probably due to the time elapsed between symptom onset and serum sample collection, as confirmed by the presence of CHIKV IgG in most patients. No false-positive or invalid results were recorded with the rapid test on 30 CHIKV-negative serum samples .Rapid and appropriate diagnostic tools are needed to slow or stop the worldwide spread of CHIKV. Rapid POC tests are highly cost-effective because they are easy to perform and can be disseminated to many laboratories for differentiating between diseases that are similar. Moreover, their results can easily be evaluated and shared within networks of reference laboratories.However, our findings, in agreement with those of others, show that current rapid CHIKV tests perform poorly and need major improvement  (1–5). TThe successful use of rapid immunochromatography-based assays with monoclonal antibodies to detect viral diseases  has encouraged the development of rapid immunoassays for CHIKV antigens, and preliminary results for these assays seem promising (In conclusion, returning travelers are sentinels of the rapidly changing epidemiology of CHIKV; thus, they require a prompt diagnosis and careful surveillance for their possible role in subsequent autochthonous disease transmission. Implementation of user-friendly, rapid, and easily deliverable POC tests for a prompt and accurate laboratory diagnosis is therefore needed to improve patient management and disease control measures.


We argue the presence of these behaviors among marine tetrapods may be limited by limb mobility and evolutionary history, rather than foraging ecology or social learning. These behaviors may also be remnant of ancestral forelimb-use that have been maintained due to a semi-aquatic life history.The use of limbs for foraging is documented in both marine and terrestrial tetrapods. These behaviors were once believed to be less likely in marine tetrapods due to the physical constraints of body plans adapted to locomotion in a fluid environment. Despite these obstacles, ten distinct types of limb-use while foraging have been previously reported in nine marine tetrapod families. Here, we expand the types of limb-use documented in marine turtles and put it in context with the diversity of marine tetrapods currently known to use limbs for foraging. Additionally, we suggest that such behaviors could have occurred in ancestral turtles, and thus, possibly extend the evolutionary timeline of limb-use behavior in marine tetrapods back approximately 70 million years. Through direct observation  Marine turtles  and most other marine tetrapods, have evolved body forms that are best suited to move, orient, and minimize drag in a fluid environment rather than using their articulating limbs to directly aid in prey capture or processing . Due to Despite the predictions of Why limb-use develops in some marine tetrapods, but not others, is not well understood. Marine turtles are the oldest extant line of marine tetrapods but some still maintain a semi-aquatic lifestyle for thermoregulation and breeding . Like maChelonia mydas), hawksbill (Eretmochelys imbricata), and loggerhead (Caretta caretta)—using limbs in the wild to aid in foraging in ways which have not been previously assessed in detail. We set these observations in context with other marine tetrapods known to use their flippers, forelimbs, or tails as direct aids in obtaining or processing food and discuss the role of behavioral, morphological and ecological factors that may limit or promote this behavior.Here, we describe three marine turtle species—green , and the published literature.For this study, limb-use for feeding was defined as the intentional use of flippers, paws, tails, or feet to directly aid in the capture, processing, or transport of the animal’s food while in the marine environment. If we did not find limb-use feeding described in the published literature , we conducted broader internet searches for video and images using the species’ common name or group (“green turtle” or “sea turtle”) combined with feeding terms . Once an initial record was found, we conducted more in-depth searches for that species or group to determine the ecological context of the behaviors. Feeding strategies were grouped into broad behavioral categories and feeding stages based on previous study definitions , Table 1Ursus maritimus) as there is significant genetic admixture with a fully terrestrial species  demonstrated the most diverse and complex forms of limb-use for foraging, including pounding prey against tools . Sea otst tools . To our st tools , uploadiWe compared the prey type, relative prey size, and habitat across the marine tetrapods listed above to determine if distinct ecological factors promoted the development of limb-use . HoweverThe regular use of limbs for tasks beyond swimming may also promote the development of limb-use. As noted in Limb mobility may play the largest role in the development of limb-use across marine tetrapods. Foreflipper mobility varies across marine tetrapods due to trade-offs for maneuverability, stability, and propulsion . Taylor The origin of limb-use in marine turtles is currently unknown. Unlike other foraging strategies (such as lunge feeding), that can be analyzed via skull structure in extinct and extant species , it is cAlthough flipper morphology and foraging ecologies likely evolved via convergent evolution across marine tetrapods  it is unThe use of limbs to directly aid in foraging, while still relatively rare, is a strategy used by a variety of marine tetrapods. Despite being the oldest extant line of marine tetrapods, this is the first time such a wide range of limb-use has been described in marine turtles. We argue that these limb-use behaviors across marine tetrapods are limited by limb mobility and that the frequent use of forelimbs for other behaviors may promote the development of these feeding strategies. These observations provide additional insight into the diversity and possible evolution of limb-use behaviors.10.7717/peerj.4565/supp-1Table S1Click here for additional data file.10.7717/peerj.4565/supp-2Figure S1Odonus niger). Video shot by Simon Enderby, ©http://www.Scubazoocom and provided with permission from Dr. Nicolas Pilcher.A series of frame grabs from a video recorded at night in Maldives shows a Hawksbill sea turtle using its foreflippers to capture and hold a red-toothed triggerfish (Click here for additional data file.


The most common tool that clinicians use to predict outcomes after radical cystectomy is still the tumor-node-metastasis (TNM) staging system, with lymph node involvement representing the most important prognostic factor. However, the predictive accuracy of staging and grading systems are limited, and nomograms incorporating clinical and pathologic factors can improve prediction of bladder cancer outcomes. One limitation of current staging is the fact that tumors of a similar stage and grade can have significantly different biology. The integration of molecular markers, especially in a panel approach, has the potential to further improve the accuracy of predictive models and may also identify targets for therapeutic intervention or patients who will respond to systemic therapies.Bladder cancer is a major cause of morbidity and mortality. At initial diagnosis, 75% of patients present with non—muscle-invasive disease and 25% of patients have muscle-invasive or metastatic disease.Patients with noninvasive disease suffer from a high rate of recurrence and 10–30% will have disease progression. Patients with muscle-invasive disease are primarily treated with radical cystectomy, but frequently succumb to their disease despite improvements in surgical technique. In non–muscle-invasive disease, multiplicity, tumor size, and prior recurrence rates are the most important predictors for recurrence, while tumor grade, stage, and carcinoma