The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. By using selected exemplary tools and open-access resources for cancer research and differential network analysis, we highlight disturbed signaling components in brain cancer subtypes of glioma. The understanding of complex diseases such as cancer requires insight into high dimensional data, underlying domain knowledge and multiple networks that provide relevant relationships among biological entities . We therCancer databases include various data types ranging from biological and pharmacological data, including information on genome, proteome as well as metabolome, and clinical information on experiments, incidence, mortality, prevalence and survival. Common issues of data retrieval are access restrictions or poor annotation due to sharing reluctance and fear about lack of control over its usage and personal credit . Still, In this paper, we focus on gene expression and PPI data.The unique pattern of gene expression for a given cell or tissue is referred to its molecular signature and defines a particular class of tumor.Each subtype holds distinct biological properties affecting clinical matters, such as metastasis likelihood and patient survival prognosis as well as tailored therapy strategies. Differential gene-expression data can be used for deriving marker genes indicating multiple types of cancers or specific to individual cancers . In refeDifferential gene expression data can be aligned to differences between cell-lines, wild-type and mutated or knock-outs, between disease and control samples or simply different disease subtypes. Gene expression is mostly assessed by transcriptomic methods . Whole tIdentifying patterns of gene expression supports characterizing subtypes of cancer towards a more personal treatment approach, such as in the case of glioblastoma . DiscrepProtein interactions determine cellular communication based on signal transduction cascades. These resemble molecular circuits consisting of receptor proteins, kinases, primary and secondary messengers which modulate the gene transcription or the activity of other proteins. Databases provide disease-specific as well as general PPI information ,29,30,31PPI networks are commonly modeled via graphs whose nodes represent proteins and whose undirected edges connect pairs of interacting proteins . These gThere are several graph-level features that suit the comparison task according to the existing literature on graph comparison ,39,40. NCancer is based on oncogenic mutations resulting in aberrant signaling in tumor cells and effecting increased mitogenesis, prevention of apoptosis, as well as increased cell motility and invasion . CanceroWe identified NetworkAnalyst , NavigatConstructed PPI graphs from the different network analysis tools using filtered gene expression data from EMBL-EBI Expression Atlas as input are illustrated in The comparison of graphs in https://github.com/schokine/Cytoscape-glioma-CF.Merged intersections and unions of the different disease- and database-specific networks as well as their unique differences among each other are summarized in https://github.com/schokine/Cytoscape-glioma-CF/. Filtered datasets were used to create PPI networks using BioGRID and StringDB, illustrated in The GO-term proliferation has been originally used to filter overexpressed genes within the extensive datasets of each general glioma, glioblastoma multiforme and low-grade astrocytoma. Proliferation is related to malignancy and was thereby chosen as exemplary key term for further analysis. This filtering step was computationally necessary due to the high number of genes which could not properly function as input for the diverse tools without error-free processing. The list of genes was thereby reduced from the magnitude of multiple thousands to less than hundred entries. Filtered gene lists that were used as input for network creation can be found for each of the three glioma subtypes on The difference networks from unique nodes to each sample dataset, isolated by subtraction from the intersection of all three sample networks, were used for further GO analysis to highlight significant biological functions. Exemplary GO-terms with low p-values within all three sample networks are presented in Within There are several matching genes within the top hub nodes of networks constructed by BioGRID compared to the far smaller ones by StringDB, presented in Some of the identified genes are hub nodes within clusters, as specified in In case of the StringDB constructed networks, there were hardly any clusters isolated due to the smaller number of nodes and edges. Still, in case of glioblastoma multiforme, HER2 was identified to be a part of cluster 1 also involving other top hub nodes of proto-oncogenes KRAS, HRAS and NRAS.The epidermal growth factor receptor  is a major regulator of proliferation in tumor cells and a well-known target in glioblastoma treatment . The humWe compared StringDB to BioGRID networks by mapping BioGRID table columns via Biomart different node identifiers. While, by using Ensembl gene identifiers, we could find 41 similar nodes within both glioblastoma multiforme networks, by using the Ensembl protein identifiers, we could find 42 matching nodes, and by using BioGRID’s human readable label within Cytoscape to map with StringDB’s label provided by NetworkAnalyst, similar to HUGO Gene Nomenclature Committee (HGNC) symbols, we found 137 intersecting nodes between the two GBM networks.We then tried to use Cytoscape’s build-in column mapping tool by mapping HGNC symbols to Ensembl Gene IDs. Since HGNC labels are written differently depending on database, format and tool, this mapping is far from comprehensive. We further tried to map Entrez gene ids to Ensembl and could map over 80% of the nodes. Missing 30 Ensembl gene identifier were added manually to the Ensembl gene id column of the imported network from Biogrid. The column was then complete but one gene. Moreover, ensembl has limitations, such as there being no ensembl gene id for the recombining binding protein suppressor of hairless pseudogene 3 (RBPJP3), though of no relevance in our use case. We experienced comparable column mapping results insofar as mapping HGNC symbols resulted only in less than half of the Ensembl gene identifier, while adding them up with Entrez mappings to complete nearly all .https://github.com/schokine/Cytoscape-glioma-CF.We further merged disease-specific networks from StringDB and BioGrid, respectively, by using the Ensembl Gene Id as intersecting nodes. Top hub nodes, for each glioma sub-type presented in The construction of PPI networks on the basis of overexpressed genes within disease samples can vary according to the applied tools and web resources. The extensive datasets on gene expression within chosen cancer samples posed the first challenge. These data had to be scaled down in order to be applicable as input for the diverse tools. Filtering data to a required minimum expression value will reduce entries. But it has to be kept in mind that low changes in expression levels can still be significant and could present a relevant or even crucial biological impact. Data entries in the five to six-digit range exceeded computing power and resources for online information retrieval from data repositories by the selected tools. In order to downsize sample data entries, we concentrated genes associated to the general biological function of proliferation as basic principle corresponding to cancer. This filtering step is one of many possibilities to analyse selected datasets in more detail. Other biological functions as apoptosis or migration could function likewise as approach to answer various questions for cancer research.We constructed our PPI networks on expression profiles from upregulated genes within disease samples. Likewise, PPI graphs could be compared on the basis of downregulated genes which could equally possess significant biological impact such as regulation of apoptosis and prevent an imbalance of proliferation.Differential graph analysis allowed us to compare the differences as well as similarities among datasets of selected disease types. GO analysis of dissected sample networks could highlight unique characteristics to disease subtypes and even point to possible biomarkers or novel molecular targets for treatment.Calculating PPI networks from gene lists is based on estimations and therefore connected to an uncertainty ,73. We cHubs presenting high degree nodes can be used to evaluate signaling key points within samples. These can be of interest for understanding molecular mechanisms up to possible targets for treatment. Still, well-known and highly investigated proteins will be more likely assigned to a multiplicity of interactions than unstudied proteins. Thus, nodes with low number of interactions or even isolated outliers could hold relevant biological function within the disease. Results from corresponding BioGRID and StringDB high degree nodes list several genes that have been investigated to a certain extent or have been postulated to be involved in glioma signaling. The difference in top hubs between low-grade and high-grade glioma in comparison to general glioma can further point to tumor progression and malignancy. Further studies on unconnected nodes seem to be equally of interest. Differential graph analysis pinpoints three example genes which could be essential to glioma signaling. They have been indicated as possible prognostic biomarkers in different cancer diseases and require further evaluation respectively. Comparative Toxicogenomics Database lists HDAC4 an PP2R5A listing inferred gene-disease associations to glioma, mainly curated via chemicals, and no association between glioma and MAP2K7. Hub nodes within clusters could point to protein complexes since numerous proteins function within interacting aggregates. These interactions relate to biological functions and can be pointed out as signaling steps in disease. The analysis of the first ten top high-degree nodes already depicted several possible interacting complexes such as HER-signaling interrelated with cell cycle proteins which have been given much attention as targets in cancer treatment . The exaWe further included data from a comparison of gene expression profiles of anaplastic glioma with or without the mutated IDH1/2 gene . Using tStill, most of the example signaling components have been evaluated within various non-brain tumors and yet have to be studied in more detail for the various glioma diseases.The main idea is to compare gene expression in general glioma including GBM and low-grade astrocytoma via graph-based analysis of different PPI databases using network analysis tools. At first, we use EMBL-EBI Expression Atlas  to downlWe used NetworkAnalyst  and Cytowww.biomart.org/biomart/martview) and g:Profiler g:convert (available online: https://biit.cs.ut.ee/gprofiler/convert) including the removal of duplicates, and also used the column mapping functions in Cytoscape. In order to compare data for glioblastoma multiforme to other projects, we repeated the same steps, downloading the data for the disease types of general glioma data from the PCAWG study [We manually filtered the BioGRID-based networks by human nodes within Cytoscape by filtering on the column taxonomy id 9606 for human. We further processed the network data by using gene name mapping to PPI data via BIomart Martview service  and log2fold cutoff 1 in experiment E-GEOD-52942. The list of genes was further filtered by upregulated genes only, on 20 Dec 2019 at 20:02:12.Genomic data on glioblastoma multiforme, general glioma and low-grade astrocytoma and anaplastic glioma with or without the mutated IDH1/2 gene were obtained from EMBL-EBI Expression Atlas  from theAmiGO version 2.5.12 BinGO version 3.0.3 Biomart, Ensembl release 98, 2019-09 ClusterOne version 1.0 ClusterViz version 1.0.3 Comparative Toxicogenomics Database, revision 15923 Cytoscape version 3.7.2 EMBL-EBI Expression Atlas release 31, 2019-05 Gene Ontology release 2019-07-01 ,93g:Profiler release 2019-10-02 NetworkAnalyst release 2019-10-07 Omicsnet release 2019-08-07 PantherDB version 14.1 https://github.com/schokine/Cytoscape-glioma-CF.Generated data can be found on There are several open-access resources available for cancer research. We present and compare exemplary web-based and stand-alone tools for differential network analysis using open gene expression data on various glioma diseases as input. This approach highlights disturbed signaling components in general glioma, glioblastoma multiforme, as well as low-grade astrocytoma.


There is little information on how to prioritize testis cancer (TC) patients' care during COVID-19 pandemic in order to relieve its pressure on the health care systems.To describe the recommendations for diagnosis, treatment and follow-up of patients with TC amidst COVID- 19 pandemic.Pubmed search and review of the main urological association guidelines on TC.The biology of TC requires immediate care of patients during diagnosis, initial surgical therapy and management of recurrent disease. Active surveillance is the first choice of management and should be offered to all compliant clinical stage I TC patients provided they understand the need to self-isolate. Active surveillance may also help decrease the demand for intensive care unit beds, ventilators, personal protective equipment, and other critical hospital and human resources by minimizing surgeries without compromising patient outcomes. Complications of therapy and symptomatic patients represent medical emergencies and should be treated immediately. Telemedicine may be useful during follow-up periods.Most stages of testis cancer require urgent care; however, all recommendations must be adapted to local health care priorities considering that most of these patients are at low risk of severe COVID-19 infection. Testicular cancer (TC), although rare, is the commonest, solid-organ cancer in men aged 15 -44 years. As the tumor is promptly identified and treated, the overall prognosis is excellent even after late diagnosis. While some authors have reported a significant relation between survival and delay in diagnosis,    others Actually, the American Urological Association (AUA),    EuropeaNotwithstanding, it is generally assumed that delays in diagnosis affect the stage of disease at presentation and therefore disease prognosis   . That iThe coronavirus disease 2019 (COVID-19) pandemic has created major dilemmas for providers in all areas of health care delivery, including cancer centers, forcing them to make substantial changes. While medical institutions may request that elective surgeries be postponed until the strain on the health care system from COVID-19 has been relieved, the characteristics of elective surgeries in urology oncology are context-dependent and have not been well defined in the current crisis.Fortunately, TC patients are usually young and healthy. Their risk of severe disease compared favorably with the risk reported in the general population of patients presenting with Covid-19. However, they cannot be excluded from the unprecedented measures taken in health systems worldwide  TCManagement of primary metastatic TCManagement of residual disease post chemotherapy.Unfortunately, there might not be high--quality evidence for the compromises proposed but it is anticipated the new information will function as an additional guide to the management of urological conditions during the current COVID-19 pandemic.The EAU categorized recommendations with increasing degrees of priorities as follows   :LOW PRIORITY: Clinical harm  very unlikely if postponed 6 months.INTERMEDIATE PRIORITY: Cancel but reconsider in case of increase in capacity  possible if postponed 3-4 months but unlikely.HIGH PRIORITY: The last to cancel, prevent delay of > 6 weeks. Clinical harm  very likely if postponed > 6 weeks.EMERGENCY: Cannot be postponed for more 24 hours. Life-threatening situation.All patients with suspicion of TC should undergo a bilateral testicular ultrasound within 24 hours of clinical examination, which should include physical examination of supraclavicular, cervical, axillary and inguinal lymph nodes, breasts and testicles.Like normally done outside any pandemic state, serum tumor markers should be evaluated before and after orchiectomy.Non contrast-enhanced CT scan of the chest and contrast-enhanced CT scan of the abdomen and pelvis should be done in patients with a diagnosis of TC ideally before orchidectomy. In case of iodine allergy or other limiting factors perform MRI of the abdomen and pelvis. According to the EAU recommendations, if diagnostic imaging studies had not been performed before orchidectomy, they may be postponed awaiting pathology result but no more than 7 days.Radical orchiectomy should be performed as soon as possible because it is an outpatient procedure and will guide further treatment   . EAU exMRI of the brain (or brain CT if not available) should be indicated on an emergency basis in patients with central nervous system symptoms, multiple lung metastases, high β-hCG values, or those in the poor-prognosis IGCCCG risk group. MRI of the brain could eventually be postponed until chest CT or marker results are available, but then becomes an emergency.Patients at high-risk for contralateral germ cell neoplasia in situ are recommended to undergo biopsy of the contralateral testis during orchidectomy. They include patients with an atrophic contralateral testis (< 20 cc volume on ultrasound) who present before the age of 31 years,    azoospeSperm banking is another low priority procedure, particularly in those patients who had not done it prior to orchiectomy and do not need adjuvant chemotherapy or radiotherapy. In patients scheduled for adjuvant treatment sperm banking becomes an emergency and should be done prior to starting treatment.There is currently no evidence of vertical transmission of COVID-19. However, patients may be offered testing at their discretion at the time of performing standard serology (i.e. HIV/Hepatitis testing) prior to sperm cryopreservation if specific covid-19 diagnostic tests are available.Active surveillance is the first choice of management in compliant CSI TC patients, particularly during COVID-19 pandemic. Active surveillance should be offered to all these patients with seminoma and low risk (no lymphovascular invasion) non seminoma germ cell tumors (NSGCT) provided they understand the need to self-isolate   .Unless the patient has contraindications to other forms of therapy, RPLND should be discouraged in order to eventually avoid use of an intensive care unit bed or a ventilator machine, and decrease patient length of hospital stay, thus, decreasing his chances of becoming Covid-19 infected.CSI seminoma or NSGCT patients not accepting active surveillance need to be treated. They are considered high priority and should be treated within 6 weeks of histologic confirmation (High priority). This group of patients with CSI seminoma should be treated with one course of carboplatin at AUC7. Experts agree that in spite of the lack of evidence on the association of bleomycin with severe lung COVID disease, bleomycin should be avoided when possible and hematopoietic growth factors (G-CSF) should be co-administered to diminish the incidence of neutropenia and infection in all patients with germ cell tumor (GCT) receiving chemotherapy.Patients with low-risk NSGCT CSI not willing or unsuitable to undergo active surveillance should receive one cycle of BEP and G-CSF. Patients with high risk CSI-NSCGT (presence of lymphovascular invasion) should be treated with one course of BEP and G-CSF if they are not willing to accept AS.Primary nerve-sparing RPLND should only be indicated in CSI -NSGCT patients with contraindication to adjuvant chemotherapy and unwilling to accept active surveillance, or in those with teratoma with somatic-type malignancy.Except for patients with clinical stage IIA seminoma who can be treated with either radio-therapy or chemotherapy within 6 weeks of histologic confirmation, all other patients with metastatic disease at presentation should be treated immediately.Patients in a good general condition may delay the initiation of chemotherapy for 7 days. In addition, short planned delays in chemotherapy for good-risk GCT patients (≤7 days per cycle) also appear to be acceptable since they may prevent serious toxicity in this curable patient population   .Clinical stage IIB seminoma patients should be treated with chemotherapy according to the International Germ Cell Consensus Classification (IGCCC) good risk group. (3x BEP o 4x EP + G-CSF)   , 19  RaPatients with stage ≤ IIC seminoma should receive primary chemotherapy based on the same principles used for NSGCT. IGCCC good risk NSGCT should be treated with 3x BEP o 4x EP + G-CSF while the recommended therapy for IGCCC intermediate or poor risk groups is 4x VIP or 4x BEP + G-CSF.    CarneirIn a life-threatening situation due to extensive metastasis, patients should be hospitalized and commence chemotherapy prior to orchidectomy .Post-chemotherapy full bilateral RPLND of either residual masses after chemotherapy for NSGCT with negative serum levels of tumor markers or growing teratoma are considered high priority and the surgery should be performed within 6 weeks of completed chemotherapy.Patients with Seminoma and NSGCT CSI on AS or after adjuvant chemotherapy are recommended to be followed within 6 weeks of the original appointment (High priority). EAU experts recommend not to postpone follow-up beyond 3 to 6 months of the original appointment in patients with metastatic disease after adjuvant treatment or complete remission.Direct-to-consumer (or on-demand) telemedicine may allow patients to be efficiently followed, as it is both patient-centered and conducive to self-quarantine, and it protects patients, clinicians, and the community from exposure. It can allow physicians and patients to communicate any time as needed, using smartphones or webcam-enabled computers   .Patients with symptomatic brain metastases following treatment, post-obstructive polyuria or symptomatic postoperative complications , intractable pain or symptomatic neutropenia during or after chemotherapy  represent medical emergencies and should be treated immediately.Urologists can make a substantial contribution to the health care systems by decreasing the demand for hospital beds, ventilators, personal protective equipment, and other critical hospital and human resources by minimizing surgeries without compromising patient outcomes whenever possible   .Medical specialists in general and urologists in particular are encouraged to weigh the impact of nonsurgical therapies such as systemic chemotherapy  and surgical risks against the natural history of the disease in case it is not timely treated.Generally speaking, considerations should include nonsurgical treatments whenever available or deferral of surgery until patient risks of in-hospital COVID-19 infection, demand for ventilators and inpatient beds diminish. The recommendation for different stages of disease in patients with testis cancer are summarizes in the The impact of surgical wait time on the outcome of testis tumors remains controversial.   – 24  ThRegarding treatment options in patients with low volume stage II seminomas (IIA and IIB), some authors recommend radiotherapy to avoid the use of chemotherapy   . HoweveThe same authors also recommend 4 cycles of VIP  in patients with intermediate or poor risk metastatic GCT, instead of the 4x BEP, to avoid the use of bleomycin. Although there is no evidence on the association of bleomycin with severe lung COVID disease, it is generally agreed to avoid bleomycin when possible. Hematopoietic growth colony stimulating factors (G-CSF) are recommended in all patients with germ cell tumor (GCT) receiving chemotherapy to diminish the incidence of neutropenia and infection   , 12 .Disasters and pandemics pose unique challenges to health care delivery and the multiple potential benefits of telemedicine are not new   . More tNeedless to say, all recommendations are mindful of significant differences between countries and regions. Depending on resources, doctors will need to make decisions according to local health care priorities. Countries or even provinces that have not had high rates of death from COVID-19 could consider similar approaches that involve balancing pandemic control with providing continued cancer care   .


Recent advancements in high-throughput sequencing technologies have generated an unprecedented amount of genomic data that must be stored, processed, and transmitted over the network for sharing. Lossy genomic data compression, especially of the base quality values of sequencing data, is emerging as an efficient way to handle this challenge due to its superior compression performance compared to lossless compression methods. Many lossy compression algorithms have been developed for and evaluated using DNA sequencing data. However, whether these algorithms can be used on RNA sequencing (RNA-seq) data remains unclear.In this study, we evaluated the impacts of lossy quality value compression on common RNA-seq data analysis pipelines including expression quantification, transcriptome assembly, and short variants detection using RNA-seq data from different species and sequencing platforms. Our study shows that lossy quality value compression could effectively improve RNA-seq data compression. In some cases, lossy algorithms achieved up to 1.2-3 times further reduction on the overall RNA-seq data size compared to existing lossless algorithms. However, lossy quality value compression could affect the results of some RNA-seq data processing pipelines, and hence its impacts to RNA-seq studies cannot be ignored in some cases. Pipelines using HISAT2 for alignment were most significantly affected by lossy quality value compression, while the effects of lossy compression on pipelines that do not depend on quality values, e.g., STAR-based expression quantification and transcriptome assembly pipelines, were not observed. Moreover, regardless of using either STAR or HISAT2 as the aligner, variant detection results were affected by lossy quality value compression, albeit to a lesser extent when STAR-based pipeline was used. Our results also show that the impacts of lossy quality value compression depend on the compression algorithms being used and the compression levels if the algorithm supports setting of multiple compression levels.Lossy quality value compression can be incorporated into existing RNA-seq analysis pipelines to alleviate the data storage and transmission burdens. However, care should be taken on the selection of compression tools and levels based on the requirements of the downstream analysis pipelines to avoid introducing undesirable adverse effects on the analysis results. In recent years, high-throughput genome sequencing has become an essential tool in biomedical and medical research with a wide range of applications in basic biomedical research, clinical diagnostic, drug discovery, forensic medicine, etc. The fast growing applications of genomic data have produced a large amount of sequencing data, for which efficient and effective data compression technologies are desired to cope with the corresponding growth in data storage and transmission costs.To address such a need, genomic data compression algorithms have been proposed in the literature . Many ofTo further improve the data size reduction rate of genomic data compression, lossy compression algorithms of quality values , 6 have As genomic data compression algorithms were designed for standard sequencing data formats such as FASTQ and SAM, they can be used to compress both DNA and RNA sequencing data directly. However, most existing genomic data compression algorithms were designed for and evaluated on DNA sequencing data from whole genome sequencing (WGS), whole exome sequencing (WES) or targeted amplicon sequencing, etc. . The impIn this paper, we provide a systematic evaluation on the impacts of lossy quality compression on common RNA-seq data analysis pipelines including gene expression quantification , transcrThe compression ratio of quality values varied depending on the datasets and the lossy compression algorithms and their corresponding coding parameters being used Fig. . As a baAs quality values occupy a significant portion of the total sequencing data file, the overall compressed file sizes are highly related to the sizes of quality values after compression Fig. . OverallSTAR  and HISAWe compared the alignment rates of HISAT2 with original and lossy compressed quality values Fig. . Noticeak-mers  or a reKallisto  and Salmp-value smaller than 0.05 were considered as DE genes. Reads counts were used in our benchmarking without further normalization since the total read counts were fixed in each split samples. As shown in Fig. For each dataset, we evaluated the number of genes that were identified as differentially expressed (DE) after lossy quality value compression on the quantification results from three technical replicates. Here, we analysed the variances of read counts between and within groups of quantification results from original and lossy compressed quality values for all the genes from each dataset, where within-group variances reflect randomized effects due to sampling and pipeline processing, and between-group variances represent the impacts of lossy compression. Significance were evaluated using one-way ANOVA and genes with We included two alignment-based transcriptome assembly algorithms, namely, StringTie and Scallop, in our evaluation. Since both tools use only alignment information in their transcriptome assembly process, we used HISAT2 with these two tools to study the impact of lossy compression on alignment-based transcriptome assembly. In our test, we compared the assembled transcriptomes using GffCompare  against Sensitivity = TP / (TP + FN),Precision = TP / (TP + FP),F1 score = 2 × Sensitivity × Precision / (Sensitivity + Precision).Here, TP (true positive) is the number of transcripts in query in agreement with the corresponding reference, FP  is the number of transcripts in query that are not present in the reference, and FN  is the number of transcripts that are present in the reference but not in the query data.Based on the results  took about 30 and 2 minutes respectively to complete the compression and decompression operations for the same file. In terms of memory consumption, Quartz had the highest peak memory consumption (69GB) while Crumble used only around 100MB to perform the compression operation.We asked if there are any effect on run-time and memory consumption of the downstream RNA-seq data analysis tools if the quality values are lossy compressed. Interestingly, we observed that the differences in run-times and memory consumption resulting from different lossy quality value compression algorithms were actually smaller than those resulting from run-to-run variations when the same algorithm was performed on different technical replicates , indicating that the impact of lossy quality value compression to the run-time and memory consumption of the downstream analysis tools is negligible.Different RNA-seq tools show different sensitivities to lossy quality compression. For pipelines that do not take base quality values into consideration, e.g., STAR-based expression quantification, analysis results will be reproduced either perfectly after lossy compression or with fluctuations that are irrelevant to quality values if the analysis process is not deterministic. In these scenarios, quality values can be heavily compressed with lossy compression algorithms or can be simply discarded without affecting the analysis results. However, for pipelines that utilize quality values, such as HISAT2 and GATK HC, lossy quality value compression should be used with care in cases where data re-analysis is expected. Short variant discovery is usually not the top-priority application in RNA-seq data analysis. In addition, according to our evaluation, the variations in variant calling results from lossy compressed RNA-seq data among different compression methods were smaller than those among replicates. Hence, we may conclude that quality values can be compressed more aggressively for variant calling applications. However, if re-alignment using a quality value-aware aligner such as HISAT2 is necessary, it is expected that we should only keep the original values intact with lossless compression, or choose a lossy compression algorithm with proper compression ratio to minimize its impact on the alignment results.When using lossy quality values compression on RNA-seq data, care should also be taken to make sure that the selected tools match the characteristics of the RNA-seq data in hand. For example, Quartz needs a bin directory which was generated according to the human reference genome. Therefore, it does not match the characteristics of sequencing data from other species. As a result, compressing the mouse, rice, and arabidopsis datasets using Quartz actually led to data size increments compared to lossless quality value compression. Some lossy quality compression algorithms were developed primarily for DNA sequencing data analysis. For example, CALQ used an internal statistical model to determine the compression level of quality values from different loci according to their significance. As the model was heavily tuned towards genotyping of DNA sequencing data, CALQ did not perform very well in many RNA-seq tasks in our study. LEON performed well in our benchmarking test as it delivered excellent compression while maintained the accuracy of downstream analysis. However, it does not provide the option to adjust the compression ratio, which makes it inconvenient when the default model does not provide the desired compression level. ScaleQC is a promising tool for RNA-seq data compression as it supports both lossless and lossy quality compression with seamless integration with SAM/CRAM tools, and it provides the flexibility to truncate a bit-stream of lower data rate from that of a higher data rate directly without expensive transcoding. In addition, it was among the compressors that achieved the best trade-off between the compression ratio and impacts to RNA-seq data analysis in our test.Finally, manufacturers of sequencing platforms have already started to incorporate lossy compression of base quality values into their sequencing hardware platforms to mitigate the storage burden of NGS data. For example, in April 2014, Illumina updated the firmware of HiSeq platforms to enable quality scores binning setting by default. Moreover, currently Illumina Novaseq uses 2-color chemistry, and only consists of four possible quality values which are 2, 12, 23 and 37. The effect of Illumina binning operation on RNA-seq data analysis was studied in this paper using the DSRC implementation, which shows that it has little impact to the downstream analysis of RNA-seq data. However, our study suggests that sequencing data with binned quality values can be further compressed using lossy compression schemes such as LEON or ScaleQC if further file size reduction is desired.To overcome the challenge in storage and transmission of NGS data from the increasing production of high-throughput sequencing technologies, compression methods specific for sequencing data have been developed. In these methods, compression of quality values is the most important contributing factor to the overall compression ratio due to the high entropy in quality values. The recent developments in lossy quality value compression methods have brought a new angle to further decrease the data size of NGS data beyond lossless compression. Unfortunately, most of the lossy quality value compressors were developed for and evaluated on DNA sequencing data while their impact on RNA-seq data analysis has yet to be elucidated. In this paper, we provide the first systematic evaluation of existing lossy quality value compression methods on RNA-seq data analysis. Our results reveal that it is viable to further reduce RNA-seq data size without introducing significant adverse effects to downstream analysis, and a suitable choice of the lossy compressor and/or compression ratio parameters heavily depends on the actual pipelines being adopted, and the target applications of the data. Furthermore, given the increasing importance of RNA-seq data analysis in biomedical and clinical studies, it is desirable that established RNA-seq data processing pipelines should be considered in the future development of sequencing data compression algorithms to ensure the applicability of the developed tools on both DNA and RNA sequencing data. Our study thus provides a useful evaluation framework for this development.In this study, we compressed the base quality values in the raw RNA-seq data using different lossy compression tools. The compressed quality data were then decompressed and merged with the other fields of the original RNA-seq data to produce either FASTQ or BAM files for re-analyzing with different pipelines Fig. . The anahttps://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR10509596), with a total of 35.1 billion bases. We used human hg38 as the reference genome for this dataset. Both the genome sequences and annotation files were download from Ensembl Release 90. SRR10433000 is extracted from mouse endometrial epithelial cells and sequenced using NovaSeq 6000 [Oryza sativa japonica (rice) group, and contains a total of 32.5 billion bases [Arabidopsis thaliana (Columbia accession) using HiSeq X Ten. Reference genome TAIR10 was selected, and both the genome sequences and annotation files were downloaded from Ensembl Plants Release 45.We enrolled four datasets of four different species and platforms in our study (Supplementary Table). Briefly, SRR10509596 was sequenced by HiSeq2000 for the HEK293T human cell line, available from NCBI SRA  for all datasets was performed using fastp (v0.19.6)  before dFinally, reads in each dataset were divided equally into three parts  by round-robin before further analysis.We included eight different lossy quality value compression algorithms  as suggested in the original paper . ScaleQCAfter compression and decompression, in case the decompressed quality values were stored with aligned reads in SAM format, the reads were converted back to FASTQ file format using “samtools fastq” for further processing.We used the RNA-seq data processing tools encapsulated in the RNA-cocktail toolkits docker image (v0.3.1)  in our eSubsequently, we used featureCounts (v2.0.0)  for aligTo evaluate the processing time and memory expense of different lossy quality value compression algorithms and downstream analysis tools on RNA-seq data with lossy-compressed quality values, we used reads mapped to chromosome 22 of hg38 reference genome extracted from SRR1050959 (the human cell line dataset) as input data (Supplementary Table). All compression tools were tested in a docker container with the number of CPU threads limited to four. Memory consumptions of compression tools were collected using the top command of the Linux OS every 1 second and the peak memory consumptions were recorded for each tool. CPU run-times were also collected from log files produced by top. For RNA-seq data analysis tools, we collected the CPU run-time and peak memory consumption directly from Nextflow with the number of CPU threads limited to six for each container.All the software tools were run on a single server with dual Intel Xeon E5 2696 v4 , 512 GB DDR4 RAM, quad stripped raid 10 hard disk with 8TB available capacity in total running Ubuntu 16.04.Additional file 1 Supplementary Data for “Performance evaluation of lossy quality compression algorithms for RNA-seq data”. Supplementary information on software tools, datasets, and additional results in Tables and Figures.


The best treatment for perforated colonic diverticulitis with generalized peritonitis is still under debate. Concurrent strategies are resection with primary anastomosis (PRA) with or without diverting ileostomy (DI), Hartmann’s procedure (HP), laparoscopic lavage (LL) and damage control surgery (DCS). This review intends to systematically analyze the current literature on DCS.DCS consists of two stages. Emergency surgery: limited resection of the diseased colon, oral and aboral closure, lavage, vacuum-assisted abdominal closure. Second look surgery after 24–48 h: definite reconstruction with colorectal anastomosis (−/ + DI) or HP after adequate resuscitation. The review was conducted in accordance to the PRISMA-P Statement. PubMed/MEDLINE, Cochrane central register of controlled trials (CENTRAL) and EMBASE were searched using the following term: (Damage control surgery) AND (Diverticulitis OR Diverticulum OR Peritonitis).Eight retrospective studies including 256 patients met the inclusion criteria. No randomized trial was available. 67% of the included patients had purulent, 30% feculent peritonitis. In 3% Hinchey stage II diverticulitis was found. In 49% the Mannheim peritonitis index (MPI) was greater than 26. Colorectal anastomosis was constructed during the course of the second surgery in 73%. In 15% of the latter DI was applied. The remaining 27% received HP. Postoperative mortality was 9%, morbidity 31% respectively. The anastomotic leak rate was 13%. 55% of patients were discharged without a stoma.DCS is a safe technique for the treatment of acute perforated diverticulitis with generalized peritonitis, allowing a high rate of colorectal anastomosis and stoma-free hospital discharge in more than half of the patients.The online version contains supplementary material available at 10.1186/s12893-021-01130-5. Perforated diverticulitis of the colon is among the most common emergencies in abdominal surgery in industrialized Western countries. To date, the best treatment approach is still a matter of controversy. Between 2010 and 2019, ten relevant international guidelines focusing on that topic were published –10. The Hypothesis of the presented systematic review is, that the application of the damage control strategy defined above leads to a lower stoma rate than the use of concurrent approaches, without negatively influencing morbidity and mortality.The systematic review is constructed in accordance to the “Preferred Reporting Items for Systematic Reviews and Meta-analyses” (PRISMA) statement as well as to the suggestions of the Cochrane Handbook for systematic reviews , 14. TheThe PICOS of this systematic review is depicted in Table DCS is defined as a two-stage procedure: first, a limited resection of the diseased colonic segment with oral and aboral blind closure, lavage, and temporary vacuum-assisted abdominal closure is performed during emergency surgery. Vacuum assistance was the only technique used for temporary abdominal closure within the analyzed cohort. 24–48 h later, the patient undergoes a second-look operation and definite reconstruction with colorectal anastomosis (−/ + diverting ileostomy) or end-colostomy (secondary HP) under optimized conditions after adequate resuscitation. Due to a lack of precise grading systems for the evaluation of the remission of peritonitis, it was coded binary as complete macroscopic clearance of the abdominal cavity without remaining pus or feces. Prior, this could be shown to have a significant impact on the clinical outcome of affected patients [th, 2020. The search strategy is depicted in Fig. PubMed/MEDLINE, Cochrane central register of controlled trials (CENTRAL) and EMBASE were systematically screened. Therefore, the below mentioned search-term was developed: (Damage control surgery) AND (Diverticulitis OR Diverticulum OR Peritonitis). To extend potential hits, the “related articles” function of PubMed was used. Additionally, all references of selected articles were screened by hand-search for additional publications matching to the inclusion criteria. As additional sources, the Clinical Trials Registry Platform Search Portal and ClinicalTrials.gov were screened for ongoing or recently completed studies. To avoid unnecessary double-publication, the PROSPERO-Database and the Review Registry Database for systematic reviews and metaanalyses were checked for similar systematic reviews currently underway or finalized. All abstracts and full-text articles were screened for the below mentioned inclusion criteria by two independent researchers. The search was completed June 30All articles identified by database search were stored in a Microsoft Excel database. In case of exclusion of a publication, reasons were attributed. After completed selection of all full-text articles, data were extracted using standardized data extraction forms by MS and PR.All reports were independently screened for predefined data items by two authors  through each phase of the review. If any inconsistency occurred concerning in- or exclusion of a study, data was presented to a third independent researcher (DW) to draw a final decision. In cases with incomplete data, the authors of the original studies were contacted to provide lacking information.The following parameters were assessed: ASA, Hinchey stage (presence of purulent or feculent peritonitis), Mannheim peritonitis index (MPI) –18 at inStoma rate at discharge from the hospitalPrimary outcome parameterRate of colorectal anastomosis at second surgeryAnastomotic leak rateMorbidityMortalityRate of fascia closureSecondary outcome parameterAccording to the recommendations of the Cochrane network, the Risk of Bias in Non-randomized Studies—of Interventions tool (ROBINS-I)  was usedA narrative synthesis of the results was performed since meta-analysis was not reasonably possible due to inhomogeneous inclusion criteria and follow-up workflow/follow-up examinations as well as partly lacking control groups. After a thorough analysis of the raw data from the original studies by respective authors or coauthors, a relevant overlap of cohorts was found in all centers with more than one publication on DCS. In a next step multiply analyzed patients were excluded. The review authors decided to report on the adjusted data from the different study groups and not on those given in the original articles. Therefore, data from five study groups rather than eight original studies are presented in Table Overall, six retrospective cohort studies and two prospective observational studies from five centers, referring to five different study cohorts, met the inclusion criteria –27 Fig.. There wAlthough perforated colonic diverticulitis complicated by generalized peritonitis constitutes a frequent abdominal emergency, an internationally accepted treatment approach has yet to be established. In descending order of importance, the aim of every therapy for perforated diverticulitis should be low mortality, low morbidity, low stoma rate, ease of performance and practicability, and low cost. According to current evidence, resection with primary anastomosis and diverting ileostomy seems to be an appropriate approach for therapy in most patients with perforated diverticulitis complicated by purulent and fecal peritonitis. Meanwhile, four prospectively randomized trials demonstrated this approach to be quite safe and feasible in most cases –31. The DCS fulfills all requirements for emergency surgery: short duration, limited surgical trauma, effective elimination of the septic focus and low technical demands. Therefore, it may be considered a potential treatment option for perforated diverticulitis with both generalized purulent and feculent peritonitis. DCS leads to a low stoma rate compared to other resectional procedures.The presented study is confined by certain limitations. Data arose of non-randomized studies only. No randomized trials were identified in the study period. Thereby, publication- and selection bias could not be ruled out definitely.Additional file 1: Prisma checklist.Additional file 2: AMSTAR2 checklist.


While the link between alcohol use and male-perpetrated intimate partner violence (IPV) has been well-established, research is needed to test whether psychosocial factors interact with alcohol use to exacerbate IPV perpetration. We tested whether depressive symptoms influenced the strength and/or direction of the alcohol-IPV relationship among men with HIV in Vietnam.This study is a secondary analysis using data from a randomized controlled trial conducted in Thai Nguyen, Vietnam. Participants were clinic patients with HIV and hazardous alcohol use. Questionnaires were administered at baseline, three, six, and 12 months. Alcohol use was assessed as proportion of days alcohol abstinent. Analyses were restricted to males who reported being married/cohabitating at baseline (N = 313). Multilevel growth models were used to test whether time-varying depressive symptoms modified the time-varying effect of alcohol use on IPV perpetration.Time-varying depressive symptoms modified the effect of proportion of days alcohol abstinent on IPV perpetration. However, the pattern of effect modification was not as expected, as reporting depressive symptoms weakened the alcohol-IPV relationship. At times when participants screened negative for depressive symptoms, those who reported higher proportion of days alcohol abstinent than usual had significantly lower odds of IPV perpetration . At times when participants screened positive for depressive symptoms, there was no observed effect of alcohol use on IPV perpetration .The findings highlight the complex nature of the alcohol-IPV relationship and the need to investigate the intersection between hazardous drinking, mental health, and IPV. Men who concurrently report depressive symptoms and heightened alcohol use may be socially isolated from an intimate partner or experiencing fatigue, leading to less alcohol-related IPV perpetration. Mental health interventions addressing depression and alcohol misuse integrated into HIV services may reduce IPV perpetration. The link between alcohol use and male-perpetrated intimate partner violence (IPV) has been established –8. The aAlcohol use and IPV perpetration are highly prevalent in Vietnam and largely shaped by sociocultural norms that stem from Confucianism . Men areThe influence of depressive symptoms on the alcohol-IPV relationship is unexplored among men with HIV, a group at high risk for hazardous alcohol use, IPV perpetration, and forward HIV transmission , 28–30. Alcohol use may be associated with IPV perpetration for some individuals, but not for others. Multiple threshold and disinhibition theories posit that each individual has an aggressive threshold determined by their propensity for aggression or by the extent to which their context encourages aggressive behavior –39. ThesEmpirical evidence also suggests that the co-occurrence of alcohol use and mental health exacerbates violence outcomes. A nationally representative study in the United States found that reporting a severe mental illness did not predict violence, but reporting both a severe mental illness and substance abuse did . AnotherIn this study, we tested whether depressive symptoms influenced the strength and/or direction of the alcohol-IPV relationship among men with HIV and hazardous alcohol use in Vietnam. We investigated whether the concurrent effect of alcohol use on IPV perpetration differed at times when an individual reported having depressive symptoms versus not having depressive symptoms. Our specific hypothesis was that the time-varying association between alcohol use and IPV perpetration would be stronger at times when an individual screens positive for depressive symptoms as compared to negative.This study is a secondary analysis of data from a three-arm randomized controlled trial (RCT) comparing the effects of two evidence-based, manually guided, individually delivered interventions to reduce alcohol use and determine the impact on viral load , 43. FroRecruitment of study participants took place at seven antiretroviral treatment (ART) community clinics in Thai Nguyen. Recruitment was completed at one clinic before moving on to recruit potential participants at each subsequent clinic. Study interviewers introduced the project before administering written informed consent to those who were interested in participating in the baseline questionnaire. Those who provided consent completed an interviewer-administered screening survey. The survey included the World Health Organization (WHO) Alcohol Use Disorders Identification Test (AUDIT-C) survey items to determine eligibility for enrollment . InclusiEligible participants were asked to consent a second time to enroll in the study after interviewers explained the RCT study objectives, procedures, risks and benefits to the participants, and answered any questions. Consenting participants were assigned a unique identification number. They then completed the baseline questionnaire and Timeline Followback (TLFB) to measure daily alcohol use over the past 30 days . EligiblAt baseline, three, six, and 12 months, quantitative questionnaires and the TLFB were administered to all study participants. Each study visit lasted approximately two hours. Trained interviewers administered questionnaires through face-to-face interviews in a private room at the study site. Participants confirmed informed consent at each follow-up visit. The behavioral assessment collected quantitative data on sociodemographics, alcohol and drug use, mental health, and violence. At the end of each study visit, participants were reimbursed for their travel expenses and given 100,000 Vietnamese Dong (~$4.30 USD) as compensation for lost wages. Retention was 94% (405/430) at three months, 96% (410/427) at six months, and 94% (390/414) at 12 months excluding those who were incarcerated  or died  during the study period.The study protocol received ethical approval from the Institutional Review Boards at the University of North Carolina Gillings School of Global Public Health, the Johns Hopkins University Bloomberg School of Public Health and the Thai Nguyen Center for Preventive Medicine. The study was registered at ClinicalTrials.gov (NCT02720237).The widely used and validated six-item shortened Conflict Tactics Scale 2 (CTS2) was used to measure recent psychological, physical, and sexual IPV perpetration among any current or previous partner –49. Recaproportion of days alcohol abstinent in past 30 days (0 to 1).The TLFB was used to measure alcohol use; the tool has been shown to be valid and reliable in multiple settings , 52. TheDepressive symptoms were measured using the nine-item Patient Health Questionnaire-9 (PHQ-9) scale  , a tool Theoretical and empirical evidence was used to select variables with the potential to confound the relationship between alcohol use and IPV perpetration , 56–60. Education, age, employment status, and injection drug use in the past three months were collected via self-report. Intervention arm was also selected as a covariate and was documented using a computer-generated randomization process.For this study, analysis was restricted to male participants who reported being married or cohabitating with a partner at baseline N = 313) for two main reasons. First, a previous study conducted among men with HIV in northern Vietnam demonstrated that the alcohol-IPV relationship operates differently for men who were married or cohabitating versus those who were single, divorced, separated or widowed 3 for two, 65. SecEffect modification analyses were conducted in SAS 9.4 with multilevel growth models using maximum likelihood based on the Laplace estimation . First, All variables included in the analysis were centered . The wavAfter determining the best-fitting unconditional growth model, the adjusted conditional growth model tested the time-varying effects of alcohol use and depressive symptoms and the two-way interactions among depressive symptoms and alcohol use on IPV perpetration adjusting for covariates. Any non-significant interactions were removed from the final model. If an interaction term was significant, the effect of alcohol use on the predicted probability of IPV perpetration was graphed at both levels of the depressive symptoms variable (0 or 1) to visualize the relationships. Standard errors (SEs) and p-values were generated to test the statistical significance of the intercepts and slopes represented in the graphs. Since participants were recruited from different ART community clinics, recruitment site was initially tested as a fixed effect to assess if it influenced results. As it did not change the results, it was removed to make models more parsimonious.The sample included 313 male participants who were married or cohabitating at baseline  at baseline . At threThe best fitting unconditional growth model for IPV perpetration comprised a random intercept with linear and fixed effects for time. The odds of IPV perpetration significantly decreased over time . At baseline, the variance in IPV perpetration significantly differed between participants .Depressive symptoms significantly modified the effect of proportion of days alcohol abstinent on IPV perpetration . HoweverIn this study, alcohol use and depressive symptoms did not act synergistically to increase the odds of IPV perpetration. At times when participants reported having depressive symptoms, the effect of alcohol use on IPV perpetration became non-significant. However, at times when participants reported having no depressive symptoms, more alcohol use was associated with significantly higher odds of IPV perpetration. This finding diverges from empirical and theoretical evidence suggesting that alcohol use and depression interact to exacerbate violence outcomes –41, 68. Our study findings do not align with the multiple threshold and disinhibition theories, which suggest that people who use alcohol and experience depressive symptoms may have higher odds of IPV perpetration as compared to those who only use alcohol –39. HoweAnother potential explanation may be the unique intersection between depressive symptoms, alcohol use, and social isolation in Vietnam. Men may respond to experiences of depression with social isolation , 73, leaDue to the high prevalence of hazardous drinking and depressive symptoms among men with HIV globally and in Vietnam , 74, intA large proportion of the participants currently or previously injected drugs because the HIV epidemic in Vietnam is largely driven by injection drug use , 77. PWIWe are not able to characterize the gender of all participants' partners due to missing data (N = 42/313). All participants with available data reported recently having female sexual partners only and having female main partners. Additionally, we did not collect data on the length of participants' intimate relationships. Participants whose relationships ended during the study may have been less likely to report IPV perpetration after their relationships ended. However, the vast majority of participants reported stable relationship statuses across study visits.Variables measured using self-report may have been biased due to social desirability, resulting in more conservative estimates of IPV perpetration and depressive symptoms , 82. ThiParticipants who dropped out of the study may have been more likely to perpetrate IPV than those who were retained in the study, resulting in an underestimation of IPV perpetration. We also used a binary measure of depressive symptoms in analyses, which may have led to a loss of meaningful information and attenuated effects.Despite these limitations, this longitudinal study contributes important findings on the intersection between hazardous alcohol use, depressive symptoms, and IPV perpetration in a high-risk, understudied population. Unexpectedly, having depressive symptoms was found to weaken the alcohol-IPV relationship. These results suggest that men who reported higher alcohol use and depressive symptoms than usual may be experiencing extreme social isolation from an intimate partner, leading to less opportunity for alcohol-related IPV perpetration. Alternatively, men with HIV who are concurrently using alcohol and experiencing depressive symptoms may have fatigue or reduced energy, decreasing risk of alcohol-related IPV perpetration. Previous mental health interventions aiming to reduce IPV perpetration have either targeted participants who misuse alcohol or those who screen positive for depressive symptoms . This st


Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and have attracted significant interest in understanding if and how they may be targeted using small molecules for therapeutic purposes. While most existing studies have focused on extending the traditional structure-centric drug design strategies and emphasized exploring pre-existing structure features of IDPs for specific binding, several examples have also emerged to suggest that small molecules could achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. These dynamic interactions can modulate the disordered conformational ensemble and often lead to modest compaction to shield functionally important interaction sites. Much work remains to be done on further elucidation of the molecular basis of the dynamic small molecule–IDP interaction and determining how it can be exploited for targeting IDPs in practice. These efforts will rely critically on an integrated experimental and computational framework for disordered protein ensemble characterization. In particular, exciting advances have been made in recent years in enhanced sampling techniques, Graphic Processing Unit (GPU)-computing, and protein force field optimization, which have now allowed rigorous physics-based atomistic simulations to generate reliable structure ensembles for nontrivial IDPs of modest sizes. Such de novo atomistic simulations will play crucial roles in exploring the exciting opportunity of targeting IDPs through dynamic interactions. Proteins are central components of regulatory networks that dictate virtually all aspects of cellular decision-making . Demand The dynamic and heterogeneous nature of unbound IDPs presents substantial challenges for characterization and this has proven to be a major bottleneck for establishing a reliable sequence–structure–function–disease relationship of IDPs ,24,25,26In this review, we will first summarize important recent advances in physics-based de novo simulations of disordered protein ensembles, including Graphic Processing Unit (GPU) computing, enhanced sampling, and re-balanced protein force fields, and then focus on emerging examples that suggest the exciting possibility of targeting IDPs by directly modulating the disordered ensembles through dynamic and transient interactions. We will discuss the promise of such a broader view of how IDPs may be targeted as well as key challenges and required methodological developments to support targeting IDPs via dynamic interactions.A principal challenge in understanding the druggability and best targeting strategy of IDPs resides in the difficulty of detailed characterization of disordered protein states ,23,24,56Experimentally, a wide range of biophysical methods can be applied to characterize disordered protein states, including NMR, circular dichroism (CD), small-angle X-ray scattering (SAXS), Förster resonance energy transfer (FRET), hydrogen/deuterium (H/D) exchange, mass spectrometry, and others ,58. ThesGiven the fundamental challenges of disordered ensemble modeling based on experimental restraints alone, physics-based atomistic simulations have a crucial role to play in helping elucidate the conformational properties of IDPs and establishing a reliable molecular basis of their function and regulation ,74,75,76One of the most important recent advances in molecular dynamics (MD) simulations is the widespread availability of efficient GPU-enabled algorithms in virtually all major molecular simulation packages ,80,81,82The importance of enhanced sampling for the generation of converged ensembles cannot be over emphasized. For example, The dramatically improved sampling capability has facilitated extensive efforts to reparametrize general-purpose protein force fields to achieve greater balance of describing protein conformational equilibria. Studies of disordered protein states have been a key driver of these developments and several well-characterized IDPs have been widely used as training systems and/or benchmarks for force field optimization ,97,98,99In a recent benchmark study, six of the latest protein force fields were evaluated using the 61-residue N-terminal transactivation domain (TAD) of tumor suppressor p53, which is a very challenging system due to its size and complex conformational features . It has We note that implicit solvent protein force fields have also been developed and deployed for atomistic simulations of IDPs with various levels of success ,98,115. To date, small molecular targeting of IDPs has mostly focused on proteins involved in neurodegenerative diseases, such as amyloid β (Aβ) peptides, α-synuclein, and tau protein, and disordered regions of cancer-associated transcription factors, such as p53, c-Myc, EWS-FLI1, KLF5, and others ,117. Adv402-412 can confer sequence specificity, even though the interaction involves many transient contacts instead of well-defined specific ones [402-412 was dominated by the entropic contribution  [Kip1 found little evidence of ligand-induced conformational space expansion [One of the earliest examples of dynamic interactions between small molecules and IDPs concerns c-Myc inhibitors ,28. NMR,fic ones . It has fic ones . Indeed, kJ/mol) . The cavxpansion . InsteadC. elegans. The observation that dynamic interactions between a small molecule and IDP could be functionally effective both in vitro and in vivo is very encouraging and supports the promise of targeting IDPs using dynamic interactions for therapeutics.Dynamic interactions were also found to underlie the mechanism of α-synuclein aggregation inhibition by analogs of cyclized nordihydroguaiaretic acid (cNDGA) . The str42 with and without tramiprosate  and scyllo-inositol (SI) were calculated using REST2 simulations in the CHARMM36m force field that lasted 10 μs per replica, making them the most extensive atomistic simulations of Aβ42 to date. The resulting ensembles are well converged and appear consistent with the NMR chemical shifts. Comparing the ensembles with and without the ligand showed that both HT and SI mainly reduced the β propensity in the C-terminal region with minimal secondary structure perturbation in the rest of the peptide. Intriguingly, both HT and SI were found to induce modest compaction of the conformational ensemble, particularly in the C-terminal segment that is known to be important for amyloid fibril formation , modulates the disordered unbound state of p53-TAD . EGCG isIDPs have remained an extremely challenging class of proteins to target using small molecules. Albeit limited, successful inhibitors have been discovered and designed for several IDPs involved in cancers and neurodegenerative diseases, suggesting that IDPs are not undruggable. Nonetheless, the unstructured and dynamic nature of IDPs is distinct from typical protein targets with well-defined binding pockets. It requires new conceptional frameworks to guide the development of novel strategies for discovering and designing small molecules that can modulate IDP functions. Traditional structure-based screening and lead optimization strategies are clearly inadequate, even though some success has been demonstrated in deploying existing tools to identify possible binding pockets and target pre-existing structural elements. Such structural elements are lightly populated and generally too small to harbor significant pockets for small molecular binding that relies on specific interactions to achieve high affinity. In fact, there is a great uncertainty on whether high-affinity binding to IDPs is feasible with small molecules . It is encouraging that examples are emerging that small molecules could modulate the IDP ensembles entirely through dynamic nonspecific interactions. Importantly, there is evidence that high-affinity binding may not be necessary to induce functional responses in vitro and in vivo. This may reflect a fundamental nature of how IDPs mediate function in biology, in that the disordered ensemble of an IDP is poised to respond sensitively to a wide array of cellular signals to support signal transduction and cellular regulation . TherefoIt is noteworthy that IDPs have been found to play central roles in mediating liquid–liquid phase separation (LLPS) that underlies a range of cellular processes ,136,137.Elucidating the molecular details of dynamic interactions between IDPs and small molecules will require further development and integration of new experimental and computational methodologies. The capability for reliable disordered ensemble characterization with and without small molecules will almost certainly be required for any future design and optimization strategy to discover drugs that target IDPs through dynamic interactions. This unfortunately remains a formidable task. Bulk experimental measurements on average properties alone are not sufficient to uniquely define the disordered ensemble. The dynamic and transient nature of molecular contacts can be very difficult to detect and resolve experimentally ,139. Lev


First, we discuss the generation and function of in vitro skeletal muscle models. We then discuss the genetic, neural, and hormonal factors regulating skeletal muscle fiber-type in vivo and the ability of current in vitro models to study muscle fiber-type regulation. We also evaluate the potential of these systems to be utilized in a patient-specific manner to accurately model and gain novel insights into diseases such as Duchenne muscular dystrophy (DMD) and volumetric muscle loss. We conclude with a discussion on future developments required for tissue-engineered skeletal muscle models to become more mature, biomimetic, and widely utilized for studying muscle physiology, disease, and clinical use.Skeletal muscle possesses remarkable plasticity that permits functional adaptations to a wide range of signals such as motor input, exercise, and disease. Small animal models have been pivotal in elucidating the molecular mechanisms regulating skeletal muscle adaptation and plasticity. However, these small animal models fail to accurately model human muscle disease resulting in poor clinical success of therapies. Here, we review the potential of  Small animal studies, particularly comparative biology and genetic manipulations, have been pivotal in elucidating the molecular mechanisms regulating skeletal muscle function and plasticity  tissue engineered skeletal muscle culture systems have been developed that better mimic the native muscle microenvironment, permit functional testing, and enable prolonged culture durations  that pump calcium back to the SR and the high affinity calcium binding protein parvalbumin found in fast skeletal muscle that quickens relaxation rate  which connects to the t-tubule at the specialized terminal cisternae. The SR stores calcium at a significantly higher concentration than seen in the sarcoplasm due to the calcium-binding protein calsequestrin (CSQ) . Calciumion rate .in vitro culture of whole skeletal muscles is impossible due to hypoxia and resultant loss of viability. To minimize hypoxic stress, muscles such as the extensor digitorum longus (EDL) and soleus (SOL) can be dissected to generate muscle strips that can be cultured for up to 12 h in highly oxygenated media  of fusion and ease of the system, this model is the most frequently used system to assess the impact of genetic manipulations, growth factors, or small molecules on muscle differentiation and fusion. However, the assessment of longer-term (<7 days) experimental interventions are often prevented due to the detachment of myotubes due to spontaneous contractions of developing myotubes . FurtherTo overcome the limitations of 2D cell culture, several 3D skeletal muscle culture models have been developed over the past 30 years . Two culThe majority of engineered tissues are generated from three-dimensional hydrogels derived from natural ECM proteins such as collagen and fibrin. Hydrogels should: (1) provide a high surface area for cell adhesion, (2) provide mechanical support and/or topical guidance to maximize, (3) minimize diffusion distances, and (4) fully degrade once sufficient cell-derived ECM is deposited to generate densely packed muscle tissue supported by its own ECM. Hydrogel based tissues are typically formed from expanded MPCs that are embedded at high density within or on top of these hydrogels. The hydrogels are cast between two fixed anchor points that enable cellular forces to remodel the hydrogel and maintain the tissues under tension that promotes tissue alignment, rapid fusion, and muscle hypertrophy .TM, a commercially available basal lamina extract isolated from murine Engelbreth-Holm-Swarm tumors, at the time of tissue formation. Collagen-matrigel hydrogels improve muscle structure but still generate lower contractile forces than fibrin based tissues and consequently are being used less frequently for studies measuring contractile function  or type 2 fast-twitch (FT) fiber types based on myosin heavy chain (MYH) isoform expression. While ST fibers express type I myosin (MYH7), FT fibers can be further classified into three subtypes, IIa (MYH1), IIx (MYH2), and IIb (MYH4), resulting in four fiber-type classifications. However, Type IIb fibers which possess the fastest contractile phenotype, are absent in human skeletal muscle resulting in humans only possessing three fiber-types . During development and muscle regeneration, the embryonic (MYH3) and neonatal (MYH8) MYH isoforms are sequentially expressed before being down regulated and replaced by the adult MYH isoforms . Importantly, approximately 25% of muscle fibers are “hybrid” and express two or more MYH isoforms that arise to provide a functional continuum for optimal contractile performance or reflect transitionary states during development and regeneration . In addiOver the past 30 years, significant advances in elucidating the complex molecular and transcriptomic regulation of fiber-type have been achieved. A combination of epigenetic imprinting, neuronal activity, oxygen tension, environmental factors, and metabolic and hormonal influences regulate signaling pathway cascades and transcription factor activity . A key rComplete muscle development and maintenance of adult muscle mass and fiber-type requires functional innervation. A key difference between slow and fast fiber-types is the motor input received with the frequency neural impulses differing between slow (10–30 Hz) and fast (50–100 Hz) muscle fibers . Additioin vitro model to study factors regulating excitability and to screen factors that promote muscle excitability  result in multiple neuromuscular diseases such as myasthenia gravis (MG) and amyotrophic lateral sclerosis (ALS) . The firThe first 3D tissue engineered muscle motor-neuron co-cultures utilized neonatal rat MPCs and embryonic spinal cord explants . Neural in vitro and in vivo.A fundamental question underlying muscle plasticity is if the satellite cells that make typically slow  or fast  muscle fibers are distinct and predisposed to generate a specific fiber-type. As discussed above, the adaptive ranges of muscle fibers suggest that fiber-type is predetermined. Slow fiber-type muscles contain a higher level of satellite cells than fast fiber type tissues . This diin vitro by the application of stretch to tissue cultures using deformable membranes  the continual increase in muscle length seen during development (ramp stretch/stimulation); and; (2) muscle strain that occurs during locomotion and exercise (cyclic stretch/stimulation). Ramp stretch results in concomitant proliferation and differentiation of MPCs  is a fatal X-linked recessive disorder that affects approximately 1 in 5000 male births due to mutations in the dystrophin gene. Dystrophin is part of the dystrophin-glycoprotein complex (DGC) that functions to efficiently transmit contractile force to the ECM and stabilize the sarcolemmal membrane during contraction to prevent muscle damage. The increased susceptibility to muscle injury due to compromised membrane stability and impaired regenerative response of satellite cells results in constant cycles of muscle degeneration and regeneration. Ultimately, this leads to progressive muscle weakness, loss of ambulation, and fatal respiratory failure by the age of 20. Currently, there is no curative treatment with standard-of-care corticosteroid (prednisone and deflazacort) therapy extending life expectancy up to the fourth decade by delaying disease progression .cv2–5) and on the DBA/2J backgrounds  . In the kgrounds . The mdx studies . Mouse m studies . These d studies  and card studies  disease efficacy . For exaefficacy , and inh in vivo . Therefonisolone  and deflnisolone . More renisolone  which wanisolone . The usein vitro skeletal muscle models of DMD have been reported using primary cells. The first utilized immortalized dystrophic mouse myoblasts and identified 11 compounds that increased contractile force generation (in vitro. Widespread in vitro personalized medicine models of DMD or any other myopathy will require the use of hiPSC-derived muscle due to the ethical considerations and proliferative limitations of taking muscle biopsies from myopathic patients. To date, the majority of hiPSC studies of DMD have been performed in 2D cell culture. These studies have demonstrated disease phenotypes such as calcium overload (in vitro and improved mdx morphology and function in vitro (To date, two 3D neration . More reneration . Whilst overload , fusion overload , and eleoverload . Interesoverload . Recentlin vitro . In addiin vitro . A furthin vitro . Overallde novo muscle formation necessitating novel therapeutic approaches (Skeletal muscle regenerative capacity can be overwhelmed by extensive muscle loss seen with trauma, blast injuries, and surgical resection. In animal models, this is typically modeled by the surgical removal of 20-40% of muscle mass . This leproaches .in vitro controls (in vitro not only enables the study of muscle regeneration in controlled conditions but also correlates to tissue survival upon implantation (in vitro but the addition of macrophages supports in vitro regeneration and increased regenerative ability and functionality upon implantation in vivo (Injection of satellite cells alone into VML injury models does not support muscle regeneration, highlighting the need for a satellite cell niche and myofiber guidance for successful regenerative outcomes . In non-controls . In thescontrols . Encouracontrols , suggestcontrols  – the keantation , 2018. T in vivo .The recent advances and progress made in tissue engineering more biomimetic muscle tissues has provided researchers a novel model to complement traditional 2D cell culture and animal models. Here, we have discussed the utility of these engineered tissues to study muscle physiology, regeneration, exercise, and disease. However, the highest functioning engineered muscle tissues have the functionality of neonatal muscle tissue and do not possess the developmental maturity of adult skeletal muscle . Given tFor engineered muscle tissues to be more widely utilized, a shift to serum-free culture conditions is also required to increase reproducibility and permit clinical translation of cellular therapies. This is highlighted by the fact that geographical origin of serum can impact the contractile kinetics and isoform expression of calcium-handling proteins in engineered tissues . FurtherThe majority of studies on engineered muscle tissue function are derived of cultures only containing muscle and contaminating or added fibroblasts. While this enables the ability to isolate muscle-specific effects, native muscle tissue is comprised of multiple cell types that are required for complete muscle development and function. The incorporation of motor neurons , sensoryin vivo studies as 2D systems have been for decades. Future advances in tissue maturation, generation of more complex heterocellular tissues, and coupling to other organ systems will generate improved models to study muscle disease and increase the chance of identifying novel biological and pharmaceutical therapeutics.Overall, tissue engineered muscle systems are a powerful tool to study skeletal muscle function, development, plasticity, and disease. These systems can be used for stand-alone studies, add functional translational components, or be used to supplement AK wrote, edited, and generated figures for the entire manuscript.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Acute aortic dissection (AAD) is a rare, but a life-threatening condition which can lead to coronary, brachiocephalic or branch vessel malperfusion, as well as aortic valve insufficiency, or aortic rupture. Mortality of surgical treatment in high-risk or elderly patients with Type A Acute aortic dissection (TAAAD) still remains high, and treatment for such patients remains controversial.A new surgical approach which entails “stepwise external wrapping (SEW)” using a zero-porosity artificial graft was developed in extremely high-risk patients with TAAAD. Herein, we described its surgical details and showed two representative cases which was successfully done.Our SEW procedure is a feasible alternative to conventional graft replacement for TAAAD in extremely high-risk or aged patients, although the gold standard consists of surgical replacement of the dissected aorta. (129 words). Acute aortic dissection (AAD) is a rare, but a life-threatening condition which can lead to coronary, brachiocephalic or branch vessel malperfusion, as well as aortic valve insufficiency, or aortic rupture . The IntWe developed a new surgical approach which entails “stepwise external wrapping (SEW)” using a zero-porosity artificial graft. Herein, we reported two cases with major preoperative comorbidities and described surgical details.From June 2016 to March 2017, 2 patients with TAAAD underwent SEW procedure of the ascending aorta. Institutional review board approval was provided before publication of this article and reporting of the information. Informed consent was obtained by all patients or patients’ family in cases in which the patient was unconscious. Patient 1 was an 83-year-old man with tamponade and cardiogenic shock. Patient 2 was a 78-year-old woman also suffering from shock vitals and preoperative coma. A computed tomographic scan showed that entire aorta was dissected. Echocardiography confirmed pericardial effusion and no severe aortic regurgitation in both patients.Median sternotomy was made and cardiopulmonary bypass was implemented through femoral arterial cannulation and single two-stage venous cannulation via right atrial appendage. The ascending aorta was carefully separated from the pulmonary artery trunk and the right pulmonary artery. Most care was taken during the dissection to avoid tearing the false lumen of the dissected aorta. Pieces of artificial graft was tailored, placed around the aorta from the coronary ostia up to the innominate artery in a stepwise fashion, and approximated with a running suture of 4–0 Prolene  to tightly wrap the dissected ascending aorta Fig. . We usedThe concept of external wrapping surgery is not new, and it was first reported by Poppe JK for successful treatment of syphilitic aneurysms of the thoracic aorta in 1946 .Recently, Demondion P et al. reported a less invasive approach consisting of off-pump wrapping of the dissected ascending aorta with favorable short and midterm results . There wIn the present cases, there was no incidence of brain injury, re-exploration for bleeding, renal failure, respiratory failure, or hospital death among the sick patients who underwent SEW. There are many advantages in SEW procedure over conventional graft replacement. SEW procedure enables us to significantly shorten the CPB and operative durations. In high risk patients, it is believed shorter operation times provide better outcomes by way of reducing the surgical stress. Since SEW procedure does not require deep hypothermia the inherent risks and harm associated with CPB on coagulation system, lungs, and other organs is avoided. In addition, no brain protection or cardiac arrest was necessary. These advantages finally helped to prevent severe complications in treating high-risk patients conventionally.In conclusion, our SEW procedure is a feasible alternative to conventional graft replacement for TAAAD in extremely high-risk or aged patients, although the gold standard consists of surgical replacement of the dissected aorta. Further careful follow-up care will be needed.


Alterations in extracellular matrix composition and organization are known to promote tumor growth and metastatic progression in breast cancer through interactions with tumor cells as well as stromal cell populations. Macrophages display a spectrum of behaviors from tumor-suppressive to tumor-promoting, and their function is spatially and temporally dependent upon integrated signals from the tumor microenvironment including, but not limited to, cytokines, metabolites, and hypoxia. Through years of investigation, the specific biochemical cues that recruit and activate tumor-promoting macrophage functions within the tumor microenvironment are becoming clear. In contrast, the impact of biomechanical stimuli on macrophage activation has been largely underappreciated, however there is a growing body of evidence that physical cues from the extracellular matrix can influence macrophage migration and behavior. While the complex, heterogeneous nature of the extracellular matrix and the transient nature of macrophage activation make studying macrophages in their native tumor microenvironment challenging, this review highlights the importance of investigating how the extracellular matrix directly and indirectly impacts tumor-associated macrophage activation. Additionally, recent advances in investigating macrophages in the tumor microenvironment and future directions regarding mechano-immunomodulation in cancer will also be discussed. Macrophoduction , 9, for In cancer, macrophages infiltrate the tumor microenvironment (TME) in response to tumor-secreted chemotactic signals and exhibit a tumor-supportive phenotype similar to the M2 phenotype. High macrophage infiltration has been associated with a poor prognosis and increased rates of metastasis in several cancer types, as tumor-associated macrophages (TAMs) can facilitate blood vessel formation to support expanding tumor growth and aid tumor cell intravasation into vasculature , 11–13. Many cancers, including breast cancer, exhibit aberrant deposition, and organization of extracellular matrix proteins surrounding a tumor –18. The in vitro. Importantly, the same mechanism of macrophage-tumor cell migration has been observed in vivo, where macrophage-tumor cell trafficking can be visualized along collagen fibers  mice, tumor growth and immunosuppressive cytokine mRNA levels are enhanced relative to wild type mice, whereas constitutive activation of the αM integrin by a point mutation knock in (C57BL/6 ITGA-M I332G) inhibits tumor growth, despite increased IL-6 mRNA levels (Itgam−/− mice (relative to Itgam+/− control mice) when challenged with TLR ligands  is the most promiscuous integrin of the β2 integrin family. It is also the most studied of the integrins expressed by macrophages, however its impact on macrophage activation remains disputed. In A levels . In cont ligands . However ligands  and by t ligands . On the  ligands , 85. Add ligands , 86, 87.In addition to αMβ2, collagen specific adhesion receptors have also been shown to mediate macrophage activation. The importance of macrophage adhesion to collagen is underscored by the fact that the ECM in human primary breast cancers contains higher levels of collagen  compared to normal breast tissue , 89. TheIL4+IL13 macrophages compared to MLPS+IFNγ, and its knockdown resulted in increased TNF-α secretion relative to the non-treated control , for example [reviewed extensively in ]. Rostamronments –113. Usironments –116.+ and NADH (in vivo. One emerging signature of macrophage activation is the use of fluorescence lifetime. Fluorescence Lifetime Imaging Microscopy (FLIM) reports the time a fluorophore remains in the excited state before transitioning back to ground state, and differences in fluorescent lifetimes of NADH and FAD+ can indicate whether the cofactors are free or protein bound. Changes in the relative concentrations of bound vs. free NADH and FAD+ can provide information on metabolic states at the single cell level  , anotherand NADH  can be uand NADH . This teand NADH , 122. Whll level , 124. Will level . Along tin vitro , thus wain vivo, here we highlight studies that investigate the relationship and crosstalk between biophysical properties of the ECM and macrophage activation. Further investigation into downstream signaling pathways activated by integrin ligand binding and mechanical stimuli is necessary to identify potential therapeutic interventions to shift TAMs away from a tumor promoting phenotype. One expanding area is the use of metabolic reprogramming to shift macrophage phenotypes. Classically and alternatively activated macrophages favor differing metabolic mechanisms, and differences in the fluorescence lifetime signatures of metabolic cofactors lends support to the use of metabolism as a phenotypic marker. Moreover, integrin activation through the α2β1 integrin can induce activation the PI3K-Akt pathway (Taming tumor-associated macrophages has been a long-time goal for cancer therapy, and much work remains to fully understand the crosstalk between macrophages and the tumor microenvironment. While a causal mechanistic link between biomechanical properties of the ECM and macrophage activation has yet to be fully established  pathway , and mac pathway . MetabolEH wrote the first draft of the manuscript. All authors contributed to manuscript and figure conceptualization and design, revision, read and approved the submitted version.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.