bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Outcomes in Breast Augmentation in Trans-Women: A 20-Year Experience
Authors: Fakin Richard M , Zimmermann Simon , Kaye Kai , Lunger Lukas , Weinforth Geraldine , Giovanoli Pietro 
Published: June 2018

Abstract

Background
Breast augmentation in trans-women requires special consideration and thorough preoperative planning.

Objectives
This study aimed to present our long-term outcome and experience gained over the past 21 years.

Methods
Trans-women who have undergone breast augmentation since 1995 were reviewed for primary surgery, type of incision, implant site, implant size and shape, and revisions.

Results
A total of 138 patients with a follow-up of 4.6 years (range, 2.0-13.3) were included. In 112 patients (82.4%), the inframammary incision was chosen. Subpectoral implantation was performed in 70 patients (51.5%). Round breast implants (91 patients, 66.9%, P = 0.010) with low projection (103 patients, 75.7%, P &lt; 0.001) were favored. The implant size used during 2011-2016 of 363.3 ± 97.3 cc was significantly increased as compared to the implant size reported during 1995-1999 (mean difference, +142.1 cc, P &lt; 0.001) and 2000-2004 (mean difference, +113.5 cc, P &lt; 0.001). Simultaneously, revision rates dropped significantly over time (52.9% during 1995-1999 as compared to 6.9% during 2011-2016, P &lt; 0.001). Overall, request for larger implants was the most common indication for revision (13 patients, 9.4%) after 6 months (range, 4.0-18.7). At revision, implant volume was 355.4 ± 132.8 cc, showing significant increase of 107.0 ± 48.1 cc as compared to primary implants (+30.0%, P = 0.048).

Conclusions
Request for larger breast implants was the most common reason for revision. Depending on the various degrees of breast tissue growth due to hormonal therapy, whenever applicable, we recommend round, low projection implants with a mean size of 360 cc in the prepectoral pocket.

Level of Evidence: 4
dbCID: a manually curated resource for exploring the driver indels in human cancer
Authors: Yue Zhenyu , Zhao Le , Cheng Na , Yan Hua , Xia Junfeng 
Published: June 2018

AbstractWhile recent advances in next-generation sequencing technologies have enabled the creation of a multitude of databases in cancer genomic research, there is no comprehensive database focusing on the annotation of driver indels (insertions and deletions) yet. Therefore, we have developed the database of Cancer driver InDels (dbCID), which is a collection of known coding indels that likely to be engaged in cancer development, progression or therapy. dbCID contains experimentally supported and putative driver indels derived from manual curation of literature and is freely available online at http://bioinfo.ahu.edu.cn:8080/dbCID. Using the data deposited in dbCID, we summarized features of driver indels in four levels (gene, DNA, transcript and protein) through comparing with putative neutral indels. We found that most of the genes containing driver indels in dbCID are known cancer genes playing a role in tumorigenesis. Contrary to the expectation, the sequences affected by driver frameshift indels are not larger than those by neutral ones. In addition, the frameshift and inframe driver indels prefer to disrupt high-conservative regions both in DNA sequences and protein domains. Finally, we developed a computational method for discriminating cancer driver from neutral frameshift indels based on the deposited data in dbCID. The proposed method outperformed other widely used non-cancer-specific predictors on an external test set, which demonstrated the usefulness of the data deposited in dbCID. We hope dbCID will be a benchmark for improving and evaluating prediction algorithms, and the characteristics summarized here may assist with investigating the mechanism of indel–cancer association.
Predicting clone genotypes from tumor bulk sequencing of multiple samples
Authors: Miura Sayaka , Gomez Karen , Murillo Oscar , Huuki Louise A , Vu Tracy , Buturla Tiffany , Kumar Sudhir 
Published: June 2018

AbstractMotivationAnalyses of data generated from bulk sequencing of tumors have revealed extensive genomic heterogeneity within patients. Many computational methods have been developed to enable the inference of genotypes of tumor cell populations (clones) from bulk sequencing data. However, the relative and absolute accuracy of available computational methods in estimating clone counts and clone genotypes is not yet known.ResultsWe have assessed the performance of nine methods, including eight previously-published and one new method (CloneFinder), by analyzing computer simulated datasets. CloneFinder, LICHeE, CITUP and cloneHD inferred clone genotypes with low error (&lt;5% per clone) for a majority of datasets in which the tumor samples contained evolutionarily-related clones. Computational methods did not perform well for datasets in which tumor samples contained mixtures of clones from different clonal lineages. Generally, the number of clones was underestimated by cloneHD and overestimated by PhyloWGS, and BayClone2, Canopy and Clomial required prior information regarding the number of clones. AncesTree and Canopy did not produce results for a large number of datasets. Overall, the deconvolution of clone genotypes from single nucleotide variant (SNV) frequency differences among tumor samples remains challenging, so there is a need to develop more accurate computational methods and robust software for clone genotype inference.Availability and implementationCloneFinder is implemented in Python and is available from https://github.com/gstecher/CloneFinderAPI.Supplementary informationSupplementary data are available at Bioinformatics online.
gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations
Authors: Irrgang M Eric , Hays Jennifer M , Kasson Peter M 
Published: June 2018

Abstract

Summary
Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that i) allows custom potential functions without modifying the simulation package code, ii) maintains the optimized performance of GROMACS and iii) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.

Availability and implementation
LGPLv2.1 source and instructions are available at https://github.com/kassonlab/gmxapi.

Supplementary information
Supplementary data are available at Bioinformatics online.
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
Authors: Simon L M , Karg S , Westermann A J , Engel M , Elbehery A H A , Hense B , Heinig M , Deng L , Theis F J 
Published: June 2018

Abstract

Background
With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts.

Findings
We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource.

Conclusions
Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.
Kelch-like protein 14 promotes B-1a but suppresses B-1b cell development
Authors: Li Shuyin , Liu Jun , Min Qing , Ikawa Tomokatsu , Yasuda Shoya , Yang Yang , Wang Yan-Qing , Tsubata Takeshi , Zhao Yaofeng , Wang Ji-Yang 
Published: June 2018

Abstract
B-1 cells are innate-like B-cell population and produce natural antibodies that contribute to the first line of host defense. There are two subsets of B-1 cells: B-1a and B-1b. B-1a cells are the main producer of poly-reactive and autoreactive natural IgM antibodies, whereas B-1b cells can respond specifically to T-cell-independent antigens. Despite the functional significance of B-1a and B-1b cells, little information is available about what regulates the development of these two subsets. We found that Kelch-like protein 14 (KLHL14) was expressed at high levels in B cells but only at low levels in a few non-lymphoid tissues. Although mice lacking KLHL14 died right after birth, the heterozygotes developed normally with no gross abnormalities by appearance. B-cell development in the bone marrow and maturation and activation in the spleen were not affected in the heterozygous mice. However, the number of peritoneal B-1a cells was significantly reduced while B-1b cells were increased in Klhl14 heterozygous mice compared with wild-type (WT) mice. Consistently, Rag1−/− mice reconstituted with Klhl14−/− fetal liver cells had a more severe reduction of B-1a and an increase of B-1b cells in the peritoneal cavity. KLHL14 did not affect the turnover or apoptosis of B-1a and B-1b cells in vivo. Moreover, Klhl14−/− fetal liver contained a similar proportion and absolute numbers of the B-1 progenitor cells as did WT fetal liver. These results suggest that KLHL14 promotes B-1a development in mice.
Trial by Statistics: Is a High Probability of Guilt Enough to Convict?
Authors: Di Bello Marcello 
Published: June 2018

AbstractSuppose one hundred prisoners are in a yard under the supervision of a guard, and at some point, ninety-nine of them collectively kill the guard. If, after the fact, a prisoner is picked at random and tried, the probability of his guilt is 99%. But despite the high probability, the statistical chances, by themselves, seem insufficient to justify a conviction. The question is why. Two arguments are offered. The first, decision-theoretic argument shows that a conviction solely based on the statistics in the prisoner scenario is unacceptable so long as the goal of expected utility maximization is combined with fairness constraints. The second, risk-based argument shows that a conviction solely based on the statistics in the prisoner scenario lets the risk of mistaken conviction surge potentially too high. The same, by contrast, cannot be said of convictions solely based on DNA evidence or eyewitness testimony. A noteworthy feature of the two arguments in the paper is that they are not confined to criminal trials and can in fact be extended to civil trials.
Diagnostic Approach for Classic Compared With Localized Whipple Disease
Authors: Crews Nicholas R , Cawcutt Kelly A , Pritt Bobbi S , Patel Robin , Virk Abinash 
Published: June 2018

Abstract

Background
Whipple disease (WD), a rare systemic infection caused by Tropheryma whipplei, can be a diagnostic challenge due to its variable presentation. The role of T. whipplei polymerase chain reaction (PCR) is unclear as small bowel biopsy with Periodic acid-Schiff (PAS) staining remains the diagnostic gold standard. Individualized diagnostic approaches based on variable clinical manifestations are underutilized. We investigated the methodologies employed at our institution to diagnose WD.

Methods
We retrospectively collected all cases of WD diagnosed from 1994 to 2016. Microbiology laboratory and anatomic pathology databases were queried. Case characteristics and disease clinical phenotypes (classical, localized WD arthritis, and localized central nervous system [CNS] disease) were described. The diagnostic approach and testing yield were analyzed and reported.

Results
Thirty-three cases of WD were diagnosed (18 classic WD [CWD], 9 localized WD arthritis [LWD], 6 CNS WD). Misdiagnosis and delay in diagnosis were frequent. Diagnostic approach and test yield differed by classical vs localized WD involvement. Small bowel tissue biopsy PAS stain/PCR was overwhelmingly positive (86%/92%) in CWD, yet seldom positive (12%/42%) in LWD (P &lt; .001). Affected joint synovial fluid PCR was frequently positive in both CWD (100%, 3/3) and LWD (85%, 6/7).

Conclusions
These results support the role of small bowel biopsy PAS stain/PCR in the diagnosis of CW, though this approach may be of limited utility in LWD or CNS WD without gastrointestinal symptoms. Affected joint synovial fluid or cerebrospinal fluid PCR was frequently positive in both CWD and LWD, supporting its diagnostic usefulness.
Abundance of C‐terminal binding protein isoform is a prerequisite for exit from pluripotency in mouse embryonic stem cells
Authors: Suh Min Young , Kim Tae Wan , Lee Han‐Teo , Shin Jihoon , Kim Jae‐Hwan , Jang Hyonchol , Kim Hye Ji , Kim Seong‐Tae , Cho Eun‐Jung , Youn Hong‐Duk 
Published: June 2018

ABSTRACTUnlike lower organisms, mammals have 2 C‐terminal binding protein (Ctbp) isoforms, Ctbp1 and Ctbp2. Ctbp2 is revealed as a key factor involved in determining cell fate decisions by regulating the epigenetic state in active embryonic stem cell (ESC) genes. However, the molecular mechanism underlying how Ctbp1 and Ctbp2 have different roles remains elusive. Here we demonstrate that Ctbp isoform abundance is important for mouse embryonic ESCs (mESCs) to exit from pluripotency. Temporal expression patterns of Ctbp isoforms were quite different; Ctbp2 is more highly expressed in mESCs and decreases during differentiation, while Ctbp1 is constantly expressed at a lower level. Ctbp2 knockdown, but not Ctbpl knockdown, in mESCs resulted in impaired exit from pluripotency. Interestingly, Ctbp1 and Ctbp2 overexpression in Ctbp2‐knockdown mESCs leads to exiting from pluripotency in a manner similar to that of wild‐type mESCs. Quantification of Ctbp1 and Ctbp2 revealed that differentiation ability correlates with abundance of Ctbp isoform in undifferentiated mESCs, suggesting that a sufficient amount of Ctbp isoform is a prerequisite for exiting from pluripotency. The results support the contention that 2 redundant Ctbp isoforms regulate elaborate differentiation via temporally distinctive regulatory patterns in mESCs.—Suh, M. Y., Kim, T. W., Lee, H.‐T., Shin, J., Kim, J.‐H., Jang, H., Kim, H. J., Kim, S.‐T., Cho, E.‐J., Youn, H.‐D. Abundance of C‐terminal binding protein isoformis a prerequisite for exit from pluripotency in mouse embryonic stem cells. FASEB J. 32, 6423–6435 (2018). www.fasebj.org
Galectin‐3 and N‐acetylglucosamine promote myogenesis and improve skeletal muscle function in the mdx model of Duchenne muscular dystrophy
Authors: Rancourt Ann , Dufresne Sébastien S. , St‐Pierre Guillaume , Lévesque Julie‐Christine , Nakamura Haruka , Kikuchi Yodai , Satoh Masahiko S. , Frenette Jéôme , Sato Sachiko 
Published: June 2018

ABSTRACTThe muscle membrane, sarcolemma, must be firmly attached to the basal lamina. The failure of proper attachment results in muscle injury, which is the underlying cause of Duchenne muscular dystrophy (DMD), in which mutations in the dystrophin gene disrupts the firm adhesion. In patients with DMD, even moderate contraction causes damage, leading to progressive muscle degeneration. The damaged muscles are repaired through myogenesis. Consequently, myogenesis is highly active in patients with DMD, and the repeated activation of myogenesis leads to the exhaustion of the myogenic stem cells. Therefore, approaches to reducing the risk of the exhaustion are to develop a treatment that strengthens the interaction between the sarcolemma and the basal lamina and increases the efficiency of the myogenesis. Galectin‐3 is an oligosaccharide‐binding protein and is known to be involved in cell–cell interactions and cell–matrix interactions. Galectin‐3 is expressed in myoblasts and skeletal muscle, although its function in muscle remains elusive. In this study, we found evidence that galectin‐3 and the monosaccharide N‐acetylglucosamine, which increases the synthesis of binding partners (oligosaccharides) of galectin‐3, promote myogenesis in vitro. Moreover, in the mdx mouse model of DMD, treatment with N‐acetylglucosamine increased muscle‐force production. The results suggest that treatment with N‐acetylglucosamine might mitigate the burden of DMD.—Rancourt, A., Dufresne, S. S., St‐Pierre, G., Levesque, J.‐C., Nakamura, H., Kikuchi, Y., Satoh, M. S., Frenette, J., Sato, S. Galectin‐3 and N‐acetylglucosamine promote myogenesis and improve skeletal muscle function in the mdx model of Duchenne muscular dystrophy. FASEB J. 32, 6445–6455 (2018). www.fasebj.org
Succinate receptor deficiency attenuates arthritis by reducing dendritic cell traffic and expansion of Th17 cells in the lymph nodes
Authors: Saraiva André L. , Veras Flávio P. , Peres Raphael S. , Talbot Jhimmy , de Lima Kalil A. , Luiz João P. , Carballido José M. , Cunha Thiago M. , Cunha Fernando Q. , Ryffel Bernhard , Alves‐Filho Jose C. 
Published: June 2018

ABSTRACTRheumatoid arthritis is a chronic inflammatory disease that leads to significant changes in metabolic activity. Succinate, an intermediate of the tricarboxylic acid cycle, has emerged as a metabolic mediator of the innate immune response. However, the involvement of succinate in the generation of the adaptive immune response and establishment of autoimmune response has not been addressed thus far. Here we demonstrated that the succinate‐sensing receptor (Sucnr1/GPR91) plays a critical role in the development of immune‐mediated arthritis. We found that Sucnr1 acts as a chemotactic gradient sensor that guides dendritic cells (DCs) into the lymph nodes, orchestrating the expansion of the Thelper(Th)17‐cell population and the development of experimental antigen‐induced arthritis. Sucnr1−/− mice show reduced articular hyperalgesia, neutrophil infiltration and inflammatory cytokines in the joint, and reduced frequency of Th17 cells in draining lymph nodes. Adoptive transfer of wild‐type (WT) DCs into Sucnr1−/− mice restored the development of arthritis. Moreover, DC‐depleted mice transferred with Sucnr1−/− DCs developed less arthritis than mice transferred with WT DCs. In contrast, succinate given together with the immunization boosted the recruitment of DCs and the frequency of Th17 cells in draining lymph nodes, increasing arthritis severity. Therefore, the blockade of Sucnr1 may represent a novel therapeutic target of arthritis.—Saraiva, A. L., Veras, F. P., Peres, R. S., Talbot, J., de Lima, K. A., Luiz, J. P., Carballido, J. M., Cunha, T. M., Cunha, F. Q., Ryffel, B., Alves‐Filho, J. C. Succinate receptor deficiency attenuates arthritis by reducing dendritic cell traffic and expansion of Th17 cells in the lymph nodes. FASEB J. 32, 6550–6558 (2018). www.fasebj.org
High-throughput Screening in Larval Zebrafish Identifies Novel Potent Sedative-hypnotics
Authors: Yang Xiaoxuan , Jounaidi Youssef , Dai Jennifer B. , Marte-Oquendo Francisco , Halpin Elizabeth S. , Brown Lauren E. , Trilles Richard , Xu Wenqing , Daigle Renee , Yu Buwei , Schaus Scott E. , Porco John A. , Forman Stuart A. 
Published: June 2018

Abstract

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
Many general anesthetics were discovered empirically, but primary screens to find new sedative-hypnotics in drug libraries have not used animals, limiting the types of drugs discovered. The authors hypothesized that a sedative-hypnotic screening approach using zebrafish larvae responses to sensory stimuli would perform comparably to standard assays, and efficiently identify new active compounds.

Methods
The authors developed a binary outcome photomotor response assay for zebrafish larvae using a computerized system that tracked individual motions of up to 96 animals simultaneously. The assay was validated against tadpole loss of righting reflexes, using sedative-hypnotics of widely varying potencies that affect various molecular targets. A total of 374 representative compounds from a larger library were screened in zebrafish larvae for hypnotic activity at 10 µM. Molecular mechanisms of hits were explored in anesthetic-sensitive ion channels using electrophysiology, or in zebrafish using a specific reversal agent.

Results
Zebrafish larvae assays required far less drug, time, and effort than tadpoles. In validation experiments, zebrafish and tadpole screening for hypnotic activity agreed 100% (n = 11; P = 0.002), and potencies were very similar (Pearson correlation, r > 0.999). Two reversible and potent sedative-hypnotics were discovered in the library subset. CMLD003237 (EC50, ~11 µM) weakly modulated γ-aminobutyric acid type A receptors and inhibited neuronal nicotinic receptors. CMLD006025 (EC50, ~13 µM) inhibited both N-methyl-d-aspartate and neuronal nicotinic receptors.

Conclusions
Photomotor response assays in zebrafish larvae are a mechanism-independent platform for high-throughput screening to identify novel sedative-hypnotics. The variety of chemotypes producing hypnosis is likely much larger than currently known.