bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoscopic and Histological Assessment, Correlation, and Relapse in Clinically Quiescent Ulcerative Colitis (MARQUEE)
Authors: Osterman Mark T , Scott Frank I , Fogt Franz F , Gilroy Erin D , Parrott Susan , Galanko Joseph , Cross Raymond , Moss Alan , Herfarth Hans H , Higgins Peter D R 
Published: March 2020

Abstract

Objective
It is difficult to predict relapse in quiescent ulcerative colitis (UC), but newer endoscopic and histological indices could improve this. This study aimed to determine in UC patients in clinical remission (1) the prevalence of active endoscopic and histological disease; (2) the correlation between endoscopic and histological scores; and (3) the predictive power of these scores for clinical relapse.

Design
This multicenter prospective cohort study conducted by the Crohn’s and Colitis Foundation Clinical Research Alliance included 100 adults with UC in clinical remission undergoing surveillance colonoscopy for dysplasia. Endoscopic activity was assessed using the Mayo endoscopic score (MES), ulcerative colitis endoscopic index of severity (UCEIS), and ulcerative colitis colonoscopic index of severity (UCCIS). Histology was assessed with the Riley index subcomponents, total Riley score, and basal plasmacytosis.

Results
Only 5% of patients had an MES of 0, whereas 38% had a score of 2 to 3; using the UCEIS, the majority of patients had at least mild activity, and 15% had more severe activity. Many patients also had evidence of histological disease activity. The correlations among endoscopic indices, histological subcomponents, and total score were low; the highest correlations occurred with the subcomponent architectural irregularity (ρ = 0.43–0.44), total Riley score (ρ = 0.35–0.37), and basal plasmacytosis (ρ = 0.35–0.36). Nineteen patients relapsed clinically over 1 year, with the subcomponent architectural irregularity being the most predictive factor (P = 0.0076).

Conclusions
This multicenter prospective study found a high prevalence of both endoscopic and histological disease activity in clinically quiescent UC. The correlations between endoscopy and histology were low, and the power to predict clinical relapse was moderate.
Automated classification of schools of the silver cyprinid Rastrineobola argentea in Lake Victoria acoustic survey data using random forests
Authors: Proud Roland , Mangeni-Sande Richard , Kayanda Robert J , Cox Martin J , Nyamweya Chrisphine , Ongore Collins , Natugonza Vianny , Everson Inigo , Elison Mboni , Hobbs Laura , Kashindye Benedicto Boniphace , Mlaponi Enock W , Taabu-Munyaho Anthony , Mwainge Venny M , Kagoya Esther , Pegado Antonio , Nduwayesu Evarist , Brierley Andrew S 
Published: March 2020

AbstractBiomass of the schooling fish Rastrineobola argentea (dagaa) is presently estimated in Lake Victoria by acoustic survey following the simple “rule” that dagaa is the source of most echo energy returned from the top third of the water column. Dagaa have, however, been caught in the bottom two-thirds, and other species occur towards the surface: a more robust discrimination technique is required. We explored the utility of a school-based random forest (RF) classifier applied to 120 kHz data from a lake-wide survey. Dagaa schools were first identified manually using expert opinion informed by fishing. These schools contained a lake-wide biomass of 0.68 million tonnes (MT). Only 43.4% of identified dagaa schools occurred in the top third of the water column, and 37.3% of all schools in the bottom two-thirds were classified as dagaa. School metrics (e.g. length, echo energy) for 49 081 manually classified dagaa and non-dagaa schools were used to build an RF school classifier. The best RF model had a classification test accuracy of 85.4%, driven largely by school length, and yielded a biomass of 0.71 MT, only c. 4% different from the manual estimate. The RF classifier offers an efficient method to generate a consistent dagaa biomass time series.
Survival outcomes of patients with high-grade and poorly differentiated thymic neuroendocrine carcinoma
Authors: Hamaji Masatsugu , Omasa Mitsugu , Nakagawa Tatsuo , Miyahara So , Suga Michiharu , Kawakami Kenzo , Aoyama Akihiro , Date Hiroshi 
Published: March 2020

Abstract
High-grade and poorly differentiated thymic neuroendocrine carcinoma is the rarest entity in thymic epithelial tumours. The aim of this study is to report survival data in a multi-institutional database in comparison to data in the literature. Retrospective chart review was performed on the basis of our multi-institutional database to identify patients undergoing the resection of poorly differentiated thymic neuroendocrine carcinoma between 1991 and 2018. Relevant factors were extracted, and survival analysis was performed using the Kaplan–Meier method. Twenty-one patients were identified. Five-year overall survival and recurrence-free survival were 64.6% and 51.8%, respectively. Twelve (57.1%) patients had recurrences. Due to the scarcity of data reported in the literature, our data may be used as a standard in high-grade and poorly differentiated thymic neuroendocrine carcinoma.
Environmental Complexity and Research Outcomes
Authors: Pritchett-Corning Kathleen R 
Published: March 2020

AbstractEnvironmental complexity is an experimental paradigm as well as a potential part of animals’ everyday housing experiences. In experimental uses, researchers add complexity to stimulate brain development, delay degenerative brain changes, elicit more naturalistic behaviors, and test learning and memory. Complexity can exacerbate or mitigate behavioral problems, give animals a sense of control, and allow for expression of highly driven, species-typical behaviors that can improve animal welfare. Complex environments should be designed thoughtfully with the animal’s natural behaviors in mind, reported faithfully in the literature, and evaluated carefully for unexpected effects.
Mammographic Screening in Older Women: When Is It Time to Stop?
Authors: Butler Reni , Philpotts Liane 
Published: March 2020

Abstract
Mammographic screening guidelines in women aged 75 and older are inconsistent due to a lack of data from prospective randomized controlled trials, such as those that exist for women between 40–74 years of age. In addition, older women are perceived as less likely to benefit from early detection due to increased comorbidities and a greater proportion of biologically favorable cancers. With increasing life expectancy and quality of life in the elderly, the question of when to stop mammographic screening merits renewed discussion. Observational data support a survival benefit from regular screening in older women with no severe comorbidities. In addition, screening mammography in this age group has been shown to perform better than in younger age groups, tipping the balance toward greater benefits than harms. Early studies of digital breast tomosynthesis (DBT) in older women suggest that performance metrics are further improved with DBT screening. While a biennial schedule in older women preserves some of the benefit of screening, annual mammography achieves the greatest reductions in breast cancer mortality and morbidity. As the medical community strives to offer personalized care for all age groups, health care providers are well positioned to offer shared decision-making based on existing data and tailored to each woman’s individual risk profile, comorbid conditions, and personal values.
Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage
Authors: Mbadinga Mbadinga Duchesse Lacour , Li Qiang , Ranocha Philippe , Martinez Yves , Dunand Christophe 
Published: March 2020

AbstractThe non-animal peroxidases belong to a superfamily of oxidoreductases that reduce hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, a number of studies have provided an understanding of the origin and evolution of this protein family. Here, we report a comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences that have been centralized in a dedicated database, we have been able to use phylogenetic reconstructions to increase our understanding of the evolutionary processes underlying the diversification of non-animal peroxidases. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlates with the presence or absence of certain organelles or with specific biological processes. Examination of almost 2000 organisms determined that ascorbate peroxidases (APxs) and cytochrome c peroxidases (CcPs) are present in those containing chloroplasts and mitochondria, respectively. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prxs) are only found in fungi with wood-decay and plant-degradation abilities. Class III peroxidases (CIII Prxs) are only found in streptophyte algae and land plants, and have been subjected to large family expansion. Biochemical activities of APx, CcP, and CIII Prx assessed using protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of the non-animal peroxidase encoding sequences.
A Rare Cohort of Two Rhnull Individuals
Authors: Gammon Richard R , Delk Alexander , Houtz Patricia , Alvarez Harold , Benitez Nancy 
Published: March 2020

Abstract

Objective
A 77 year old female was admitted with a subdural hematoma requiring 1 unit of apheresis platelets. She was a study subject in the 1960s and was found to be Rhnull, along with another individual who previously served as a directed donor for her.

Methods
Serologic testing performed by the immunohematology reference laboratory (IRL) confirmed that the patient was Rhnull and expressed anti-Rh29 antibodies. While searching for red blood cells (RBCs) for possible transfusion, it was discovered that the individual from the original study had recently donated an autologous unit.

Results
The IRL discovered that the donor’s antigen typing was r’r’. Testing had been performed using a molecular human erythrocyte antigen BeadChip (HBC). Due to the discrepancy between current and historical testing results, a donor segment was thawed and by tube testing confirmed to be Rhnull. A limitation of HBC is that many null phenotypes will be missed.

Conclusion
This case demonstrated that Rhnull evaluation of the donor required both serological and molecular methods.
Four Paradigms of Legal Change: American Conservative Halachic Rulings on Women’s Roles in Synagogue Practice
Authors: Haklai Iddo 
Published: March 2020

Abstract
Conservative Judaism in North America has undergone significant changes over the last seventy years regarding the issue of women’s roles within the synagogue. A review of different halachic responsa addressing women’s participation in three central functions of public prayer—receiving aliyot to the Torah, leading public prayer, and being counted in the prayer quorum, the minyan—reveals four different paradigms of legal change within the Conservative Movement and allows us to recognize certain trends throughout time.
Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations
Authors: Cicconardi Francesco , Krapf Patrick , D’Annessa Ilda , Gamisch Alexander , Wagner Herbert C , Nguyen Andrew D , Economo Evan P , Mikheyev Alexander S , Guénard Benoit , Grabherr Reingard , Andesner Philipp , Wolfgang Arthofer , Di Marino Daniele , Steiner Florian M , Schlick-Steiner Birgit C 
Published: March 2020

Abstract
Understanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesized two parallel patterns would occur in a genome adapting to an extreme habitat: 1) strong positive selection on genes related to adaptation and 2) a relaxation of previous purifying selection. We tested this hypothesis by sequencing the high-elevation specialist Tetramorium alpestre and four other phylogenetically related species. In support of our hypothesis, we recorded a strong shift of selective forces in T. alpestre, in particular a stronger magnitude of diversifying and relaxed selection when compared with all other ants. We further disentangled candidate molecular adaptations in both gene expression and protein-coding sequence that were identified by our genome-wide analyses. In particular, we demonstrate that T. alpestre has 1) a higher level of expression for stv and other heat-shock proteins in chill-shock tests and 2) enzymatic enhancement of Hex-T1, a rate-limiting regulatory enzyme that controls the entry of glucose into the glycolytic pathway. Together, our analyses highlight the adaptive molecular changes that support colonization of high-altitude environments.
Empowering Women Survivors of Domestic Violence
Authors: Hernandez-Ruiz Eugenia 
Published: March 2020

Abstract
Domestic violence is a pervasive public health problem with high societal costs. Domestic violence shelters provide services to women and their children to support their journey away from violence. Music therapy in shelters can be a vehicle of empowerment for these women. In this clinical portrait, I share my experience as a music therapist in a domestic violence shelter, incorporating an overview of the services and theoretical framework we used, reflecting on the function that music may have in this situation, and illustrating it with the case of one of the women that I was honored to meet.
Academic and Cultural Adjustment Among Asian Students in Graduate Music Therapy Programs
Authors: Lan Huei-Yi Whitney 
Published: March 2020

Abstract
Institute of International Education (Open doors report on international educational exchange: International student enrollment trends, 1948/49–2017/18) data indicated that during the 2017–2018 academic year, 1,094,792 international students were studying at a college or university in the United States, of which 62% came from Asian countries such as China, Indonesia, Japan, Malaysia, South Korea, Taiwan, and Vietnam. Recognizing the importance of a diverse student body, universities have developed programs to assist international students in adapting to the U.S. culture and education system. Music therapy programs, particularly at the graduate level, continue to attract students from Asian countries, although the exact number of students is unknown. Furthermore, little is known about the extent to which music therapy programs provide support for Asian international students, or how Asian international students themselves adjust to, and experience, the first few years of their academic training. Within this context, the purpose of this study was to interview Asian international students studying in graduate music therapy programs in order to understand their experiences during their first 3 years in the United States, particularly the cultural and educational challenges they encountered. Six students and five new professionals were interviewed, with interview transcripts analyzed using methods consistent with qualitative content analysis. Results indicated that almost all the Asian international students interviewed experienced challenges associated with cultural and academic adjustment. Recommendations for students and educators suggest ways to support Asian students as they adapt and integrate into U.S. cultural and academic environments.
The role of Sp1 in the detection and elimination of cells with persistent DNA strand breaks
Authors: Loshchenova Polina S , Sergeeva Svetlana V , Fletcher Sally C , Dianov Grigory L 
Published: March 2020

Abstract
Maintenance of genome stability suppresses cancer and other human diseases and is critical for organism survival. Inevitably, during a life span, multiple DNA lesions can arise due to the inherent instability of DNA molecules or due to endogenous or exogenous DNA damaging factors. To avoid malignant transformation of cells with damaged DNA, multiple mechanisms have evolved to repair DNA or to detect and eradicate cells accumulating unrepaired DNA damage. In this review, we discuss recent findings on the role of Sp1 (specificity factor 1) in the detection and elimination of cells accumulating persistent DNA strand breaks. We also discuss how this mechanism may contribute to the maintenance of physiological populations of healthy cells in an organism, thus preventing cancer formation, and the possible application of these findings in cancer therapy.
Joint single cell DNA-seq and RNA-seq of gastric cancer cell lines reveals rules of in vitro evolution
Authors: Andor Noemi , Lau Billy T , Catalanotti Claudia , Sathe Anuja , Kubit Matthew , Chen Jiamin , Blaj Cristina , Cherry Athena , Bangs Charles D , Grimes Susan M , Suarez Carlos J , Ji Hanlee P 
Published: March 2020

Abstract
Cancer cell lines are not homogeneous nor are they static in their genetic state and biological properties. Genetic, transcriptional and phenotypic diversity within cell lines contributes to the lack of experimental reproducibility frequently observed in tissue-culture-based studies. While cancer cell line heterogeneity has been generally recognized, there are no studies which quantify the number of clones that coexist within cell lines and their distinguishing characteristics. We used a single-cell DNA sequencing approach to characterize the cellular diversity within nine gastric cancer cell lines and integrated this information with single-cell RNA sequencing. Overall, we sequenced the genomes of 8824 cells, identifying between 2 and 12 clones per cell line. Using the transcriptomes of more than 28 000 single cells from the same cell lines, we independently corroborated 88% of the clonal structure determined from single cell DNA analysis. For one of these cell lines, we identified cell surface markers that distinguished two subpopulations and used flow cytometry to sort these two clones. We identified substantial proportions of replicating cells in each cell line, assigned these cells to subclones detected among the G0/G1 population and used the proportion of replicating cells per subclone as a surrogate of each subclone's growth rate.
GSAn: an alternative to enrichment analysis for annotating gene sets
Authors: Ayllon-Benitez Aaron , Bourqui Romain , Thébault Patricia , Mougin Fleur 
Published: March 2020

Abstract
The revolution in new sequencing technologies is greatly leading to new understandings of the relations between genotype and phenotype. To interpret and analyze data that are grouped according to a phenotype of interest, methods based on statistical enrichment became a standard in biology. However, these methods synthesize the biological information by a priori selecting the over-represented terms and may suffer from focusing on the most studied genes that represent a limited coverage of annotated genes within a gene set. Semantic similarity measures have shown great results within the pairwise gene comparison by making advantage of the underlying structure of the Gene Ontology. We developed GSAn, a novel gene set annotation method that uses semantic similarity measures to synthesize a priori Gene Ontology annotation terms. The originality of our approach is to identify the best compromise between the number of retained annotation terms that has to be drastically reduced and the number of related genes that has to be as large as possible. Moreover, GSAn offers interactive visualization facilities dedicated to the multi-scale analysis of gene set annotations. Compared to enrichment analysis tools, GSAn has shown excellent results in terms of maximizing the gene coverage while minimizing the number of terms.
Getting Personal: How Childhood Vaccination Policies Shape the Landscape of Vaccine Exemptions
Authors: Garnier Romain , Nedell Emma R , Omer Saad B , Bansal Shweta 
Published: March 2020

Abstract

Background
State-mandated school entry immunization requirements in the United States play an important role in achieving high vaccine coverage, but variations in vaccine exemption policies result in a patchwork of vaccine coverage across the country.

Methods
In this study, we evaluate epidemiological effects and spatial variations in nonmedical exemption (NME) rates in the context of vaccine policies. We first analyze the correlation between NME rates and vaccine coverage for 3 significant childhood vaccinations. Furthermore, we assess the effects of policy changes in a subset of states, using a correlative approach at the state level and performing a clustering analysis at the county level.

Results
We find that higher rates of exemptions are associated with lower vaccination rates of school-aged children in all cases. In a subset of states where exemption policy has recently changed, we show that the effects on statewide NME rates vary widely and that decreases in NMEs can lead to an increase in other types of exemptions. Finally, our clustering analysis in California, Illinois, and Connecticut shows that policy changes affect the spatial distribution of NMEs.

Conclusions
Our work suggests that vaccination policies have significant impacts on patterns of herd immunity. Our findings can be used to develop evidence-based vaccine legislation.
Endovascular Embolization of a Lateral Sacral Fistula: 2-Dimensional Operative Video
Authors: Rahme Rudy J , Abi-Aad Karl R , Almekkawi Ahmad Kareem , Patra Devi P , Bendok Bernard R 
Published: March 2020

Abstract
Spinal dural arteriovenous fistulas are the most common vascular malformations of the spine. They are localized in the sacral spine in 5% to 14% of the cases. They can be fed by the median or the lateral sacral arteries. These lesions present with nonspecific symptoms such as radiculopathy and/or myelopathy, which often leads to a delay in diagnosis. In this video, we present the case of a 65-yr-old gentleman with a lateral sacral dural arteriovenous fistula. The patient was referred to our institution after the outside facility workup was nondiagnostic. He presented with spastic paraparesis and bilateral radiculopathy. After patient informed consent was obtained, we performed a spinal diagnostic angiogram with catheterization and angiography of the internal iliac artery, which revealed the fistula. Onyx (Medtronic, Dublin, Ireland) embolization was performed, which led to a complete occlusion of the fistula. The patient had complete neurological recovery, and at 2-yr follow-up, imaging remained negative for a fistula. In this video, we discuss the nuances and key points related to the epidemiology, diagnosis, and treatment of lateral sacral fistulas.
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