bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of tapering on neuromuscular and metabolic fitness in team sports: a systematic review and meta‐analysis
Authors: Vachon Adrien , Berryman Nicolas , Mujika Iñigo , Paquet Jean‐Baptiste , Arvisais Denis , Bosquet Laurent
Published: March 2020

Purpose: To assess the effects of a taper strategy on neuromuscular and metabolic fitness in team sport athletes, through a systematic review and meta‐analysis. Method: To be included in this meta‐analysis, studies had to involve competitive team sport athletes and a tapering intervention providing details about the procedures used to decrease the training load, as well as competition or field‐based criterion performance and all necessary data to calculate effect sizes. Four databases were searched according to these criteria, which led to the identification of 895 potential studies and the subsequent inclusion of 14 articles. Independent variables were training intensity, volume and frequency, as well as the pattern of taper and its duration. The dependent variable was performance obtained in various neuromuscular and metabolic tests. Results: There was limited evidence of a moderate taper‐induced improvement in repeated sprint ability (Standardized Mean Difference (SMD) (95%IC;I2) = 0.41 (0.26–0.55;0%)) and moderate evidence of a moderate increase in maximal power (SMD (95%IC;I2) = 0.44 (0.32–0.56;15%)), change of direction speed (SMD (95%IC;I2) = 0.38 (0.15–0.60;28%)) and maximal oxygen uptake (SMD (95%IC;I2) = 0.76 (0.43–1.09;37%)). Conclusion: Tapering is an effective training strategy to improve maximal power, maximal oxygen uptake, repeated sprint ability and change of direction speed in team sports. However, the literature lacks studies using various tapering strategies to compare their effectiveness and make evidence‐based recommendations. Future original studies should focus on this major issue.
Effect of allopurinol on phosphocreatine recovery and muscle function in older people with impaired physical function: a randomised controlled trial
Authors: Witham Miles D , Clarke Clare L , Hutcheon Anita , Gingles Christopher , Gandy Stephen , Priba Lukasz , Nicholas Richard S , Cavin Ian , Sumukadas Deepa , Struthers Allan D , George Jacob
Published: March 2020

Background

Allopurinol has vascular antioxidant effects and participates in purinergic signalling within muscle. We tested whether allopurinol could improve skeletal muscle energetics and physical function in older people with impaired physical performance.

Methods

We conducted a randomised, double blind, parallel group, placebo-controlled trial, comparing 20 weeks of allopurinol 600 mg once daily versus placebo. We recruited community-dwelling participants aged 65 and over with baseline 6-min walk distance of <400 m and no contraindications to magnetic resonance imaging scanning. Outcomes were measured at baseline and 20 weeks. The primary outcome was post-exercise phosphocreatine (PCr) recovery rate measured using 31P magnetic resonance spectroscopy of the calf. Secondary outcomes included 6-min walk distance, short physical performance battery (SPPB), lean body mass measured by bioimpedance, endothelial function and quality of life.

Results

In total, 124 participants were randomised, mean age 80 (SD 6) years. A total of 59 (48%) were female, baseline 6-min walk distance was 293 m (SD 80 m) and baseline SPPB was 8.5 (SD 2.0). Allopurinol did not significantly improve PCr recovery rate (treatment effect 0.10 units [95% CI, −0.07 to 0.27], P = 0.25). No significant changes were seen in endothelial function, quality of life, lean body mass or SPPB. Allopurinol improved 6-min walk distance (treatment effect 25 m [95% 4–46, P = 0.02]). This was more pronounced in those with high baseline oxidative stress and urate.

Conclusion

Allopurinol improved 6-min walk distance but not PCr recovery rate in older people with impaired physical function. Antioxidant strategies to improve muscle function for older people may need to be targeted at subgroups with high baseline oxidative stress.
Psychophysiological Correlates of Emotional- and Alcohol-Related Cues Processing in Offspring of Alcohol-Dependent Patients
Authors: Dominguez-Centeno I , Jurado-Barba R , Sion A , Martínez-Maldonado A , Castillo-Parra G , López-Muñoz F , Rubio G , Martínez-Gras I
Published: March 2020

Aims

To determinate if offspring of alcohol-dependent patients (OA) process affective stimuli and alcohol-related cues in a different manner than control subjects do.

Methods

Event-related potentials (early posterior negativity [EPN]/ late positive potential [LPP]) and event-related oscillations (Theta) were obtained by electroencephalographic (EEG) recording during the viewing of International Affective Picture System (IAPS) images with positive, negative and neutral valence, as well as alcohol-related cues. The total sample was comprised of 60 participants, divided into two groups: one group consisted of OA (30) and the control group of participants with negative family history of alcohol use disorders (30).

Results

Theta power analysis implies a significant interaction between condition, region and group factors. Post-hoc analysis indicates an increased theta power for the OA at different regions, during pleasant (frontal, central, parietal, occipital, right temporal); unpleasant (frontal, central, occipital); alcohol (frontal, central, parietal, occipital, right and left temporal) and neutral (occipital) cues. There are no group differences regarding any of the event-related potential measurements (EPN/LPP).

Conclusions

There is evidence of alterations in the processing of affective stimuli and alcohol-related information, evidenced by changes in theta brain oscillations. These alterations are characterized by an increased emotional reactivity, evidenced by increased theta at posterior sites. There is also an increased recruitment of emotion control, which could be a compensation mechanism, evidenced by increased theta power at anterior sites during affective stimuli and alcohol cues.
SG-LSTM-FRAME: a computational frame using sequence and geometrical information via LSTM to predict miRNA–gene associations
Authors: Xie Weidun , Luo Jiawei , Pan Chu , Liu Ying
Published: March 2020

Motivation

MircroRNAs (miRNAs) regulate target genes and are responsible for lethal diseases such as cancers. Accurately recognizing and identifying miRNA and gene pairs could be helpful in deciphering the mechanism by which miRNA affects and regulates the development of cancers. Embedding methods and deep learning methods have shown their excellent performance in traditional classification tasks in many scenarios. But not so many attempts have adapted and merged these two methods into miRNA–gene relationship prediction. Hence, we proposed a novel computational framework. We first generated representational features for miRNAs and genes using both sequence and geometrical information and then leveraged a deep learning method for the associations’ prediction.

Results

We used long short-term memory (LSTM) to predict potential relationships and proved that our method outperformed other state-of-the-art methods. Results showed that our framework SG-LSTM got an area under curve of 0.94 and was superior to other methods. In the case study, we predicted the top 10 miRNA–gene relationships and recommended the top 10 potential genes for hsa-miR-335-5p for SG-LSTM-core. We also tested our model using a larger dataset, from which 14 668 698 miRNA–gene pairs were predicted. The top 10 unknown pairs were also listed.

Availability

Our work can be download in https://github.com/Xshelton/SG_LSTM

Contact

luojiawei@hnu.edu.cn

Supplementary information

Supplementary data are available at Briefings in Bioinformatics online.
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications
Authors: Pratt Henry , Weng Zhiping
Published: March 2020

Sequence logos were introduced nearly 30 years ago as a human-readable format for representing consensus sequences, and they remain widely used. As new experimental and computational techniques have developed, logos have been extended: extra symbols represent covalent modifications to nucleotides, logos with multiple letters at each position illustrate models with multi-nucleotide features and symbols extending below the x-axis may represent a binding energy penalty for a residue or a negative weight output from a neural network. Web-based visualization tools for genomic data are increasingly taking advantage of modern web technology to offer dynamic, interactive figures to users, but support for sequence logos remains limited. Here, we present LogoJS, a Javascript package for rendering customizable, interactive, vector-graphic sequence logos and embedding them in web applications. LogoJS supports all the aforementioned logo extensions and is bundled with a companion web application for creating and sharing logos.

Availability and implementation

LogoJS is implemented both in plain Javascript and ReactJS, a popular user-interface framework. The web application is hosted at logojs.wenglab.org. All major browsers and operating systems are supported. The package and application are open-source; code is available at GitHub.

Contact

zhiping.weng@umassmed.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Asymptomatic Bacteriuria and Pyuria in Premenopausal Women
Authors: Hooton Thomas M , Roberts Pacita L , Stapleton Ann E
Published: March 2020

Background

Asymptomatic bacteriuria and pyuria in healthy women often trigger inappropriate antimicrobial treatment, but there is a paucity of data on their prevalence and persistence.

Methods

To evaluate the prevalence and persistence of asymptomatic bacteriuria and pyuria in women at high risk of recurrent urinary tract infection, we conducted an observational cohort study in 104 healthy premenopausal women with a history of recurrent urinary tract infection with daily assessments of bacteriuria, pyuria, and urinary symptoms over a 3-month period.

Results

The mean age of participants was 22 years, and 74% were white. Asymptomatic bacteriuria events (urine cultures with colony count ≥105 CFU/mL of a uropathogen on days with no symptomatic urinary tract infection diagnosed) occurred in 45 (45%) women on 159 (2.5%) of 6283 days. Asymptomatic bacteriuria events were most commonly caused by Escherichia coli, which was present on 1.4% of days, with a median duration of 1 day (range, 1–10). Pyuria occurred in 70 (78%) of 90 evaluable participants on at least 1 day and 25% of all days on which no symptomatic urinary tract infection was diagnosed. The positive predictive value of pyuria for E. coli asymptomatic bacteriuria was 4%.

Conclusions

In this population of healthy women at high risk of recurrent urinary tract infection, asymptomatic bacteriuria is uncommon and, when present, rarely lasts more than 2 days. Pyuria, on the other hand, is common but infrequently associated with bacteriuria or symptoms. These data strongly support recommendations not to screen for or treat asymptomatic bacteriuria or pyuria in healthy, nonpregnant women.
Sraffa on non-self-replacing systems: a note
Authors: Ravagnani Fabio
Published: March 2020

In two passages of Production of Commodities, Sraffa states very concisely that the analysis presented also applies to viable economic systems in which the means of production consumed are not fully replaced. This aspect of the book has been nearly ignored for a long time, and, only in the last two decades have some scholars begun to discuss it in depth. These scholars, however, base their discussion on the terse references to non-self-replacing systems appearing in Sraffa’s published works—except for a single author, who also takes into account three brief passages drawn from Sraffa’s manuscripts. In the present note, we carry out instead an exhaustive examination of the unpublished manuscripts in order to ascertain as accurately as possible what exactly Sraffa’s position was concerning the nature and relevance of non-self-replacing systems. In the light of this examination, we briefly comment in the final section on some debatable aspects of current renditions of Sraffa’s theory.
Education as inefficient resource against depressive symptoms in the Czech Republic: cross-sectional analysis of the HAPIEE study
Authors: Cermakova Pavla , Pikhart Hynek , Kubinova Ruzena , Bobak Martin
Published: March 2020

Background

Increasing educational level of the population could be a strategy to prevent depression. We investigated whether education may offer a greater benefit for mental health to women and to individuals living in socioeconomically disadvantaged areas.

Methods

We performed a cross-sectional study using data on 6964 Czech participants of the Health, Alcohol and Psychosocial factors in Eastern Europe study (on average 58 years old; 53% women). Binary logistic regression was used to examine the association of education with depressive symptoms, adjusting for several groups of covariates. Interactions were tested between education and sex as well as between education and socioeconomic advantage of the area of residence.

Results

Higher education was strongly associated with lower odds of depressive symptoms, independently of sociodemographic characteristics, health behavior and somatic diseases. This association was attenuated after adjusting for other markers of individual socioeconomic position (work activity, material deprivation and household items). There were no interactions between education and either sex or socioeconomic advantage of the area of residence.

Conclusions

We did not find an independent association between education and depressive symptoms after controlling for other socioeconomic markers in a sample with a formative history of communistic ideologies. Women or individuals from socioeconomically disadvantaged areas do not seem to gain a larger mental health benefit from education.
Estimating Price Dynamics in the Aftermath of Forest Disturbances: The Biscuit Fire in Southwest Oregon
Authors: Zhai Jun , Kuusela Olli-Pekka
Published: March 2020

Catastrophic forest disturbances, such as wildfires, insect outbreaks, and hurricanes, have become more frequent in recent decades. Such disturbances can create supply disruptions in regional timber markets, with potentially significant short-run and long-run price effects. We review the time-series intervention models that have been used to analyze the impacts of forest disturbances. We apply the intervention models to investigate the market effects of the Biscuit Fire that burned nearly 500,000 acres (202,000 hectares) of forest land in southwest Oregon in 2002, thus creating an unexpected supply shock in the regional timber markets. Most of the burned area was located on federal lands. Although almost two billion board feet were available for harvesting by some estimates, the salvage logging on public lands after the Biscuit Fire amounted to 60 million board feet by the end of 2005. We use a univariate and reduced-form model to estimate the effect of the Biscuit Fire on regional Douglas-fir log markets. We find that the fire did not cause immediate price effects; however, we detect positive effects during the salvage logging period in some of the markets, whereas a negative long-run effect has persisted since the salvage logging period was completed.
How Accumulated Wealth Affects Driving Reduction and Cessation
Authors: Vivoda Jonathon M , Walker Ryan Michael , Cao Jiawei , Koumoutzis Athena
Published: March 2020

Background and Objectives

Older adults can expect to live between 6 and 10 years after they give up driving, but driving reduction and cessation (DRC) are not equally experienced by all groups. Individual characteristics such as poor health, impaired vision, older age, and female gender are known to affect DRC. Using cumulative disadvantage theory as a guide, this study assessed the role played by wealth in DRC among older adults.

Research Design and Methods

Data from the National Health and Aging Trends Study were analyzed using multinomial logistic regression techniques. This allowed for the effect of each predictor on the odds of engagement in a given driving status (full driving, driving reduction [DR], and driving cessation [DC]) to be compared to each of the others.

Results

The final sample included 6,387 participants. After controlling for the effect of covariates, less wealth was associated with higher odds of DR compared to full driving, DC compared to full driving, and DC compared to DR. Confirming previous research, several other factors were also significantly related to driving status including age, health, vision, gender, race, education, relationship status, household size, and work status.

Discussion and Implications

The influence of wealth on driving status among older adults represents another disadvantage unequally distributed to some in older adulthood. Those with less wealth will have fewer resources to meet their mobility needs using alternatives and may already be facing additional financial constraints due to worse health and other challenges associated with lower socioeconomic status.
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
Authors: Hörtenhuber Matthias , Mukarram Abdul K , Stoiber Marcus H , Brown James B , Daub Carsten O
Published: March 2020

Background

Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial.

Findings

We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality.

Conclusions

We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts.
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

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

Biomass 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

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

Environmental 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

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

The 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

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

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

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

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

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

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

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

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

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

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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Frontal Ethmoidal Dural Arteriovenous Fistula: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: March 2020

Anterior cranial fossa dural arteriovenous fistulas (DAVFs) are an infrequent subtype of cranial DAVFs. These lesions are most commonly derived from the ophthalmic artery. These lesions are often best treated utilizing endovascular embolization; however, this modality can be challenging because of the difficulty in catheterizing the ophthalmic or ethmoidal arteries. Surgical intervention is therefore indicated and requires approaching the proximal portion of the drainage vein to appropriately obliterate the fistulous point. For ethmoidal DAVFs, this is frequently along the dura of the cranial base adjacent to the cribriform plate. This patient had a right frontal hematoma with a typical ethmoidal DAVF. The fistula was exposed through a frontal craniotomy, and the ethmoidal branch was identified at the fistulous point. Intraoperative angiography was used to test for obliteration, which revealed a contralateral DAVF. The contralateral fistula was then obliterated in a similar manner, demonstrated on a second intraoperative angiogram. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Pterional Craniotomy for Anterior Temporal Artery to Middle Cerebral Artery Bypass: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: March 2020

Broad-based aneurysms of the middle cerebral artery M1 bifurcation usually involve aneurysmal inclusion of an M2 vessel wall within the neck. This necessitates a consideration of performing a bypass to preserve the patency of distal perfusion. The patient in this video is a 17-yr-old man who presented after experiencing a small stroke and was found to have a partially thrombosed giant middle cerebral artery M1 bifurcation aneurysm with an M2 branch arising from the aneurysm. To maintain the perfusion of the M2 brain, the anterior temporal artery was used to perform a side-to-side anastomosis with the M2 brain at risk. A distal clip was determined to be not necessary for aneurysm occlusion because the aneurysm was almost completely thrombosed before the operation and the bypass flow was anticipated to be sufficient to facilitate complete thrombosis. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Epidemiologic and clinical characteristics of 91 hospitalized patients with COVID-19 in Zhejiang, China: a retrospective, multi-centre case series
Authors: Qian G -Q , Yang N -B , Ding F , Ma A H Y , Wang Z -Y , Shen Y -F , Shi C -W , Lian X , Chu J -G , Chen L , Wang Z -Y , Ren D -W , Li G -X , Chen X -Q , Shen H -J , Chen X -M
Published: March 2020

Background

Recent studies have focused on initial clinical and epidemiological characteristics of the coronavirus disease 2019 (COVID-19), which is the mainly revealing situation in Wuhan, Hubei.

Aim

This study aims to reveal more data on the epidemiological and clinical characteristics of COVID-19 patients outside of Wuhan, Zhejiang, China.

Design

This study was a retrospective case series.

Methods

Eighty-eight cases of laboratory-confirmed and three cases of clinically confirmed COVID-19 were admitted to five hospitals in Zhejiang province, China. Data were collected from 20 January 2020 to 11 February 2020.

Results and discussion

Of all 91 patients, 88 (96.70%) were laboratory-confirmed COVID-19 with throat swab samples that tested positive for SARS-Cov-2, three (3.30%) cases were clinically diagnosed. The median age of the patients was 50 (36.5–57) years, and female accounted for 59.34%. In this sample, 40 (43.96%) patients had contracted the disease from local cases, 31 (34.07%) patients had been to Wuhan/Hubei, eight (8.79%) patients had contacted with people from Wuhan, and 11 (12.09%) patients were diagnosed after having flown together in the same flight with no passenger that could later be identified as the source of infection. In particular within the city of Ningbo, 60.52% cases can be traced back to an event held in a temple. The most common symptoms were fever (71.43%), cough (60.44%) and fatigue (43.96%). The median of incubation period was 6 (interquartile range 3–8) days and the median time from the first visit to a doctor to the confirmed diagnosis was 1 (1–2) days. According to the chest computed tomography scans, 67.03% cases had bilateral pneumonia.

Conclusions

Social activity cluster, family cluster and flying alongside with persons already infected with COVID-19 were how people got infected with COVID-19 in Zhejiang.
Identifying insomnia-related chemicals through integrative analysis of genome-wide association studies and chemical–genes interaction information
Authors: Kafle Om Prakash , Cheng Shiqiang , Ma Mei , Li Ping , Cheng Bolun , Zhang Lu , Wen Yan , Liang Chujun , Qi Xin , Zhang Feng
Published: March 2020

Study Objectives

Insomnia is a common sleep disorder and constitutes a major issue in modern society. We provide new clues for revealing the association between environmental chemicals and insomnia.

Methods

Three genome-wide association studies (GWAS) summary datasets of insomnia (n = 113,006, n = 1,331,010, and n = 453,379, respectively) were driven from the UK Biobank, 23andMe, and deCODE. The chemical–gene interaction dataset was downloaded from the Comparative Toxicogenomics Database. First, we conducted a meta-analysis of the three datasets of insomnia using the METAL software. Using the result of meta-analysis, transcriptome-wide association studies were performed to calculate the expression association testing statistics of insomnia. Then chemical-related gene set enrichment analysis (GSEA) was used to explore the association between chemicals and insomnia.

Results

For GWAS meta-analysis dataset of insomnia, we identified 42 chemicals associated with insomnia in brain tissue (p < 0.05) by GSEA. We detected five important chemicals such as pinosylvin (p = 0.0128), bromobenzene (p = 0.0134), clonidine (p = 0.0372), gabapentin (p = 0.0372), and melatonin (p = 0.0404) which are directly associated with insomnia.

Conclusion

Our study results provide new clues for revealing the roles of environmental chemicals in the development of insomnia.