bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes
Authors: Kloub Lina , Gosselin Sophia , Fullmer Matthew , Graf Joerg , Gogarten Johann Peter , Bansal Mukul S 
Published: February 2021

AbstractHorizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multigene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale data set of over 22,000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multigene transfer. Among other insights, we find that 1) the observed relative frequency of HMGT increases as divergence between genomes increases, 2) HMGTs often have conserved gene functions, and 3) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.
A Location-Based Outcome Analysis of the Most Common Microsurgically Clipped Cerebral Aneurysms: A Single-Center Experience
Authors: Nisson Peyton L , Meybodi Ali Tayebi , Berger Garrett K , Thompson Austen , Morshed Ramin A , Lawton Michael T 
Published: February 2021

ABSTRACT

BACKGROUND
Intracranial aneurysms of the anterior communicating artery (AComA), posterior communicating artery (PComA), and the middle cerebral artery (MCA) comprise the majority of all aneurysms encountered and treated by vascular neurosurgeons.

OBJECTIVE
To analyze and compare outcomes between these locations using multivariable logistic regression and to assess what clinical features may differ between them.

METHODS
Solitary aneurysms microsurgically clipped by the senior author were included from a prospective database of patients treated between January 2010 and April 2013 at a tertiary academic medical center. Neurological status was assessed using the modified Rankin Scale (mRS). Neurological outcomes were dichotomized, with mRS scores 0-2 considered “good” and 3-6 considered “poor.”

RESULTS
A total of 196 patients were treated; 69 aneurysms were located at the MCA, 77 at the AComA, and 50 at the PComA. A total of 48% (97/196) of patients presented with a ruptured aneurysm and 14% (25/180) were considered large. PComA was more commonly presented as a ruptured aneurysm (64%) compared to AComA (56%) and MCA (28%) (P ≤ .001), and when ruptured, PComA aneurysms were 1.6 times more likely to experience a favorable outcome compared to MCA aneurysms (P = .01). Regression analysis revealed PComA was associated with a lower risk for poor outcomes (odds ratio [OR] 0.19, P = .01) controlling for age, presentation type, and vasospasm.

CONCLUSION
Patients who underwent microsurgical clipping of ruptured PComA aneurysms experienced significantly better outcomes, while those with MCA aneurysms suffered the worst. Further investigation on this topic and the potential reasons that may account for these differences is warranted.
FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas
Authors: Sharaf Radwa , Pavlick Dean C , Frampton Garrett M , Cooper Maureen , Jenkins Jacqueline , Danziger Natalie , Haberberger James , Alexander Brian M , Cloughesy Timothy , Yong William H , Liau Linda M , Nghiemphu Phioanh L , Ji Matthew , Lai Albert , Ramkissoon Shakti H , Albacker Lee A 
Published: February 2021

Abstract

Background
Molecular profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify clinical trial options for primary and recurrent tumors. This study aimed to determine the accuracy of reporting the whole arm 1p19q codeletion status from the FoundationOne platform.

Methods
Testing was performed on glioma samples as part of clinical care and analyzed up to 395 cancer-associated genes (including IDH1/2). The whole arm 1p19q codeletion status was predicted from the same assay using a custom research-use only algorithm, which was validated using 463 glioma samples with available fluorescence in-situ hybridization (FISH) data. For 519 patients with available outcomes data, progression-free and overall survival were assessed based on whole arm 1p19q codeletion status derived from sequencing data.

Results
Concordance between 1p19q status based on FISH and our algorithm was 96.7% (449/463) with a positive predictive value (PPV) of 100% and a positive percent agreement (PPA) of 91.0%. All discordant samples were positive for codeletion by FISH and harbored genomic alterations inconsistent with oligodendrogliomas. Median overall survival was 168 months for the IDH1/2 mutant, codeleted group, and 122 months for IDH1/2 mutant-only (hazard ratio (HR): 0.42; P &lt; .05).

Conclusions
1p19q codeletion status derived from FoundationOne testing is highly concordant with FISH results. Genomic profiling may be a reliable substitute for traditional FISH testing while also providing IDH1/2 status.
Caregiver perceptions of end-of-life care in patients with high-grade glioma
Authors: Fortunato John T , Van Harn Meredith , Haider Sameah A , Phillips Joel , Walbert Tobias 
Published: February 2021

AbstractBackgroundPatients dying from high-grade gliomas (HGG) suffer from high symptom burden in the end-of-life (EoL) phase. Family caregivers are most informed about the patient’s symptoms and disease course. The aim of this study is to assess caregiver perception on quality of EoL care of HGG patients.MethodsCaregivers prospectively participated in the Toolkit After-Death Bereaved Family Member Interview, part of the Toolkit of Instruments to Measure End-of-Life Care (TIME survey). This validated survey assesses EoL care in areas such as physical comfort and emotional support, advance care planning, focus on the individual, attention to family, and coordination of care. The quality of EoL care was measured by domain scores (0 = care was always optimal, 1 = care was always suboptimal) or with a 0-10 scale.ResultsOf the 55 enrolled family caregivers, 44 completed the interview and rated the overall care high (8.90 ± 1.36/10), perceived that patients’ wishes were respected (9.46 ± 0.95) and that they died in dignity (9.65 ± 0.98). Caregivers perceived high satisfaction with information and decision-making (0.18), advance care planning (0.19), focus on the individual (0.16), and care coordination (0.11). Attention to family (0.25) needed improvement. Only 41% of caregivers were confident that they knew what to do at the time of death and 46% felt that the healthcare team did not provide them with someone to turn to in distress.ConclusionsCaregivers reported high overall satisfaction with EoL HGG care, though attention to family and communication needed improvement. Focus should therefore be on improved caregiver communication to improve EoL care, caregiver burnout, and bereavement in HGG populations.
Atomically dispersed Ir/α-MoC catalyst with high metal loading and thermal stability for water-promoted hydrogenation reaction
Authors: Li Siwei , Cao Ruochen , Xu Mingquan , Deng Yuchen , Lin Lili , Yao Siyu , Liang Xuan , Peng Mi , Gao Zirui , Ge Yuzhen , Liu Jin-Xun , Li Wei-Xue , Zhou Wu , Ma Ding 
Published: February 2021

ABSTRACT
Synthesis of atomically dispersed catalysts with high metal loading and thermal stability is challenging but particularly valuable for industrial application in heterogeneous catalysis. Here, we report a facile synthesis of a thermally stable atomically dispersed Ir/α-MoC catalyst with metal loading as high as 4 wt%, an unusually high value for carbide supported metal catalysts. The strong interaction between Ir and the α-MoC substrate enables high dispersion of Ir on the α-MoC surface, and modulates the electronic structure of the supported Ir species. Using quinoline hydrogenation as a model reaction, we demonstrate that this atomically dispersed Ir/α-MoC catalyst exhibits remarkable reactivity, selectivity and stability, for which the presence of high-density isolated Ir atoms is the key to achieving high metal-normalized activity and mass-specific activity. We also show that the water-promoted quinoline hydrogenation mechanism is preferred over the Ir/α-MoC, and contributes to high selectivity towards 1,2,3,4-tetrahydroquinoline. The present work demonstrates a new strategy in constructing a high-loading atomically dispersed catalyst for the hydrogenation reaction.
Reactivation of Chagas Disease in a Patient With an Autoimmune Rheumatic Disease: Case Report and Review of the Literature
Authors: Czech Mary M , Nayak Ashwin K , Subramanian Kavitha , Suarez Jose F , Ferguson Jessica , Jacobson Karen Blake , Montgomery Susan P , Chang Michael , Bae Gordon H , Raghavan Shyam S , Wang Hannah , Miranti Eugenia , Budvytiene Indre , Shoor Stanford Mervyn , Banaei Niaz , Rieger Kerri , Deresinski Stan , Holubar Marisa , Blackburn Brian G 
Published: February 2021

Abstract
Reactivation of Chagas disease has been described in immunosuppressed patients, but there is a paucity of literature describing reactivation in patients on immunosuppressive therapies for the treatment of autoimmune rheumatic diseases. We describe a case of Chagas disease reactivation in a woman taking azathioprine and prednisone for limited cutaneous systemic sclerosis (lcSSc). Reactivation manifested as indurated and erythematous cutaneous nodules. Sequencing of a skin biopsy specimen confirmed the diagnosis of Chagas disease. She was treated with benznidazole with clinical improvement in the cutaneous lesions. However, her clinical course was complicated and included disseminated CMV disease and subsequent septic shock due to bacteremia. Our case and review of the literature highlight that screening for Chagas disease should be strongly considered for patients who will undergo immunosuppression for treatment of autoimmune disease if epidemiologically indicated.
Alternating Current Is More Fatigable Than Pulsed Current in People Who Are Healthy: A Double-Blind, Randomized Crossover Trial
Authors: Paz Isabel de Almeida , Rigo Graciane Taglian , Sgarioni Amanda , Baroni Bruno Manfredini , Frasson Viviane Bortoluzzi , Vaz Marco Aurélio 
Published: February 2021

AbstractObjectiveTolerance level and rapid fatigue onset are limitations in the use of neuromuscular electrical stimulation (NMES) as an electrotherapeutic resource in rehabilitation and training protocols; however, it is unclear if pulsed current (PC) and alternating current (AC) produce different fatigue levels when applied at submaximal contraction level. The purpose of this study was to compare fatigue and discomfort levels between PC and AC during a submaximal contraction protocol in people who are healthy.MethodsIn this double-blind, randomized crossover trial conducted in a laboratory setting, 30 male volunteers [23.23 years of age (SD = 4.59)] performed 2 submaximal fatigue protocols (with a 7-day interval) in a randomized order: PC (pulse duration = 2 milliseconds, pulse frequency = 100 Hz) and AC (2.5 kHz, pulse duration = 0.4 milliseconds, burst frequency = 100 Hz). NMES currents were applied to the knee extensor motor point of the dominant limb. The NMES protocol consisted of 80 evoked contractions (time on:off = 5:10 seconds) and lasted 20 minutes. The current was maintained at a constant intensity throughout the NMES protocol. The primary outcome measures were maximal voluntary isometric contraction, fatigue index (evoked torque decline), fatigability (number of contractions for a 50% drop in evoked-torque from the protocol start), total evoked torque-time integral (TTI), decline in TTI, and discomfort level.ResultsAC at 2.5 kHz demonstrated higher maximal voluntary isometric contraction decline post-fatigue, higher fatigue index, higher fatigability (ie, fewer contractions to reach the 50% evoked torque decline from the protocol start), smaller total TTI, and higher TTI decline compared with PC. No between-currents difference was observed in discomfort level.ConclusionPC is less fatigable than AC at 2.5 kHz.ImpactBased on this study, PC is the preferred current choice when the NMES goal is to generate higher muscle work, higher mechanical load, and smaller fatigability during training both for athletes who are healthy and for rehabilitation programs for people with disease or injury.
Nutrition in Physical Therapist Practice: Setting the Stage for Taking Action
Authors: Berner Patrick , Bezner Janet R , Morris David , Lein Donald H 
Published: February 2021

AbstractDiet and nutrition are critical components of health, recovery from disease and illness, performance, and normal growth across the lifespan. Thus, it is important for physical therapists to be knowledgeable about nutrition and to have competency in providing information and guidance to patients/clients. Yet, there is an overwhelming amount of diet and nutrition information available from numerous sources, which makes it difficult to reach conclusions and determine the importance and relevance to patient care. The purpose of this perspective paper is to increase the knowledge and skills of physical therapists by providing guidelines for healthy eating and outlining diet and nutrition information most relevant for physical therapist practice and to clarify professional scope of practice related to diet and nutrition, including boundaries created by law, and the connection between healthy eating and health outcomes, muscle strength, bone health, and wound healing.
Blood-Flow–Restricted Strength Training Combined With High-Load Strength and Endurance Training in Pulmonary Rehabilitation for COPD: A Case Report
Authors: Kohlbrenner Dario , Aregger Céline , Osswald Martin , Sievi Noriane A , Clarenbach Christian F 
Published: February 2021

Abstract

Objective
The purpose of this report is to describe the case of a patient with chronic obstructive pulmonary disease (COPD) who was load compromised and being referred for outpatient pulmonary rehabilitation. Low-load blood flow restriction strength training (LL-BFRT) was applied to prepare for and increase tolerability of subsequently applied high-load strength training.

Methods (Case Description)
A 62-year-old woman with COPD GOLD 2 B presented with severe breathlessness. Lower limb strength was severely reduced while functional exercise capacity was preserved. The patient was severely load compromised and had high risk to be intolerant of the high training loads required to trigger the desired adaptations. LL-BFRT was applied during the first 12 training sessions and high-load strength training in the subsequent 12 training sessions of the rehabilitation program. Endurance training on a cycle ergometer was performed throughout the program.

Results
Symptom burden in the COPD assessment test was reduced by 6 points (40%). Lower limb strength improved by 95.3 Nm (521%) and 88.4 Nm (433%) for the knee extensors and by 33.8 Nm (95%) and 56 Nm (184%) for the knee flexors, respectively. Functional exercise capacity improved by 44 m (11%) in the 6-minute walk test and 14 repetitions (108%) in the 1-minute sit-to stand test. The patient did not experience any adverse events related to the exercise training.

Conclusion
Clinically relevant changes were observed in both strength-related functional and self-reported outcomes. The achievements translated well into daily living and enabled functioning according to the patients’ desires. LL-BFRT was reported to be well tolerated and implementable into an outpatient pulmonary rehabilitation program.

Impact
The description of this case encourages the systematic investigation of LL-BFRT in COPD. LL-BFRT has the potential to increase benefits as well as tolerability of strength training in pulmonary rehabilitation. Consideration of the physiological changes achieved through LL-BFRT highlights potential in targeting peripheral muscle dysfunction in COPD.
Dynamic Asset Pricing with Interactions between Short-Sale and Borrowing Constraints
Authors: Shi Lei , Xiao Yajun 
Published: February 2021

Abstract
This paper studies the joint effect of borrowing and short-sale constraints under heterogeneous beliefs and risk aversions. Although the constraints never simultaneously bind in equilibrium, interesting economics emerge in the anticipatory effects of potentially future binding constraints. In particular, the risk-free rate and Sharpe ratio experience endogenous jumps at a critical state, where two equilibria coexist. Moreover, a short-sale ban can lead to a lower stock price and higher volatility depending on the relative tightness between the constraints, and tightening the borrowing constraint during a short-sale ban can also make returns more volatile. (JEL G11, G12)
Parts of Speech: The Grammar of Redemption in De Worde’s Printed Interludes
Authors: Ridley Jacob 
Published: February 2021

Abstract
This essay proposes that Hyckescorner and The Worlde and the Chylde, playbooks printed by Wynkyn De Worde in 1515–1522, were made to resemble his Latin schoolbooks, or grammars, in order to function like textbooks of virtue and vice. Using De Worde’s output as a linchpin, the essay considers the plays’ personified abstractions (such as Contemplation, Manhood, and Free Will) in ‘grammatical’ terms and refers to standard school-texts of the day—from the so-called Auctores octo to the contemporary grammars of Robert Whittington—which might have helped lay readers to mine the plays for moral teaching. The teaching of elementary Latin provides a surprisingly apt metaphor throughout. I also suggest that The Worlde and the Chylde was published because it transposed the recent pedagogical controversy of the Grammarians’ War of 1519–1521 into the sphere of spiritual education, depicting the dangers of blind imitation and the fruits of preceptive instruction. The essay challenges the prevailing scholarly view that dramatic dialogue was the foremost feature which printers sought to emphasize when they first began publishing English plays. It also posits ‘pedagogical’ reading, shaped explicitly by schoolroom practice, as one tool which printers and book designers anticipated in publishing didactic works, and demonstrates how interpretatively fruitful De Worde’s sometimes confusing, and often maligned, blackletter quartos can be.
The relationship between chronotype and sleep behavior during rotating shift work: a field study
Authors: Kervezee Laura , Gonzales-Aste Fernando , Boudreau Phillipe , Boivin Diane B 
Published: February 2021

Abstract
Shift work, an essential part of our 24/7 society, inevitably leads to displacement of the habitual sleep period and thereby to misalignment of the internal circadian timing system with the rest–activity cycle and the environment. How interindividual differences in circadian organization affect sleep duration and timing during rotating shift work is not fully understood. The objective of this study was to assess the effect of chronotype, shift type, and their interaction on actigraphy-based sleep behavior in 74 police officers (20 women and 54 men; age [mean ± SD]: 32.1 ± 5.4 years) involved in rotating shift work throughout a 28- to 35-day work cycle consisting of morning, evening, and night shifts. Using linear mixed modeling, we found that chronotype was associated with sleep duration depending on the shift type: increasing morningness was correlated with longer sleep duration during series of consecutive morning shifts, while increasing eveningness was correlated with longer sleep duration during series of evening shifts. During series of night shifts, increasing eveningness was associated with a longer duration of the main sleep episode, but this relationship was attenuated and no longer significant when naps were taken into account due to increased napping in morning chronotypes during series of night shifts. Providing a detailed within-subject characterization of sleep behavior across a complete work cycle consisting of morning, evening, and night shifts, this study advances the understanding of the relationship between chronotype and sleep in rotating shift workers and supports the implementation of work schedules that take into account chronobiological principles.
The Contexts of Spiritual Seeking: How Ghanaians in the United States Navigate Changing Normative Conditions of Religious Belief and Practice
Authors: Manglos-Weber Nicolette D 
Published: February 2021

AbstractTwo concurrent agendas in the sociology of religion explore how conditions of secularism in the United States result in widespread norms of “spiritual seeking”, and how religion functions as a basis of belonging for U.S. immigrants. This study brings these subfields together by asking whether new immigrants from Ghana, West Africa, also exhibit an orientation of spiritual seeking in their religious trajectories, and how they engage with normative conditions of spiritual seeking within institutional contexts. I find strong evidence of spiritual seeking in their narratives, and I identify processes within the social institutions of family and coethnic networks, higher education, and African Evangelical Christianity that support a seeking orientation. I argue for more focus on the counter-impulses of seeking versus dwelling in immigrant religion, and that more studies of religion and culture should explicitly analyze the institutional contexts that mediate between normative culture and trajectories of social practice.