bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving performance of finishing pigs with added valine, isoleucine, and tryptophan: validating a meta-analysis model
Authors: Kerkaert Hayden R , Cemin Henrique S , Woodworth Jason C , DeRouchey Joel M , Dritz Steve S , Tokach Mike D , Goodband Robert D , Haydon Keith D , Hastad Chad W , Post Zach B 
Published: February 2021

Abstract
Based on results of a recent meta-analysis, we hypothesized that increased dietary Val, Ile, or Trp could correct possible amino acid interactions because of excess Leu in diets containing high levels of corn protein, namely dried distiller’s grains with solubles (DDGS). A total of 1,200 pigs (PIC TR4 × (Fast LW × PIC L02); initially 33.6 ± 0.6 kg) were used in a 103-d study. The 6 dietary treatments were corn–soybean meal (SBM)-DDGS-based as follows: (1) high SBM and low level of l-Lys HCl (HSBM), (2) high l-Lys HCl and moderate Ile, Val, Trp (AA above NRC 2012 estimates; NC), (3) moderate l-Lys HCl and high Ile, Val, and Trp (PC), and PC with either increased (4) L-Val (PC+Val), (5) L-Ile (PC+Ile), or (6) L-Trp (PC+Trp). Pigs fed the NC diet were predicted to have the poorest average daily gain (ADG), the PC diet to be intermediate, and pigs fed the HSBM, PC+Val, PC+Ile, and PC+Trp have the same and highest predicted ADG. In the grower period (34 to 90 kg), ADG was greater (Ρ &lt; 0.05) for the pigs fed HSBM and PC+Val diets than the NC with pigs fed other diets intermediate. Pigs fed HSBM were more (Ρ &lt; 0.05) efficient (G:F) than the NC and PC with pigs fed other diets intermediate. In the finisher period (90 to 136 kg), ADG was greater (Ρ &lt; 0.05) for pigs fed PC+Ile than that of the NC with pigs fed other diets intermediate. Pigs fed PC+Val had greater (Ρ &lt; 0.05) average daily feed intake (ADFI) than the NC with pigs fed other diets intermediate. However, PC+Ile pigs were more (Ρ &lt; 0.05) efficient than PC+Val with pigs fed other diets intermediate. Overall, ADG was greater (Ρ &lt; 0.05) for pigs fed HSBM, PC+Val, and PC+Ile diets than the NC with pigs fed other diets intermediate. Pigs fed the PC+Val diet had greater (Ρ &lt; 0.05) ADFI than the NC with pigs fed other diets intermediate. No differences were detected between treatments for overall G:F or other carcass characteristics. In conclusion, increasing Val or Ile in high l-Lys-HCl-DDGS-based diets improved growth performance compared with pigs fed diets containing high levels of l-Lys HCl without added Val and Ile. These results present evidence that the recently developed meta-analysis can predict the relative differences in overall ADG for pigs fed the NC, PC, PC+Val, and PC+Ile diets; however, the predicted G:F was less accurate. The data demonstrate that the negative effects of high Leu concentrations in corn-DDGS-based diets can be reversed by increasing the ratios of Val and Ile relative to Lys.
Psychopharmacology in Cancer Care
Authors: Roth Andrew , Nelson Chris 
Published: February 2021

Abstract
Clinicians who care for adult cancer patients have many tools to manage symptoms of depression, anxiety, cognitive changes, insomnia, and fatigue. Non-prescribing clinicians, such as psychologists, nurses, social workers, and occupational and physical therapists, provide frontline psychosocial interventions and physical support for cancer patients. Psychotropic treatments are sometimes required to resolve complex syndromes that mingle both medical and psychiatric features. Psychiatric medications are most frequently prescribed to cancer patients by oncologists, general medical practitioners, general psychiatrists, and psychiatric advanced practice providers such as nurse practitioners and physician assistants, as few oncology practices have dedicated psycho-oncologists. Non-prescribing practitioners who care for people with cancer are often the first to identify a psychiatric syndrome that requires a referral for psychopharmacologic intervention. They can also play an important role in educating patients about how psychopharmacologic agents can augment their cancer care. After psychotropic medications are started, non-prescribers can observe for improvement and detect problematic side effects if they arise, thus improving adherence with medication regimens. Practitioners who read this book will benefit from the highlighted clinical pearls to follow, and the potholes to avoid, regarding the tricky diagnostics and pharmacologic treatment of psychiatric syndromes. All clinicians will learn communication strategies that bridge distances of professional specialty and geography so that treatment by multiple providers may be more seamless, which it is hoped will enrich outcomes, both medical and emotional.
Longitudinal change in fine motor skills after brain radiotherapy and in vivo imaging biomarkers associated with decline
Authors: Salans Mia , Tibbs Michelle D , Karunamuni Roshan , Yip Anthony , Huynh-Le Minh-Phuong , Macari Anna Christina , Reyes Anny , Tringale Kathryn , McDonald Carrie R , Hattangadi-Gluth Jona A 
Published: February 2021

AbstractBackgroundWe explored fine motor skills (FMS) before and after brain radiotherapy (RT), analyzing associations between longitudinal FMS and imaging biomarkers of cortical and white matter (WM) integrity in motor regions of interest (ROIs).MethodsOn a prospective trial, 52 primary brain tumor patients receiving fractionated brain RT underwent volumetric brain MRI, diffusion tensor imaging, and FMS assessments (Delis-Kaplan Executive Function System Trail Making Test Motor Speed [DKEFS-MS], Grooved Pegboard Dominant Hands [PDH], and Grooved Pegboard Nondominant Hands [PNDH]) at baseline and 3-, 6-, and 12-month post-RT. Motor ROIs autosegmented included: sensorimotor cortices and superficial WM, corticospinal tracts, cerebellar cortices and WM, and basal ganglia. Volume (cc) was measured in all ROIs at each timepoint. Diffusion biomarkers (FA [fractional anisotropy] and MD [mean diffusivity]) were additionally measured in WM ROIs. Linear mixed-effects models assessed biomarkers as predictors of FMS scores. P values were corrected for multiple comparisons.ResultsHigher RT dose was associated with right paracentral cortical thinning (β = −2.42 Gy/(month × mm), P = .03) and higher right precentral WM MD (β = 0.69 Gy/(month × µm2/ms), P = .04). Higher left (β = 38.7 points/(month × µm2/ms), P = .004) and right (β = 42.4 points/(month × µm2/ms), P = .01) cerebellar WM MD, left precentral cortical atrophy (β = −8.67 points/(month × mm), P = .02), and reduced right cerebral peduncle FA (β = −0.50 points/month, P = .01) were associated with worse DKEFS-MS performance. Left precentral cortex thinning was associated with worse PDH scores (β = −17.3 points/(month × mm), P = .02). Left (β = −0.87 points/(month × cm3), P = .001) and right (β = −0.64 points/(month × cm3), P = .02) cerebellar cortex, left pons (β = −19.8 points/(month × cm3), P = .02), and right pallidum (β = −10.8 points/(month × cm3), P = .02) atrophy and reduced right internal capsule FA (β = −1.02 points/month, P = .03) were associated with worse PNDH performance.ConclusionsBiomarkers of microstructural injury in motor-associated brain regions were associated with worse FMS. Dose avoidance in these areas may preserve FMS.
Developing a Professionalism and Harassment Policy for Organized Neurosurgery
Authors: Air Ellen L , Orrico Katie O , Benzil Deborah L , Scarrow Alan M , Bean James R , Mazzola Catherine A , Liau Linda M , Rutka James T , Muraszko Karin M 
Published: February 2021

Abstract
Annual conferences, educational courses, and other meetings draw a diverse community of individuals, yet also create a unique environment without the traditional guard rails. Unlike events held at one's home institution, clear rules and jurisdiction have not been universally established. To promote the open exchange of ideas, as well as an environment conducive to professional growth of all participants, the leading neurosurgical professional organizations joined forces to delineate the expectations for anyone who participates in sponsored events. The One Neurosurgery Summit Taskforce on Professionalism and Harassment developed a foundational policy that establishes common expectations for behavior and a unified roadmap for the prompt response to untoward events. We hope that publishing this policy will inspire other medical organizations to establish their own meeting and conference policies. More importantly, we wish to bring greater attention to everyone's responsibility for ensuring a safe and respectful space for education, scientific debate, and networking during organized events.
Efficacy and comorbidities of hypofractionated and single-dose radiosurgery for vestibular schwannomas: a systematic review and meta-analysis
Authors: Tosi Umberto , Guadix Sergio , An Anjile , Wright Drew , Christos Paul J , Pannullo Susan , Brandmaier Andrew , Knisely Jonathan P S , Stieg Philip E , Ramakrishna Rohan 
Published: February 2021

Abstract

Background
Vestibular schwannomas (VS) are tumors of the cerebellopontine angle with significant morbidity, causing hearing loss, tinnitus, and trigeminal and facial nerve compromise. An effective alternative to microsurgical resection is stereotactic radiosurgery (SRS), which can be delivered in either single-fraction (SRS) or hypofractionated stereotactic radiotherapy (hSRT) (3-5 treatments) regimens. It remains unclear which fractionation regimen provides superior outcomes.

Methods
Ovid MEDLINE, EMBASE, CINAHL, and Cochrane Reviews were searched for studies either comparing hSRT with SRS or focusing on hSRT alone in treating VS. Primary endpoints included tumor control, serviceable hearing, tinnitus, and cranial nerve V and VII symptoms. A random-effects analysis was employed to compare pre- and post-treatment effects (hSRT alone) or SRS and hSRT outcomes (two-arm studies).

Results
This analysis included 21 studies focusing on hSRT alone and 13 studies comparing SRS and hSRT. Significant heterogeneity was observed. Overall, when hSRT was analyzed alone, crude tumor control was achieved in 94% (95% CI: 88%, 99%) of 1571 patients. There was no difference between pre- and post-treatment odds ratios (OR) of tinnitus, facial, or trigeminal impairment. Serviceable hearing was diminished following hSRT (OR = 0.60, 95% CI: 0.44, 0.83). Comparison with SRS showed no difference with respect to tumor control, serviceable hearing, trigeminal or facial nerve impairment.

Conclusions
hSRT achieved excellent tumor control and, with the exception of serviceable hearing, did not result in worse post-treatment cranial nerve symptomatology. Analysis of comparative studies between hSRT and SRS did not reveal any significant difference in either tumor control or treatment morbidities.
Prospective Cohort of Fluvoxamine for Early Treatment of Coronavirus Disease 19
Authors: Seftel David , Boulware David R 
Published: February 2021

Abstract
We report a real-world experience using fluvoxamine for coronavirus disease 19 (COVID-19) in a prospective cohort in the setting of a mass outbreak. Overall, 65 persons opted to receive fluvoxamine (50 mg twice daily) and 48 declined. Incidence of hospitalization was 0% (0 of 65) with fluvoxamine and 12.5% (6 of 48) with observation alone. At 14 days, residual symptoms persisted in 0% (0 of 65) with fluvoxamine and 60% (29 of 48) with observation.
How Do Pathogens Evolve Novel Virulence Activities?
Authors: Sacristán Soledad , Goss Erica M. , Eves-van den Akker Sebastian 
Published: February 2021

This article is part of the Top 10 Unanswered Questions in MPMI invited review series. We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Hybrid Genome Assembly and Gene Repertoire of the Root Endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes)
Authors: Peng Long , Shan Xiaoliang , Wang Yuchen , Martin Francis , Vilgalys Rytas , Yuan Zhilin 
Published: February 2021

Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefitting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10, isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50 = 3.3 Mb) with 49.2% GC content. Of them, 10 contigs approached the length of intact chromosomes, and three had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4%, using Basidiomycota_odb10 lineage data. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of transposable elements (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters, and 361 genes encoding putative carbohydrate-active enzymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees and will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Pristine microstructures in pseudotachylytes formed in dry lower crust, Lofoten, Norway
Authors: Dunkel Kristina G. , Morales Luiz F. G. , Jamtveit Bjørn 
Published: February 2021

Feldspar-rich pseudotachylytes from the island of Moskenesøya, Lofoten, formed in dry granulites under lower crustal conditions during the Caledonian orogeny. The central parts of the pseudotachylytes, where the cooling rates were slowest, are characterized by microlites and spherulites of plagioclase and K-feldspar. K-feldspar surrounding plagioclase is consistent with crystallization from a melt during cooling instead of devitrification as the origin of the spherulites. Very thin (a few micrometres wide) injection veins, which experienced very rapid quenching, contain amorphous or cryptocrystalline material. The preservation of this material and of the fine-grained microstructures shows that, under fluid-absent conditions, recrystallization and reactions are slow and the original microstructures of the pseudotachylytes can be preserved.
This article is part of a discussion meeting issue ‘Understanding earthquakes using the geological record’.
What’s down there? The structures, materials and environment of deep-seated slow slip and tremor
Authors: Behr Whitney M. , Bürgmann Roland 
Published: February 2021

Deep-seated slow slip and tremor (SST), including slow slip events, episodic tremor and slip, and low-frequency earthquakes, occur downdip of the seismogenic zone of numerous subduction megathrusts and plate boundary strike-slip faults. These events represent a fascinating and perplexing mode of fault failure that has greatly broadened our view of earthquake dynamics. In this contribution, we review constraints on SST deformation processes from both geophysical observations of active subduction zones and geological observations of exhumed field analogues. We first provide an overview of what has been learned about the environment, kinematics and dynamics of SST from geodetic and seismologic data. We then describe the materials, deformation mechanisms, and metamorphic and fluid pressure conditions that characterize exhumed rocks from SST source depths. Both the geophysical and geological records strongly suggest the importance of a fluid-rich and high fluid pressure habitat for the SST source region. Additionally, transient deformation features preserved in the rock record, involving combined frictional-viscous shear in regions of mixed lithology and near-lithostatic fluid pressures, may scale with the tremor component of SST. While several open questions remain, it is clear that improved constraints on the materials, environment, structure, and conditions of the plate interface from geophysical imaging and geologic observations will enhance model representations of the boundary conditions and geometry of the SST deformation process.This article is part of a discussion meeting issue ‘Understanding earthquakes using the geological record’.
HTSlib - C library for reading/writing high-throughput sequencing data
Authors: Bonfield James K. , Marshall John , Danecek Petr , Li Heng , Ohan Valeriu , Whitwham Andrew , Keane Thomas , Davies Robert M. 
Published: February 2021

AbstractBackgroundSince the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.FindingsWe present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.ConclusionSince the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19).Widespread adoption has seen HTSlib downloaded over a million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT / BSD license.Contactsamtools@sanger.ac.uk
Modeling the potential impact of indirect transmission on COVID-19 epidemic
Authors: David Jummy , Iyaniwura Sarafa A. , Yuan Pei , Tan Yi , Kong Jude , Zhu Huaiping 
Published: February 2021

AbstractThe spread of SARS-CoV-2 through direct transmission (person-to-person) has been the focus of most studies on the dynamics of COVID-19. The efficacy of social distancing and mask usage at reducing the risk of direct transmission of COVID-19 has been studied by many researchers. Little or no attention is given to indirect transmission of the virus through shared items, commonly touch surfaces and door handles. The impact of the persistence of SARS-CoV-2 on hard surfaces and in the environment, on the dynamics of COVID-19 remain largely unknown. Also, the current increase in the number of cases despite the strict non-pharmaceutical interventions suggests a need to study the indirect transmission of COVID-19 while incorporating testing of infected individuals as a preventive measure. Assessing the impact of indirect transmission of the virus may improve our understanding of the overall dynamics of COVID-19. We developed a novel deterministic susceptible-exposed-infected-removed-virus-death compartmental model to study the impact of indirect transmission pathway on the spread of COVID-19, the sources of infection, and prevention/control. We fitted the model to the cumulative number of confirmed cases at episode date in Toronto, Canada using a Markov Chain Monte Carlo optimization algorithm. We studied the effect of indirect transmission on the epidemic peak, peak time, epidemic final size and the effective reproduction number, based on different initial conditions and at different stages. Our findings revealed an increase in cases with indirect transmission. Our work highlights the importance of implementing additional preventive and control measures involving cleaning of surfaces, fumigation, and disinfection to lower the spread of COVID-19, especially in public areas like the grocery stores, malls and so on. We conclude that indirect transmission of SARS-CoV-2 has a significant effect on the dynamics of COVID-19, and there is need to consider this transmission route for effective mitigation, prevention and control of COVID-19 epidemic.
Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus - Georgia Institute of Technology, Fall 2020
Authors: Gibson Greg , Weitz Joshua S. , Shannon Michael P. , Holton Benjamin , Bryksin Anton , Liu Brian , Bramblett Sandra , Williamson JulieAnne , Farrell Michael , Ortiz Alexander , Abdallah Chaouki T. , García Andrés J. 
Published: February 2021

AbstractA SARS-CoV-2 testing program combining pooled saliva sample surveillance leading to diagnosis and intervention surveyed over 112,000 samples from 18,029 students, staff and faculty, as part of integrative efforts to mitigate transmission at the Georgia Institute of Technology in Fall 2020. Cumulatively, 1,508 individuals were confirmed diagnostically. The surveillance strategy, including focused intensification of testing given case clusters, was effective in disrupting transmission following rapid case increases upon entry in August 2020, and again in November 2020. Owing to broad adoption by the campus community, the program protected higher risk staff while allowing some normalization of research activities.