bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decentralized Virtual Reality Training of Mastoidectomy Improves Cadaver Dissection Performance: A Prospective, Controlled Cohort Study
Authors: Frendø Martin , Konge Lars , Cayé-Thomasen Per , Sørensen Mads Sølvsten , Andersen Steven Arild Wuyts 
Published: December 2019

Objective:
Virtual reality (VR) simulation training can improve temporal bone (TB) cadaver dissection skills and distributed, self-regulated practice is optimal for skills consolidation. Decentralized training (DT) at the trainees’ own department or home offers more convenient access compared with centralized VR simulation training where the simulators are localized at one facility. The effect of DT in TB surgical training is unknown. We investigated the effect of decentralized VR simulation training of TB surgery on subsequent cadaver dissection performance.

Study Design:
Prospective, controlled cohort study.

Setting:
Otorhinolaryngology (ORL) teaching hospitals and the Danish national TB course.

Participants:
Thirty-eight ORL residents: 20 in the intervention cohort (decentralized training) and 18 in the control cohort (standard training during course).

Intervention:
Three months of access to decentralized VR simulation training at the local ORL department or the trainee's home. A freeware VR simulator (the visible ear simulator [VES]) was used, supplemented by a range of learning supports for directed, self-regulated learning.

Main Outcome Measure:
Mastoidectomy final-product scores from the VR simulations and cadaver dissection were rated using a modified Welling Scale by blinded expert raters.

Results:
Participants in the intervention cohort trained decentrally a median of 3.5 hours and performed significantly better than the control cohort during VR simulation (p < 0.01), which importantly also transferred to a 76% higher performance score during subsequent cadaver training (mean scores: 8.8 versus 5.0 points; p < 0.001).

Conclusions:
Decentralized VR simulation training of mastoidectomy improves subsequent cadaver dissection performance and can potentially improve implementation of VR simulation surgical training.
The Direct Costs of Microsurgical Resection of Vestibular Schwannomas
Authors: Saliba Joe , Mohammadzadeh Amir , Tawfik Kareem O. , Carriere Junie S. , Schwartz Marc S. , Nguyen Quyen T. , Friedman Rick A. 
Published: December 2019

Objective:
To determine and itemize surgical costs associated with the translabyrinthine (TL), retrosigmoid (RS), and middle cranial fossa (MCF) approaches for microsurgical excision of vestibular schwannoma (VS).

Study Design:
Retrospective cost analysis study.

Setting:
Tertiary referral center.

Patients:
Thirty consecutive adult patients underwent microsurgical excision of VS by either TL, RS, or MCF approach (10 per approach).

Interventions:
Microsurgical excision of VS by one of the three major approaches. Medical and financial data were collected.

Main Outcome Measures:
Total operating room time (minutes), skin-to-skin time (minutes), operating room cost ($US), and surgical supplies cost ($US).

Results:
The MCF approach was associated with the shortest skin-to-skin time (230.3 min, p < 0.001). Mean overall nonsurgical room time was 94.7 minutes and not significantly different among approaches (p = 0.55). Mean total surgical supplies cost was $5,028 and was the highest for the RS ($7,116; p < 0.001) but not significantly different between TL and MCF. Mean operating room services charges were $68,417 overall and were the lowest for the MCF group ($53,306; p = 0.01). Tumor size was not correlated with surgical supplies cost (p = 0.74). The items associated with the highest average cost per case were the surgical aspirator ($1,062), drill burs ($928), and titanium implants ($575). There was redundancy in multiple surgical items such as drill burs, hemostatic agents, and sutures.

Conclusion:
This study is the first to provide a detailed itemization of the surgical expenses specific to VS resection. Elevated nonsurgical room time and supply redundancy provides the opportunity for decreasing surgical costs and waste.
Effect of Head-of-Bed Elevation on Nocturnal Reflux Symptoms of Esophageal Cancer Patients With Esophagectomy and Reconstruction
Authors: Huang Hui-Chen , Chang Ying-Ju , Tseng Yau-Lin , Fang Su-Ying 
Published: December 2019

Background
Studies revealed the symptom of gastroesophageal reflux (GE reflux) disturb patients following esophageal reconstruction.

Objective
To examine the effect of head-of-bed elevation by using the wedge-shaped pillow (WSP) on the reflux symptoms of patients with esophageal cancer following esophagectomy and reconstruction.

Methods
Fourteen patients with nocturnal reflux symptoms following esophagectomy and gastric tube reconstruction were enrolled and randomized into 2 groups. A 2-week crossover trial was performed using 2 sequences (drug only and drug plus WSP). The WSP was designed with a height of 20 cm, a length of 62 cm, and an elevation angle of 20 degrees and used with fabricated from memory foam. After 2 weeks, all of the patients received combined drug and WSP intervention for 3 months. Reflux symptoms were measured by Dysfunction After Upper Gastrointestinal Surgery for Cancer and examined by endoscopic observations prior to intervention and follow-up for 3 months.

Result
The average reflux symptom score for the combined drug and WSP treatment in the beginning 2 weeks was lower than that for the drug-only sequence. The severity of esophagitis was improved in 46.1%, and 38.5% showed a stabilization after 3 months.

Conclusions
Combined drug and WSP treatment may be beneficial in improving GE reflux symptoms.

Implications for Practice
Nursing care professionals would suggest patients find a similar WSP to elevate the head of the bed to reduce the severity of nocturnal reflux symptoms after esophagectomy and gastric tube reconstruction.
Urological Evidence of Tick Bites in Children
Authors: Shields Lisa B.E. , Peppas Dennis S. , Rosenberg Eran 
Published: December 2019

Abstract
Ticks pose a serious threat to individuals of all ages owing to numerous physical illnesses including chills, aches, and a rash. Tick-borne illnesses range from a mild fever that may be treated at home to a severe disease necessitating hospitalization. Children are at an increased risk of tick bites owing to to their exposure to tick-infested areas during the summer. We report 2 cases of boys aged 3 and 8 years who sustained tick bites to the hemiscrotum and penis. Overnight hospitalization and a course of antibiotics were mandatory. In the first case, the child experienced significant scrotal cellulitis with erythema and edema extending to the suprapubic area with induration of the right anterior scrotum at the site of the tick bite. A scrotal ultrasound demonstrated swelling of the scrotal wall. In the second case, considerable swelling and induration of the distal penis and glans, pruritis of the left groin and penis, and an erythematous rash over the entire anterior pelvis were observed. A high index of suspicion is warranted because a tick bite may present as penile edema. Pediatric emergency physicians should be aware of the risks associated with tick bites and accurately diagnose and initiate treatment to prevent morbidity and mortality.
Focusing on Families and Visitors Reduces Healthcare Associated Respiratory Viral Infections in a Neonatal Intensive Care Unit
Authors: Linam W. Matthew , Marrero Elizabeth M. , Honeycutt Michele D. , Wisdom Christy M. , Gaspar Anna , Vijayan Vini 
Published: December 2019

Introduction:
Healthcare-associated respiratory viral infections (HARVIs) result in significant harm to infants in the neonatal intensive care unit (NICU). Healthcare workers and visitors can serve as transmission vectors to patients. We hypothesized that improved family and visitor hand hygiene (FVHH) and visitor screening would reduce HARVIs by at least 25%.

Methods:
This quality improvement project took place in a large tertiary NICU to reduce HARVIs. Interventions primarily focused on improving FVHH and reducing visitation by symptomatic family members and visitors. We defined correct FVHH as hand hygiene performed immediately before touching their child. Hand hygiene observations were performed by direct observation by NICU staff using a standardized tool. Interventions to improve FVHH included education of staff and visitors, reminder signs, and immediate reminders to families to prevent lapses in hand hygiene. Staff screened family and visitors before NICU entry. Symptomatic individuals were asked to defer visitation until symptoms resolved. HARVIs were identified during prospective surveillance by infection preventionists using standard definitions.

Results:
Baseline FVHH was 27% in 2015. After May 2017, the average FVHH remained at 85%. When reminded, family members and visitors performed hand hygiene 99% of the time. Staff screened ~129,000 people for FVHH. Between January 2013 and March 2019, there were 74 HARVIs; 80% were rhinovirus/enterovirus. After the implementation of improved FVHH, the HARVI rate decreased from 0.67 to 0.23/1,000 patient days.

Conclusions:
Adding interventions to improve FVHH and visitor management to existing healthcare worker prevention efforts can help reduce HARVIs in the NICU.
PULP-NN: accelerating quantized neural networks on parallel ultra-low-power RISC-V processors
Authors: Garofalo Angelo , Rusci Manuele , Conti Francesco , Rossi Davide , Benini Luca 
Published: December 2019

We present PULP-NN, an optimized computing library for a parallel ultra-low-power tightly coupled cluster of RISC-V processors. The key innovation in PULP-NN is a set of kernels for quantized neural network inference, targeting byte and sub-byte data types, down to INT-1, tuned for the recent trend toward aggressive quantization in deep neural network inference. The proposed library exploits both the digital signal processing extensions available in the PULP RISC-V processors and the cluster’s parallelism, achieving up to 15.5 MACs/cycle on INT-8 and improving performance by up to 63 × with respect to a sequential implementation on a single RISC-V core implementing the baseline RV32IMC ISA. Using PULP-NN, a CIFAR-10 network on an octa-core cluster runs in 30 × and 19.6 × less clock cycles than the current state-of-the-art ARM CMSIS-NN library, running on STM32L4 and STM32H7 MCUs, respectively. The proposed library, when running on a GAP-8 processor, outperforms by 36.8 × and by 7.45 × the execution on energy efficient MCUs such as STM32L4 and high-end MCUs such as STM32H7 respectively, when operating at the maximum frequency. The energy efficiency on GAP-8 is 14.1 × higher than STM32L4 and 39.5 × higher than STM32H7, at the maximum efficiency operating point.
This article is part of the theme issue ‘Harmonizing energy-autonomous computing and intelligence’.
Developing a pseudotype model to test infectivity among different Zika virus mutants
Authors: Jimenez Fernando Ruiz , Olais Jose Humberto Perez , Ball Jonathan 
Published: December 2019

Viral infections pose a massive threat to the public health; recently several viral outbreaks had occurred across the globe, including Ebola virus, Middle East respiratory syndrome and Zika virus (ZIKV). ZIKV had great importance due to the appearance of malformation and neurological syndromes in newborns. One of the things that are worth noting is that ZIKV has been present in nature since the second half of the 1900s but only until the outbreak of 2015 in Brazil it gained a prominent spot in the public health surveillance.
The main goal of the project was to develop a suitable method to test different mutations that occurred naturally throughout several outbreaks of the virus across the globe, with particular emphasis in the Asian and American epidemics between 2007 and 2016. To achieve the objectives, the strategy previously used in other viruses known as pseudotyping was proposed. Pseudotyping poses a safe alternative to life virus work due to the lack of a productive infectious cycle, the use of a retroviral backbone supplemented with the glycoprotein of interest has been used in hazardous viruses such as Ebola or Hepatitis C. This system also allows to test individual mutations and the impact in the infectivity of the virus discarding any other accessory protein within the wild type virus. HIV-1 and MLV backbones were tested using a matrix of different ratios of glycoprotein and retrovirus plasmid to find the best set of concentrations; different cell lines were also tested, and protein expression viral proteins were detected.
Discovery of novel endogenous viral elements in Aedes spp. mosquitoes
Authors: Pischedda Elisa , Palatini Umberto , Crava Maria Cristina , Mattia Annamaria , Bonizzoni Mariangela 
Published: December 2019

The genomes of Aedes spp. mosquitoes contain integrated sequences from nonretroviral RNA viruses that are enriched in piRNA clusters, are embedded next to transposable elements (TEs) and produce piRNAs. The parallelism between TEs and viral integrations led to the hypothesis that viral integrations may constitute an archive of past viral infections and potentially have an immunity impact on novel infection with cognate viruses, similarly to how the piRNA pathway interacts with TEs. A corollary of this hypothesis is that the landscape of viral integrations should be variable across populations depending on their viral exposure. The highly repetitive nature of Aedes spp. genomes make the discovery of viral integrations from whole genome sequencing data of wild mosquitoes a daunting task.
Here we describe a novel bioinformatic pipeline to rigorously identify viral integrations using Next Generation Sequencing (NGS) data. Libraries from single or pools of mosquitoes, reference genome statistics, the landscape of TEs and the geographic origin of the analyzed samples are the actors of the analysis.
This pipeline has been tested in Ae. aegypti and Ae. albopictus mosquitoes, allowing to compare the performance of the analyses on genome assemblies of different completeness. We identified novel viral integrations in both genomes. Additionally, we show that the landscape of viral integrations is dynamic, with a population-specific behavior that we can leverage to formulate hypothesis on mechanisms of integration and the biological role of viral integrations.
Concerted cutting by Spo11 illuminates DNA break mechanisms and initiates gap repair during meiosis
Authors: Johnson Dominic , Crawford Margaret , Cooper Tim , Bouuaert Corentin Claeys , Keeney Scott , Llorente Bertrand , Garcia Valerie , Neale Matthew J. 
Published: December 2019

SummaryGenetic variation arises during meiosis via repair of DNA double-strand breaks (DSBs) created by the topoisomerase-like Spo11 protein. These DSBs are thought to always occur sparsely across the genome, with isolated DSBs generating discrete recombination events. We challenge this view, demonstrating that hyper-localised coincident DSBs frequently form within hotspots in bothS. cerevisiaeand mouse—a process suppressed by the DNA damage response kinase Tel1/ATM. Remarkably, the distances separating coincident DSBs vary with ∼10.5 bp periodicity, invoking a model where adjacent Spo11 molecules have a fixed orientation relative to the DNA helix. Deep sequencing of meiotic progeny identifies recombination scars consistent with gap repair initiated by adjacent DSBs. Our results revise current thinking about how genetic recombination initiates, reviving original concepts of meiotic recombination as double-strand gap repair.
Tracking self-citations in academic publishing
Authors: Kacem Ameni , Flatt Justin W. , Mayr Philipp 
Published: December 2019

AbstractCitation metrics have value because they aim to make scientific assessment a level playing field, but urgent transparency-based adjustments are necessary to ensure that measurements yield the most accurate picture of impact and excellence. One problematic area is the handling of self-citations, which are either excluded or inappropriately accounted for when using bibliometric indicators for research evaluation. Here, in favor of openly tracking self-citations we report on self-referencing behavior among various academic disciplines as captured by the curated Clarivate Analytics Web of Science database. Specifically, we examined the behavior of 385,616 authors grouped into 15 subject areas like Biology, Chemistry, Science & Technology, Engineering, and Physics. These authors have published 3,240,973 papers that have accumulated 90,806,462 citations, roughly five percent of which are self-citations. Up until now, very little is known about the buildup of self-citations at the author-level and in field-specific contexts. Our view is that hiding self-citation data is indefensible and needlessly confuses any attempts to understand the bibliometric impact of one’s work. Instead we urge academics to embrace visibility of citation data in a community of peers, which relies on nuance and openness rather than curated scorekeeping.
Human tauopathies are not associated with an activated unfolded protein response
Authors: Pitera A. P. , Hartnell I. J. , Boche D. , O’Connor V. , Deinhardt K. 
Published: December 2019

AbstractTauopathies are the neurodegenerative diseases associated with the accumulation of misfolded tau protein. Despite many years of investigation, the mechanisms underpinning tau dependent proteinopathy remains to be elucidated. A protein quality control pathway within the endoplasmic reticulum (ER), called unfolded protein response (UPR), has been suggested as a possible response implicated in the misfolded tau-mediated neurodegeneration. However, the question arose: how does the cytosolic protein tau that does not enter the ER induce a response stemming from this compartment? In this study we investigated three different human tauopathies to establish whether these diseases are associated with the activation of UPR. We probed for the modulation of several reliable UPR markers in mRNA and proteins extracted from 20 brain samples from Alzheimer’s disease (AD) patients, 11 from Pick’s disease (PiD) and 10 from Progressive Supranuclear Palsy (PSP) patients coupled to equal numbers of age-matched non-demented controls. This showed that different markers of UPR are not changed in any of the human tauopathies investigated. Interestingly, UPR signatures were often observed in non-demented controls. These data from human tissue further support the emerging evidence that the accumulation of misfolded cytosolic tau does not drive a diseased associated activation of UPR.
EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA
Authors: Vaisvila Romualdas , Ponnaluri V. K. Chaithanya , Sun Zhiyi , Langhorst Bradley W. , Saleh Lana , Guan Shengxi , Dai Nan , Campbell Matthew A. , Sexton Brittany S. , Marks Katherine , Samaranayake Mala , Samuelson James C. , Church Heidi E. , Tamanaha Esta , Corrêa Ivan R. , Pradhan Sriharsa , Dimalanta Eileen T. , Evans Thomas C. , Williams Louise , Davis Theodore B. 
Published: December 2019

AbstractBisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).
Sympatric ecological divergence with coevolution of niche preference
Authors: Payne Pavel , Polechová Jitka 
Published: December 2019

AbstractReinforcement, the increase of assortative mating driven by selection against unfit hybrids, is conditional on pre-existing divergence. Yet, for ecological divergence to precede the evolution of assortment, strict symmetries between fitnesses in niches must hold, and/or there must be low gene flow between the nascent species. It has thus been argued that conditions favouring sympatric speciation are rarely met in nature. Indeed, we show that under disruptive selection, violating symmetries in niche sizes and increasing strength of the trade-off in selection between the niches quickly leads to loss of genetic variation, instead of evolution of specialists. The region of the parameter space where polymorphism is maintained further narrows with increasing number of loci encoding the diverging trait and the rate of recombination between them. Yet, evolvable assortment and pre-existing assortment both substantially broaden the parameter space within which polymorphism is maintained. Notably, pre-existing niche preference speeds up further increase of assortment, thus facilitating reinforcement in the later phases of speciation. We conclude that in order for sympatric ecological divergence to occur, niche preference must co-evolve throughout the divergence process. Even if populations come into secondary contact, having diverged in isolation, niche preference substantially broadens the conditions for coexistence in sympatry and completion of the speciation process.
HIV Care Prioritization using Phylogenetic Branch Length
Authors: Moshiri Niema , Smith Davey M. , Mirarab Siavash 
Published: December 2019

AbstractIn HIV epidemics, the structure of the transmission network can be dictated by just a few individuals. Public health intervention, such as ensuring people living with HIV adhere to antiretroviral therapy (ART) and are continually virally-suppressed, can help control the spread of the virus. However, such intervention requires utilizing the limited public health resource allocations. As a result, the ability to determine which individuals are most at-risk of transmitting HIV could allow public health officials to focus their limited resources on these individuals. Molecular epidemiology suggests an approach: prioritizing people living with HIV based on patterns of transmission inferred from their sampled viral sequences. In this paper, we introduce ProACT (Prioritization usingAnCesTral edge lengths), a phylogenetic approach for prioritizing individuals living with HIV. ProACT uses a simple idea: ordering individuals by their terminal branch length in the phylogeny of their virus. In simulations and also on a dataset of HIV-1 subtype Bpolsequences obtained in San Diego, we show that this simple strategy improves the effectiveness of prioritization compared to state-of-the-art methods that rely on monitoring the growth of transmission clusters defined based on genetic distance.