bluuebunny/crossref_metadata_2025 huggingface dataset:
PKM2-dependent glycolysis promotes skeletal muscle cell pyroptosis by activating the NLRP3 inflammasome in dermatomyositis/polymyositis
Authors: Liu Di , Xiao Yizhi , Zhou Bin , Gao Siming , Li Liya , Zhao Lijuan , Chen Weilin , Dai Bingying , Li Qiuxiang , Duan Huiqian , Zuo Xiaoxia , Luo Hui , Zhu Honglin
Published: July 2020

Objectives

Muscle cell necrosis is the most common pathological manifestation of idiopathic inflammatory myopathies. Evidence suggests that glycolysis might participate in it. However, the mechanism is unclear. This study aimed to determine the role of glycolysis in the muscle damage that occurs in DM/PM.

Methods

Mass spectrometry was performed on muscle lesions from DM/PM and control subjects. The expression levels of pyruvate kinase isozyme M2 (PKM2), the nucleotide-binding and oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) inflammasome and pyroptosis-related genes in muscle tissues or plasma were determined by real-time PCR, western blot analysis, IF and ELISA. In addition, IFNγ was used to stimulate myotubes, and the relationships among PMK2 expression, NLRP3 inflammasome activation and pyroptosis were investigated.

Results

Mass spectrometry and bioinformatics analysis suggested that multiple glycolysis processes, the NLRP3 inflammasome and programmed cell death pathway-related proteins were dysregulated in the muscle tissues of DM/PM. PKM2 and the NLRP3 inflammasome were upregulated and positively correlated in the muscle fibres of DM/PM. Moreover, the pyroptosis-related proteins were increased in muscle tissues of DM/PM and were further increased in PM. The levels of PKM2 in muscle tissues and IL-1β in plasma were high in patients with anti-signal recognition particle autoantibody expression. The pharmacological inhibition of PKM2 in IFNγ-stimulated myotubes attenuated NLRP3 inflammasome activation and subsequently inhibited pyroptosis.

Conclusion

Our study revealed upregulated glycolysis in the lesioned muscle tissues of DM/PM, which activated the NLRP3 inflammasome and leaded to pyroptosis in muscle cells. The levels of PKM2 and IL-1β were high in patients with anti-signal recognition particle autoantibody expression. These proteins might be used as new biomarkers for muscle damage.
The Use of Psychological Patient Reported Outcome Measures to Identify Adolescent Athletes at Risk for Prolonged Recovery Following an ACL Reconstruction
Authors: Ellis Henry B. , Sabatino Meagan , Nwelue Emmanuel , Wagner K. John , Force Erica , Wilson Philip
Published: July 2020

Background:

Psychological response to injury and the recovery process impact return to play and can put an athlete at risk for prolonged recovery. The purpose of this study was to investigate the psychological changes that occur surrounding an anterior cruciate ligament (ACL) reconstruction utilizing a set of patient reported outcomes measures (PROMs) that focus on psychological factors.

Methods:

Consecutive patients undergoing a primary ACL reconstruction, ages 12 to 18, were recruited. Patients were included if they verbalized a desire to return to the same sport and a baseline Tegner of >6. Functional and psychological PROMs were administered preoperatively, 6 months, and 1 year postoperatively. A Y-Balance Test was utilized to assess for clearance.

Results:

Of the 68 participants, 36 were female (52.9%) and 32 male, with a mean age of 14.5 years. On average, participants were cleared to return to sport 259.1 days postoperatively. Of the measures given preoperatively, only the Athletic Coping Skills Inventory-28 (ACSI)-28 correlated with delayed recovery time (r
s=−0.291, P=0.04). Lower baseline ACSI-28 subscale scores in coachability (r
s=−0.298, P=0.03) and Coping with Adversity (r
s=−0.341, P=0.01) were correlated with delayed recovery. Participants that took longer than average to recover scored significantly lower on the ACSI-28 preoperatively than those with a shorter recovery time (62.04 vs. 54.8, P<0.01). Participants that scored <58 on their preoperative ACSI-28 took 2 months longer to recover than participants who scored ≥58 (9.6 vs. 7.65 mo, P<0.01). At 6 months postoperatively, higher ACSI-28 subscale Concentration (r
s=−0.357, P<0.01) and Peaking Under Pressure (r
s=−0.274, P=0.04) scores correlated with shorter recovery time.

Conclusions:

The ACSI-28 significantly correlated with recovery time following ACL reconstruction. A baseline score of 58 may be a valuable cutoff to identify youth athletes at risk for prolonged recovery.

Level of Evidence:

Level II—prospective study.
Targeting microRNA in hematologic malignancies
Authors: Han Zhen , Rosen Steven T. , Querfeld Christiane
Published: July 2020

Purpose of review

MiRNAs are critical regulators for gene expression. Numerous studies have revealed how miRNAs contribute to the pathogenesis of hematologic malignancies.

Recent findings

The identification of novel miRNA regulatory factors and pathways crucial for miRNA dysregulation has been linked to hematologic malignancies. miRNA expression profiling has shown their potential to predict outcomes and treatment responses. Recently, targeting miRNA biogenesis or pathways has become a promising therapeutic strategy with recent miRNA-therapeutics being developed.

We provide a comprehensive overview of the role of miRNAs for diagnosis, prognosis, and therapeutic potential in hematologic malignancies.
Comparison of Urban and Rural Physical Activity and Outdoor Play Environments of Childcare Centers and Family Childcare Homes
Authors: Dinkel Danae , Dev Dipti , Guo Yage , Sedani Ami , Hulse Emily , Rida Zainab , Abel Kayla
Published: July 2020

The purpose of this study was to examine the physical activity environment in childcare programs across type (childcare centers [CCCs] and family childcare homes [FCCHs]) and geographic location (urban and rural) as assessed by physical activity best practices according to the Go Nutrition and Physical Activity Self-assessment in Child Care. Results showed CCCs compared with FCCHs reported higher achievement of best practices. Further, urban childcare programs (CCCs and FCCHs) reported higher achievement of best practices in comparison to rural childcare programs. There is a need to deliver targeted interventions that promote children's physical activity in FCCHs and CCCs in rural areas.
A digital health psychological intervention (WebMAP Mobile) for children and adolescents with chronic pain: results of a hybrid effectiveness-implementation stepped-wedge cluster randomized trial
Authors: Palermo Tonya M. , de la Vega Rocio , Murray Caitlin , Law Emily , Zhou Chuan
Published: July 2020

Although psychological treatments benefit youth with chronic pain, treatment is not accessible in most communities. Digital health interventions offer promise for expanding access and reach to this population. Using a stepped-wedge cluster randomized trial design, we evaluated effectiveness and implementation of a digital health delivered psychological intervention for pediatric chronic pain. One hundred forty-three youth, aged 10 to 17 years, with chronic pain and a caregiver were recruited from 8 clinics in the United States. Active intervention included access to the Web-based Management of Adolescent Pain (WebMAP) Mobile app and the WebMAP parent web site to learn pain self-management skills. Effectiveness outcomes included pain intensity, disability, and patient global impression of change, while Reach, Adoption, Implementation, and Maintenance were implementation outcomes. Results showed that youth in both treatment conditions (WebMAP vs Usual Care) had similar changes over time in pain and disability. Youth in the WebMAP condition perceived greater improvement (patient global impression of change) at post-treatment and follow-up (d's = 0.54 and 0.44, P < 0.05) compared with youth receiving usual care. Use of the digital health intervention was modest and variable; approximately 30% of youth and parents completed treatment. Greater engagement (number of completed modules) was associated with significantly greater reductions in pain and disability from pre-treatment to follow-up (d's = −0.57 and −0.38, P < 0.05). Parents, youth, and providers found treatment acceptable; providers had positive attitudes and demonstrated referrals over a maintenance period. Further research is needed to understand how to enhance treatment engagement with digital health interventions and optimize implementation.
Evaluation of Pathologic Response on Overall Survival After Neoadjuvant Therapy in Pancreatic Ductal Adenocarcinoma
Authors: Sell Naomi M. , Lee Grace C. , Fernández-Del Castillo Carlos , Ferrone Cristina R. , Warshaw Andrew L. , Hong Theodore S. , Blaszkowsky Lawrence S. , Lillemoe Keith D. , Qadan Motaz
Published: July 2020

Objectives

Single-institution studies have shown improved outcomes among patients with a pathologic complete response (pCR) following neoadjuvant therapy. We sought to evaluate the impact of pCR and near-complete response (nCR) on overall survival (OS) using a large national database.

Methods

The National Cancer Database was queried for patients given a diagnosis of pancreatic cancer from 2004 to 2014. A pCR was defined as no tumor identified in the pancreas after surgical resection. An nCR was defined as a primary tumor less than 1 cm without lymph node metastases. The primary outcome was OS.

Results

A total of 5364 patients underwent neoadjuvant chemotherapy and/or radiation followed by pancreatectomy. Forty-one patients (0.8%) had a pCR, 54 (1%) had an nCR, and the remaining 5266 (98.2%) had an otherwise incomplete response. Patients with pCR had a median OS of 43 months compared with 24 months for nCR and 23 months for incomplete response (P < 0.0001). Only pCR was associated with improved OS on adjusted Cox regression.

Conclusions

For patients given a diagnosis of pancreatic cancer who underwent neoadjuvant treatment and surgical resection, achieving a pCR was associated with improved OS compared with those with residual tumor. An association between nCR and improved survival was not observed.
Pancreatic Neuroendocrine Neoplasms and Gastrointestinal Stromal Tumors
Authors: Milanetto Anna Caterina , Pacciani Sabrina , Fassan Matteo , Pasquali Claudio
Published: July 2020

Objective

Pancreatic neuroendocrine neoplasms (pNENs) and gastrointestinal stromal tumors (GISTs) represent rare neoplasms. Nonsyndromic cases of pNENs associated with a synchronous GIST were evaluated, and a review of the literature was performed.

Methods

We evaluated clinicopathologic features, postoperative outcome, and follow-up of patients operated on for nonsyndromic synchronous pNENs and GISTs in our unit (2003–2017).

Results

Five (3.2%) of 156 patients with a pNEN had an associated GIST (3 male/2 female; average age, 67 years). They were diagnosed with a pNEN preoperatively and underwent pancreatic surgery. In 4 patients, GISTs were detected intraoperatively. Histology showed 3 G1 and 2 G2 pNENs. All GISTs were low risk (median size, 0.9 cm). Two patients were alive without disease 108 and 132 months after surgery. In the literature, 7 cases were described. They had low-risk GISTs, with a gastric location in 6 cases (median size, 2.85 cm).

Conclusions

Sporadic pNENs coexisting with a GIST have been demonstrated in 12 cases. This association is considered fortuitous, and its true incidence may be underestimated. Surgery should be performed on the GIST during the pancreatic surgery. The prognosis strictly depends on the pancreatic NENs.
The Role of Laparoscopic Cholecystectomy After Severe and/or Necrotic Pancreatitis in the Setting of Modern Minimally Invasive Management of Pancreatic Necrosis
Authors: Ackermann Travis G. , Cashin Paul A. , Alwan Mostafa , Wewelwala Chamila C. , Tan Darius , Vu Anh N. , Bowers Kaye A. , Berry Roger , Croagh Daniel G.
Published: July 2020

Objectives

The trend toward minimally invasive procedures (MIP) in necrotizing pancreatitis is increasing. The optimal timing and technique of cholecystectomy in severe/necrotizing pancreatitis is unclear. This study aims to determine the role of laparoscopic cholecystectomy after severe/necrotizing pancreatitis in the context of MIP.

Methods

Retrospective analysis of a prospective database was performed for consecutive patients after cholecystectomy for gallstone pancreatitis between January 2011 and January 2018 at Monash Health, Melbourne, Australia.

Results

Three hundred fifty-five patients with gallstone pancreatitis underwent laparoscopic cholecystectomy with 2 conversions. Patients with severe pancreatitis were older (P = 0.002), with a more even sex distribution when compared with mild pancreatitis. Females predominated in the mild pancreatitis group.

Patients with moderate/severe pancreatitis (P = 0.002) and necrosis (P > 0.001) were more likely to have delayed cholecystectomy compared with mild pancreatitis. There was no increase in biliary presentations while awaiting cholecystectomy. Length of stay for patients with severe/necrotizing pancreatitis (P = 0.001) was increased, surgical complications appeared similar.

Conclusions

Laparoscopic cholecystectomy can be performed safely and effectively for pancreatitis, irrespective of severity. The paradigm shift in the management of severe necrotizing pancreatitis away from open necrosectomy toward MIP can be extended to encompass laparoscopic cholecystectomy.
Continuous Video Monitoring
Authors: Abbe JacQualine Renee , O'Keeffe Christian
Published: July 2020

Background:

Sitters are often used in the inpatient setting as a measure to ensure safety of patients with cognitive and behavioral concerns.

Problem:

Sitters are costly, and evidence is lacking that their presence produces safer outcomes. Continuous video monitoring is a safe alternative; yet, there is a lack of best practices and implementation strategies.

Approach:

A large academic medical center in the Pacific Northwest introduced continuous video monitoring as an adjunct measure to replace sitter use when appropriate. Adoption of the technology was influenced by nurse enculturation, leader standard work (standard parameters used by nurse leaders for process improvement), data tracking management, and patient/family feedback.

Outcomes:

Continuous video monitoring is a bridge for the nursing staff to enhance safety for patients and an additional safety intervention when sitter use is not reasonable.

Conclusion:

Utilizing technology such as continuous video monitoring can relieve sitters to allow for optimal productivity, increased safety, cost reduction, and nurse/family satisfaction.
A Roadmap for Practice-Based Evidence
Authors: Kaiser Jennifer , Wills Nicole , Reilly Therese , Pratt Jessica , Tumbleson Valerie , Niemeyer Marissa , Mindling Glenna
Published: July 2020

Background:

To ensure successful integration and implementation of evidence into practice, validation of measures and interventions should be performed in the population and setting in which they will be used.

Purpose:

This article provides a method for evaluating the predictive performance of a risk tool using the Hester Davis fall risk tool as an example.

Methods:

A retrospective matched-pairs sample of fallers and nonfallers was created. Psychometric properties were calculated using 2 × 2 contingency tables and compared to data in the original report.

Results:

In this study sample, the risk tool showed minimal ability to distinguish patients at risk for falling from those not at risk.

Conclusions:

Organizations are urged to assess the performance of risk tools in their own patient population. This article provides a practical approach for the validation of evidence into the practice setting.
Using a Post Fall Assessment Simulation to Examine Nurse Thought Processes
Authors: Allen Latricia , Bulat Tatjana , Uphold Constance R. , Johnson Theodore , Winkler Sandra L.
Published: July 2020

The prevalence of injurious falls is high in the Veterans Health Administration (VHA) and a major patient safety issue. The VHA is embracing technology such as simulation to improve patient care. Little is known regarding nurse thought processes while undergoing a post fall assessment simulation in the VHA. This article examines the benefit of using an evidence-based post fall simulation to improve nurse assessment skills while providing opportunity for practice without harm to patients.
Time-to-Task Validation in Sequential Simulations as a Component of Nursing Student Competency
Authors: Shinnick Mary Ann
Published: July 2020

Background

Time goals have not been tested as a component of nursing competence.

Methods

Using a known-groups approach, a multisite study was performed on prelicensure nursing students (novices) and experienced nurses (experts) who participated in 2 simulations of patient deterioration with time goals. Video capture was achieved with an eye tracker.

Results

While all novices did not achieve the time goals in both simulations, there was a significant improvement between the 2 simulations (P = .04). Experts were more successful in achieving the time-to-task goals in both simulations (44% and 95%, respectively). Statistical significance was found between the novice and expert groups in achieving the time goal for both simulations (P < .01).

Conclusions

This study was able to differentiate the expert group as being more proficient in a timed assessment, although the novices showed improvement between 2 simulations. This illustrates an opportunity for skill development among novices in managing patient deterioration amenable to time as an objective assessment.
Pilot Paramedic Survey of Benefits, Risks, and Strategies for Pediatric Prehospital Telemedicine
Authors: Boyle Tehnaz P. , Liu James , Dyer K. Sophia , Nadkarni Vinay M. , Camargo Carlos A. , Feldman James A.
Published: July 2020

Objective

A national survey found prehospital telemedicine had potential clinical applications but lacked provider opinion on its use for pediatric emergency care. We aimed to (1) estimate prehospital telemedicine use, (2) describe perceived benefits and risks of pediatric applications, and (3) identify preferred utilization strategies by paramedics.

Methods

We administered a 14-question survey to a convenience sample of 25 Massachusetts paramedics attending a regional course in 2018. Volunteer participants were offered a gift card. We compared respondents to a state database for sample representativeness. We present descriptive statistics and summarize qualitative responses.

Results

Twenty-five paramedics completed the survey (100% response); 23 (96%) were male, 21 (84%) 40 years or older, and 23 (92%) in urban practice. Respondents were older and more experienced than the average Massachusetts paramedic. Few had used prehospital telemedicine for patients younger than 12 years (8%; 95% confidence interval, 10–26%). Potential benefits included paramedic training (80%), real-time critical care support (68%), risk mitigation (68%), patient documentation (72%), decision support for hospital team activation (68%), and scene visualization (76%). Time delays from telemedicine equipment use (76%) and physician consultation (64%), broadband reliability (52%), and cost (56%) were potential risks. Respondents preferred video strategies for scene visualization, physician-assisted assessment and care. More respondents felt pediatric telemedicine applications would benefit rural/suburban settings than urban ones.

Conclusions

Paramedics reported prehospital telemedicine is underutilized for children but identified potential benefits including provider telesupport, training, situational awareness, and documentation. Concerns included transportation delays, cost, and broadband availability. Video was preferred for limited pediatric exposure settings. These results inform which telemedicine applications and strategies paramedics favor for children.
Brief Report: Toll-like Receptor 9-1635A/G Polymorphism Is Associated With HIV-1 Rebound After Four Weeks of Interruption of Antiretroviral Therapy
Authors: Vallejo Alejandro , Molina-Pinelo Sonia , de Felipe Beatriz , Abad-Fernández María , González-Escribano María Francisca , Leal Manuel , Soriano-Sarabia Natalia
Published: July 2020

Objectives:

This study aims to analyze the association of the presence of common polymorphisms [single nucleotide polymorphisms (SNPs)] on Toll-like receptors (TLRs), such as TLR9-1635A/G, TLR2-1892A/C, TLR2-2258G/A, TLR4-899A/G, and TLR4-1196C/T, with the viral rebound after stopping antiretroviral treatment (ART). CCR5-Δ32 deletion and HLA-A/HLA-B alleles were also analyzed.

Design:

Interruption of ART may be required to investigate the outcome of strategies aimed to achieve drug-free HIV remission or cure. However, interruption of ART is currently not indicated. This was a retrospective longitudinal study that included 57 long-term suppressed HIV-1-infected individuals.

Methods:

TLR SNPs were detected by real-time polymerase chain reaction (PCR). CCR5-Δ32 was analyzed by conventional PCR and HLA-A and HLA-B alleles by PCR-SSOP Luminex.

Results:

HIV-1 RNA rebound at week 4 after treatment interruption positively correlated with pre-ART HIV-1 load (P = 0.025). The TLR9-1635AA genotype was independently associated with a higher HIV-1 rebound compared with those with AG + GG genotype (multivariate stepwise regression analysis, P = 0.004). Women had lower HIV-1 RNA load both at rebound and during the 72 weeks of follow-up compared with men (P < 0.05 at all time-points), whereas CD4 nadir and CD4 count set-point were similar according to sex. The pre-ART viral load was independently associated with the viral set-point (P = 0.001), whereas the presence of the HLA-A01 allele (P = 0.027) and the CD4 nadir (P = 0.001) were associated with the CD4 count set-point.

Conclusions:

The association of the TLR9-1635AA genotype with a higher HIV-1 rebound suggests that this SNP may affect the results from strategies requiring interruption of ART aimed to cure HIV-1 infection.
Anthropometric Parameters for Nose Evaluation and Nasal Surgery Planning
Authors: Piombino Pasquale , Zace Pamela , Grassia Maria Gabriella , Cataldo Rosanna , Marino Marina , De Riu Giacomo , Testa Domenico , Bonavolontà Paola , Califano Luigi
Published: July 2020

Background:

The esthetic characteristics of face and nose are commonly evaluated before rhinoplasty using a completely subjective method, due to the lack of validated and reliable methods for quantifying facial esthetics and for accurate nose treatment planning. The aim of the study was to review the literature to determine and evaluate the points, distances, and angles commonly used in the treatment planning for rhinoplasty.

Methods:

Research based on anthropometric studies of the face and nose, published from 1987 to 2018 was included. Finally, 138 papers were selected after a statistical analysis through a simple random and non-random sample selection, and all papers were evaluated in their entirety.

Results:

According to the frequency of citation, 198 points, 336 distances, and 199 angles were listed. The first quartile of each distribution was eliminated, and frequency of more than 25% was selected. A group of 49 points, 77 distances, and 11 angles, were classified according to their anatomical region, that is, bone and soft tissues, was obtained.

Conclusions:

An enormous inhomogeneity and lack of standardized anthropometric measurement system, specifically of the nose, was evident, as the studies were conducted by authors of different origins. According to universally accepted parameters, the importance of a reliable method for nose surgery planning is highlighted.
Cancer Surgery Scheduling During and After the COVID-19 First Wave
Authors: Tzeng Ching-Wei D. , Teshome Mediget , Katz Matthew H. G. , Weinberg Jeffrey S. , Lai Stephen Y. , Antonoff Mara B. , Bird Justin E. , Shafer Aaron , Davis John W. , Adelman David M. , Moon Bryan , Reece Gregory , Prabhu Sujit S. , DeSnyder Sarah M. , Skibber John M. , Mehran Reza , Schmeler Kathleen , Roland Christina L. , Tran Cao Hop S. , Aloia Thomas A. , Caudle Abigail S. , Swisher Stephen G. , Vauthey Jean-Nicolas
Published: July 2020

Objective:

To summarize the multi-specialty strategy and initial guidelines of a Case Review Committee in triaging oncologic surgery procedures in a large Comprehensive Cancer Center and to outline current steps moving forward after the initial wave.

Summary of Background Data:

The impetus for strategic rescheduling of operations is multifactorial and includes our societal responsibility to minimize COVID-19 exposure risk and propagation among patients, the healthcare workforce, and our community at large. Strategic rescheduling is also driven by the need to preserve limited resources. As many states have already or are considering to re-open and relax stay-at-home orders, there remains a continued need for careful surgical scheduling because we must face the reality that we will need to co-exist with COVID-19 for months, if not years.

Methods:

The quality officers, chairs, and leadership of the 9 surgical departments in our Division of Surgery provide specialty-specific approaches to appropriately triage patients.

Results:

We present the strategic approach for surgical rescheduling during and immediately after the COVID-19 first wave for the 9 departments in the Division of Surgery at The University of Texas MD Anderson Cancer Center in Houston, Texas.

Conclusions:

Cancer surgeons should continue to use their oncologic knowledge to determine the window of opportunity for each surgical procedure, based on tumor biology, preoperative treatment sequencing, and response to systemic therapy, to safely guide patients through this cautious recovery phase.
Aquirufa ecclesiirivi sp. nov. and Aquirufa beregesia sp. nov., isolated from a small creek and classification of Allopseudarcicella aquatilis as a later heterotypic synonym of Aquirufa nivalisilvae
Authors: Pitt Alexandra , Koll Ulrike , Schmidt Johanna , Hahn Martin W.
Published: July 2020

Two bacterial strains, 50A-KIRBAT and 50C-KIRBAT, were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to

Aquirufa nivalisilvae

of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the new strains represent two new species of the genus

Aquirufa

. Pairwise calculated whole-genome average nucleotide identity (gANI) values ranging from 85.4 to 87.5 % confirmed this conclusion. Phenotypic, chemotaxonomic and genomic traits were investigated. Like strains of other

Aquirufa

species, 50A-KIRBAT and 50C-KIRBAT grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented and motile, most likely by gliding. They could be distinguished by slight differences in the chemotaxonomic features. We propose to establish for strain 50A-KIRBAT (=CIP 111735T=LMG 31080T) as type strain the name Aquirufa ecclesiirivi and for strain 50C-KIRBAT (=CIP 111736T=LMG 31501T) as type strain the name Aquirufa beregesia. Furthermore, the relationship between the type strains of

Aquirufa nivalisilvae

(59G-WUEMPELT) and

Allopseudarcicella aquatilis

(HME7025T) was investigated. Results of polyphasic analyses, especially a gANI value of 97.6 %, as well as the genome-based phylogenetic reconstruction, suggested that

Allopseudarcicella aquatilis

is a heterotypic synonym of

Aquirufa nivalisilvae

. According to rule 24b of the International Code of Nomenclature of Prokaryotes we propose to classify strain HME7025 as

Aquirufa nivalisilvae

and provide an emended description for the latter.
Unsuspected prevalent tree occurrences in high elevation sky-islands of the western Alps
Authors: André Gilles , Lavergne Sébastien , Carcaillet Christopher
Published: July 2020

The present note intends to challenge, based on field observations, the definition of treeline and argues for considering the upper occurrences of tree-species as an integrative result of historical and contemporary processes acting on high-altitude socio-ecosystems. A field survey ofPinus cembragrowing above 2800 m asl was conducted, in an ecoregion of southwestern Alps, straddling France and Italy (Queyras-Mt Viso area). Pines were described (height, density) and their habitats were contextualized (altitude, slope degree and exposure, bedrock). Individuals ofPinus cembraare commonly growing between 2800 and 3200 m asl, generally on east-facing, steep and rocky slopes, with a pine density decreasing with altitude. Pines are generally dwarf-shaped, sometimes erected or prostrated. Their needles are half the size compared to those of pines growing in subalpine forests. Pine morphology indicates harsh growing conditions, notably strong wind, aridity and frost. These habitats constitute visually emerging objects attractive for the nutcracker caching behaviour. This setting acts as a positive passive driver for pine at high altitudes, which is further favoured by intense atmospheric moisture supplied by the east from the Po valley. Steep and rocky slopes exclude livestock, likely explaining why these pines are located in grass-less habitats. These tree clusters constitute remarkable “sky-island” populations.Larix deciduaandPinus uncinatawere also recorded at exceptional altitudes butP. cembrais the most frequent species in high alpine conditions. These observations altogether highlight a complex pattern of tree-species line in the western Alps, and probably beyond.
Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors
Authors: Chen Wenhan , Wu Yang , Zheng Zhili , Qi Ting , Visscher Peter M , Zhu Zhihong , Yang Jian
Published: July 2020

Summary statistics from genome-wide association studies (GWAS) have facilitated the development of various summary data-based methods, which typically require a reference sample for linkage disequilibrium (LD) estimation. Analyses using these methods may be biased by errors in GWAS summary data and heterogeneity between GWAS and LD reference. Here we propose a quality control method, DENTIST, that leverages LD among genetic variants to detect and eliminate errors in GWAS or LD reference and heterogeneity between the two. Through simulations, we demonstrate that DENTIST substantially reduces false-positive rate (FPR) in detecting secondary signals in the summary-data-based conditional and joint (COJO) association analysis, especially for imputed rare variants (FPR reduced from >28% to <2% in the presence of heterogeneity between GWAS and LD reference). We further show that DENTIST can improve other summary-data-based analyses such as fine-mapping analysis, and integrative analysis of GWAS and expression quantitative trait locus data.
Worth the effort? A practical examination of random effects in hidden Markov models for animal telemetry data
Authors: McClintock Brett T.
Published: July 2020

Hidden Markov models (HMMs) that include individual-level random effects have recently been promoted for inferring animal movement behaviour from biotelemetry data. These “mixed HMMs” come at significant cost in terms of implementation and computation, and discrete random effects have been advocated as a practical alternative to more computationally-intensive continuous random effects. However, the performance of mixed HMMs has not yet been sufficiently explored to justify their widespread adoption, and there is currently little guidance for practitioners weighing the costs and benefits of mixed HMMs for a particular research objective.

I performed an extensive simulation study comparing the performance of a suite of fixed and random effect models for individual heterogeneity in the hidden state process of a 2-state HMM. I focused on sampling scenarios more typical of telemetry studies, which often consist of relatively long time series (30 – 250 observations per animal) for relatively few individuals (5 – 100 animals).

I generally found mixed HMMs did not improve state assignment relative to standard HMMs. Reliable estimation of random effects required larger sample sizes than are often feasible in telemetry studies. Continuous random effect models performed reasonably well with data generated under discrete random effects, but not vice versa. Random effects accounting for unexplained individual variation can improve estimation of state transition probabilities and measurable covariate effects, but discrete random effects can be a relatively poor (and potentially misleading) approximation for continuous variation.

When weighing the costs and benefits of mixed HMMs, three important considerations are study objectives, sample size, and model complexity. HMM applications often focus on state assignment with little emphasis on heterogeneity in state transition probabilities, in which case random effects in the hidden state process simply may not be worth the additional effort. However, if explaining variation in state transition probabilities is a primary objective and sufficient explanatory covariates are not available, then random effects are worth pursuing as a more parsimonious alternative to individual fixed effects.

To help put my findings in context and illustrate some potential challenges that practitioners may encounter when applying mixed HMMs, I revisit a previous analysis of long-finned pilot whale biotelemetry data.
Kinetic assays of DNA polymerase fidelity: a new theoretical perspective beyond Michaelis-Menten kinetics
Authors: Li Qiu-Shi , Shu Yao-Gen , Ou-Yang Zhong-Can , Li Ming
Published: July 2020

The high fidelity of DNA polymerase (DNAP) is critical for the faithful replication of DNA. There are several quantitative approaches to measure DNAP fidelity. Directly counting the error frequency in the replication products gives the true fidelity but it turns out very hard to implement in practice. Two biochemical kinetic approaches, the steady-state assay and the transient-state assay, were then suggested and widely adopted. In these assays, the error frequency is indirectly estimated by using kinetic theories combined with the measured apparent kinetic rates. However, whether it is equivalent to the true fidelity has never been clarified theoretically, and in particular there are different strategies using these assays to quantify the proofreading efficiency of DNAP but often lead to inconsistent results. In this paper, we make a comprehensive examination on the theoretical foundation of the two kinetic assays, based on the theory of DNAP fidelity recently proposed by us. Our studies show that while the conventional kinetic assays are generally valid to quantify the discrimination efficiency of DNAP, they are valid to quantify the proofreading efficiency of DNAP only when the kinetic parameters satisfy some constraints which will be given explicitly in this paper.These results may inspire more carefully-designed experiments to quantify DNAP fidelity.
GAN-based anomaly detection in multi-modal MRI images
Authors: Benson Sean , Beets-Tan Regina
Published: July 2020

Generative adversarial networks (GANs) are known to be a powerful tool in order to correct image aberrations, and even predict entirely synthetic images. We describe and demonstrate a method to use GANs trained from multi-modal magnetic resonance images as a 3-channel input. The training of the generative network was performed using only healthy images together with pseudo-random irregular masks. The dataset consisted of just 20 people. The resulting model was then used to detect anomalies real patient images in which the anomaly was a tumour. The search was performed using no prior knowledge of the tumour location, if indeed a tumour was present. Resulting accuracies are observed to vary significantly on the size of the anomaly. The area under the receiver operator characteristic curve is observed to be greater than 0.75 for anomaly sizes greater than 4 cm2.
A modelling framework for the prediction of the herd-level probability of infection from longitudinal data
Authors: Madouasse Aurélien , Mercat Mathilde , van Roon Annika , Graham David , Guelbenzu Maria , Santman Berends Inge , van Schaik Gerdien , Nielen Mirjam , Frössling Jenny , Ågren Estelle , Humphry Roger , Eze Jude , Gunn George , Henry Madeleine K. , Gethmann Jörn , More Simon J. , Toft Nils , Fourichon Christine
Published: July 2020

The collective control programmes (CPs) that exist for many infectious diseases of farm animals rely on the application of diagnostic testing at regular time intervals for the identification of infected animals or herds. The diversity of these CPs complicates the trade of animals between regions or countries because the definition of freedom from infection differs from one CP to another. In this paper, we describe a statistical model for the prediction of herd-level probabilities of infection from longitudinal data collected as part of CPs against infectious diseases of cattle. The model was applied to data collected as part of a CP against bovine viral diarrhoea virus (BVDV) infection in Loire-Atlantique, France. The model represents infection as a herd latent status with a monthly dynamics. This latent status determines test results through test sensitivity and test specificity. The probability of becoming status positive between consecutive months is modelled as a function of risk factors (when available) using logistic regression. Modelling is performed in a Bayesian framework, using either Stan or JAGS. Prior distributions need to be provided for the sensitivities and specificities of the different tests used, for the probability of remaining status positive between months as well as for the probability of becoming positive between months. When risk factors are available, prior distributions need to be provided for the coefficients of the logistic regression, replacing the prior for the probability of becoming positive. From these prior distributions and from the longitudinal data, the model returns posterior probability distributions for being status positive for all herds on the current month. Data from the previous months are used for parameter estimation. The impact of using different prior distributions and model implementations on parameter estimation was evaluated. The main advantage of this model is its ability to predict a probability of being status positive in a month from inputs that can vary in terms of nature of test, frequency of testing and risk factor availability/presence. The main challenge in applying the model to the BVDV CP data was in identifying prior distributions, especially for test characteristics, that corresponded to the latent status of interest, i.e. herds with at least one persistently infected (PI) animal. The model is available on Github as an R package (https://github.com/AurMad/STOCfree) and can be used to carry out output-based evaluation of disease CPs.
Nursery habitat use by juvenile blue crabs in created and natural marshes
Authors: Bilkovic D.M. , Isdell R.E. , Stanhope D. , Angstadt K.T. , Havens K.J. , Chambers R.M.
Published: July 2020

Climate change and coastal development pressures have intensified the need for shoreline protection. Nature-first approaches that use natural habitats, particularly marshes, are being promoted globally as ecologically-beneficial alternatives to grey infrastructure. The ability of these novel shorelines to provide nursery habitat to blue crab, an ecologically and economically important species along the Atlantic and Gulf coasts of the United States, has not been quantified.

We quantified the abundance and size distribution of juvenile blue crabs from a chronosequence of living shorelines (created fringing marshes) spanning 2 to 16 years in age (since construction) and compared with paired natural fringing marshes in the southern Chesapeake Bay.

Both created and natural fringing marshes are being used by blue crabs as primary nursery habitats. While there were interannual differences in abundance, young blue crabs (≤ 2.5 cm carapace width) were observed in similar densities and sizes at living shoreline and natural marshes. There was no relationship between the age of the living shoreline and blue crab density, indicating that even the youngest living shorelines (2 years) were providing primary nursery habitat. Young blue crabs were more abundant in more isolated marshes and those that were inundated for longer periods of time each tidal cycle, which may be evidence for habitat-limitation.

Synthesis and applications:We provide evidence that juvenile blue crabs are comparably using natural and created fringing salt marshes as primary nursery habitat. Although the relative importance of salt marshes as young crab nursery habitat is not fully understood and likely varies by system, the value of marshes within a suite of available structural nursery habitats may increase under a changing climate. The potential for living shorelines to serve as nursery habitat for an economically important species may provide additional incentives to implement these climate adaptation strategies.
Is the “end-of-study guess” a valid measure of sham blinding during transcranial direct current stimulation?
Authors: Turner Christopher , Jackson Catherine , Learmonth Gemma
Published: July 2020

Studies using transcranial direct current stimulation (tDCS) typically incorporate afade-in, short-stimulation, fade-outsham (placebo) protocol, which is assumed to be indistinct from a 10-30min active protocol on the scalp. However, many studies report that participants can dissociate active stimulation from sham, even during low-intensity 1mA currents. We recently identified differences in the perception of an active (10min of 1mA) and a sham (20s of 1mA) protocol that lasted for 5 mins after the cessation of sham. In the present study we assessed whether delivery of a higher-intensity 2mA current would exacerbate these differences. Two protocols were delivered to 32 adults in a double-blinded, within-subjects design (active:10min of 2mA, andsham:20s of 2mA), with the anode over the left primary motor cortex and the cathode on the right forehead. Participants were asked “Is the stimulation on?” and“How sure are you?”at 30s intervals during and after stimulation. The differences between active and sham were more consistent and sustained during 2mA than during 1mA. We then quantified how well participants were able to track the presence and absence of stimulation (i.e. their sensitivity) during the experiment using cross-correlations. Current strength was a good classifier of sensitivity during active tDCS, but exhibited only moderate specificity during sham. The accuracy of theend-of-study guesswas no better than chance at predicting sensitivity. Our results indicate that the traditional end-of-study guess poorly reflects the sensitivity of participants to stimulation, and may not be a valid method of assessing sham blinding.
Whole-proteome Tree of Insects: Grouping and phylogeny without sequence alignment
Authors: Choi JaeJin , Kim Byung-Ju , Kim Sung-Hou
Published: July 2020

An “organism tree” of insects, the largest and most species-diverse group of all living animals, can be considered as a conceptual tree to capture a simplified narrative of the complex evolutionary courses of the extant insects. Currently, the most common approach has been to construct a “protein tree”, as a surrogate for the organism tree, by Multiple Sequence Alignment (MSA) of highly homologous regions of a set of select proteins to represent each organism. However, such selected regions account for a very small fraction of the whole-proteome of each organism.

Information Theory provides a method of comparing two sets of all proteins, two whole-proteomes, without MSA: By treating each whole-proteome sequence as a “book” of amino acid alphabets, the information contents of two whole-proteomes can be quantitatively compared using the text comparison method of the theory, without sequence alignment, providing an opportunity to construct a “whole-proteome tree” of insects as a surrogate for an organism tree of insects.

A whole-proteome tree of the insects in this study shows that: (a) all the founders of the major groups of the insects have emerged in an explosive “burst” near the root of the tree, (b) the most basal group of all the insects is a subgroup of Hemiptera consisting of aphids and psyllids, and (c) there are other notable differences in the phylogeny of the groups compared to those of the recent protein trees of insects.
Lateral phase differences in a population model of the visual cortex are sufficient for the development of rhythmic spatial sampling
Authors: Yi Justin D. , Arisaka Katsushi
Published: July 2020

When attending to many spatially distributed visual stimuli, attention is reweighted rhythmically at 4-8 Hz. The probability of detection depends on the phase at which a stimulus is deployed relative to this intrinsic rhythm. The reweighting oscillations can be observed both electrophysiologically and behaviorally, and appear to be regulated by the pulvinar. Based on these findings, we considered the computational consequences of allowing feedback to shape the distribution of inhibitory oscillations from the thalamus, as measured by a local field potential (LFP) phases in the 8 Hz low alpha-band, across laterally-connected regions of the visual cortex. We constructed a population activity model with lateral and feedforward connections. In agreement with prior models, we found that the sign of the lateral phase difference in the inhibitory low-frequency oscillations regulated the direction of communication between the laterally-connected regions. Furthermore, the phase difference induced periodicity in the dynamics of a downstream winner-takes-all attractor network such that periodic switching between states was observed. We finally simulated a simple spatial attention task. We found rhythmic 8 Hz sampling between two regions when a lateral phase difference was present—an effect that disappeared when the lateral phase difference was zero. These findings are in agreement with spatial attention literature and suggest that lateral phase differences are essential for manifesting communicational asymmetries in laterally-connected visual cortices. Our model predicts that population-specific phase differences are critical for sampling the spatial extent of stimuli.

Author summary

We conducted a computational study of the effects of lateral phase differences in a simulated model of the visual cortex. Lateral phase differences are defined to be when the phase of an intrinsic low-frequency inhibitory oscillation varies consistently across populations in the same cortical area. For example, our model was intended to capture the dynamics of a retinotopic cortex where feedback from the frotoparietal areas via the pulvinar nucleus assigned laterally-connected regions of the visual cortex different phases. We found that the sign of the phase differences influenced the direction of lateral communication. Furthermore, the phase differences introduced rhythmicity in the downstream areas, thus allowing us to simulate rhythmic spatial selection of stimuli. Prior to the current study, the influence of inter-areal phase differences in feedforward models had been well characterized. Our model provides new insights into the dynamics of population-specific lateral phase differences and predicts that the development of phase differences across the visual cortex are critical for the allocation of attention in space.