bluuebunny/crossref_metadata_2025 huggingface dataset:
PredCID: prediction of driver frameshift indels in human cancer
Authors: Yue Zhenyu , Chu Xinlu , Xia Junfeng
Published: May 2020

The discrimination of driver from passenger mutations has been a hot topic in the field of cancer biology. Although recent advances have improved the identification of driver mutations in cancer genomic research, there is no computational method specific for the cancer frameshift indels (insertions or/and deletions) yet. In addition, existing pathogenic frameshift indel predictors may suffer from plenty of missing values because of different choices of transcripts during the variant annotation processes. In this study, we proposed a computational model, called PredCID (Predictor for Cancer driver frameshift InDels), for accurately predicting cancer driver frameshift indels. Gene, DNA, transcript and protein level features are combined together and selected for classification with eXtreme Gradient Boosting classifier. Benchmarking results on the cross-validation dataset and independent dataset showed that PredCID achieves better and robust performance compared with existing noncancer-specific methods in distinguishing cancer driver frameshift indels from passengers and is therefore a valuable method for deeper understanding of frameshift indels in human cancer. PredCID is freely available for academic research at http://bioinfo.ahu.edu.cn:8080/PredCID.
Impact of Meningococcal B (4CMenB) Vaccine on Pharyngeal Neisseria meningitidis Carriage Density and Persistence in Adolescents
Authors: McMillan Mark , Walters Luke , Sullivan Thomas , Leong Lex E X , Turra Mark , Lawrence Andrew , Koehler Ann P , Finn Adam , Andrews Ross M , Marshall Helen S
Published: May 2020

Background

Higher density of Neisseria meningitidis carriage may be associated with transmission of the meningococcus. Our aim was to establish the impact of meningococcal B (4CMenB) vaccine on N. meningitidis carriage density.

Methods

We compared 4CMenB vaccine to control among 913 South Australian students aged approximately 15–18 years in a cluster randomized trial who had N. meningitidis carriage at 12 months. Oropharyngeal swabs were collected at baseline and 12 months later to detect N. meningitidis carriage. Colony-forming units per milliliter (CFU/mL) were estimated by generating a standard curve that plotted quantitative polymerase chain reaction cycle threshold values against log-normalized CFU.

Results

Among the 913 students with N. meningitidis carriage at 12 months, there was no difference in mean carriage density between the vaccinated (n = 434; 3.80 log CFU/mL [standard deviation {SD}, 1.29]) and control group (n = 479; 3.73 log CFU/mL [SD, 1.30]; P = .51). Higher N. meningitidis carriage density at baseline was associated with an increase in the odds of persistent carriage at 12 months (n = 504; odds ratio [OR] per 1.0 log CFU/mL increase in density, 1.36 [95% confidence interval {CI}, 1.17–1.58]; P < .001). Students with baseline carriage who were vaccinated had decreased persistent N. meningitidis carriage at 12 months compared to unvaccinated students (81/260 [31%] vs 105/244 [43%]; OR, 0.60 [95% CI, .40–.90]; P = .01).

Conclusions

4CMenB vaccine did not reduce carriage density of N. meningitidis 12 months postvaccination, despite increased carriage clearance. Higher carriage density is likely to enable transmission through prolonged periods of population exposure.

Clinical Trials Registration

NCT03089086.
Deaf Community Cultural Wealth in Community College Students
Authors: Johnson Serena , Stapleton Lissa , Berrett Bryan
Published: May 2020

Deaf students are members of a linguistic and cultural minority whose background and experiences provide a unique backdrop for the navigation of higher education. Using the framework of Deaf community cultural wealth, this study examines the experiences of Deaf students in community college and their utilization of various forms of capital. Findings showed that they exhibited instances of resistant, navigational, social, and familial capital in accessing and persisting in higher education.
Myocardial infarction or acute coronary syndrome with non-obstructive coronary arteries and sudden cardiac death: a missing connection
Authors: Kosmas Nikolaos , Manolis Antonis S , Dagres Nikolaos , Iliodromitis Efstathios K
Published: May 2020

Myocardial infarction with non-obstructive coronary arteries or any acute coronary syndrome (ACS) with normal or near-normal (non-obstructive) coronary arteries (ACS-NNOCA) is an heterogeneous clinical entity, which includes different pathophysiology mechanisms and is challenging to treat. Sudden cardiac death (SCD) is a catastrophic manifestation of ACS that is crucial to prevent and treat urgently. The concurrence of the two conditions has not been adequately studied. This narrative review focuses on the existing literature concerning ACS-NNOCA pathophysiology, with an emphasis on SCD, together with risk and outcome data from clinical trials. There have been no large-scale studies to investigate the incidence of SCD within ACS-NNOCA patients, both early and late in the disease. Some pathophysiology mechanisms that are known to mediate ACS-NNOCA, such as atheromatous plaque erosion, anomalous coronary arteries, and spontaneous coronary artery dissection are documented causes of SCD. Myocardial ischaemia, inflammation, and fibrosis are probably at the core of the SCD risk in these patients. Effective treatments to reduce the relevant risk are still under research. ACS-NNOCA is generally considered as an ACS with more ‘benign’ outcome compared to ACS with obstructive coronary artery disease, but its relationship with SCD remains obscure, especially until its incidence and effective treatment are evaluated.
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
Authors: Oeyen Jan Philip , Baa-Puyoulet Patrice , Benoit Joshua B , Beukeboom Leo W , Bornberg-Bauer Erich , Buttstedt Anja , Calevro Federica , Cash Elizabeth I , Chao Hsu , Charles Hubert , Chen Mei-Ju May , Childers Christopher , Cridge Andrew G , Dearden Peter , Dinh Huyen , Doddapaneni Harsha Vardhan , Dolan Amanda , Donath Alexander , Dowling Daniel , Dugan Shannon , Duncan Elizabeth , Elpidina Elena N , Friedrich Markus , Geuverink Elzemiek , Gibson Joshua D , Grath Sonja , Grimmelikhuijzen Cornelis J P , Große-Wilde Ewald , Gudobba Cameron , Han Yi , Hansson Bill S , Hauser Frank , Hughes Daniel S T , Ioannidis Panagiotis , Jacquin-Joly Emmanuelle , Jennings Emily C , Jones Jeffery W , Klasberg Steffen , Lee Sandra L , Lesný Peter , Lovegrove Mackenzie , Martin Sebastian , Martynov Alexander G , Mayer Christoph , Montagné Nicolas , Moris Victoria C , Munoz-Torres Monica , Murali Shwetha Canchi , Muzny Donna M , Oppert Brenda , Parisot Nicolas , Pauli Thomas , Peters Ralph S , Petersen Malte , Pick Christian , Persyn Emma , Podsiadlowski Lars , Poelchau Monica F , Provataris Panagiotis , Qu Jiaxin , Reijnders Maarten J M F , von Reumont Björn Marcus , Rosendale Andrew J , Simao Felipe A , Skelly John , Sotiropoulos Alexandros G , Stahl Aaron L , Sumitani Megumi , Szuter Elise M , Tidswell Olivia , Tsitlakidis Evangelos , Vedder Lucia , Waterhouse Robert M , Werren John H , Wilbrandt Jeanne , Worley Kim C , Yamamoto Daisuke S , van de Zande Louis , Zdobnov Evgeny M , Ziesmann Tanja , Gibbs Richard A , Richards Stephen , Hatakeyama Masatsugu , Misof Bernhard , Niehuis Oliver
Published: May 2020

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
Earthquake productivity law
Authors: Shebalin P N , Narteau C , Baranov S V
Published: May 2020

Mechanisms of stress transfer and probabilistic models have been widely investigated to explain earthquake clustering features. However, these approaches are still far from being able to link individual events and to determine the number of earthquakes caused by a single event. An alternative approach based on proximity functions allows us to generate hierarchical clustering trees and to identify pairs of nearest-neighbours between consecutive levels of hierarchy. Then, the productivity of an earthquake is the number of events of the next level to which it is linked. Using a relative magnitude threshold ΔM to account for scale invariance in the triggering process, we show that the ΔM-productivity attached to each event is a random variable that follows an exponential distribution. The exponential rate of this distribution does not depend on the magnitude of triggering events and systematically decreases with depth. These results could now be used to characterize active fault systems and improve epidemic models of seismicity.
Total Abdominal Colectomies With Proctectomy Are Associated With Higher 30-Day Readmission Rates in Children With Ulcerative Colitis
Authors: Egberg Matthew D , Phillips Michael , Galanko Joseph A , Kappelman Michael
Published: May 2020

Background

Hospital readmissions are a burden on patients and families and place financial strain on the health care system. Thirty-day readmission rates for adult patients undergoing colectomy are as high as 30%, and inflammatory bowel disease is a risk factor for readmission. We used a multicenter pediatric surgical database to determine the 30-day readmission rate for pediatric patients with ulcerative colitis (UC) undergoing total abdominal colectomy (TAC) and to identify risk factors for 30-day hospital readmission.

Methods

We used the National Surgical Quality Improvement Program-Pediatrics database to identify pediatric patients with UC undergoing a TAC between 2012 and 2017. We identified patient and procedural data from the index hospitalization and used logistic regression to identify risk factors for 30-day readmission rates, adjusting for confounding factors.

Results

We identified 489 pediatric UC TAC hospitalizations between 2012 and 2017, and 19.4% were readmitted within 30 days of surgical discharge. Patient demographics and preoperative laboratory values were not associated with risk of readmission. The TAC procedures that included a proctectomy were at a 2-fold (odds ratio = 2.4; 95% confidence interval, 1.1-5.2) higher risk of 30-day readmission than TAC alone after adjusted analysis.

Conclusions

Nearly 20% of annual pediatric UC hospitalizations involving a colectomy resulted in a 30-day hospital readmission. Notably, TAC procedures that included a proctectomy had significantly higher readmission rates compared to TAC alone. These results can inform risk management strategies aimed at reducing morbidity and hospital readmissions for children with UC.
Favorable Outcomes and Anti-TNF Durability After Addition of an Immunomodulator for Anti-Drug Antibodies in Pediatric IBD Patients
Authors: Colman Ruben J , Portocarrero-Castillo Andrea , Chona Deepika , Hellmann Jennifer , Minar Phillip , Rosen Michael J
Published: May 2020

Background

Anti-drug antibodies (ADAs) to anti-tumor necrosis factor alpha (anti-TNF) drugs are associated with increased drug clearance and loss of response. We aimed to assess the effectiveness of starting an immunomodulator (IM) drug in patients with newly detected ADAs on anti-TNF monotherapy.

Methods

We reviewed the medical records of pediatric patients with inflammatory bowel disease on infliximab or adalimumab monotherapy with first-time detection of significant ADAs between 2014 and 2018. Patients who started an IM within 3 months of ADA detection were compared with those who did not (No-IM). Outcomes included steroid-free clinical and biochemical remission on the same anti-TNF , anti-TNF durability, and ADA reversal.

Results

We identified 89 patients with ADAs: 30 IM patients and 59 No-IM patients. The initial anti-TNF was stopped shortly after ADA detection in 36% of the No-IM patients vs none of the IM patients, driving longer survival on the initial anti-TNF in the IM group (P = 0.005). At 12 months, steroid-free clinical and biochemical remission on the same anti-TNF occurred in 53.9% of the IM group vs 26.8% in the No-IM group (P = 0.025). Drug levels rose higher (P = 0.003) and ADA levels fell farther (P = 0.037) in the IM group than in the No-IM group. Baseline ADA level predicted ADA reversal in the No-IM patients with an area under the receiver operating characteristic of 0.79 (P = 0.006). An ADA level <329 ng/mL had a 76.2% sensitivity and an 83.3% specificity for ADA reversal without IM.

Conclusions

Pediatric patients with inflammatory bowel disease on anti-TNF monotherapy who started an IM for significant ADA levels exhibited longer anti-TNF durability and a higher likelihood of steroid-free clinical and biochemical remission on the same anti-TNF. Patients not treated with an IM were unlikely to reverse ADAs >329 ng/mL.
From “taking” to “tending”: learning about Indigenous land and resource management on the Pacific Northwest Coast of North America
Authors: Turner Nancy J
Published: May 2020

Indigenous peoples have occupied the northwestern North American coast for at least 15 000 years—a time when much of the land was covered by a kilometre or more of ice and only patches of land were glacier free. Over the millennia, through difficult times and seasons of plenty, they have built up an immense body of local knowledge, practice, and belief—Indigenous, or Traditional Ecological Knowledge—enabling them to live well, learning about the plants and animals of terrestrial, aquatic, and marine environments on which they have depended, and how to harvest and process them into nutritious foods, healing medicines, and useful materials. Although it has been commonly assumed that these people, as so-called “hunter-gatherers”, were simply helping themselves to nature’s provisions, over decades of learning from Indigenous plant specialists and other knowledge holders as an ethnobotanist, I have come to see First Peoples as resource tenders and managers over countless generations. Their traditional land and resource management systems provide many lessons on how we humans can work with natural processes to ensure the well-being not only of ourselves but also of the species and habitats on which we rely.
The Automorphic Discrete Spectrum of Mp4
Authors: Gan Wee Teck , Ichino Atsushi
Published: May 2020

We prove the multiplicity formula for the automorphic discrete spectrum of the metaplectic group $\textrm{Mp}_4$ of rank $2$.
Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome–Similar Coronavirus
Authors: Chen Shuaiyin , Zheng Xin , Zhu Jingyuan , Ding Ronghua , Jin Yuefei , Zhang Weiguo , Yang HaiYan , Zheng Yingjuan , Li Xin , Duan Guangcai
Published: May 2020

Severe acute respiratory syndrome coronavirus (SARS-CoV) was discovered as a novel pathogen in the 2002–2003 SARS epidemic. The emergence and disappearance of this pathogen have brought questions regarding its source and evolution. Within the genome sequences of 281 SARS-CoVs, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-related CoVs (SARSr-CoVs), a ~430 bp genomic region (from 27 701 bp to 28 131 bp in AY390556.1) with regular variations was investigated. This ~430 bp region overlaps with the ORF8 gene and is prone to deletions and nucleotide substitutions. Its complexity suggested the need for a new genotyping method for coronaviruses related to SARS-similar coronaviruses (SARS-CoV, SARSr-CoV, and SARS-CoV-2). Bat SARSr-CoV presented 3 genotypes, of which type 0 is only seen in bat SARSr-CoV, type I is present in SARS in the early phase, and type II is found in all SARS-CoV-2. This genotyping also shows potential usage in distinguishing the SARS-similar coronaviruses from different hosts and geographic areas. This genomic region has important implications for predicting the epidemic trend and studying the evolution of coronavirus.
HIV-1 Gag mutations alone are sufficient to reduce darunavir susceptibility during virological failure to boosted PI therapy
Authors: Blanch-Lombarte Oscar , Santos José R , Peña Ruth , Jiménez-Moyano Esther , Clotet Bonaventura , Paredes Roger , Prado Julia G
Published: May 2020

Background

Virological failure (VF) to boosted PIs with a high genetic barrier is not usually linked to the development of resistance-associated mutations in the protease gene.

Methods

From a cohort of 520 HIV-infected subjects treated with lopinavir/ritonavir or darunavir/ritonavir monotherapy, we retrospectively identified nine patients with VF. We sequenced the HIV-1 Gag-protease region and generated clonal virus from plasma samples. We characterized phenotypically clonal variants in terms of replicative capacity and susceptibility to PIs. Also, we used VESPA to identify signature mutations and 3D molecular modelling information to detect conformational changes in the Gag region.

Results

All subjects analysed harboured Gag-associated polymorphisms in the absence of resistance mutations in the protease gene. Most Gag changes occurred outside Gag cleavage sites. VESPA analyses identified K95R and R286K (P < 0.01) as signature mutations in Gag present at VF. In one out of four patients with clonal analysis available, we identified clonal variants with high replicative capacity and 8- to 13-fold reduction in darunavir susceptibility. These clonal variants harboured K95R, R286K and additional mutations in Gag. Low susceptibility to darunavir was dependent on the Gag sequence context. All other clonal variants analysed preserved drug susceptibility and virus replicative capacity.

Conclusions

Gag mutations may reduce darunavir susceptibility in the absence of protease mutations while preserving viral fitness. This effect is Gag-sequence context dependent and may occur during boosted PI failure.
Transcriptome changes underlie alterations in behavioral traits in different types of chicken
Authors: Chen Siyu , Yan Chao , Xiang Hai , Xiao Jinlong , Liu Jian , Zhang Hui , Wang Jikun , Liu Hao , Zhang Xiben , Ou Maojun , Chen Zelin , Li Weibo , Turner Simon P , Zhao Xingbo
Published: May 2020

In recent decades, artificial selection has contributed greatly to meeting the demands for animal meat, eggs, and milk. However, it has also resulted in changes in behavior, metabolic and digestive function, and alterations in tissue development, including the brain and skeleton. Our study aimed to profile the behavioral traits and transcriptome pattern of chickens (broilers, layers, and dual-purpose breeds) in response to artificial selection. Broilers spent less time gathered as a group in a novel arena (P < 0.01), suggesting reduced fearfulness in these birds. Broilers also showed a greater willingness to approach a model predator during a vigilance test but had a greater behavioral response when first exposed to the vocalization of the predator. Genes found to be upregulated and downregulated in previous work on chickens divergently selected for fear responses also showed consistent differences in expression between breeds in our study and indicated a reduction in fearfulness in broilers. Gene ACTB_G1 (actin) was differentially expressed between breeds and is a candidate gene involved with skeletal muscle growth and disease susceptibility in broilers. Furthermore, breed-specific alterations in the chicken domestic phenotype leading to differences in growth and egg production were associated with behavioral changes, which are probably underpinned by alterations in gene expression, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways. The results highlight the change in behavior and gene expression of the broiler strain relative to the layer and a dual-purpose native breed.
The Chimeric Bud-Sport ‘Delicious’ (Red) Mutant Strain, It, Expresses Lethal-Effect Resistance Against the Obliquebanded Leafroller (Lepidoptera: Tortricidae)
Authors: Schwarz Joseph , Milnes Joshua , Brunner Jay
Published: May 2020

Three ‘Red Delicious,’ Malus domestica Borkhausen (Rosales: Rosaceae), apple plantings, each representing a different sport, were evaluated for natural resistance against the obliquebanded leafroller (OBLR), Choristoneura rosaceana (Harris). The establishment of neonate larvae on apple foliage was not different between the three ‘Red Delicious’ plantings. Of the three ‘Red Delicious’ plantings, the one that most negatively impacted OBLR was the ‘It Delicious’ genotype. The ‘It Delicious’ genotype at the Sunrise Research Orchard exhibited essentially 100% mortality against OBLR when fed on spring and summer foliage, and mortality accumulated faster across instars than on other ‘Red Delicious’ plantings. The high mortality observed in the ‘It Delicious’ genotype points to the existence of a putative gene, which we propose as Cro1. The other ‘Red Delicious’ plantings, Columbia River Orchard and Tree Fruit Research and Extension Center Research Orchard treatments, showed negative impacts, especially when exposed to foliage from the summer compared to the spring period. Development rates in these treatments in spring were higher compared to summer, and there were direct relationships between development rates, pupal weights, and adult longevity for both males and females. These latter results suggest that sublethal effects could be present in these ‘Red Delicious’ cultivars, thus offering insights to a gene-pyramiding strategy for breeders to managing leafroller pests in Washington apple.
The Urban Politics of Human Rights Practice
Authors: Fernandez-Wulff Paula , Yap Christopher
Published: May 2020

Social movement organizations are increasingly developing human rights strategies at the municipal level, particularly in European urban contexts. Yet critical scholarly work on human rights has overlooked two related realities: non-state-centric, social movement use of the tools and discourses of rights, and the strategic participation of citizen groups in municipal urban policy spaces. This article builds on critical human rights theory through the experiences of three grassroots organizations claiming and exercising social rights in urban policy spaces of Barcelona, Valladolid, and London. It engages with a number of scholarly critiques of the state and human rights, particularly focusing on those critiques that question their compatibility with autonomy, democracy, and self-government at the local level. While the value of such critical literature is undeniable, we show how urban grassroots practices and experiences with social rights-based strategies in the context of housing, water, and participation can circumvent some of these critiques on the ground, pointing at new avenues for critical legal research when infused with other critical discourses, including urban politics.
Adaptation of an Intervention to Reduce Disparities in School HRQOL for Latino Childhood Cancer Survivors
Authors: Patel Sunita K , Miranda Leticia , Delgado Nicole , Barreto Nicolas , Nolty Anne , Kelly Natalie C , Wilson Karla , Toomey Debbie , Pawlowska Anna
Published: May 2020

Objective

Survivors of childhood leukemia, especially those from low socioeconomic status households, often experience persistent neurocognitive and academic impairment. This study adapted an existing parent training intervention to improve outcomes for low-acculturated, Spanish-speaking Latino parents of children with leukemia and pilot tested that intervention for feasibility.

Methods

Semistructured interviews were conducted with a focus group of 20 Latino parents of children treated for leukemia. Ten Latino families participated in a pilot study of the adapted parenting intervention, consisting of eight sessions over 6 months.

Results

Focus groups revealed that parents unanimously supported a parenting intervention but barriers to participation included time constraints, transportation issues, and anxiety in the hospital environment. The parents also highlighted cultural factors that could contribute to the health disparity, such as lack of knowledge and efficacy in facilitating their child’s progress with learning and school. In the pilot study, adherence was 90%, establishing feasibility, and the adapted intervention was considered beneficial. The median parenting efficacy scores improved from preintervention to postintervention (median 3.40 vs. 3.94; p < .011), as did parent-reported school functioning of the child (median 50.00 vs. 60.00; p = .088).

Conclusions

This study addressed a health disparity by culturally adapting a parenting intervention, which was designed to improve school functioning, to meet the needs and preferences of low-acculturated, Spanish-speaking families of children with leukemia in Southern California. The pilot study demonstrated that the adapted intervention is feasible and acceptable in the target population. A larger trial is underway to test the efficacy of this adapted parenting intervention.
Acute Fulminant Cerebral Edema: A Newly Recognized Phenotype in Children With Suspected Encephalitis
Authors: Krishnan Preetha , Glenn Orit A , Samuel Michael C , Sheriff Heather , Foster-Barber Audrey , Sejvar James J , Roy-Burman Arup , Wadford Debra A , Preas Christopher P , Tureen Jay H , Glaser Carol A
Published: May 2020

Background

Encephalitis is a severe neurological syndrome associated with significant morbidity and mortality. The California Encephalitis Project (CEP) enrolled patients for more than a decade. A subset of patients with acute and fulminant cerebral edema was noted.

Methods

All pediatric encephalitis patients with cerebral edema referred to the CEP between 1998 and 2012 were reviewed. A case definition was developed for acute fulminant cerebral edema (AFCE) that included the CEP case definition for encephalitis and progression to diffuse cerebral edema on neuroimaging and/or autopsy, and no other recognized etiology for cerebral edema (eg, organic, metabolic, toxin). Prodromic features, demographic and laboratory data, neuroimaging, and outcomes were compared with non-AFCE encephalitis cases.

Results

Of 1955 pediatric cases referred to the CEP, 30 (1.5%) patients met the AFCE case definition. The median age for AFCE and non-AFCE cases was similar: 8.2 years (1–18 years) and 8.0 years (0.5–18 years), respectively. Asian-Pacific Islanders comprised a larger proportion of AFCE cases (44%) compared with non-AFCE cases (14%, P < .01). AFCE cases often had a prodrome of high fever, vomiting, and profound headache. Mortality among AFCE patients was significantly higher than among non-AFCE patients (80% vs 13%, P < .01). A confirmed etiology was identified in only 2 cases (enterovirus, human herpes virus type 6), while 10 others had evidence of a respiratory pathogen.

Thirty pediatric patients referred to the California Encephalitis Project with a unique, and often fatal, form of encephalitis are reported. Demographic and clinical characteristics, possible etiologies and a proposed case definition for acute fulminant cerebral edema (AFCE) are described.

Conclusions

AFCE is a recently recognized phenotype of encephalitis with a high mortality. AFCE may be triggered by common pediatric infections. Here, we propose a case definition.
Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes
Authors: Sewelam Nasser , Brilhaus Dominik , Bräutigam Andrea , Alseekh Saleh , Fernie Alisdair R , Maurino Veronica G
Published: May 2020

Environmental stresses such as drought, heat, and salinity limit plant development and agricultural productivity. While individual stresses have been studied extensively, much less is known about the molecular interaction of responses to multiple stresses. To address this problem, we investigated molecular responses of Arabidopsis to single, double, and triple combinations of salt, osmotic, and heat stresses. A metabolite profiling analysis indicated the production of specific compatible solutes depending on the nature of the stress applied. We found that in combination with other stresses, heat has a dominant effect on global gene expression and metabolite level patterns. Treatments that include heat stress lead to strongly reduced transcription of genes coding for abundant photosynthetic proteins and proteins regulating the cell life cycle, while genes involved in protein degradation are up-regulated. Under combined stress conditions, the plants shifted their metabolism to a survival state characterized by low productivity. Our work provides molecular evidence for the dangers for plant productivity and future world food security posed by heat waves resulting from global warming. We highlight candidate genes, many of which are functionally uncharacterized, for engineering plant abiotic stress tolerance.
The Polish Rider: CH Alexandrowicz and the reorientation of international law, Part I: Madras studies
Authors: Landauer Carl
Published: May 2020

This article analyses the prominent international legal historian, CH Alexandrowicz, known largely for his advocating of the East’s imprint on international law. It places his perspective of the East and South, and his diachronic narrative—the rise of naturalism, its fall to positivism, and eventual promise of return from positivism—in the context of his own traversing of geographies and his intellectual commitments, including his study of the Indian Constitution.
Posttraumatic Encapsulated Orbital Lipoma
Authors: Chorost Matthew S , Yakopson Vladimir , Chou Eva
Published: May 2020

A 43-year-old white male sought treatment for swelling of the left brow, which started after sustaining direct blunt trauma to the left bony orbit 6 months prior. Magnetic resonance imaging with contrast showed a 5.6 × 2.7 mm T1 bright focus at the anterior aspect of the left supraorbital rim. On the postgadolinium fat-saturated axial T1 images, the lesion demonstrated fat signal but was not suppressed in T1 with fat suppression. Upon excision, the lesion was found to be an encapsulated orbital rim lipoma, which was unexpected given the hyperintensity on T1 with fat suppressed magnetic resonance imaging. The lesion did not return after excision. Orbital lipomas are rare benign neoplasms with only a handful of cases in literature. This is the first report of a posttraumatic encapsulated lipoma presenting on the brow or orbit. Although rare, lipomas should be on the differential of post-traumatic lesions affecting the orbit and the orbital rim.
A Comparison of Improvised and Commercially Available Point-of-Wounding Tourniquets in Simulated Traumatic Amputation with Catastrophic Hemorrhage
Authors: Hay-David Aurélie G C , Herron Jonathan B T , Thurgood Andrew , Whittle Craig , Mahmood Ansar , Bodger Owen , Hodgetts Timothy J , Pallister Ian
Published: May 2020

Introduction

Catastrophic hemorrhage is the leading cause of preventable trauma deaths in the military and civilian populations. The use of tourniquets by first responders (medical and nonmedically trained) is supported and has the potential to save lives if applied correctly.

Aims

We sought to examine the use of 5 tourniquets: 1 improvised and 4 commercially available tourniquets to investigate the time taken to stop simulated bleeding and to secure the device; evidence of rebleeding when the “blood pressure” was restored and to gain qualitative feedback on their application.

Materials and Methods

Four commercially available tourniquets (Combat Application Tourniquet [C-A-T], Special Operations Forces Tactical Tourniquet - Wide (SOFTT-W), stretch, wrap, and tuck tourniquet [SWAT-T], and the Tourni-key) and an improvised tourniquet (tie & wooden spoon) were tested on a complex silicone simulation model used to replicate catastrophic hemorrhage from a blast injury with above traumatic knee amputation (SAM 4.1 Trauma Simulation Ltd, UK). To limit the user variability, the same investigator applied each tourniquet and each was tested 3 times. No ethical approval was required to conduct this study.

Results

None of the devices took longer than 1 minute to secure. The C-A-T and SOFTT-W were quickest to occlude and secure. Although the Tourni-key took longer statistically, this was unlikely to be a clinically important difference. Compared to the others, the SOFTT-W rebled on 2 out of 3 applications. The improvised tourniquet had an obvious ligature effect because of its narrowness, followed by the Tourni-key. This effect was least evident with the SWAT-T; however, particular care was needed to ensure it was safely secured as it was slippery when wet.

Conclusions

All tourniquets tested were effective and swift to apply. The Tourni-key’s antipinch card seems helpful in reducing local pain under the windlass. Reinspection for rebleeding is important and should be routinely performed irrespective of the device. The width of the SWAT-T may be beneficial, thereby, reducing the risk of crush injury.
New multilocus sequence typing primers to enable genotyping of AD hybrids within the Cryptococcus neoformans species complex
Authors: Cogliati Massimo , Roger Frederic , Meyer Wieland , Robert Vincent , Bertout Sébastien
Published: May 2020

Although AD hybrids within the Cryptococcus neoformans species complex represent about 20% of the isolates identified in Europe, phylogenetic and population genetic studies are lacking due to the inability to use the standardized typing method. The aim of the present study was to design new molecular type specific primers in order to apply the standard ISHAM consensus multilocus sequence typing (MLST) scheme to AD hybrids. The new primers are able to specifically amplify VNI and VNIV alleles of the seven MLST loci in both haploid and diploid or aneuploid hybrid strains. This study forms the basis for future molecular epidemiology studies of AD hybrids.

Lay abstract

We designed and tested new specific primers to amplify the two alleles of each of the seven MLST loci in C. neoformans species complex hybrids. The sequences obtained from hybrids can be compared with those present in the Cryptococcus global MLST database for future molecular epidemiology studies.
Pneumocystis jirovecii and microsporidia: An unusual coinfection in HIV patients?
Authors: de Armas Yaxsier , Capó Virginia , Bornay-Linares Fernando Jorge , del Águila Carmen , Matos Olga , Calderón Enrique J
Published: May 2020

Pneumocystis jirovecii and microsporidia species are recognized as opportunistic infectious pathogens in AIDS patients. Coinfection of both in one patient has been rarely reported. The aim of the present study was to investigate the coinfection of P. jirovecii and microsporidia in different tissues from AIDS deceased patients. Post mortem histological finding of P. jirovecii and microsporidia was demonstrated by means of the Grocott's methenamine silver and Brown Brenn staining, respectively. Molecular technique was used for identification and characterization of both fungi. Out of the 514 autopsied cases P. jirovecii and microsporidia species were identified in 53 (10.3%) and 62 (12.1%) cases respectively. A total of five cases (0.97%) coinfected with Pneumocystis and microsporidia were recovered from all analyzed autopsies. Coinfection of Pneumocystis and microsporidia is very challenging and raises interesting issues about host-parasite relationship. The early diagnosis of both pathogens must be crucial to establish correct and early treatments, improve the patient's evolution, reducing the risk of death.
Dynamical orbital classification of selected N-rich stars with Gaia Data Release 2 astrometry
Authors: Fernández-Trincado José G , Chaves-Velasquez Leonardo , Pérez-Villegas Angeles , Vieira Katherine , Moreno Edmundo , Ortigoza-Urdaneta Mario , Vega-Neme Luis
Published: May 2020

We have used the galaxy modelling algorithm gravpot16, to explore the most probable orbital elements of a sample of 64 selected N-rich stars across the Milky Way. We use the newly measured proper motions from Gaia Data Release 2 with existing line-of-sight velocities from the second generation of the Apache Point Observatory Galactic Evolution Experiment (APOGEE-2) and spectrophotometric distance estimations from starhorse. We adopted a set of high-resolution particle simulations evolved in the same steady-state Galactic potential model with a bar, in order to identify the groups of N-rich stars that have a high probability of belonging to the bulge/bar, disc and stellar halo component. We find that the vast majority of the N-rich stars show typically maximum height from the Galactic plane below 3 kpc, and develop eccentric orbits (e > 0.5), which means that these stars appear to have bulge/bar-like and/or halo-like orbits. We also show that ∼66 per cent of the selected N-rich stars currently reside in the inner Galaxy inside the corotation radius, whilst ∼ 14 per cent are in halo-like orbits. Among the N-rich stars in the inner Galaxy, ∼ 27 per cent share orbital properties in the boundary between bulge/bar and disc, depending on the bar pattern speeds. Our dynamical analysis also indicates that some of the N-rich stars are likely to be halo interlopers, which suggests that halo contamination is not insignificant within the bulge area.
Weak lensing measurement of filamentary structure with the SDSS BOSS and Subaru Hyper Suprime-Cam data
Authors: Kondo Hiroto , Miyatake Hironao , Shirasaki Masato , Sugiyama Naoshi , Nishizawa Atsushi J
Published: May 2020

We report the weak lensing measurement of filaments between Sloan Digital Sky Survey (SDSS) III/Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxy pairs at z ∼ 0.55, using the Subaru Hyper Suprime-Cam (HSC) first-year galaxy shape catalogue. Despite of the small overlap of 140 deg2 between these surveys, we detect the filament lensing signal at 3.9σ significance, which is the highest signal-to-noise lensing measurement of filaments between galaxy-scale haloes at this redshift range. We derive a theoretical prediction and covariance using mock catalogues based on full-sky ray-tracing simulations. We find that the intrinsic scatter of filament properties and the fluctuations in a large-scale structure along the line of sight are the primary component of the covariance and the intrinsic shape noise from source galaxies no longer limits our lensing measurement. This fact demonstrates the statistical power of the HSC survey due to its deep observations and high number density of source galaxies. Our result is consistent with the theoretical prediction and supports the ‘thick’ filament model. As the HSC survey area increases, we will be able to study detailed filament properties such as the dark matter distributions and redshift evolution of filaments.
Deep learning assisted data inspection for radio astronomy
Authors: Mesarcik Michael , Boonstra Albert-Jan , Meijer Christiaan , Jansen Walter , Ranguelova Elena , van Nieuwpoort Rob V
Published: May 2020

Modern radio telescopes combine thousands of receivers, long-distance networks, large-scale compute hardware, and intricate software. Due to this complexity, failures occur relatively frequently. In this work, we propose novel use of unsupervised deep learning to diagnose system health for modern radio telescopes. The model is a convolutional variational autoencoder (VAE) that enables the projection of the high-dimensional time–frequency data to a low-dimensional prescriptive space. Using this projection, telescope operators are able to visually inspect failures thereby maintaining system health. We have trained and evaluated the performance of the VAE quantitatively in controlled experiments on simulated data from HERA. Moreover, we present a qualitative assessment of the model trained and tested on real LOFAR data. Through the use of a naïve SVM classifier on the projected synthesized data, we show that there is a trade-off between the dimensionality of the projection and the number of compounded features in a given spectrogram. The VAE and SVM combination scores between 65 per cent and 90 per cent accuracy depending on the number of features in a given input. Finally, we show the prototype system-health-diagnostic web framework that integrates the evaluated model. The system is currently undergoing testing at the ASTRON observatory.
Evolutionary Genomics at the Human–Environment Interface in Africa
Authors: Svardal Hannes , Rusuwa Bosco , Linderoth Tyler , Kiran Anmol , Charmantier Anne , Lattorff H Michael G , Cagan Alex , Ommeh Sheila C , Kamng’ona Arox , Katongo Cyprian , Santos M Emília , Durbin Richard , Kumwenda Benjamin , Visscher Peter M , von der Heyden Sophie ,   and the Participants of SMBE Malawi
Published: May 2020

We report on the first meeting of SMBE in Africa. SMBE Malawi was initiated to bring together African and international researchers who use genetics or genomics to study natural systems impacted by human activities. The goals of this conference were 1) to reach a world-class standard of science with a large number of contributions from Africa, 2) to initiate exchange between African and international researchers, and 3) to identify challenges and opportunities for evolutionary genomics research in Africa. As repored, we think that we have achieved these goals and make suggestions on the way forward for African evolutionary genomics research.
Sarcopenia as a Prognostic Factor for 90-Day and Overall Mortality in Patients Undergoing Spine Surgery for Metastatic Tumors: A Multicenter Retrospective Cohort Study
Authors: Zakaria Hesham Mostafa , Wilkinson Brandon Michael , Pennington Zach , Saadeh Yamaan S , Lau Darryl , Chandra Ankush , Ahmed A Karim , Macki Mohamed , Anand Sharath Kumar , Abouelleil Mohamed A , Fateh Jibran A , Rick Jonathan W , Morshed Ramin A , Deng Hansen , Chen Kai-Yuan , Robin Adam , Lee Ian Y , Kalkanis Steven , Chou Dean , Park Paul , Sciubba Daniel M , Chang Victor
Published: May 2020

BACKGROUND

Novel methods in predicting survival in patients with spinal metastases may help guide clinical decision-making and stratify treatments regarding surgery vs palliative care.

OBJECTIVE

To evaluate whether the frailty/sarcopenia paradigm is predictive of survival and morbidity in patients undergoing surgery for spinal metastasis.

METHODS

A total of 271 patients from 4 tertiary care centers who had undergone surgery for spinal metastasis were identified. Frailty/sarcopenia was defined by psoas muscle size. Survival hazard ratios were calculated using multivariate analysis, with variables from demographic, functional, oncological, and surgical factors. Secondary outcomes included improvement of neurological function and postoperative morbidity.

RESULTS

Patients in the smallest psoas tertile had shorter overall survival compared to the middle and largest tertile. Psoas size (PS) predicted overall mortality more strongly than Tokuhashi score, Tomita score, and Karnofsky Performance Status (KPS). PS predicted 90-d mortality more strongly than Tokuhashi score, Tomita score, and KPS. Patients with a larger PS were more likely to have an improvement in deficit compared to the middle tertile. PS was not predictive of 30-d morbidity.

CONCLUSION

In patients undergoing surgery for spine metastases, PS as a surrogate for frailty/sarcopenia predicts 90-d and overall mortality, independent of demographic, functional, oncological, and surgical characteristics. The frailty/sarcopenia paradigm is a stronger predictor of survival at these time points than other standards. PS can be used in clinical decision-making to select which patients with metastatic spine tumors are appropriate surgical candidates.
Indoor Air Quality and Passive E-cigarette Aerosol Exposures in Vape-Shops
Authors: Son Yeongkwon , Giovenco Daniel P , Delnevo Cristine , Khlystov Andrey , Samburova Vera , Meng Qingyu
Published: May 2020

Introduction

Direct emissions of nicotine and harmful chemicals from electronic cigarettes (e-cigarettes) have been intensively studied, but secondhand and thirdhand e-cigarette aerosol (THA) exposures in indoor environments are understudied.

Aims and Methods

Indoor CO2, NO2, particulate matter (PM2.5), aldehydes, and airborne nicotine were measured in five vape-shops to assess secondhand exposures. Nicotine and tobacco-specific nitrosamines were measured on vape-shop surfaces and materials (glass, paper, clothing, rubber, and fur ball) placed in the vape-shops (14 days) to study thirdhand exposures.

Results

Airborne PM2.5, formaldehyde, acetaldehyde, and nicotine concentrations during shop opening hours were 21, 3.3, 4.0, and 3.8 times higher than the levels during shop closing hours, respectively. PM2.5 concentrations were correlated with the number of e-cigarette users present in vape-shops (ρ = 0.366–0.761, p < .001). Surface nicotine, 4-(N-methyl-N-nitrosamino)-4-(3-pyridyl)butanal (NNA), and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) were also detected at levels of 223.6 ± 313.2 µg/m2, 4.78 ± 11.8 ng/m2, and 44.8 ± 102.3 ng/m2, respectively. Substantial amounts of nicotine (up to 2073 µg/m2) deposited on the materials placed within the vape-shops, and NNA (up to 474.4 ng/m2) and NNK (up to 184.0 ng/m2) were also formed on these materials. The deposited nicotine concentrations were strongly correlated with the median number of active vapers present in a vape-shop per hour (ρ = 0.894–0.949, p = .04–.051). NNK levels on the material surfaces were significantly associated with surface nicotine levels (ρ=0.645, p = .037).

Conclusions

Indoor vaping leads to secondhand and THA exposures. Thirdhand exposures induced by e-cigarette vaping are comparable or higher than that induced by cigarette smoking. Long-term studies in various microenvironments are needed to improve our understanding of secondhand and THA exposures.

Implications

This study adds new convincing evidence that e-cigarette vaping can cause secondhand and THA exposures. Our findings can inform Occupational Safety and Health Administration, state authorities, and other government agencies regarding indoor air policies related to e-cigarette use, particularly in vape-shops. There is an urgent need to ensure that vape-shops maintain suitable ventilation systems and cleaning practices to protect customers, employees, and bystanders. Our study also demonstrates that nicotine can deposit or be adsorbed on baby’s clothes and toys, and that tobacco-specific nitrosamines can form and retain on baby’s clothes, highlighting children’s exposure to environmental e-cigarette aerosol and THA at home is of a particular concern.