bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’-type lung adenocarcinomas
Authors: Hamada Kenichi , Tian Ying , Fujimoto Mao , Takahashi Yoriko , Kohno Takashi , Tsuta Koji , Watanabe Shun-ichi , Yoshida Teruhiko , Asamura Hisao , Kanai Yae , Arai Eri
Published: October 2020

Although some previous studies have examined epigenomic alterations in lung adenocarcinomas, correlations between epigenomic events and genomic driver mutations have not been fully elucidated. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of adjacent normal lung tissue (N) and the corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF and HER2 and fusions involving ALK, RET and ROS1, were examined. DNA methylation levels in 12 629 probes from N samples were significantly correlated with recurrence-free survival. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver aberrations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups. After small interfering RNA knockdown of ZNF132, which showed DNA hypermethylation only in the pan-negative group and was correlated with vascular invasion, the proliferation, apoptosis and migration of cancer cell lines were examined. ZNF132 knockdown led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’ lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression.
Human Brain Ages With Hierarchy-Selective Attenuation of Prediction Errors
Authors: Hsu Yi-Fang , Waszak Florian , Strömmer Juho , Hämäläinen Jarmo A
Published: October 2020

From the perspective of predictive coding, our brain embodies a hierarchical generative model to realize perception, which proactively predicts the statistical structure of sensory inputs. How are these predictive processes modified as we age? Recent research suggested that aging leads to decreased weighting of sensory inputs and increased reliance on predictions. Here we investigated whether this age-related shift from sensorium to predictions occurs at all levels of hierarchical message passing. We recorded the electroencephalography responses with an auditory local–global paradigm in a cohort of 108 healthy participants from 3 groups: seniors, adults, and adolescents. The detection of local deviancy seems largely preserved in older individuals at earlier latency (including the mismatch negativity followed by the P3a but not the reorienting negativity). In contrast, the detection of global deviancy is clearly compromised in older individuals, as they showed worse task performance and attenuated P3b. Our findings demonstrate that older brains show little decline in sensory (i.e., first-order) prediction errors but significant diminution in contextual (i.e., second-order) prediction errors. Age-related deficient maintenance of auditory information in working memory might affect whether and how lower-level prediction errors propagate to the higher level.
Transfer of Odor Perception From the Retronasal to the Orthonasal Pathway
Authors: He Rui , Dukes Talicia C , Kay Leslie M
Published: October 2020

Although orthonasal odorants are often associated with the external environment, retronasal odorants are accompanied by consummatory behaviors and indicate an internal state of an animal. Our study aimed to examine whether the same odorants may generate a consistent perceptual experience when 2 olfactory routes potentiate variations in concentration in the nasal cavity and orosensory activation. A customized lick spout with vacuum removing odorants around the animal’s nares was used to render a pure retronasal exposure experience. We found that pre-exposing rats to odorants retronasally with positive or negative reinforcers (sweet or bitter) lead to a significant learning rate difference between high- and low-vapor-pressure odorants. This effect was not observed for novel odorants, suggesting that odorants may generate similar perceptual quality in a volatility-dependent manner.
Invasive Pneumococcal Strain Distributions and Isolate Clusters Associated With Persons Experiencing Homelessness During 2018
Authors: Metcalf Benjamin J , Chochua Sopio , Walker Hollis , Tran Theresa , Li Zhongya , Varghese Jasmine , Snippes Vagnone Paula M , Lynfield Ruth , McGee Lesley , Li Yuan , Pilishvili Tamara , Beall Bernard
Published: October 2020

Background

We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the United States during 2018 and examine within-serotype propensities of isolates to form related clusters.

Methods

We predicted strain features using whole genome sequencing obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention’s Active Bacterial Core surveillance (ABCs), which has a surveillance population of approximately 34.5 million individuals distributed among 10 states. Phylogenetic analysis was provided for serotypes accounting for ≥27 isolates.

Results

Thirteen-valent pneumococcal conjugate vaccine (PCV13) serotypes together with 6C accounted for 23 of 105 (21.9%) of isolates from children aged <5 years and 820 of 2780 (29.5%) isolates from those aged ≥5 years. The most common serotypes from adult IPD isolates were serotypes 3 (413/2780 [14.9%]), 22F (291/2780 [10.5%]), and 9N (191/2780 [6.9%]). Among child IPD isolates, serotypes 15BC (18/105 [17.1%]), 3 (11/105 [10.5%]), and 33F (10/105 [9.5%]) were most common. Serotypes 4, 12F, 20, and 7F had the highest proportions of isolates that formed related clusters together with the highest proportions of isolates from persons experiencing homelessness (PEH). Among 84 isolates from long-term care facilities, 2 instances of highly related isolate pairs from co-residents were identified.

Conclusions

Non-PCV13 serotypes accounted for >70% of IPD in ABCs; however, PCV13 serotype 3 is the most common IPD serotype overall. Serotypes most common among PEH were more often associated with temporally related clusters identified both among PEH and among persons not reportedly experiencing homelessness.
Coronavirus Disease 2019 (COVID-19) Seropositivity and Asymptomatic Rates in Healthcare Workers Are Associated with Job Function and Masking
Authors: Sims Matthew D , Maine Gabriel N , Childers Karen Lins , Podolsky Robert H , Voss Daniel R , Berkiw-Scenna Natalie , Oh Joyce , Heinrich Kevin E , Keil Hans , Kennedy Richard H , Homayouni Ramin
Published: October 2020

Background

Although the risk of exposure to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is higher for frontline healthcare workers, not all personnel have similar risks. Determining infection rate is difficult due to the limits on testing and the high rate of asymptomatic individuals. Detection of antibodies against SARS-CoV-2 may be useful for determining prior exposure to the virus and assessing mitigation strategies, such as isolation, masks, and other protective equipment.

Methods

An online assessment that included demographic, clinical, and exposure information and a blood sample was collected from 20 614 participants out of ~43 000 total employees at Beaumont Health, which includes 8 hospitals distributed across the Detroit metropolitan area in southeast Michigan. The presence of anti-SARS-CoV-2 IgG was determined using the EUROIMMUN assay.

Results

A total of 1818 (8.8%) participants were seropositive between April 13 and May 28, 2020. Among the seropositive individuals, 44% reported that they were asymptomatic during the month prior to blood collection. Healthcare roles such as phlebotomy, respiratory therapy, and nursing/nursing support exhibited significantly higher seropositivity. Among participants reporting direct exposure to a Coronavirus Disease 2019 (COVID-19) positive individual, those wearing an N95/PAPR mask had a significantly lower seropositivity rate (10.2%) compared to surgical/other masks (13.1%) or no mask (17.5%).

Conclusions

Direct contact with COVID-19 patients increased the likelihood of seropositivity among employees but study participants who wore a mask during COVID-19 exposures were less likely to be seropositive. Additionally, a large proportion of seropositive employees self-reported as asymptomatic. (Funded by Beaumont Health and by major donors through the Beaumont Health Foundation)

ClinicalTrials.gov number

NCT04349202
Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability
Authors: Haro-Moreno Jose M , Coutinho Felipe Hernandes , Zaragoza-Solas Asier , Picazo Antonio , Almagro-Moreno Salvador , López-Pérez Mario
Published: October 2020

The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.
Transcriptional analysis of metabolic and virulence genes associated with biofilm formation in Piscirickettsia salmonis strains
Authors: Zúñiga A , Solis C , Cartes C , Nourdin G , Yañez A , Romero A , Haussmann D , Figueroa J
Published: October 2020

Piscirickettsia salmonis is a facultative intracellular bacterium that generates piscirickettsiosis affecting salmonids in Chile. The bacterium has the adaptability to survive in the marine environment under multiple stressful conditions. In this sense, this work focused on the analysis of a gene battery associated with biofilm formation under different culture conditions and on the adaptability of this biofilm to different media. The results indicated that the strains LF-89, IBM-034 and IBM-040 were strong biofilm producers, evidencing adaptability to the media by increasing the amount of biofilm through successive growths. Transcript levels of six genes described in various bacteria and P. salmonis, considered to have metabolic functions, and playing a relevant role in biofilm formation, were analyzed to evaluate bacterial functionality in the biofilm. The genes mazE-mazF, implicated in biofilm and stress, were markedly overexpressed in the biofilm condition in the three strains. For its part, gene gltA, an indicator of metabolic activity and related to virulence inhibition in Salmonella typhimurium, also seems to restrain the pathogenesis process in P. salmonis by inhibiting the expression of the virulence-associated genes liso and tcf. Finally, the expression of the glnA gene suggests the use of glutamine as an essential element for the growth of the biofilm.
Energy, environment and economic analyses of a parabolic trough concentrating photovoltaic/thermal system
Authors: Alayi Reza , Kumar Ravinder , Seydnouri Syed Reza , Ahmadi Mohammad Hossein , Issakhov Alibek
Published: October 2020

The present study deals with the techno-economic and environmental analysis of a parabolic trough concentrating photovoltaic/thermal system. Energy, economic and environmental issues of the purposed system have been evaluated and analyzed. The MATLAB software has been used for modeling. The outputs of this software include the amount of energy and electrical productions as well as environmental parameters for different studied areas. Finally, economic analysis and energy savings have been performed to persuade the use of this type of technology to supply the various loads of a building. One of the most important results of this study is the production of 222 060 kW of thermal and electrical energy in Bushehr, which is the largest amount of production among cities and saves energy and revenue from the sale of this amount of energy—231 983 kW and 38 533.24$, respectively. A comparative environmental analysis represents that the largest prevention of CO2 emissions is found in Bushehr with 515 tons per year and the lowest prevention of CO2 is related to Rasht with 34 tons.
Antidepressive Effect of Antipsychotics in the Treatment of Schizophrenia: Meta-Regression Analysis of Randomized Placebo-Controlled Trials
Authors: Miura Itaru , Nosaka Tadashi , Yabe Hirooki , Hagi Katsuhiko
Published: October 2020

Background

Antipsychotics improve the positive symptoms of schizophrenia. However, little is known about the extent of antidepressive effects of antipsychotics and their correlation with effects on other symptom domains in schizophrenia. The aim was to investigate whether antidepressive effects of antipsychotics have a significant correlation with the effects on specific symptom domains of schizophrenia.

Methods

Electronic databases were searched to identify eligible studies that reported antidepressive effects of antipsychotics for the treatment of adult patients with schizophrenia in double-blind, randomized placebo-controlled trials (RCTs). Mean change from baseline in depressive symptoms was meta-analyzed, and the correlation with the effects on other symptom domains was examined through meta-regression analysis.

Results

Thirty-five RCTs (13 890 patients) were included in this meta-analysis. Overall, antipsychotics showed greater efficacy than placebo in reducing depressive symptoms, with small to medium effect sizes (standardized mean difference = −0.27, 95% confidence interval −0.32 to −0.22, P < .001). All the antipsychotics, except for chlorpromazine, haloperidol, and ziprasidone, were associated with significantly greater decreases in depressive symptoms compared with placebo (standardized mean difference = −0.19 to −0.40). A higher antidepressive effect was significantly correlated with a higher improvement in Positive and Negative Syndrome Scale/Brief Psychiatric Rating Scale total, positive, and negative, and Positive and Negative Syndrome Scale-general psychopathology symptoms (β = .618, P < .001; β = .476, P < .001; β = .689, P < .001; β = .603, P < .001, respectively).

Conclusions

Second-generation antipsychotics (except for ziprasidone) were associated with small to medium effects sizes on improvement in depressive symptoms among adult patients with schizophrenia. The antidepressive effect of antipsychotics was significantly correlated with improvement in other symptom domains, with the highest correlation observed for improvement in negative symptoms.

PROSPERO registration number

CRD42019133015
Long-term efficacy of dolutegravir plus lamivudine for maintenance of HIV viral suppression in adults with and without historical resistance to lamivudine: Week 96 results of ART-PRO pilot study
Authors: Rial-Crestelo David , de Miguel Rosa , Montejano Rocío , Dominguez-Dominguez Lourdes , Aranguren-Rivas Paula , Esteban-Cantos Andrés , Bisbal Otilia , Santacreu-Guerrero Mireia , Garcia-Alvarez Mónica , Alejos Belén , Hernando Asunción , Bermejo-Plaza Laura , Cadiñanos Julen , Mayoral Mario , Castro Juan Miguel , Moreno Victoria , Martin-Carbonero Luz , Delgado Rafael , Rubio Rafael , Pulido Federico , Arribas José Ramón ,   ART-PRO, Arribas J R , Buckley R De Miguel , Montejano R , Esteban-Cantos A , Stella-Ascariz N , Cadiñanos J , Mayoral M , Castro J M , Moreno V , Martin-Carbonero L , Valencia E , Bernardino I , Busca C , Micán R , Pérez-Valero I , González J , Montes ML , Centeno J Rodríguez ,   PI16/00837-PI16/00678 study group, Pulido F , Rial-Crestelo D , Dominguez-Dominguez L , Aranguren-Rivas P , Bisbal O , Plaza L Bermejo , Garcia-Alvarez M , Santacreu-Guerrero M , de Lagarde M , Matarranz M , Luzckoviak J , Sotillo A , Delgado R , Rubio R
Published: October 2020

Background

In the ART-PRO pilot trial there were no virological failures through 48 weeks of treatment with dolutegravir plus lamivudine in suppressed individuals with and without archived lamivudine resistance-associated mutations (RAMs) detected through next-generation sequencing (NGS) but without evidence of lamivudine RAMs in baseline proviral DNA population sequencing.

Objectives

To present 96 week results from ART-PRO.

Methods

Open-label, single-arm pilot trial. At baseline, all participants switched to dolutegravir plus lamivudine. Participants were excluded if proviral DNA population genotyping detected lamivudine RAMs. To detect resistance minority variants, proviral DNA NGS was retrospectively performed from baseline samples. For this analysis the efficacy endpoint was the proportion of participants with <50 HIV-1 RNA copies/mL at week 96. Safety and tolerability outcomes were incidence of adverse events and treatment discontinuations.

Results

Forty-one participants were included, 21 with lamivudine RAMs in historical plasma RNA genotypes. Baseline proviral DNA NGS detected lamivudine RAMs (M184V/I and/or K65R/E/N) above a 5% threshold in 71.4% (15/21) and 15% (3/20) of participants with and without history of lamivudine resistance, respectively. At 96 weeks, 90.2% of participants achieved the efficacy endpoint. Between week 48 and 96 there was one discontinuation due to consent withdrawal and no discontinuations related to adverse events. Two participants had a transient viral rebound, both re-suppressed on dolutegravir plus lamivudine. Through week 96, there were no virological failures.

Conclusions

In this pilot trial, dolutegravir plus lamivudine maintained virological suppression at 96 weeks despite historical lamivudine resistance and persisting archived minority lamivudine RAMs.
Evaluation of Two-Leaf Sampling Units to Estimate Sugarcane Aphid (Hemiptera: Aphididae) Economic Thresholds in Commercial Grain Sorghum
Authors: Lindenmayer Jessica C , Payton Mark , Giles Kris L , Elliott Norman C , Knutson Allen E , Bowling Robert , Seiter Nicholas J , McCornack Brian , Brown Sebe A , Royer Tom A
Published: October 2020

Sugarcane aphid Melanaphis sacchari Zehntner is a significant economic pest of grain sorghum in the United States. Effective monitoring and early detection are cornerstones for managing invasive pests. The recently developed binomial sequential sampling plan estimates sugarcane aphid economic thresholds (ETs) based on classification whether a 2-leaf sample unit has ≤ or ≥ 50 M. sacchari. In this study, we evaluated eight 2-leaf sampling units for potential use in the sequential sampling plan. From 2016 through 2017, whole plant counts of M. sacchari were recorded non-destructively in situ on sorghum plants from 140 fields located in five states. Plant canopies were stratified into three categories. Two leaves from each stratum were used to compare linear relationships between M. sacchari numbers per two-leaf sample unit and total M. sacchari density per plant. Analysis revealed that two randomly selected leaves from the middle stratum accounted more variation for estimating M. sacchari density when compared to two leaves from the other strata. Comparison of eight two-leaf sampling units within plant growth stages were variable in quantifying variation of M. sacchari densities. When growth stages were combined, the standard uppermost + lowermost leaf sample unit and a unit consisting of two randomly selected leaves from the middle stratum revealed little difference in their enumeration of variation in M. sacchari density. Because other sample units were either less predictive and/or more variable in estimating M. sacchari density, we suggest that the (L1+U1) sample unit remain the preferred method for appraising M. sacchari ETs.
Effects of Human Settlements and Spatial Distribution of Wing Vein Length, Wing Fray Categories and Hunger Stages in Glossina morsitans morsitans (Diptera: Glossinidae) and Glossina pallidipes (Diptera: Glossinidae) in Areas Devoid of Cattle in North-Eastern Zambia
Authors: Chilongo Kalinga , Manyangadze Tawanda , Mukaratirwa Samson
Published: October 2020

The effect of human-associated habitat degradation on tsetse populations is well established. However, more insights are needed into how gradual human encroachment into tsetse fly belts affect tsetse populations. This study investigated how wing vein length, wing fray categories, and hunger stages, taken as indicators of body size, age, and levels of access to hosts, respectively, in Glossina morsitans morsitans Westwood (Diptera: Glossinidae) and Glossina pallidipes Austen (Diptera: Glossinidae), varied along a transect from the edge into inner parts of the tsetse belt, in sites that had human settlement either concentrated at the edge of belt or evenly distributed along transect line, in north-eastern Zambia. Black-screen fly round and Epsilon traps were used in a cross-sectional survey on tsetse flies at three sites, following a transect line marked by a road running from the edge into the inner parts of the tsetse belt, per site. Two sites had human settlement concentrated at or close to the edge of the tsetse belt, whereas the third had human settlement evenly distributed along the transect line. Where settlements were concentrated at the edge of tsetse belt, increase in distance from the settlements was associated with increase in wing vein length and a reduction in the proportion of older, and hungry, tsetse flies. Increase in distance from human settlements was associated with improved tsetse well-being, likely due to increase in habitat quality due to decrease in effects of human activities.
Antimullerian Hormone as a Serum Biomarker for Risk of Chemotherapy-Induced Amenorrhea
Authors: Ruddy Kathryn J , Schaid Daniel J , Batzler Anthony , Cecchini Reena S , Partridge Ann H , Norman Aaron , Fehrenbacher Louis , Stewart Elizabeth A , Trabuco Emanuel , Ginsburg Elizabeth , Couch Fergus J , Fasching Peter A , Vachon Celine , Ganz Patricia A
Published: October 2020

Antimullerian hormone (AMH) is a promising biomarker for ovarian reserve. In this study, we assessed AMH before and 1 year after initiation of adjuvant chemotherapy on National Surgical Adjuvant Breast and Bowel Project (NSABP)/NRG Oncology B-47 in female participants aged 42 years and younger (median age = 39 years). At baseline, median AMH was 1.2 ng/mL; 13 (4.7%) values were less than 0.1 ng/mL (the threshold for detectable levels, in the perimenopause and menopause range), and 57 values (20.6%) were less than 0.5 ng/mL. At 1 year, 215 (77.6%) were less than 0.1 ng/mL, and 264 (95.3%) were less than 0.5 ng/mL. Postchemotherapy menses were reported by 46.2% of participants. Multivariable logistic regression found that the odds of having postchemotherapy menses increased with younger age, higher body mass index, and higher prechemotherapy AMH, but not by trastuzumab administration or by the choice of chemotherapy (doxorubicin-cyclophosphamide followed by paclitaxel vs docetaxel-cyclophosphamide). We conclude that higher prechemotherapy AMH predicts a lower risk of chemotherapy-induced amenorrhea and that AMH 1 year after chemotherapy initiation is not informative in this setting because it is likely to be very low.
Minimally invasive esophagectomy with intrathoracic anastomosis in a situs inversus totalis patient
Authors: Meng Yunchong , Xiao Han , Zhang Zheng , Li Kuo , Huang Quanfu , Qiu Wenlin , Liao Yongde
Published: October 2020

Situs inversus totalis (SIT) is a rare congenital condition, which is characterized by abnormal placement of the thoracic and abdominal organs. The incidence of this condition is estimated to be from 1/8000 to 1/25,000. There have been minimal reports on SIT patients with esophageal cancer. In this report, we discuss a patient with SIT complicated by middle and lower esophageal cancer who underwent laparoscopic and thoracoscopic esophagectomy with intrathoracic anastomosis, and provide useful information with regards to treatment of this rare condition.
Two new cases of pediatric tumoral calcinosis
Authors: Rajaonarison Ny Ony Narindra Lova Hasina , Nirinaharimanitra Vatosoa Sarobidy , Hunald Francis Allen , Ahmad Ahmad
Published: October 2020

Tumoral calcinosis (TC) is a rare benign pathology, particularly in pediatrics. It is difficult to diagnose with its pathophysiology poorly understood. We report two pediatric cases of TC having benefited from radiological assessments and surgical excision. Final diagnosis was made by pathological examination. For the two cases, no sign of recurrence was noted ~30 months of follow-up.
CRISPR-Based Approaches for Efficient and Accurate Detection of SARS-CoV-2
Authors: Zhang Wancun , Liu Kangbo , Zhang Pin , Cheng Weyland , Li Linfei , Zhang Fan , Yu Zhidan , Li Lifeng , Zhang Xianwei
Published: October 2020

An outbreak of COVID-19, caused by infection with SARS-CoV-2 in Wuhan, China in December 2019, spread throughout the country and around the world, quickly. The primary detection technique for SARS-CoV-2, the reverse-transcription polymerase chain reaction (RT-PCR)–based approach, requires expensive reagents and equipment and skilled personnel. In addition, for SARS-CoV-2 detection, specimens are usually shipped to a designated laboratory for testing, which may extend the diagnosis and treatment time of patients with COVID-19. The latest research shows that clustered regularly interspaced short palindromic repeats (CRISPR)–based approaches can quickly provide visual, rapid, ultrasensitive, and specific detection of SARS-CoV-2 at isothermal conditions. Therefore, CRISPR-based approaches are expected to be developed as attractive alternatives to conventional RT-PCR methods for the efficient and accurate detection of SARS-CoV-2. Recent advances in the field of CRISPR-based biosensing technologies for SARS-CoV-2 detection and insights into their potential use in many applications are reviewed in this article.
Turbulent dissipation, CH+ abundance, H2 line luminosities, and polarization in the cold neutral medium
Authors: Moseley Eric R , Draine B T , Tomida Kengo , Stone James M
Published: October 2020

In the cold neutral medium, high out-of-equilibrium temperatures are created by intermittent dissipation processes, including shocks, viscous heating, and ambipolar diffusion. The high-temperature excursions are thought to explain the enhanced abundance of CH+ observed along diffuse molecular sightlines. Intermittent high temperatures should also have an impact on H2 line luminosities. We carry out simulations of magnetohydrodynamic (MHD) turbulence in molecular clouds including heating and cooling, and post-process them to study H2 line emission and hot-gas chemistry, particularly the formation of CH+. We explore multiple magnetic field strengths and equations of state. We use a new H2 cooling function for $n_{\text{H}}\le 10^5\, {\text{cm}}^{-3}$, $T\le 5000\, {\text{K}}$, and variable H2 fraction. We make two important simplifying assumptions: (i) the H2/H fraction is fixed everywhere and (ii) we exclude from our analysis regions where the ion–neutral drift velocity is calculated to be greater than 5 km s−1. Our models produce H2 emission lines in accord with many observations, although extra excitation mechanisms are required in some clouds. For realistic root-mean-square (rms) magnetic field strengths (≈10 μG) and velocity dispersions, we reproduce observed CH+ abundances. These findings contrast with those of Valdivia et al. (2017) Comparison of predicted dust polarization with observations by Planck suggests that the mean field is ≳5 µG, so that the turbulence is sub-Alfvénic. We recommend future work treating ions and neutrals as separate fluids to more accurately capture the effects of ambipolar diffusion on CH+ abundance.
Binary population synthesis with probabilistic remnant mass and kick prescriptions
Authors: Mandel Ilya , Müller Bernhard , Riley Jeff , de Mink Selma E , Vigna-Gómez Alejandro , Chattopadhyay Debatri
Published: October 2020

We report on the impact of a probabilistic prescription for compact remnant masses and kicks on massive binary population synthesis. We find that this prescription populates the putative mass gap between neutron stars and black holes with low-mass black holes. However, evolutionary effects reduce the number of X-ray binary candidates with low-mass black holes, consistent with the dearth of such systems in the observed sample. We further find that this prescription is consistent with the formation of heavier binary neutron stars such as GW190425, but overpredicts the masses of Galactic double neutron stars. The revised natal kicks, particularly increased ultra-stripped supernova kicks, do not directly explain the observed Galactic double neutron star orbital period–eccentricity distribution. Finally, this prescription allows for the formation of systems similar to the recently discovered extreme mass ratio binary GW190814, but only if we allow for the survival of binaries in which the common envelope is initiated by a donor crossing the Hertzsprung gap, contrary to our standard model.
The orbital evolution of UFDs and GCs in an evolving Galactic potential
Authors: Armstrong Benjamin M , Bekki Kenji , Ludlow Aaron D
Published: October 2020

We use the second Gaia data release to investigate the kinematics of 17 ultra-faint dwarf galaxies (UFDs) and 154 globular clusters (GCs) in the Milky Way, focusing on the differences between static and evolving models of the Galactic potential. An evolving potential modifies a satellite’s orbit relative to its static equivalent, though the difference is small compared to existing uncertainties on orbital parameters. We find that the UFD Boötes II is likely on its first passage around the Milky Way. Depending on the assumed mass of the Milky Way, the UFDs Triangulum II, Hydrus I, Coma Berenices, Draco II, and Ursa Major II, as well as the GC Pyxis, may also be on first infall so may be useful for constraining the mass of the Galaxy. We identify a clear kinematic distinction between metal-rich ([Fe/H] > −1.1) and metal-poor GCs ([Fe/H] ≤ −1.1). Although most metal-rich clusters occupy predominately prograde orbits, with low eccentricities (e ≈ 0.35) and similar specific angular momenta and orbital planes as the Galactic disc, seven show potentially retrograde orbits, the origin of which is unclear. Metal-poor clusters have more diverse orbits, higher eccentricities (e ≈ 0.65), and half of them have orbital planes offset from the disc by 60° to 120°—twice as many as the metal-poor GCs. The UFDs have similar θ and ϕ to the metal-poor GCs, suggesting a similar origin. We provide a catalogue of orbital parameters for UFDs and GCs for two different Galaxy masses and their observational uncertainties.
Non-Piecemeal Pluralism
Authors: Miller Elizabeth
Published: October 2020

I argue that Schaffer fails to provide a non-question-begging argument for priority monism. Despite his suggestion to the contrary, Humean pluralists need not, and plausibly do not, endorse his tiling constraint on metaphysically basic objects. Moreover, the distinction between supervenience—of the sort at issue in Humean doctrine—and metaphysical necessitation—of the sort at issue in Schaffer’s tiling constraint—points toward an alternative treatment of the phenomena initially inspiring Schafferian monism. There is an important possibility, one that Humeans can or should embrace, that Schaffer overlooks when drawing his monistic conclusion.
Lepus europaeus(Lagomorpha: Leporidae)
Authors: Bock Anni
Published: October 2020

Lepus europaeus Pallas, 1778, commonly called the European hare, is one of 32 species of Lepus. It is widely distributed in Europe and Asia where it was not native but introduced by humans for sport. L. europaeus does not burrow, nor hibernate, and gives birth to precocial young (leverets). It prefers open grassland, fields, agricultural farmland, and pastures with hedgerows and bushes. Declining populations in several countries since the 1960s led to increased research to investigate the reasons; L. europaeus is considered threatened in several countries, but of “Least Concern” by the International Union for Conservation of Nature and Natural Resources.
OrthoDB in 2020: evolutionary and functional annotations of orthologs
Authors: Zdobnov Evgeny M , Kuznetsov Dmitry , Tegenfeldt Fredrik , Manni Mosè , Berkeley Matthew , Kriventseva Evgenia V
Published: October 2020

OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number of available organisms. OrthoDB is leading in the coverage and genomic diversity sampling of Eukaryotes, Prokaryotes and Viruses, and the sampling of Bacteria is further set to increase three-fold. The user interface has been enhanced in response to the massive growth in data. OrthoDB provides three views on the data: (i) a list of orthologous groups related to a user query, which are now arranged to visualize their hierarchical relations, (ii) a detailed view of an orthologous group, now featuring a Sankey diagram to facilitate navigation between the levels of orthology, from more finely-resolved to more general groups of orthologs, as well as an arrangement of orthologs into an interactive organism taxonomy structure, and (iii) we added a gene-centric view, showing the gene functional annotations and the pair-wise orthologs in example species. The OrthoDB standalone software for delineation of orthologs, Orthologer, is freely available. Online BUSCO assessments and mapping to OrthoDB of user-uploaded data enable interactive exploration of related annotations and generation of comparative charts. OrthoDB strives to predict orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations, and to compute evolutionary annotations such as evolutionary rate and phyletic profile. OrthoDB data can be assessed via SPARQL RDF, REST API, downloaded or browsed online from https://orthodb.org.
ATACdb: a comprehensive human chromatin accessibility database
Authors: Wang Fan , Bai Xuefeng , Wang Yuezhu , Jiang Yong , Ai Bo , Zhang Yong , Liu Yuejuan , Xu Mingcong , Wang Qiuyu , Han Xiaole , Pan Qi , Li Yanyu , Li Xuecang , Zhang Jian , Zhao Jun , Zhang Guorui , Feng Chenchen , Zhu Jiang , Li Chunquan
Published: October 2020

Accessible chromatin is a highly informative structural feature for identifying regulatory elements, which provides a large amount of information about transcriptional activity and gene regulatory mechanisms. Human ATAC-seq datasets are accumulating rapidly, prompting an urgent need to comprehensively collect and effectively process these data. We developed a comprehensive human chromatin accessibility database (ATACdb, http://www.licpathway.net/ATACdb), with the aim of providing a large amount of publicly available resources on human chromatin accessibility data, and to annotate and illustrate potential roles in a tissue/cell type-specific manner. The current version of ATACdb documented a total of 52 078 883 regions from over 1400 ATAC-seq samples. These samples have been manually curated from over 2200 chromatin accessibility samples from NCBI GEO/SRA. To make these datasets more accessible to the research community, ATACdb provides a quality assurance process including four quality control (QC) metrics. ATACdb provides detailed (epi)genetic annotations in chromatin accessibility regions, including super-enhancers, typical enhancers, transcription factors (TFs), common single-nucleotide polymorphisms (SNPs), risk SNPs, eQTLs, LD SNPs, methylations, chromatin interactions and TADs. Especially, ATACdb provides accurate inference of TF footprints within chromatin accessibility regions. ATACdb is a powerful platform that provides the most comprehensive accessible chromatin data, QC, TF footprint and various other annotations.
Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals
Authors: Liu Jianheng , Huang Tao , Zhang Yusen , Zhao Tianxuan , Zhao Xueni , Chen Wanying , Zhang Rui
Published: October 2020

mRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a downstream G-rich triplet motif and are computationally predicted to be located at the 5′ end of putative hairpin structures, are methylated by NSUN2. Type II m5C sites contain a downstream UCCA motif and are computationally predicted to be located in the loops of putative hairpin structures. However, their biogenesis remains unknown. Here we identified NSUN6, a methyltransferase that is known to methylate C72 of tRNAThr and tRNACys, as an mRNA methyltransferase that targets Type II m5C sites. Combining the RNA secondary structure prediction, miCLIP, and results from a high-throughput mutagenesis analysis, we determined the RNA sequence and structural features governing the specificity of NSUN6-mediated mRNA methylation. Integrating these features into an NSUN6-RNA structural model, we identified an NSUN6 variant that largely loses tRNA methylation but retains mRNA methylation ability. Finally, we revealed a weak negative correlation between m5C methylation and translation efficiency. Our findings uncover that mRNA m5C is tightly controlled by an elaborate two-enzyme system, and the protein-RNA structure analysis strategy established may be applied to other RNA modification writers to distinguish the functions of different RNA substrates of a writer protein.
Secondhand Smoke Exposure at Home and/or in a Vehicle: Differences Between Urban and Non-Urban Adolescents in the United States, From 2015 to 2018
Authors: Mantey Dale S , Omega-Njemnobi Onyinye , Barroso Cristina S
Published: October 2020

Introduction

Secondhand smoke exposure during adolescence is linked to increased risk for cigarette smoking susceptibility and initiation. Non-urban youth may encounter a disproportionate number social and environmental risk factors for secondhand smoke exposure. Research is needed to explore geographic disparities in secondhand smoke exposure.

Aims and Methods

Four years of National Youth Tobacco Survey (2015–2018) data were pooled. Participants were 69 249 middle and high school students. Multivariable logistic regression examined the relationship between geographic region and secondhand smoke exposure (1) at home and (2) in a vehicle. A multivariable, multinomial logistic regression examined the relationship between geographic region and number of sources of secondhand smoke exposure (ie, 0, 1 source, 2 sources). Covariates included sex, race/ethnicity, grade level, past 30-day tobacco use, and living with a tobacco user.

Results

From 2015 to 2018, ~28.4% of middle and high school students reported secondhand smoke exposure either at home, in a vehicle, or both. Non-urban youth had greater odds of reporting secondhand smoke exposure at home (Adj OR: 1.26; 95% CI: 1.15 to 1.38) and in a vehicle (Adj OR: 1.50; 95% CI: 1.35 to 1.65), compared with urban youth. Similarly, non-urban youth had greater odds of reporting secondhand smoke exposure via one source (RRR: 1.21; 95% CI: 1.11 to 1.31) and two sources (RRR: 1.61; 95% CI: 1.42 to 1.82), relative to no exposure, than urban youth.

Conclusion

Secondhand smoke exposure at home and/or in a vehicle varies across geographic region. Targeted interventions should be developed and implemented to reduce secondhand smoke exposure among at-risk youth.

Implications

Findings showcase the need to address secondhand smoke exposure in non-urban areas and how it impacts adolescents. Public health interventions and regulatory policies aimed at improving social norms and expanding health infrastructure in rural communities should be designed and implemented in order to prevent and reduce secondhand smoke exposure among non-urban youth.
Raising ethnicity recording in NHS Lothian from 3% to 90% in 3 years: processes and analysis of data from Accidents and Emergencies
Authors: Davidson Emma M , Douglas Anne , Villarroel Nazmy , Dimmock Katy , Gorman Dermot , Bhopal Raj S
Published: October 2020

Background

The disproportionate burden of COVID-19 on ethnic minority populations has recently highlighted the necessity of maintaining accessible, routinely collected, ethnicity data within healthcare services. Despite 25 years of supportive legislation and policy in the UK, ethnicity data recording remains inconsistent, which has hindered needs assessment, evaluation and decision-making. We describe efforts to improve the completeness, quality and usage of ethnicity data within our regional health board, NHS Lothian.

Methods

The Ethnicity Coding Task Force was established with the aim of increasing ethnicity recording within NHS Lothian secondary care services from 3 to 90% over 3 years. We subsequently analysed these data specifically focusing on Accident and Emergency (A&E) use by ethnic group.

Results

We achieved 91%, 85% and 93% completeness of recording across inpatients, outpatients and A&E, respectively. Analysis of A&E data found a mixed pattern of attendance amongst ethnic minority populations and did not support the commonly perceived relationship between lower GP registration and higher A&E use within this population.

Conclusions

We identified a successful approach to increase ethnicity recording within a regional health board, which could potentially be useful in other settings, and demonstrated the utility of these data in informing assessment of healthcare delivery and future planning.
The role of metrics in peer assessments
Authors: Langfeldt Liv , Reymert Ingvild , Aksnes Dag W
Published: October 2020

Metrics on scientific publications and their citations are easily accessible and are often referred to in assessments of research and researchers. This paper addresses whether metrics are considered a legitimate and integral part of such assessments. Based on an extensive questionnaire survey in three countries, the opinions of researchers are analysed. We provide comparisons across academic fields (cardiology, economics, and physics) and contexts for assessing research (identifying the best research in their field, assessing grant proposals and assessing candidates for positions). A minority of the researchers responding to the survey reported that metrics were reasons for considering something to be the best research. Still, a large majority in all the studied fields indicated that metrics were important or partly important in their review of grant proposals and assessments of candidates for academic positions. In these contexts, the citation impact of the publications and, particularly, the number of publications were emphasized. These findings hold across all fields analysed, still the economists relied more on productivity measures than the cardiologists and the physicists. Moreover, reviewers with high scores on bibliometric indicators seemed more frequently (than other reviewers) to adhere to metrics in their assessments. Hence, when planning and using peer review, one should be aware that reviewers—in particular reviewers who score high on metrics—find metrics to be a good proxy for the future success of projects and candidates, and rely on metrics in their evaluation procedures despite the concerns in scientific communities on the use and misuse of publication metrics.
Can We Panelize Seizure?
Authors: Roberts Ruth , Authier Simon , Mellon R Daniel , Morton Michael , Suzuki Ikuro , Tjalkens Ronald B , Valentin Jean-Pierre , Pierson Jennifer B
Published: October 2020

Seizure liability remains a significant cause of attrition in drug discovery and development, leading to loss of competitiveness, delays, and increased costs. Current detection methods rely on observations made in in vivo studies intended to support clinical trials, such as tremors or other abnormal movements. These signs could be missed or misinterpreted; thus, definitive confirmation of drug-induced seizure requires a follow-up electroencephalogram study. There has been progress in in vivo detection of seizure using automated video systems that record and analyze animal movements. Nonetheless, it would be preferable to have earlier prediction of seizurogenic risk that could be used to eliminate liabilities early in discovery while there are options for medicinal chemists making potential new drugs. Attrition due to cardiac adverse events has benefited from routine early screening; could we reduce attrition due to seizure using a similar approach? Specifically, microelectrode arrays could be used to detect potential seizurogenic signals in stem-cell-derived neurons. In addition, there is clear evidence implicating neuronal voltage-gated and ligand-gated ion channels, GPCRs and transporters in seizure. Interactions with surrounding glial cells during states of stress or inflammation can also modulate ion channel function in neurons, adding to the challenge of seizure prediction. It is timely to evaluate the opportunity to develop an in vitro assessment of seizure linked to a panel of ion channel assays that predict seizure, with the aim of influencing structure-activity relationship at the design stage and eliminating compounds predicted to be associated with pro-seizurogenic state.
Genome Sequence of the Biocontrol Agent Coniothyrium minitans Conio (IMI 134523)
Authors: Patel Denise , Shittu Taiwo A. , Baroncelli Riccardo , Muthumeenakshi Sreenivasaprasad , Osborne Thomas H. , Janganan Thamarai K. , Sreenivasaprasad Surapareddy
Published: October 2020

Coniothyrium minitans (synonym, Paraphaeosphaeria minitans) is a highly specific mycoparasite of the wide host range crop pathogen Sclerotinia sclerotiorum. The capability of C. minitans to destroy the sclerotia of S. sclerotiorum has been well recognized and it is available as a widely used biocontrol product Contans WG. We present the draft genome sequence of C. minitans Conio (IMI 134523), which has previously been used in extensive studies that formed part of a registration package of the commercial product. This work provides a distinctive resource for further research into the molecular basis of mycoparasitism to harness the biocontrol potential of C. minitans.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .