bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of the Cerambycidae (Coleoptera) Community in a Tropical Deciduous Forest in Northern Morelos, Mexico
Authors: Martínez-Hernández José Guadalupe , Corona-López Angélica María , Flores-Palacios Alejandro , Toledo-Hernández Víctor Hugo 
Published: February 2022

AbstractThe purpose of this study was to determine the structure of the community and seasonality of the Cerambycidae family in the tropical deciduous forest (TDF) of San Andrés de la Cal, Tepoztlán in Morelos, Mexico. Following a year of systematic collections, and with the addition of data obtained from breeding chambers and sporadic collections, 155 species, 91 genera, 35 tribes, and 4 subfamilies were recorded. Thirty-three of these species, &gt;21% are new records for the state of Morelos. Sample coverage was 97% and, according to the Chao 1 richness estimator, we found 80% of the species present in the study area. Greater species richness, abundance, and diversity were found during the rainy season, which generates a significant difference between seasons. The ordering of faunal similarities between months indicated a marked seasonality in the composition. The data suggest that the diversity of TDF insects is not completely known (i.e., new records were found), but comprises a diverse community, composed of a high proportion (78%) of rare species. Our findings reinforce the need to continue documenting insect diversity in TDF, especially considering that this is among the least protected of the ecosystems, and one that is negatively affected to a greater degree by anthropogenic activities and climate change.
PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features
Authors: Yan Cheng , Duan Guihua , Li Na , Zhang Lishen , Wu Fang-Xiang , Wang Jianxin 
Published: February 2022

Abstract

Motivation
Many studies have shown that microRNAs (miRNAs) play a key role in human diseases. Meanwhile, traditional experimental methods for miRNA–disease association identification are extremely costly, time-consuming and challenging. Therefore, many computational methods have been developed to predict potential associations between miRNAs and diseases. However, those methods mainly predict the existence of miRNA–disease associations, and they cannot predict the deep-level miRNA–disease association types.

Results
In this study, we propose a new end-to-end deep learning method (called PDMDA) to predict deep-level miRNA–disease associations with graph neural networks (GNNs) and miRNA sequence features. Based on the sequence and structural features of miRNAs, PDMDA extracts the miRNA feature representations by a fully connected network (FCN). The disease feature representations are extracted from the disease–gene network and gene–gene interaction network by GNN model. Finally, a multilayer with three fully connected layers and a softmax layer is designed to predict the final miRNA–disease association scores based on the concatenated feature representations of miRNAs and diseases. Note that PDMDA does not take the miRNA–disease association matrix as input to compute the Gaussian interaction profile similarity. We conduct three experiments based on six association type samples (including circulations, epigenetics, target, genetics, known association of which their types are unknown and unknown association samples). We conduct fivefold cross-validation validation to assess the prediction performance of PDMDA. The area under the receiver operating characteristic curve scores is used as metric. The experiment results show that PDMDA can accurately predict the deep-level miRNA–disease associations.

Availability and implementation
Data and source codes are available at https://github.com/27167199/PDMDA.
NPRL3 loss alters neuronal morphology, mTOR localization, cortical lamination and seizure threshold
Authors: Iffland Philip H , Everett Mariah E , Cobb-Pitstick Katherine M , Bowser Lauren E , Barnes Allan E , Babus Janice K , Romanowski Andrea J , Baybis Marianna , Elziny Soad , Puffenberger Erik G , Gonzaga-Jauregui Claudia , Poulopoulos Alexandros , Carson Vincent J , Crino Peter B 
Published: February 2022

AbstractMutations in nitrogen permease regulator-like 3 (NPRL3), a component of the GATOR1 complex within the mTOR pathway, are associated with epilepsy and malformations of cortical development. Little is known about the effects of NPRL3 loss on neuronal mTOR signalling and morphology, or cerebral cortical development and seizure susceptibility.We report the clinical phenotypic spectrum of a founder NPRL3 pedigree (c.349delG, p.Glu117LysFS; n = 133) among Old Order Mennonites dating to 1727. Next, as a strategy to define the role of NPRL3 in cortical development, CRISPR/Cas9 Nprl3 knockout in Neuro2a cells in vitro and in foetal mouse brain in vivo was used to assess the effects of Nprl3 knockout on mTOR activation, subcellular mTOR localization, nutrient signalling, cell morphology and aggregation, cerebral cortical cytoarchitecture and network integrity. The NPRL3 pedigree exhibited an epilepsy penetrance of 28% and heterogeneous clinical phenotypes with a range of epilepsy semiologies, i.e. focal or generalized onset, brain imaging abnormalities, i.e. polymicrogyria, focal cortical dysplasia or normal imaging, and EEG findings, e.g. focal, multi-focal or generalized spikes, focal or generalized slowing. Whole exome analysis comparing a seizure-free group (n = 37) to those with epilepsy (n = 24) to search for gene modifiers for epilepsy did not identify a unique genetic modifier that explained the variability in seizure penetrance in this cohort. Nprl3 knockout in vitro caused mTOR pathway hyperactivation, cell soma enlargement and the formation of cellular aggregates seen in time-lapse videos that were prevented with the mTOR inhibitors rapamycin or torin1. In Nprl3 knockout cells, mTOR remained localized on the lysosome in a constitutively active conformation, as evidenced by phosphorylation of ribosomal S6 and 4E-BP1 proteins, even under nutrient starvation (amino acid-free) conditions, demonstrating that Nprl3 loss decouples mTOR activation from neuronal metabolic state. To model human malformations of cortical development associated with NPRL3 variants, we created a focal Nprl3 knockout in foetal mouse cortex by in utero electroporation and found altered cortical lamination and white matter heterotopic neurons, effects which were prevented with rapamycin treatment. EEG recordings showed network hyperexcitability and reduced seizure threshold to pentylenetetrazol treatment.NPRL3 variants are linked to a highly variable clinical phenotype which we propose results from mTOR-dependent effects on cell structure, cortical development and network organization.
Intermittent administration of tacrolimus enhances &#x2028;anti-tumor immunity in melanoma-bearing mice
Authors: Chen Ting , Zhang Qi , Zhang Nianhai , Liu Bo , Chen Junying , Huang Fei , Lin Jianhua , Lan Ruilong , Xie Xianhe , Wang Zili 
Published: February 2022

AbstractOne key reason for T cell exhaustion is continuous antigen exposure. Early exhausted T cells can reverse exhaustion and differentiate into fully functional memory T cells if removed from persisting antigen stimulation. Therefore, this study viewed T cell exhaustion as an over-activation status induced by chronic antigen stimuli. This study hypothesized that blocking TCR signal intermittently to terminate over-activation signal can defer the developmental process of T cell exhaustion. In this study, melanoma-bearing mice were treated with tacrolimus (FK506) every 5 days. The tumor size and tumor-infiltrating lymphocytes (TILs) were analyzed. We found that intermittent administration of tacrolimus significantly inhibited tumor growth, and this effect was mediated by CD8+T cells. Intermittent tacrolimus treatment facilitated the infiltration of CD8+TILs. RNA-seq and quantitative RT-PCR of sorted CD8+TILs showed the expression of Nr4a1 (an exhaustion-related transcription factor) and Ctla4 (a T cell inhibitory receptor) was remarkably downregulated. These results indicated that intermittently blocking TCR signal by tacrolimus can promote anti-tumor immunity and inhibit the tumor growth in melanoma-bearing mice, inhibiting the transcription of several exhaustion-related genes, such as Nr4a1 and Ctla4.
New Insights into Mitochondrial–Nuclear Interactions Revealed through Analysis of Small RNAs
Authors: Pozzi Andrea , Dowling Damian K 
Published: February 2022

Abstract
Mitochondrial sequence variants affect phenotypic function, often through interaction with the nuclear genome. These “mitonuclear” interactions have been linked both to evolutionary processes and human health. The study of these interactions has focused on mechanisms regulating communication between mitochondrial and nuclear proteins; the role of mitochondrial (mt) RNAs has received little attention. Here, we show that small mt-RNAs bind to the nuclear protein Argonaute 2, and that nuclear miRNAs bind to mt-mRNAs. We identify one small mt-RNA that binds to Argonaute 2 in human tissues whose expression and sequence remain unchanged across vertebrates. Although analyses of CLEAR-CLIP sequencing data sets of human and mouse did not reveal consistent interactions between small mt-RNAs and nuclear mRNAs, we found that MT-ND4 and MT-ATP6 mRNAs are bound by different nuclear miRNAs in humans and mice. Our work homes in on previously unknown interactions between nuclear and small mt-RNAs, which may play key roles in intergenomic communication.
Fast rupture of the 2009Mw 6.9 Canal de Ballenas earthquake in the Gulf of California dynamically triggers seismicity in California
Authors: Fan Wenyuan , Okuwaki Ryo , Barbour Andrew J , Huang Yihe , Lin Guoqing , Cochran Elizabeth S 
Published: February 2022

SUMMARYIn the Gulf of California, Mexico, the relative motion across the North America–Pacific boundary is accommodated by a series of marine transform faults and spreading centres. About 40 M&gt; 6 earthquakes have occurred in the region since 1960. On 2009 August 3, an Mw 6.9 earthquake occurred near Canal de Ballenas in the region. The earthquake was a strike-slip event with a shallow hypocentre that is likely close to the seafloor. In contrast to an adjacent M7 earthquake, this earthquake triggered a ground-motion-based earthquake early warning algorithm being tested in southern California (∼600 km away). This observation suggests that the abnormally large ground motions and dynamic strains observed for this earthquake relate to its rupture properties. To investigate this possibility, we image the rupture process and resolve the slip distribution of the event using a P-wave backprojection approach and a teleseismic, finite-fault inversion method. Results from these two independent analyses indicate a relatively simple, unilateral rupture propagation directed along-strike in the northward direction. However, the average rupture speed is estimated around 4 km s−1, suggesting a possible supershear rupture. The supershear speed is also supported by a Rayleigh wave Mach cone analysis, although uncertainties in local velocity structure preclude a definitive conclusion. The Canal de Ballenas earthquake dynamically triggered seismicity at multiple sites in California, with triggering response characteristics varying from location-to-location. For instance, some of the triggered earthquakes in California occurred up to 24 hr later, suggesting that nonlinear triggering mechanisms likely have modulated their occurrence.
Assessment of causal effects of visceral adipose tissue on risk of cancers: a Mendelian randomization study
Authors: Lu Yao , Tang Haibo , Huang Peiyuan , Wang Jie , Deng Peizhi , Li Yalan , Zheng Jie , Weng Liang 
Published: February 2022

AbstractBackgroundDespite the established association between obesity and cancer risk, it remains unclear whether visceral obesity is causally related to cancer risk and whether it is more pro-oncogenic than total body fat.MethodsWe conducted two-sample Mendelian randomization (MR) analysis to assess the causal effects of visceral adipose tissue (VAT) on six common cancers. For exposure data, 221 genetic variants associated with the predicted volume of VAT in 325 153 Europeans from UK Biobank were used as instrumental variables. Genetic association data of six common cancers (breast, lung, colorectal, ovarian, pancreatic and prostate cancers) were obtained from large-scale consortia with an average of 19 576 cases and 43 272 controls. We performed univariable MR with five MR methods [inverse-variance weighted (IVW), MR-Egger regression, weighted median, MR-Pleiotropy Residual Sum and Outlier (MR-PRESSO) and Radial MR] and multivariable MR to estimate the effect of VAT independent of body mass index (BMI). Finally, we performed a series of sensitivity analyses as validation of primary MR results.ResultsTwo associations survived the false discovery rate correction for multiple testing (q-value &lt; 0.05): in IVW, the odds ratios (95% CIs) per unit increase in genetically determined VAT were 1.65 (1.03 to 2.62) for pancreatic cancer and 1.47 (1.20 to 1.82) for lung squamous-cell carcinoma, respectively, which showed the same directions and overlapped confidence intervals with MR-Egger regression and weighted median results. There were no outlier variants identified by MR-PRESSO and no evidence supporting the presence of heterogeneity and pleiotropy in sensitivity analyses, although with wider confidence intervals that included the null, multivariable MR results for these two cancers showed the same directions and similar effect sizes as in IVW, which were independent of the effect from BMI. There was no evidence for a causal effect of VAT on the risk of other types of cancer.ConclusionOur findings suggest that lifelong exposure to elevated volumes of VAT might increase the risk of pancreatic cancer and lung squamous-cell carcinoma, highlighting the importance of revealing the underlying mechanisms for intervention targets.
Pre-trauma predictors of severe psychiatric comorbidity 5 years following traumatic experiences
Authors: Gradus Jaimie L , Rosellini Anthony J , Szentkúti Péter , Horváth-Puhó Erzsébet , Smith Meghan L , Galatzer-Levy Isaac , Lash Timothy L , Galea Sandro , Schnurr Paula P , Sørensen Henrik T 
Published: February 2022

Abstract

Background
A minority of persons who have traumatic experiences go on to develop post-traumatic stress disorder (PTSD), leading to interest in who is at risk for psychopathology after these experiences. Complicating this effort is the observation that post-traumatic psychopathology is heterogeneous. The goal of this nested case-control study was to identify pre-trauma predictors of severe post-traumatic psychiatric comorbidity, using data from Danish registries.

Methods
The source population for this study was the population of Denmark from 1994 through 2016. Cases had received three or more psychiatric diagnoses (across all ICD-10 categories) within 5 years of a traumatic experience (n = 20 361); controls were sampled from the parent cohort using risk-set sampling (n = 81 444). Analyses were repeated in samples stratified by pre-trauma psychiatric diagnoses. We used machine learning methods (classification and regression trees and random forest) to determine the important predictors of severe post-trauma psychiatric comorbidity from among hundreds of pre-trauma predictor variables spanning demographic and social variables, psychiatric and somatic diagnoses and filled medication prescriptions.

Results
In the full sample, pre-trauma psychiatric diagnoses (e.g. stress disorders, alcohol-related disorders, personality disorders) were the most important predictors of severe post-trauma psychiatric comorbidity. Among persons with no pre-trauma psychiatric diagnoses, demographic and social variables (e.g. marital status), type of trauma, medications used primarily to treat psychiatric symptomatology, anti-inflammatory medications and gastrointestinal distress were important to prediction. Results among persons with pre-trauma psychiatric diagnoses were consistent with the overall sample.

Conclusions
This study builds on the understanding of pre-trauma factors that predict psychopathology following traumatic experiences, by examining a broad range of predictors of post-trauma psychopathology and comorbidity beyond PTSD.
Cascade relationship between flow field characteristics and smoke emissions in the industrial reheating furnace
Authors: Lipo Yang , Yunpeng Liu , Yingwu Hou , Yongshun Zhang 
Published: February 2022

Abstract
The temperature control process of reheating furnace is time delay and highly nonlinear to result in large temperature difference fluctuation and low temperature accuracy, because the complex flow field characteristics obviously affect the on-line temperature distribution of furnace and slab. Up to date, it is urgent to find out the heat balance cascade law between the key factors. Therefore, it is necessary to deeply study the coupling characteristics of key flow field parameters such as the nozzle injection angle, the air–gas ratio and the preheating temperature on the combustion mechanism and the smoke emission, so as to ensure that the temperature control accuracy and the environmental protection as well as the energy saving requirements are met. Firstly, the dynamic equivalent heat transfer coefficient could be obtained according to the flow field law of air and gas in the furnace. Secondly, according to coupling characteristics of the combustion model, the radiation model and the NOx generation model, the cascade relationship among the key combustion parameters, the temperature accuracy and the smoke emission was deeply analyzed. Finally, based on the actual engineering case, the combustion process optimization was implemented, and the practical problems such as the unstable furnace temperature and the excessive emission of pusher reheating furnace were successfully solved. On the basis of strictly controlling the temperature, the gas consumption and flue gas pollutant emission were significantly reduced via the new methods, which not only matched the downstream production but also satisfied the requirement of environmental protection.
An R2P Commission: A Proposal for Holding States Accountable to Their Responsibility to Protect
Authors: Illingworth Richard 
Published: February 2022

AbstractIn 2005, the United Nations (UN) committed to a “responsibility to protect” (R2P) against four mass-atrocity crimes of genocide, war crimes, crimes against humanity, and ethnic cleansing. This was a clear commitment acknowledging that states hold responsibilities to consider the protection needs of domestic, and outside, populations. However, holding actors accountable to their R2P commitments is difficult due to the politicization of the norm and the international institutions for implementing it. The result is that the UN lacks the mechanisms for promoting R2P's successful implementation, meaning R2P breaches are all too common and that there is an urgent need to find ways to hold states accountable to their pledges. Applying transitional cosmopolitanism, which calls for an incremental approach in the pursuit of cosmopolitan solutions to contemporary global challenges, this article examines an entirely new and supplementary mechanism to assist in R2P's implementation. The article calls for the creation of an “R2P Commission.” This is a suggestion for a body composed of independent elected experts to scrutinize state practice across R2P's “three pillars.” It argues that an R2P Commission would provide an effective and feasible supplementary body to enhance R2P's implementation via determinations of where manifest R2P failures have occurred, review of international practice vis-à-vis atrocity prevention and response, and recommendations for altering practice and potential response action.
Population Structure and Genetic Diversity of the Pepper Weevil (Coleoptera: Curculionidae) Using the COI Barcoding Region
Authors: Fernández D Catalina , VanLaerhoven Sherah L , Rodríguez-Leyva Esteban , Zhang Y Miles , Labbé Roselyne 
Published: February 2022

Abstract
The pepper weevil Anthonomus eugenii Cano (Coleoptera: Curculionidae) is a pest of economic importance for Capsicum species pepper in North America that attacks the reproductive structures of the plant. The insect is distributed across Mexico, the United States, and the Caribbean, and is occasionally found during the pepper growing season in southern Ontario, Canada. Continuous spread of the insect to new areas is partially the result of global pepper trade. Here, we describe the genetic diversity of the pepper weevil using the mitochondrial COI barcoding region across most of its geographic range. In this study, 44 (H1–H44) highly similar haplotypes were identified, the greatest number of haplotypes and haplotype diversity were observed among specimens from its native Mexico, followed by specimens from the United States. Unlike Mexico, a low haplotype diversity was found among specimens from Canada, the Dominican Republic, Italy, and the Netherlands. Out of these 44 haplotypes, 29 are reported for the first time. Haplotype diversity in the Canadian population suggests either multiple and continuous introductions of the pepper weevil into this area or a single introduction of genetically diverse individuals. We discuss the importance of such population genetic data in tailoring pepper weevil management programs, using Canada as an example.
Epidemiology and Management of Orbital Cellulitis in Children
Authors: Anosike Brenda I , Ganapathy Veena , Nakamura Mari M 
Published: February 2022

AbstractBackgroundThe epidemiology of orbital cellulitis likely has evolved due to the emergence of methicillin-resistant Staphylococcus aureus (MRSA) and the adoption of pneumococcal conjugate vaccination. In the absence of published guidelines, management is highly variable. We characterized epidemiology and management over an 11-year period.MethodsA retrospective cohort study of children 0 to 21 years of age with orbital cellulitis +/− subperiosteal orbital abscess hospitalized at a large quaternary children’s hospital from January 2008 to June 2018. We reviewed charts for demographic characteristics, clinical features, management, and outcomes. Using multivariable logistic regression, we evaluated predictors of surgical intervention and assessed whether corticosteroid use or antibiotic duration was related to clinical outcomes.ResultsAmong 220 patients, methicillin-susceptible S. aureus was the most common organism (26.3%), with MRSA found in only 5.0%. Rates of vancomycin use fluctuated annually from 40.9% to 84.6%. Surgery was performed in 39.5% of the patients. Corticosteroids, used in 70 patients (32.1%), were unrelated to treatment failure (n = 9), defined as persistent signs and symptoms or initial clinical improvement followed by worsening (P = .137). The median antibiotic duration was 17 days (interquartile range 14-26). After controlling for age, gender, proptosis, eye pain with movement, eyelid swelling, neutrophil count, and corticosteroid use, treatment failure was not significantly associated with receipt of ≥ 3 weeks of antibiotic therapy (8/84, 9.5%) compared with &gt; 2 but &lt; 3 weeks (0/51, 0.0%) or ≤ 2 weeks (1/85, 1.2%) (adjusted odds ratio = 5.83 for ≥ 3 vs ≤2 weeks; 95% confidence interval: 0.58, 59.0).ConclusionsAlthough MRSA was rare, empiric vancomycin use was high. Treatment failure was uncommon in patients who received ≤ 2 weeks of therapy, suggesting that shorter durations are adequate in some patients.