bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal relationship of serum nutritional factors with osteoarthritis: a Mendelian randomization study
Authors: Qu Zihao , Yang Fangkun , Hong Jianqiao , Wang Wei , Li Sihao , Jiang Guangyao , Yan Shigui 
Published: August 2020

Abstract

Objectives
OA is the most common form of arthritis worldwide and has a major impact on the quality of life among the older population. This study aimed at determining the potential causal effects of several serum nutritional factors on OA.

Methods
A total of seven serum nutritional factors were identified from genome-wide association studies. Summary statistics for OA were obtained from UK Biobank (194 153 for women and 166 988 for men) and a large genome-wide association studies meta-analysis based on the European population (455 221, 393 873 and 403 124 for overall, hip and knee OA, respectively). Two-sample Mendelian randomization approach was used to estimate the causal association between the selected nutritional factors and the risk of OA.

Results
The Mendelian randomization analyses suggested that serum calcium levels were inversely associated with overall OA (95% CI, 0.595, 0.850), hip OA (95% CI, 0.352, 0.799) and knee OA (95% CI, 0.461, 0.901). Serum retinol levels were also inversely associated with hip OA (95% CI, 0.257, 0.778). Moreover, sex-specific associations were observed between serum calcium levels (95% CI, 0.936, 0.998), iron levels (95% CI, 1.000, 1.012), selenium levels (95% CI, 0.923, 0.999) and OA in women.

Conclusion
In this study, an inverse causal association between serum calcium levels and OA was established. Serum retinol levels were inversely associated with hip OA. In addition, we provide evidence for the causal effect of serum calcium, iron and selenium on the risk of OA in women.
The Care of the Patients With Alcohol Intoxication in the Emergency Department of a Central Hospital
Authors: Hakala Tiina , Kylmä Jari , Paavilainen Eija , Koivunen Marita 
Published: August 2020

Abstract

Aim
The aim of the study was to describe nurses' skills, knowledge of care, and attitudes toward the care of patients with alcohol intoxication in the emergency department.

Method
The data were collected using theme interviews in 2016. The study participants were nurses working in the emergency department (n = 6) that has a sobering unit. The data were analyzed using inductive content analysis.

Results
On the basis of the interviewees' descriptions, five main categories were formed: the skills to discuss the use of alcohol on arrival, safety skills, teamwork skills, the skills to organize follow-up care, and nurses' attitudes and ethics in patients' care. Asking about the use of alcohol as well as the use of a screening tool varied. The interviewees emphasized the skills to anticipate the risk of violence as well as ensuring the safety of the working environment. Nurses' attitudes were seen as the ability to regulate negative emotions raised by the patient. Factors related to nurses' attitudes emerged in patients' behavioral disorders and commitment to treatment. Despite some negative feelings toward patients, nurses thought that it is important to ensure ethicality in patients' care.

Conclusions
The nurses' skills and knowledge of care and attitudes toward patients with alcohol intoxication varied. There is a need for additional training on issues relating to the treatment of patients with alcohol intoxication.
Analysis of Factors Related to Social Network Service Addiction Among Korean High School Students
Authors: Kim Mi-Ran , Oh Jae-Woo , Huh Bo-Yun 
Published: August 2020

Abstract
We employed a descriptive survey to determine the effects of excessive social network service (SNS) usage. Measures of SNS addiction, SNS fatigue, anxiety, and school life adjustment were employed with 209 high school students (85.2% female, 14.8% male). SNS addiction increased as students became more dissatisfied with school life, used SNS for a longer period, and had increased access to SNS as compared with their counterparts. SNS addiction was positively correlated with SNS fatigue (r = .24, p < .001) and anxiety (r = .20, p = .003). SNS fatigue and anxiety were positively correlated (r = .30, p < .001), and school adjustment and anxiety were negatively correlated (r = −.25, p < .001). SNS daily use (in both frequency and number of minutes) and anxiety were associated with SNS addiction (adjusted R
2 = 38.4%). It is necessary to develop intervention programs for vulnerable groups and promote early screening for SNS addiction.
Nursing Attitudes Toward Patients With Substance Use Disorders
Authors: Jackman Kevon-Mark , Scala Elizabeth , Nwogwugwu Charlotte , Huggins Delcora , Antoine Denis G. 
Published: August 2020

Abstract

Background
Negative healthcare provider attitudes toward patients with substance use disorder (SUD) may adversely impact the quality of care and treatment outcomes.

Purpose
In this article, we aim to characterize the effects of an 8-hour educational workshop on attitudes toward patients with SUD among nurses from an urban inpatient psychiatric hospital.

Methods
The Drug and Drug Problems Perceptions Questionnaire, a 22-item scale consisting of six subscales, was used to assess nurse attitudes to patients with SUD at pretest (n = 38), posttest (n = 36), and 30-day follow-up (n = 20). Generalized estimating equation models adjusted for gender and years of work experience were used to measure changes in Drug and Drug Problems Perceptions Questionnaire scores.

Results
Positive attitudes significantly increased at posttest (β = −12.09, 95%CI [−16.83, −7.34]; p < .001) and were sustained at 30-day follow-up (β = 1.71, 95% CI [−3.11, 6.53]; p = .49). Subscales of motivation (β = −0.26, 95% CI [−0.87, 0.35]; p = .41) and task-specific self-esteem (β = −0.56, 95% CI [−1.44, 0.32]; p = .21) did not significantly change at posttest.

Conclusions
Our findings show workshop effectiveness in improving nurse attitudes toward patients with SUD. Future research may test similar interventions at a larger scale and with other health professionals.
Spatiotemporal dynamics of dengue in Colombia in relation to the combined effects of local climate and ENSO
Authors: Muñoz Estefanía , Poveda Germán , Arbeláez M. Patricia , Vélez Iván D. 
Published: August 2020

AbstractDengue virus (DENV) is an endemic disease in the hot and humid low-lands of Colombia. We characterize diverse temporal and spatial patterns of monthly series of dengue incidence in diverse regions of Colombia during the period 2007-2017 at different spatial scales, and their association with indices of El Niño/Southern Oscillation (ENSO) at the tropical Pacific and local climatic variables. For estimation purposes, we use linear analysis tools including lagged cross-correlations (Pearson test), cross wavelet analysis (wavelet cross spectrum, and wavelet coherence), as well as a novel nonlinear causality method, PCMCI, that allows identifying common causal drivers and links among high dimensional simultaneous and time-lagged variables. Our results evidence the strong association of DENV cases in Colombia with ENSO indices and with local temperature and rainfall. El Niño (La Niña) phenomenon is related to an increase (decrease) of dengue cases nationally and in most regions and departments, with maximum correlations occurring at shorter time lags in the Pacific and Andes regions, closer to the Pacific Ocean. This association is mainly explained by the ENSO-driven increase in temperature and decrease in rainfall, especially in the Andes and Pacific regions. The influence of ENSO is not stationary (there is a reduction of DENV cases since 2005) and local climate variables vary in space and time, which prevents to extrapolate results from one site to another. The association between DENV and ENSO varies at national and regional scales when data are disaggregated by seasons, being stronger in DJF and weaker in SON. Specific regions (Pacific and Andes) control the overall relationship between dengue dynamics and ENSO at national scale, and the departments of Antioquia and Valle del Cauca determine those of the Andes and Pacific regions, respectively. Cross wavelet analysis indicates that the ENSO-DENV relation in Colombia exhibits a strong coherence in the 12 to 16-months frequency band, which implies the frequency locking between the annual cycle and the interannual (ENSO) timescales. Results of nonlinear causality metrics reveal the complex concomitant effects of ENSO and local climate variables, while offering new insights to develop early warning systems for DENV in Colombia.
Heightened resistance to type 1 interferons characterizes HIV-1 at transmission and following analytical treatment interruption
Authors: Gondim Marcos V. P. , Sherrill-Mix Scott , Bibollet-Ruche Frederic , Russell Ronnie M. , Trimboli Stephanie , Smith Andrew G. , Li Yingying , Liu Weimin , Avitto Alexa N. , DeVoto Julia , Connell Jesse , Fenton-May Angharad E. , Pellegrino Pierre , Williams Ian , Papasavvas Emmanouil , Lorenzi Julio C. C. , Salantes D. Brenda , Mampe Felicity , Monroy M. Alexandra , Cohen Yehuda Z. , Heath Sonya , Saag Michael S. , Montaner Luis J. , Collman Ronald G. , Siliciano Janet M. , Siliciano Robert F. , Plenderleith Lindsey , Sharp Paul M. , Caskey Marina , Nussenzweig Michel C. , Shaw George M. , Borrow Persephone , Bar Katharine J. , Hahn Beatrice H. 
Published: August 2020

AbstractType 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their anti-viral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally-derived HIV-1 isolates from plasma and CD4+ T cells of 26 individuals sampled longitudinally following transmission and/or after antiretroviral therapy (ART) and analytical treatment interruption (ATI). Determining the concentration of IFNα2 and IFNβ that reduced HIV-1 replication by 50% (IC50), we found remarkably consistent changes in the sensitivity of viruses to IFN-I inhibition, both across individuals and over time. IFN-I resistance was uniformly high during acute infection, decreased in all subjects in the first year post-infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in subjects with accelerated disease. Isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just prior to ART initiation. However, viruses that rebounded following treatment interruption displayed the highest levels of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate immune responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control impacted by both ART and ATI. Although elevated at transmission, IFN-mediated pressures are the highest during viral rebound, limiting the viruses that successfully reactivate from latency.One Sentence SummaryHIV-1 resistance to IFN-I is highest during acute infection and following analytic treatment interruption, indicating a dynamic interplay between host innate immunity and virus biology.
Universal properties of the dynamics of the Covid-19 pandemic
Authors: Chruściel Piotr T. , Szybka Sebastian J. 
Published: August 2020

AbstractWe present evidence for existence of a universal lower bound for the initial growth rate of the epidemic curve of the SARS-CoV-2 coronavirus. This can be used to infer that, on average, an asymptomatic infected individual is infectious during 5.6 ± 0.3 days. We further present evidence of an average time scale of 12 days for halving the number of new cases, or new deaths, during the extinction period of the first phase of the epidemic.
Automatic late blight lesion recognition and severity quantification based on field imagery of diverse potato genotypes by deep learning
Authors: Gao Junfeng , Westergaard Jesper Cairo , Sundmark Ea Høegh Riis , Bagge Merethe , Liljeroth Erland , Alexandersson Erik 
Published: August 2020

AbstractThe plant pathogenPhytophthora infestanscauses the severe disease late blight in potato, which results in a huge loss for potato production. Automatic and accurate disease lesion segmentation enables fast evaluation of disease severity and assessment of disease progress for precision crop breeding. Deep learning has gained tremendous success in computer vision tasks for image classification, object detection and semantic segmentation. To test whether we could extract late blight lesions from unstructured field environments based on high-resolution visual field images and deep learning algorithms, we collected ~500 field RGB images in a set of diverse potato genotypes with different disease severity (0-70%), resulting in 2100 cropped images. 1600 of these cropped images were used as the dataset for training deep neural networks. Finally, the developed model was tested on the 250 cropped images. The results show that the intersection over union (IoU) values of background (leaf and soil) and disease lesion classes in the test dataset are 0.996 and 0.386, respectively. Furthermore, we established a linear relationship (R2= 0.655) between manual visual scores of late blight and the number of lesions at the canopy level. We also learned that imbalance weights of lesion and background classes improved segmentation performance, and that fused masks based on the majority voting of the multiple masks enhanced the correlation with the visual scores. This study demonstrates the feasibility of using deep learning algorithms for disease lesion segmentation and severity evaluation based on proximal imagery for crop resistance breeding in field environments.
New insights on species divergence in red panda
Authors: Joshi Bheem Dutt , Dalui Supriyo , Singh Sujeet Kumar , Mukherjee Tanoy , Chandra Kailash , Sharma Lalit Kumar , Thakur Mukesh 
Published: August 2020

AbstractWith the recent classification of red panda into two phylogenetic species, we propose ‘Siang river’ as a potential boundary for species divergence between the Himalayan red panda (Ailurus fulgens) and the Chinese red panda (Ailurus styani). Bayesian based phylogeny and MJ network splited all the sequences into two distinct clusters in accordance to the origin of the samples collected from the east and west side of the Siang river. The clade 1, that represented Himalayan red panda, was formed by inclusion of samples originated from the north West Bengal, Sikkim, and central Arunachal Pradesh and South Tibet. While, clade 2 represented Chinese red panda by inclusion of the samples originated from Dibang valley of eastern Arunachal Pradesh, India and Southwest China. We suggest being associated with diverse habitats, threats and transboundary distribution, both species of red panda require regional as well as multilateral cooperation for making species survival plan.
Structural characterization ofMyxococcus xanthusMglC, a component of polarity control system, and its interactions with MglB
Authors: Kapoor Srajan , Kodesia Akriti , Kalidas Nidhi , Ashish  , Thakur Krishan Gopal 
Published: August 2020

AbstractMyxococcus xanthusdisplays two types of motilities i.e. Social (S) and Adventurous (A). The pole-to-pole reversals of these motility regulator proteins is the key to this process. Here, we determined ~1.85 Å resolution crystal structure of MglC, which revealed that despite sharing <9% sequence identity, both MglB and MglC adoptRegulatoryLightChain 7 (RLC7) family fold. Interestingly, MglC is structurally unique compared to the other known RLC7 family proteins having ~30°-40° shift in the orientation of functionally important α2 helix. Using isothermal titration calorimetry and gel filtration chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using combination of small angle X-ray scattering and molecular docking studies, we show that MglBC complex is formed by MglC homodimer sandwiched between two homodimers of MglB.In BriefKapooret al. report the crystal structure ofMyxococcus xanthusMglC, aRoadblockLightChain 7 (RLC7) family protein, involved in polarity reversal. The structure reveals a distinct orientation of α2 helix compared to other RLC7 proteins. They also demonstrate that MglC binds a GTPase activating protein, MglB, with submicromolar range dissociation constant.HighlightsMglC adopts RLC7 fold and has distinct structural features.MglC interacts MglB to form a stable complex having submicromolar range dissociation constant.MglC homodimer is sandwiched between two MglB homodimers to form a 2:4 stoichiometric complex.
Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae
Authors: Brock Kinsey M. , McTavish Emily Jane , Edwards Danielle L. 
Published: August 2020

ABSTRACTColor polymorphism – two or more heritable color phenotypes maintained within a single breeding population – is an extreme type of intra-specific diversity widespread across the tree of life but rarely studied in a comparative framework. Color polymorphism is thought to be an engine for speciation, where morph loss or divergence between distinct color morphs within a species results in the rapid evolution of new lineages, and thus, color polymorphic lineages are expected to display elevated diversification rates. Lizards of the family Lacertidae have evolved multiple lineages with color polymorphism, but lack of a complete and robust phylogeny for the group has made comparative analysis difficult. Here, we produce a comprehensive species-level phylogeny of the lizard family Lacertidae to reconstruct the evolutionary history of color polymorphism and test if color polymorphism has been a driver of diversification. Accounting for phylogenetic uncertainty, we estimate an ancient macroevolutionary origin of color polymorphism within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most likely evolved several times in the Lacertidae and has been lost at a much faster rate than gained. Evolutionary transitions to color polymorphism are associated with shifts in increased net diversification rate in this family of lizards. Taken together, our empirical results support long-standing theoretical expectations that color polymorphism is a driver of diversification.
The novel roles of choline transporter-like 1 and 2 in ethanolamine transport
Authors: Taylor Adrian , Grapentine Sophie , Ichhpuniani Jasmine , Bakovic Marica 
Published: August 2020

AbstractWe examined a novel function of mammalian Choline-Transporter-Like proteins CTL1/SLC44A1 and CTL2/SLC44A2 in ethanolamine transport. We established two distinct ethanolamine transport systems of a high affinity (K1= 55.6 - 66.5 μM), mediated by CTL1, and of a low affinity (K2= 275 - 299 μM), mediated by CTL2. Both types of transport are Na+-independent and mediated in a pH dependent manner, as expected for ethanolamine/H+antiporters. Primary human fibroblasts with separate frameshift mutations (M1=SLC44A1ΔAsp517and M2=SLC44A1ΔSer126) are devoid of CTL1 ethanolamine transport but maintain unaffected CTL2 transport. The lack of CTL1 or CTL2 reduced the ethanolamine transport, the flux by the CDP-ethanolamine Kennedy pathway and PE synthesis. Overexpression of CTL1 inSLC44A1ΔSer126(M2) cells improved the ethanolamine transport and PE synthesis. TheSLC44A1ΔSer126cells are reliant on CTL2 function and CTL2 siRNA almost completely abolished ethanolamine transport in the whole cells and mitochondria. Overexpression of CTL1 and CTL2 cDNAs increased ethanolamine transport in control andSLC44A1ΔSer126cells. CTL1 and CTL2 facilitated mitochondrial ethanolamine uptake, but the transport mediated by CTL1 is predominant in the whole cells and mitochondria. These data firmly established that CTL1 and CTL2 are the first identified ethanolamine transporters in the whole cells and mitochondria, with intrinsic roles inde novoPE synthesis by the CDP-Etn Kennedy pathway and compartmentation of intracellular ethanolamine.SignificanceThe lack of Choline Transporter Like 1 (SLC44A1/CTL1) is the primary cause of a new neurodegenerative disorder with elements of childhood-onset parkinsonism and mitochondrial dysfunction.SLC44A2/CTL2 encodes the human neutrophil antigen 3, causes autoimmune hearing loss and Meniere’s disease, and has been recently identified as the main risk factor for thrombosis-the major cause of death in Covid-19 patients. Our investigation provides insights into the novel functions of CTL1 and CTL2 as intrinsic ethanolamine transporters. CTL1 and CTL2 are high and low affinity transporters, with direct roles in the membrane phospholipid synthesis. The work contributes to new knowledge for CTL1 and CTL2 independent transport functions and the optimization of prevention and treatment strategies in those various diseases.
Base Pairing and Functional Insights intoN3-methylcytidine (m3C) in RNA
Authors: Mao Song , Haruehanroengra Phensinee , Ranganathan Srivathsan V. , Shen Fusheng , Begley Thomas J. , Sheng Jia 
Published: August 2020

ABSTRACTN3-methylcytidine (m3C) is present in both eukaryotic tRNA and mRNA and plays critical roles in many biological processes. We report the synthesis of the m3C phosphoramidite building block and its containing RNA oligonucleotides. The base-pairing stability and specificity studies show that the m3C modification significantly disrupts the stability of the Watson-Crick C:G pair. Further m3C decreases the base pairing discrimination between C:G and the other mismatched C:A, C:U, and C:C pairs. Our molecular dynamic simulation study further reveals the detailed structural insights into the m3C:G base pairing pattern in an RNA duplex. More importantly, the biochemical investigation of m3C using reverse transcription shows thatN3-methylation specifies the C:A pair and induces a G to A mutation using HIV-1-RT, MMLV-RT and MutiScribe™-RT enzymes, all with relatively low replication fidelity. For other reverse transcriptases with higher fidelity like AMV-RT, the methylation could completely shut down DNA synthesis.
Genome-wide analysis ofcis-regulatory changes in the metabolic adaptation of cavefish
Authors: Krishnan Jaya , Seidel Chris W. , Zhang Ning , VanCampen Jake , Peuß Robert , Xiong Shaolei , Kenzior Alexander , Li Hua , Conaway Joan W. , Rohner Nicolas 
Published: August 2020

AbstractChanges in cis-regulatory elements play important roles in adaptation and phenotypic evolution. However, their contribution to metabolic adaptation of organisms is less understood. Here we have utilized a unique vertebrate model,Astyanax mexicanus,different morphotypes of which survive in nutrient-rich surface and nutrient-deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide epigenetic profiling in the liver tissue of one surface and two independently derived cave populations. We find that many cis-regulatory elements differ in their epigenetic status/chromatin accessibility between surface fish and cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. These differentially accessible regions are associated with genes of key pathways related to lipid metabolism, circadian rhythm and immune system that are known to be altered in cavefish. Usingin vitroandin vivofunctional testing of the candidate cis-regulatory elements, we find that genetic changes within them cause quantitative expression differences. We characterized one cis-regulatory element in thehpdbgene and found a genomic deletion in cavefish that abolishes binding of the transcriptional repressor IRF2in vitroand derepresses enhancer activity in reporter assays. Genetic experiments further validated a cis-mediated role of the enhancer and suggest a role of this deletion in the upregulation ofhpdbin wild cavefish populations. Selection of this mutation in multiple independent cave populations supports its importance in the adaptation to the cave environment, providing novel molecular insights into the evolutionary trade-off between loss of pigmentation and adaptation to a food-deprived cave environment.