bluuebunny/crossref_metadata_2025_split huggingface dataset:
Event shape engineering and multiplicity dependent study of identified particle production in proton + proton collisions at

s

= 13 TeV using PYTHIA8
Authors: Khuntia Arvind , Tripathy Sushanta , Bisht Ashish , Sahoo Raghunath 
Published: August 2020

Abstract
Small system collectivity observed at the LHC energies along with enhancement of strangeness makes high-multiplicity proton + proton (pp) collisions very interesting in order to look for QGP-like features, usually found in heavy-ion collisions. It may be interesting to perform a double differential study of different observables in pp collisions in terms of charged particle multiplicity and event shape in order to understand the new dimensions in high-multiplicity pp physics. We study the correlation between the number of multi-partonic interactions (nMPI), event shape (transverse spherocity) and charged particle multiplicity classes. For the first time, we report the simulation results on the spherocity and charged particle multiplicity dependent study of (π
+ + π
−), (K+ + K−), (p +

p

¯

), K∗0, ϕ and (

Λ
+

Λ

0

¯

) production in pp collisions at

s

= 13 TeV using PYTHIA8. We explore the event shape and charged particle multiplicity dependence of the transverse momentum (p
T) spectra, integrated yield, mean transverse momentum (⟨p
T⟩) and particle ratios of the identified particles. This study provides a baseline for exploring the event topology and final state multiplicity dependence of identified particle production in the LHC pp collisions.
Strength testing or strength training: considerations for future research
Authors: Spitz Robert W , Bell Zachary W , Wong Vickie , Yamada Yujiro , Song Jun Seob , Buckner Samuel L , Abe Takashi , Loenneke Jeremy P 
Published: August 2020

Abstract
Maximal strength testing is often performed to assess the efficacy of training programs or as a way to prescribe exercise load. Generally, it is believed that high load exercise is superior to low load exercise at increasing absolute strength, however this is not always the case (i.e. strength increases similarly between groups). We hypothesized that some of the discrepancy in the literature may be related to performing the strength test itself. To investigate this further we reviewed the literature looking for studies comparing high load and low load exercise. The included studies were separated into ‘no extra practice’ and ‘practice’. No extra practice means the strength test was only performed at pre and post whereas practice refers to additional strength tests performed throughout the training intervention. Our results indicated that the differences between high load and low load exercise can be reduced when the group training with a low load is allowed additional exposure to the maximal strength test. This suggests that repeated exposure to strength tests may augment low load training adaptations and influence the outcomes. We discuss potential moderators of this relationship (e.g. how low is the low load, complexity of the skill) and offer considerations for future research. Based on this it would be recommended that when investigating the effects of low load training strength tests should be limited to pre and post intervention or if a control group is utilized then the control group should receive the same number of exposures to the strength test.
Propagation effects in multipass high harmonic generation from plasma surfaces
Authors: Tietze S , Zepf M , Rykovanov S G , Yeung M 
Published: August 2020

Abstract
Multipass high harmonic generation from plasma surfaces is a promising technique to enhance the efficiency of the generation process. In this paper it is shown that there is an optimal distance between two targets where the efficiency is maximized, depending on the laser and plasma parameters. This can be explained by the Gouy phase shift, which leads to the relative phase between the colours being changed with propagation in free space. A simple model is used to mimic the propagation of light from one target to another and to observe this effect in 1D particle-in-cell (PIC) simulations. The results are also verified using 2D PIC simulations.
Increasingly uneven intra-seasonal distribution of daily and hourly precipitation over Eastern China
Authors: Chen Yang 
Published: August 2020

Abstract
It has been long appreciated that precipitation falls unevenly in time, but the degree of unevenness and its changes with warming have been seldomly quantified. These quantifications, however, matter to various sectors (e.g. crop and livestock yields) for addressing evolutionary hydro-meteorological hazards. Using gauge observations at hourly- and daily-resolution, precipitation unevenness is measured by the number of wettest days/hours for half of seasonal precipitation totals over Eastern China, a major breadbasket vulnerable to precipitation volatility intra-seasonally. Across the region, half of seasonal totals needs only 11 d or even more unexpectedly just 44 h to precipitate. During 1970–2017, though seasonal precipitation amount changed little, the intra-seasonal distribution of precipitation, in both frequency and amount, has been getting significantly more uneven, with more widespread and faster changes manifesting in hourly records. The regional-scale unevenness increase is unlikely modulated by internal variability alone, suggesting detectable contributions from anthropogenic climate change. The increased unevenness has led to significant lengthening of the longest dry spells, exposing the region to a more volatile precipitation mode—burstier-but-wetter storms with prolonged droughts in-between.
Climate change and shifts in cropping systems together exacerbate China’s water scarcity
Authors: Zhang Li , Chen Fu , Lei Yongdeng 
Published: August 2020

Abstract
Water shortage is regarded as the most critical constraint limiting the world’s capacity for food security. While previous studies have attributed water scarcity primarily to climate change or some natural factors (e.g. lack of fresh water), few have investigated the impacts of shifts in agricultural systems on water resources. This study quantitatively distinguished the effects of spatiotemporal changes in climatic factors (e.g. temperature and precipitation), planted area, and crop type on China’s irrigation water resources by use of logarithmic mean Divisia index. The results indicated that in the past 25 years (from 1990 to 2015), changes in planted area, crop mix, and climatic factors all led to an increase in irrigation water demand (IWD) in China. Changes in planted area had the greatest effect on IWD (+45.4 × 109 m3), followed by the climate change effect (+10.8 × 109 m3). In particular, the rapid expansion of maize and other crops in northern China in recent decades has greatly increased irrigation water consumption. It is suggested that in addition to mitigating the adverse effects of climate change, China must address its water scarcity problems by appropriately controlling the scale of some water-intensive crops. These strategies will be essential for adapting agricultural production to future climate change while ensuring food security and water sustainability.
Duality relations between spatial birth–death processes and diffusions in Hilbert space
Authors: Greenman Chris D 
Published: August 2020

Abstract
Spatially dependent birth–death processes can be modelled by kinetic models such as the BBGKY hierarchy. Diffusion in infinite dimensional systems can be modelled with Brownian motion in Hilbert space. In this work Doi field theoretic formalism is utilised to establish dualities between these classes of processes. This enables path integral methods to calculate expectations of duality functions. These are exemplified with models ranging from stochastic cable signalling to jump-diffusion processes.
Position representation of single-mode Gaussian channels beyond the Gaussian functional form
Authors: Davalos David , Moreno Camilo , Urbina Juan-Diego , Pineda Carlos 
Published: August 2020

Abstract
We study one-mode Gaussian quantum channels in continuous-variable systems by performing a black-box characterization using complete positivity and trace preserving conditions, and report the existence of two subsets that do not have a functional Gaussian form. Our study covers as a particular limit the case of singular channels, thus connecting our results with their known classification scheme based on canonical forms. Our full characterization of Gaussian channels without Gaussian functional form is completed by showing how Gaussian states are transformed under these operations, and by deriving the conditions for the existence of master equations for the non-singular cases. We show that although every functional form can be found in the vicinity of the identity, one of them does not parametrize unitary channels.
CSynth: an interactive modelling and visualization tool for 3D chromatin structure
Authors: Todd Stephen , Todd Peter , McGowan Simon J , Hughes James R , Kakui Yasutaka , Leymarie Frederic Fol , Latham William , Taylor Stephen 
Published: August 2020

Abstract

Motivation
The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools.

Results
We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool.

Availabilityand implementation
CSynth is web based and available to use at csynth.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions
Authors: Zammit Alan , Helwerda Leon , Olsthoorn René C L , Verbeek Fons J , Gultyaev Alexander P 
Published: August 2020

Abstract

Motivation
The Flavivirus genus includes several important pathogens, such as Zika, dengue and yellow fever virus. Flavivirus RNA genomes contain a number of functionally important structures in their 3′ untranslated regions (3′UTRs). Due to the diversity of sequences and topologies of these structures, their identification is often difficult. In contrast, predictions of such structures are important for understanding of flavivirus replication cycles and development of antiviral strategies.

Results
We have developed an algorithm for structured pattern search in RNA sequences, including secondary structures, pseudoknots and triple base interactions. Using the data on known conserved flavivirus 3′UTR structures, we constructed structural descriptors which covered the diversity of patterns in these motifs. The descriptors and the search algorithm were used for the construction of a database of flavivirus 3′UTR structures. Validating this approach, we identified a number of domains matching a general pattern of exoribonuclease Xrn1-resistant RNAs in the growing group of insect-specific flaviviruses.

Availability and implementation
The Leiden Flavivirus RNA Structure Database is available at https://rna.liacs.nl. The search algorithm is available at https://github.com/LeidenRNA/SRHS.

Supplementary information
Supplementary data are available at Bioinformatics online.
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein–protein binding affinity
Authors: Li Gen , Pahari Swagata , Murthy Adithya Krishna , Liang Siqi , Fragoza Robert , Yu Haiyuan , Alexov Emil 
Published: August 2020

AbstractMotivationVast majority of human genetic disorders are associated with mutations that affect protein–protein interactions by altering wild-type binding affinity. Therefore, it is extremely important to assess the effect of mutations on protein–protein binding free energy to assist the development of therapeutic solutions. Currently, the most popular approaches use structural information to deliver the predictions, which precludes them to be applicable on genome-scale investigations. Indeed, with the progress of genomic sequencing, researchers are frequently dealing with assessing effect of mutations for which there is no structure available.ResultsHere, we report a Gradient Boosting Decision Tree machine learning algorithm, the SAAMBE-SEQ, which is completely sequence-based and does not require structural information at all. SAAMBE-SEQ utilizes 80 features representing evolutionary information, sequence-based features and change of physical properties upon mutation at the mutation site. The approach is shown to achieve Pearson correlation coefficient (PCC) of 0.83 in 5-fold cross validation in a benchmarking test against experimentally determined binding free energy change (ΔΔG). Further, a blind test (no-STRUC) is compiled collecting experimental ΔΔG upon mutation for protein complexes for which structure is not available and used to benchmark SAAMBE-SEQ resulting in PCC in the range of 0.37–0.46. The accuracy of SAAMBE-SEQ method is found to be either better or comparable to most advanced structure-based methods. SAAMBE-SEQ is very fast, available as webserver and stand-alone code, and indeed utilizes only sequence information, and thus it is applicable for genome-scale investigations to study the effect of mutations on protein–protein interactions.Availability and implementationSAAMBE-SEQ is available at http://compbio.clemson.edu/saambe_webserver/indexSEQ.php#started.Supplementary informationSupplementary data are available at Bioinformatics online.
Trypanosoma brucei gambiense-iELISA: A Promising New Test for the Post-Elimination Monitoring of Human African Trypanosomiasis
Authors: Geerts Manon , Van Reet Nick , Leyten Sander , Berghmans Raf , Rock Kat S , Coetzer Theresa H T , Eyssen Lauren E-A , Büscher Philippe 
Published: August 2020

Abstract

Background
The World Health Organization targeted Trypanosoma brucei gambiense human African trypanosomiasis (gHAT) for elimination as a public health problem and for elimination of transmission. To measure gHAT elimination success with prevalences close to zero, highly specific diagnostics are necessary. Such a test exists in the form of an antibody-mediated complement lysis test, the trypanolysis test, but biosafety issues and technological requirements prevent its large-scale use. We developed an inhibition ELISA with high specificity and sensitivity that is applicable in regional laboratories in gHAT endemic countries.

Methods
The T. b. gambiense inhibition ELISA (g-iELISA) is based on the principle that binding of monoclonal antibodies to specific epitopes of T. b. gambiense surface glycoproteins can be inhibited by circulating antibodies of gHAT patients directed against the same epitopes. Using trypanolysis as reference test, the diagnostic accuracy of the g-iELISA was evaluated on plasma samples from 739 gHAT patients and 619 endemic controls and on dried blood spots prepared with plasma of 95 gHAT and 37 endemic controls.

Results
Overall sensitivity and specificity on plasma were, respectively, 98.0% (95% CI 96.7–98.9) and 99.5% (95% CI 98.6–99.9). With dried blood spots, sensitivity was 92.6% (95% CI 85.4–97.0), and specificity was 100% (95% CI 90.5–100.0). The g-iELISA is stable for at least 8 months when stored at 2–8°C.

Conclusion
The g-iELISA might largely replace trypanolysis for monitoring gHAT elimination and for postelimination surveillance. The g-iELISA kit is available for evaluation in reference laboratories in endemic countries.
Patient Characteristics and Outcomes of 11 721 Patients With Coronavirus Disease 2019 (COVID-19) Hospitalized Across the United States
Authors: Fried Michael W , Crawford Julie M , Mospan Andrea R , Watkins Stephanie E , Munoz Breda , Zink Richard C , Elliott Sherry , Burleson Kyle , Landis Charles , Reddy K Rajender , Brown Robert S 
Published: August 2020

Abstract

Background
As coronavirus disease 2019 (COVID-19) disseminates throughout the United States, a better understanding of the patient characteristics associated with hospitalization, morbidity, and mortality in diverse geographic regions is essential.

Methods
Hospital chargemaster data on adult patients with COVID-19 admitted to 245 hospitals across 38 states between 15 February and 20 April 2020 were assessed. The clinical course from admission, through hospitalization, and to discharge or death was analyzed.

Results
A total of 11 721 patients were included (majority were &gt;60 years of age [59.9%] and male [53.4%]). Comorbidities included hypertension (46.7%), diabetes (27.8%), cardiovascular disease (18.6%), obesity (16.1%), and chronic kidney disease (12.2%). Mechanical ventilation was required by 1967 patients (16.8%). Mortality among hospitalized patients was 21.4% and increased to 70.5% among those on mechanical ventilation. Male sex, older age, obesity, geographic region, and the presence of chronic kidney disease or a preexisting cardiovascular disease were associated with increased odds of mechanical ventilation. All aforementioned risk factors, with the exception of obesity, were associated with increased odds of death (all P values &lt; .001). Many patients received investigational medications for treatment of COVID-19, including 48 patients on remdesivir and 4232 on hydroxychloroquine.

Conclusions
This large observational cohort describes the clinical course and identifies factors associated with the outcomes of hospitalized patients with COVID-19 across the United States. These data can inform strategies to prioritize prevention and treatment for this disease.
Neuromuscular Junction Aging: A Role for Biomarkers and Exercise
Authors: Pratt Jedd , De Vito Giuseppe , Narici Marco , Boreham Colin 
Published: August 2020

Abstract
Age-related skeletal muscle degradation known as “sarcopenia” exerts considerable strain on public health systems globally. While the pathogenesis of such atrophy is undoubtedly multifactorial, disruption at the neuromuscular junction (NMJ) has recently gained traction as a key explanatory factor. The NMJ, an essential communicatory link between nerve and muscle, undergoes profound changes with advancing age. Ascertaining whether such changes potentiate the onset of sarcopenia would be paramount in facilitating a timely implementation of targeted therapeutic strategies. Hence, there is a growing level of importance to further substantiate the effects of age on NMJs, in parallel with developing measures to attenuate such changes. As such, this review aimed to establish the current standpoint on age-related NMJ deterioration and consequences for skeletal muscle, while illuminating a role for biomarkers and exercise in ameliorating these alterations. Recent insights into the importance of key biomarkers for NMJ stability are provided, while the stimulative benefits of exercise in preserving NMJ function are demonstrated. Further elucidation of the diagnostic and prognostic relevance of biomarkers, coupled with the therapeutic benefits of regular exercise may be crucial in combating age-related NMJ and skeletal muscle degradation.
The magnitude of intimate partner violence during pregnancy in Eldoret, Kenya: exigency for policy action
Authors: Luhumyo Loice , Mwaliko Emily , Tonui Philliph , Getanda Amos , Hann Katrina 
Published: August 2020

Abstract
Intimate partner violence (IPV) is sexual, psychological and physical coercive acts used against persons by intimate partners. When IPV occurs during pregnancy (IPVp), it can result in adverse maternal and pregnancy outcomes. No policy nor practice direction exists to address the rates and risk factors of IPVp in Kenya. Determining the prevalence, types and determinants of IPVp in Western Kenya would aid in the identification of pregnant women affected by and/or at risk of IPVp, as well as informing the development of policy, practices and programmes to support preventive interventions. In this cross-sectional study of 369 women who had given birth at Moi Teaching and Referral Hospital, participants were recruited using systematic sampling and data collected via structured questionnaires adopted from the WHO Violence Against Women Instrument. Associations were made in relation to physical or sexual violence and psychological violence. Logistic regression was used to assess the association between determinants and occurrence of IPVp. The overall prevalence of IPVp was 34.1%. Prevalence of physical or sexual violence was 22.8%. Psychological violence emerged as the most common (27.4%) form of IPVp. A lower than tertiary level of education and previous experience of IPV were individually associated with physical/sexual IPVp, whereas psychological IPVp was associated with previous experience of IPV and was prevented by the intimate partner having formal employment. Preterm birth rates were found to be higher than the country’s rates. The prevalence rates of IPVp are high in Western Kenya. Strategies that address the promotion of respectful, nonviolent relationships and that interrupt the development of risk factors are required. Policies (clinical guidelines) targeting prevention of IPVp and screening and the identification of at-risk women and survivors of IPVp are needed urgently. Primary prevention through interrupting the occurrence of predisposing factors is key in addressing IPVp.
Incidence, Clinical Characteristics, and Evolution of SARS-CoV-2 Infection in Patients With Inflammatory Bowel Disease: A Single-Center Study in Madrid, Spain
Authors: Guerra Ivan , Algaba Alicia , Jiménez Laura , Mar Aller Mª , Garza Daniel , Bonillo Daniel , Molina Esteban Laura María , Bermejo Fernando 
Published: August 2020

Abstract

Background
There are scarce data about SARS-CoV-2 infection in patients with inflammatory bowel disease (IBD). Our aim was to analyze the incidence, clinical presentation, and severity of SARS-CoV-2 infection in patients with IBD.

Methods
This is a cross-sectional, observational study. We contacted all the patients being treated at our IBD unit to identify those patients with suspected or confirmed SARS-CoV-2 infection, following the World Health Organization case definition. Data were obtained by patient electronical medical records and by phone interview.

Results
Eighty-two of 805 patients with IBD (10.2%; 95% confidence interval [CI], 8.3-12.5) were diagnosed as having confirmed (28 patients, 3.5%; 95% CI, 2.4-5.0) or suspected (54 patients, 6.7%) infection. Patient age was 46 ± 14 years, 44 patients were female (53.7%), 17.3% were smokers, 51.2% had Crohn disease (CD), and 39.0% had comorbidities. Digestive symptoms were reported in 41 patients (50.0%), with diarrhea as the most common (42.7%). One patient (1.2%) was diagnosed with IBD flare-up during SARS-CoV-2 infection. Twenty-two patients (26.8%) temporarily withdrew from their IBD treatment because of COVID-19. Most of the patients had mild disease (79.3%), and 1 patient died (1.2%). In the multivariate analysis, the presence of dyspnea was associated with moderate to severe infection (odds ratio, 5.3; 95% CI, 1.6-17.7; P = 0.01) and myalgias (odds ratio, 4.8; 95% CI, 1.3-17.9; P = 0.02) were related to a milder clinical course. Immunosuppression was not related to severity.

Conclusions
SARS-CoV-2 infection in patients with IBD is not rare. Dyspnea is associated with a more severe infection. Therapy for IBD, including immunomodulators and biologic therapy, is not related to a greater severity of COVID-19, and SARS-CoV-2 infections do not appear to be related to IBD flare-ups.