bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impaired Scaling of Step Length in Parkinsonian Postural Instability
Authors: McGovern Robert A. , Cortés Juan C. , Wilson Anne P. , McKhann Guy M. , Mazzoni Pietro 
Published: August 2020

AbstractBackgroundPostural stepping is an important strategy for recovery of balance in response to postural perturbations. It is disrupted by Parkinson’s disease (PD) and other conditions. The nature of this disruption remains poorly understood. Understanding the motor control nature of this impairment can guide the development of novel interventions.ObjectivesTo identify the motor control abnormalities responsible for parkinsonian impairment of postural stepping.MethodsWe studied four groups of participants: control, aged, PD, and normal-pressure hydrocephalus (NPH). We performed kinematic analysis of postural stepping by recording participants’ body motion during a modified version of the clinical pull test, which was performed multiple times with different amounts of pulling forcefulness.ResultsSuccessful postural stepping in the control group was accompanied by linear scaling of their first step’s length and latency to the body’s initial motion: more forceful pulls caused larger initial body acceleration, which resulted in longer steps that began earlier. PD patients exhibited reduced scaling of step length: they maintained normal reaction time but took steps that were inadequately short. Reduced step length scaling was present, but less severe, in aged individuals, and was more severe in NPH patients. Aged individuals and PD patients exhibited partial compensation for reduced step length scaling: their step length included a component that was independent of initial body acceleration, which was absent in control and NPH groups.Conclusionsthe impairment of postural stepping caused by PD and related conditions is due to inadequate scaling of movement amplitude and is thus a form of hypokinesia.
Decision models to improve healthcare-associated C. difficile PCR test use in patients with community-acquired pneumonia
Authors: Rhodes Nathaniel J. , Jozefczyk Caroline C. , Moore W. Justin , Yarnold Paul R. , Harkabuz Karolina , Sutton Sarah H. , Silkaitis Christina , Qi Chao , Wunderink Richard G. , Zembower Teresa R. 
Published: August 2020

AbstractAdults hospitalized with community-acquired pneumonia (CAP) typically receive antibiotics and thus are at increased risk of developing Clostridioides difficile infection (CDI), a disease of significant morbidity. We developed and validated a CAP-specific clinical decision algorithm to facilitate optimal diagnostic stewardship of C. difficile polymerase chain reaction (PCR) testing. The study was a single-center retrospective, case-control analysis of hospitalized adult patients empirically treated for CAP between January 1, 2014 and May 29, 2018. A series of predictive models and validity assessments were used to evaluate demographic and post-admission patient-specific risk factors as predictors of CDI case status among patients with CAP. Thirty-two PCR confirmed CDI cases were identified and 232 randomly selected controls were drawn from the total CAP population. After propensity score weighting, hospital-onset (HO) CDI was significantly associated with broad-spectrum Gram-negative antibiotic use (P=0.002) as was subsequent community-onset (CO) CDI (P=0.005). Modified-APACHE II > 8.5 (P=0.003) and broad-spectrum Gram-negative antibiotic use (P=0.002) were associated with healthcare-associated CDI and were robust in multiple validity analyses. Patients with m-APACHE II ≤ 8.5 who received broad-spectrum Gram-negative antibiotics were more likely (odds=1:2) to experience healthcare-associated CDI compared to those who did not receive these broad-spectrum agents (odds=1:125) and compared to those with m-APACHE II > 8.5 irrespective of treatment (odds=5:27). We conclude that broad-spectrum Gram-negative antibiotic use was the common factor in development of CDI in patients with CAP in all settings. Prospective studies are needed to confirm the reproducibility and clinical utility of our model when used for diagnostic test stewardship.
Short Adaptation of the Smell Test of the University of Pennsylvania (UPSIT) For the Venezuelan Population
Authors: Rosalinda Pieruzzini , Wilneg Rodríguez , Carlos Velázquez 
Published: August 2020

ABSTRACTThe objective of this study was to design a short smell test adapted to the Venezuelan population using the UPSIT test as a reference.Methodology: Preliminary surveys were carried out in 2 groups of patients (1010 patients for each group) until obtaining the most frequently recognized odors and preferred values of that population. Normosmia, hyposmia and anosmia were normalized. The results of the new Venezuelan test were compared with the UPSIT test in 169 patients. Results: Sensitivity 73%, Specificity 100% and Positive predictive value of 100 with a diagnostic accuracy of 85,21%. Conclusions: short venezuelan smell test is safe and with reliable results in the diagnosis of olfactory alterations.
Post-infection depression, anxiety and PTSD: a retrospective cohort study with mild COVID-19 patients
Authors: Ismael Flavia , Bizario João C. S. , Battagin Tatiana , Zaramella Beatriz , Leal Fabio E. , Torales Julio , Ventriglio Antonio , Marziali Megan E. , Martins Silvia S. , Castaldelli-Maia João M. 
Published: August 2020

AbstractBackgroundIt remains unclear whether COVID-19 is associated with psychiatric symptoms during or after the acute illness phase. Being affected by the disease exposes the individual to an uncertain prognosis and a state of quarantine. These factors can predispose individuals to the development of mental symptoms during or after the acute phase of the disease. There is a need for prospective studies assessing mental health symptoms in COVID-19 patients in the post-infection period.MethodsIn this retrospective cohort study, nasopharyngeal swabs for COVID-19 tests were collected at patients’ homes under the supervision of trained healthcare personnel. Patients who tested positive for COVID-19 and were classified as mild cases (N=895) at treatment intake were further assessed for the presence of mental health disorders (on average, 56.6 days after the intake). We investigated the association between the number of COVID-19 symptoms at intake and depression, anxiety and PTSD, adjusting for previous mental health status, time between baseline and outcome, and other confounders. Multivariate logistic regression and generalized linear models were employed for categorical and continuous outcomes, respectively.FindingsDepression, anxiety and PTSD were reported by 26.2% (N=235), 22.4% (N=201), and 17.3% (N=155) of the sample. Reporting an increased number of COVID-related symptoms was associated with depression (aOR=1.059;95%CI=1.002-1.119), anxiety (aOR=1.072;95%CI=1.012-1.134), and PTSD (aOR=1.092;95%CI=1.024-1.166). Sensitivity analyses supported findings for both continuous and categorical measures.InterpretationExposure to an increased number of COVID-19 symptoms may predispose individuals to depression, anxiety and PTSD after the acute phase of the disease. These patients should be monitored for the development of mental health disorders after COVID-19 treatment discharge. Early interventions, such as brief interventions of psychoeducation on coping strategies, could benefit these individuals.FundingThe city health department of São Caetano do Sul (Secretaria Municipal de Saúde da Prefeitura de São Caetano do Sul) funded the establishment and implementation of the COVID-19 platform.
Rapid genomic expansion and purging associated with habitat transitions in a clade of beach crustaceans (Haustoriidae: Amphipoda)
Authors: Hancock Zachary B. , Hardin Faith O. , Murthy Archana , Hillhouse Andrew , Johnston J. Spencer 
Published: August 2020

AbstractGenome sizes vary by orders of magnitude across the Tree of Life and lack any correlation with organismal complexity. Some crustacean orders, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that natural selection may constrain genome sizes due to physiological pressures. In this study, we examine the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncover a 6-fold genome size variation within a clade that is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. Finally, we find evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays.Significance StatementThe evolution of genome size has been a long-standing puzzle in biology. In this work, we find that genome sizes may be driven by different selection regimes following shifts to a new habitat. Dramatic genome size changes can occur rapidly, in only a few million years.Data Availability StatementRaw data sheets have been deposited on Dryad: SUBMITTED. Raw sequence reads are available at from NCBI under Bioproject SUBMITTED.
The immunodominant and neutralization linear epitopes for SARS-CoV-2
Authors: Lu Shuai , Xie Xi-xiu , Zhao Lei , Wang Bin , Zhu Jie , Yang Ting-rui , Yang Guang-wen , Ji Mei , Lv Cui-ping , Xue Jian , Dai Er-hei , Fu Xi-ming , Liu Dong-qun , zhang Lun , Hou Sheng-jie , Yu Xiao-lin , Wang Yu-ling , Gao Hui-xia , Shi Xue-han , Ke Chang-wen , Ke Bi-xia , Jiang Chun-guo , Liu Rui-tian 
Published: August 2020

ABSTRACTThe coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becomes a tremendous threat to global health. Although vaccines against the virus are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulated the three-dimensional structures of SARS-CoV-2 proteins with high performance computer, predicted the B cell epitopes on spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches, and then validated the epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. We also found that the immunodominant epitopes of domestic SARS-CoV-2 were different from that of the imported, which may be caused by the mutations on S (G614D) and N proteins. Importantly, we validated that eight epitopes on S protein elicited neutralizing antibodies that blocked the cell entry of both D614 and G614 pseudo-virus of SARS-CoV-2, three and nine epitopes induced D614 or G614 neutralizing antibodies, respectively. Our present study shed light on the immunodominance, neutralization, and conserved epitopes on SARS-CoV-2 which are potently used for the diagnosis, virus classification and the vaccine design tackling inefficiency, virus mutation and different species of coronaviruses.
Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element
Authors: Schlick T. , Zhu Q. , Jain S. , Yan S. 
Published: August 2020

ABSTRACTWith the rapid rate of Covid-19 infections and deaths, treatments and cures besides hand washing, social distancing, masks, isolation, and quarantines are urgently needed. The treatments and vaccines rely on the basic biophysics of the complex viral apparatus. While proteins are serving as main drug and vaccine targets, therapeutic approaches targeting the 30,000 nucleotide RNA viral genome form important complementary approaches. Indeed, the high conservation of the viral genome, its close evolutionary relationship to other viruses, and the rise of gene editing and RNA-based vaccines all argue for a focus on the RNA agent itself. One of the key steps in the viral replication cycle inside host cells is the ribosomal frameshifting required for translation of overlapping open reading frames. The frameshifting element (FSE), one of three highly conserved regions of coronaviruses, includes an RNA pseudoknot considered essential for this ribosomal switching. In this work, we apply our graph-theory-based framework for representing RNA secondary structures, “RAG” (RNA-As Graphs), to alter key structural features of the FSE of the SARS-CoV-2 virus. Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally-important stem and/or the pseudoknot of the FSE, potentially dismantling the virus against translation of the polyproteins. Additionally, our microsecond molecular dynamics simulations of mutant structures indicate relatively stable secondary structures. These findings not only advance our computational design of RNAs containing pseudoknots; they pinpoint to key residues of the SARS-CoV-2 virus as targets for anti-viral drugs and gene editing approaches.SIGNIFICANCESince the outbreak of Covid-19, numerous projects were launched to discover drugs and vaccines. Compared to protein-focused approaches, targeting the RNA genome, especially highly conserved crucial regions, can destruct the virus life cycle more fundamentally and avoid problems of viral mutations. We choose to target the small frame-shifting element (FSE) embedded in the Open Reading Frame 1a,b of SARS-CoV-2. This FSE is essential for translating overlapping reading frames and thus controlling the viral protein synthesis pathway. By applying graph-theory-based computational algorithms, we identify structurally crucial residues in the FSE as potential targets for anti-viral drugs and gene editing.
Tissue pressure and cell traction compensate to drive robust aggregate spreading
Authors: Yousafzai M. S. , Yadav V. , Amiri S. , Staddon M.F. , Tabatabai A. P. , Errami Y. , Jaspard G. , Amiri S. , Banerjee S. , Murrell M. 
Published: August 2020

AbstractIn liquid droplets, the balance of interfacial energies and substrate elasticity determines the shape of the droplet and the dynamics of wetting. In living cells, interfacial energies are not constant, but adapt to the mechanics of their environment. As a result, the forces driving the dynamics of wetting for cells and tissues are unclear and may be context specific. In this work, using a combination of experimental measurements and modeling, we show the surface tension of cell aggregates, as models of active liquid droplets, depends upon the size of the aggregate and the magnitude of applied load, which alters the wetting dynamics. Upon wetting rigid substrates, traction stresses are elevated at the boundary, and tension drives forward motion. By contrast, upon wetting compliant substrates, traction forces are attenuated, yet wetting occurs at a comparable rate. In this case, capillary forces at the contact line are elevated and aggregate surface tension contributes to strong outward, pressure-driven cellular flows. Thus, cell aggregates adapt to the mechanics of their environments, using pressure and traction as compensatory mechanisms to drive robust wetting.
Confinement Discerns Swarmers from Planktonic Bacteria
Authors: Chen Weijie , Mani Neha , Karani Hamid , Li Hao , Mani Sridhar , Tang Jay X. 
Published: August 2020

AbstractPowered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper flagellation have been shown to accompany the swarming phenotype. However, less noticeable, are the contrasts of collective motion between the swarming cells and the planktonic cells of comparable cell density. Here, we show that confining bacterial movement in designed dimensions allows distinguishing bacterial swarming from collective swimming. We found that on a soft agar plate, a novel bacterial strainEnterobactersp. SM3 exhibited different motion patterns in swarming and planktonic states when confined to circular microwells of a specific range of sizes. When the confinement diameter was between 40 μm and 90 μm, swarming SM3 formed a single swirl motion pattern in the microwells whereas planktonic SM3 showed multiple swirls. Similar differential behavior is observed across a range of randomly selected gram-negative bacteria. We hypothesize that the “rafting behavior” of the swarming bacteria upon dilution might account for the motion pattern difference. We verified our conjectures via numerical simulations where swarming cells are modeled with lower repulsion and more substantial alignment force. The novel technical approach enabled us to observe swarming on a non-agar tissue surface for the first time. Our work provides the basis for characterizing bacterial swarming under more sophisticated environments, such as polymicrobial swarmer detection, andin vivoswarming exploration.
“…I can use any syringe I find”: contextual determinants of HIV risk in public injecting settings in Nigeria
Authors: Nelson Ediomo-Ubong Ekpo , Nnam Macpherson Uchenna 
Published: August 2020

Purpose
The purpose of this study is to explore the contextual determinants of HIV risk among people who inject drugs (PWID) in public settings in Nigeria.

Design/methodology/approach
In-depth, individual interviews were conducted with 29 street-based PWID recruited through snowball sampling in Uyo, Nigeria. Interviews were tape-recorded, transcribed, coded and analysed hematically.

Findings
Homelessness and withdrawal pains encouraged consumption of drugs in public spaces (e.g. bunks, public parks). Conversely, the benefits of participation in street drug-use scenes, including reciprocity norms that guarantee free drugs during withdrawal and protection during overdose, fostered a preference for public injecting. Although participants recognized the need to inject with sterile syringes, scarcity of syringes compelled them to improvise with old syringes or share syringes, increasing risk for HIV transmission. HIV risk was exacerbated by unlawful and discriminatory policing practices, which deterred possession of syringes and encouraged risky behaviours such as rushing injection and sharing of equipment.

Practical implications
Contextual factors are key determinants of HIV risk for street-based PWID. Implementation of needle and syringe programmes as well as reforming legal frameworks and policing practices to support harm reduction are needed responses.

Originality/value
This is one of very few qualitative studies that explore risk factors for HIV transmission among PWID in West Africa. The focus on scarcity of sterile syringes and HIV risk is unique and has important policy implications.
The UK private housebuilding sector: social media perspectives
Authors: Craig Nigel , Pilcher Nick , MacKenzie Rebecca , Boothman Chris 
Published: August 2020

Purpose
The UK private housebuilding sector is the key supplier of new-build homes for customers, constituting a fifth of the entire UK construction industry. Yet, despite the high average cost of houses, and official reports advocating improvement, the sector remains blighted by criticism and a negative image of its quality. However, social media now offers customers new sources of advice and information. In this context, the purpose of this paper is to analyse social media forum posts from new-build homebuyers to reveal perceptions of the industry and illustrate the value of such data for others.

Design/methodology/approach
This paper presents and thematically analyses 147 comment posts from nine online Facebook forums under the themes of safety; standards; quality; workmanship; customer service; finance and money; advice; National House Building Council; ombudsman; and page closures.

Findings
Customers express frustration, anger, feelings of neglect and of an abdication of responsibility by the sector. Fundamentally, change is suggested at a systemic level, and it is urged this occurs through powerful and independent bodies.

Originality/value
To date, social media data has not been analysed in the context of the housebuilding sector. Yet, such data is key not only for its open and wide-reaching nature but also because it can be incorporated into government reports. It is hoped such data will be used by the new home ombudsman the UK Government hopes to establish in 2020 and help rectify many of the performance issues experienced and protect homebuyers.
Trust and knowledge contribution to agricultural cluster performance
Authors: Leonardo Sandra Bergamini , Silveira Marco Antonio Pinheiro , Martinez-Sánchez Paloma María Teresa , Romeiro Maria do Carmo 
Published: August 2020

PurposeThis paper aimed to analyze the contribution of the interorganizational relationship (IOR) factors trust and knowledge resources to the relational and transactional performance of a Brazilian agricultural cluster formed by small farmers.Design/methodology/approachA survey was conducted using a questionnaire divided into groups of variables, each group seeking to identify one of the three constructs: trust, knowledge resources and relational and transactional performance. A theoretical framework was elaborated and later compared with survey results, which were analyzed using exploratory factor analysis (EFA) and partial least squares–structural equation modeling (PLS-SEM).FindingsCorrelations between trust and relational and transactional cluster performance varied according to actors involved, being significant between some actors and not significant between others. Knowledge resources, on the other hand, proved to be significantly relevant for cluster performance, considering both relational and transactional measures.Research limitations/implicationsIt was made in a Brazilian single cluster and its conclusions cannot be generalized.Practical implicationsFarmers cannot innovate with the efficiency and effectiveness that the process demands. They need complementary capacity that apparently is not in the agricultural cluster. Research and development involve knowledge and techniques that empirical knowledge alone may not provide. And much of the formal knowledge is embedded in universities and research institutes. If there were investments by public entities in research and development to improve the culture and its by-products, this could contribute to improving the income of farmers.Social implicationsThis study provided a photograph of the current scenario of a Brazilian agricultural cluster. Changes in trust and knowledge resources could affect cluster relational and transactional performance. Special attention is deserved to the important role of scientific research on agricultural clusters to strengthen the capacity of critical analysis by the researcher who, with the results in hand, makes them public, hoping that the shared information can contribute with the research of other scholars and improve the quality of life of farmers involved.Originality/valueThis study offers empirical evidence that trust and knowledge resources can contribute to a Brazilian agricultural cluster performance, which can be analyzed considering both relational and transactional measures. These findings brought new fact to Singh and Shrivastava’s (2013) research.