bluuebunny/crossref_metadata_2025_split huggingface dataset:
P-Curve Analysis of the Köhler Motivation Gain Effect in Exercise Settings: A Demonstration of a Novel Technique to Estimate Evidential Value Across Multiple Studies
Authors: Hill Christopher R , Samendinger Stephen , Rymal Amanda M 
Published: October 2020

Abstract

Background
Practitioners and researchers may not always be able to adequately evaluate the evidential value of findings from a series of independent studies. This is partially due to the possibility of inflated effect size estimates for these findings as a result of researcher manipulation or selective reporting of analyses (i.e., p-hacking). In light of the possible overestimation of effect sizes in the literature, the p-curve analysis has been proposed as a worthwhile tool that may help identify bias across a series of studies focused on a single effect. The p-curve analysis provides a measure of the evidential value in the published literature and might highlight p-hacking practices.

Purpose
Therefore, the purpose of this paper is to introduce the mechanics of the p-curve analysis to individuals researching phenomena in the psychosocial aspects of behavior and provide a substantive example of a p-curve analysis using findings from a series of studies examining a group dynamic motivation gain paradigm.

Methods
We performed a p-curve analysis on a sample of 13 studies that examined the Köhler motivation gain effect in exercise settings as a means to instruct readers how to conduct such an analysis on their own.

Results
The p-curve for studies examining the Köhler effect demonstrated evidential value and that this motivation effect is likely not a byproduct of p-hacking. The p-curve analysis is explained, as well as potential limitations of the analysis, interpretation of the results, and other uses where a p-curve analysis could be implemented.
Network Pharmacology and bioinformatics analyses identify intersection genes of niacin and COVID-19 as potential therapeutic targets
Authors: Li Rong , Li Yu , Liang Xiao , Yang Lu , Su Min , Lai Keng Po 
Published: October 2020

AbstractObjectivesPatients with colorectal cancer (CRC) may be susceptible to the coronavirus disease-2019 (COVID-19). However, anti-CRC/COVID-19 treatment options are currently unavailable. Since niacin is a vitamin with cytoprotective and anti-inflammatory functions, this study aimed to evaluate the possible functional roles and underlying mechanisms of action of niacin as an anti-COVID-19 and -CRC therapy.InterventionsWe used a series of network pharmacology-based and computational analyses to understand and characterize the binding capacity, biological functions, pharmacological targets and therapeutic mechanisms of niacin in CRC/COVID-19.Measurements and main resultsWe revealed the clinical characteristics of CRC patients and COVID-19 patients, including predisposing genes, survival rate and prognosis. Moreover, the results of molecular docking analysis indicated that niacin exerted effective binding capacity in COVID-19. Further, we disclosed the targets, biological functions and signaling pathways of niacin in CRC/COVID-19. The analysis indicated that niacin could help in treating CRC/COVID-19 through cytoprotection, enhancement of immunologic functions, inhibition of inflammatory reactions and regulation of cellular microenvironment. Furthermore, five core pharmacological targets of niacin in CRC/COVID-19 were also identified, including BCL2L1, PTGS2, IL1B, IFNG and SERPINE1.ConclusionsThis study, for the first time, revealed the niacin-associated molecular functions and pharmacological targets for treating CRC/COVID-19, as COVID-19 remains a serious pandemic. But the findings were not validated in actual CRC patients infected with COVID-19, so further investigation is needed to confirm the potential use of niacin for treating CRC/COVID-19.
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
Authors: Hafez Ahmed , Futami Ricardo , Arastehfar Amir , Daneshnia Farnaz , Miguel Ana , Roig Francisco J. , Soriano Beatriz , Perez-Sánchez Jaume , Boekhout Teun , Gabaldón Toni , Llorens Carlos 
Published: October 2020

Abstract

Motivation
Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.

Result
SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets.

Availabilityand implementation
SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual.

Supplementary information
Supplementary data are available at Bioinformatics online.
Out of the OCBILs: new hypotheses for the evolution, ecology and conservation of the eucalypts
Authors: Hopper Stephen D 
Published: October 2020

Abstract
OCBIL theory is a multi-hypothesis formulation aimed towards an understanding of the evolution, ecology and conservation of biological and cultural diversity on old, climatically buffered, infertile landscapes (OCBILs). OCBILs have been in existence contemporaneously with rainforest since Gondwanan times. Such landscapes are common in areas of eucalypt species richness embraced by Australia’s two Global Biodiversity Hotspots, the Southwest Australian Floristic Region and the Forests of East Australia. Here, I summarize evidence pertaining to the eucalypts in the context of a recent reformulation of OCBIL theory into 12 evolutionary, ecological and cultural hypotheses and ten conservation management hypotheses. A compelling argument emerges for a new interpretation of the eucalypts evolving out of the OCBILs, rather than out of the rainforests as traditionally interpreted. This calls for a significant reinterpretation of best conservation management of the eucalypts. For example, traditional ideas on application of fire in eucalypt communities regarded as well adapted to this disturbance need to give way to a more nuanced and cautious view. This review of eucalypts seen as evolving out of the OCBILs helps in understanding the group from several new perspectives. Interpretation of other sedentary plant and animal groups as out of the OCBILs is commended for further study.
Alzheimer’s disease brain-derived extracellular vesicles spread tau pathology in interneurons
Authors: Ruan Zhi , Pathak Dhruba , Venkatesan Kalavai Srinidhi , Yoshii-Kitahara Asuka , Muraoka Satoshi , Bhatt Nemil , Takamatsu-Yukawa Kayo , Hu Jianqiao , Wang Yuzhi , Hersh Samuel , Ericsson Maria , Gorantla Santhi , Gendelman Howard E , Kayed Rakez , Ikezu Seiko , Luebke Jennifer I , Ikezu Tsuneya 
Published: October 2020

Abstract
Extracellular vesicles are highly transmissible and play critical roles in the propagation of tau pathology, although the underlying mechanism remains elusive. Here, for the first time, we comprehensively characterized the physicochemical structure and pathogenic function of human brain-derived extracellular vesicles isolated from Alzheimer’s disease, prodromal Alzheimer’s disease, and non-demented control cases. Alzheimer’s disease extracellular vesicles were significantly enriched in epitope-specific tau oligomers in comparison to prodromal Alzheimer’s disease or control extracellular vesicles as determined by dot blot and atomic force microscopy. Alzheimer’s disease extracellular vesicles were more efficiently internalized by murine cortical neurons, as well as more efficient in transferring and misfolding tau, than prodromal Alzheimer’s disease and control extracellular vesicles in vitro. Strikingly, the inoculation of Alzheimer’s disease or prodromal Alzheimer’s disease extracellular vesicles containing only 300 pg of tau into the outer molecular layer of the dentate gyrus of 18-month-old C57BL/6 mice resulted in the accumulation of abnormally phosphorylated tau throughout the hippocampus by 4.5 months, whereas inoculation of an equal amount of tau from control extracellular vesicles, isolated tau oligomers, or fibrils from the same Alzheimer’s disease donor showed little tau pathology. Furthermore, Alzheimer’s disease extracellular vesicles induced misfolding of endogenous tau in both oligomeric and sarkosyl-insoluble forms in the hippocampal region. Unexpectedly, phosphorylated tau was primarily accumulated in glutamic acid decarboxylase 67 (GAD67) GABAergic interneurons and, to a lesser extent, glutamate receptor 2/3-positive excitatory mossy cells, showing preferential extracellular vesicle-mediated GABAergic interneuronal tau propagation. Whole-cell patch clamp recordings of CA1 pyramidal cells showed significant reduction in the amplitude of spontaneous inhibitory post-synaptic currents. This was accompanied by reductions in c-fos+ GAD67+ neurons and GAD67+ neuronal puncta surrounding pyramidal neurons in the CA1 region, confirming reduced GABAergic transmission in this region. Our study posits a novel mechanism for the spread of tau in hippocampal GABAergic interneurons via brain-derived extracellular vesicles and their subsequent neuronal dysfunction.
Development and Validation of Stability Indicating High-Performance Liquid Chromatographic Method for Determination of Cyproheptadine Hydrochloride, its Impurity And Degradation Product
Authors: Abdelrahman Maha M , Abdelaleem Eglal A , Ali Nouruddin W , Emam Raghda A 
Published: October 2020

Abstract
This work presents a sensitive, accurate and selective RP-HPLC method for simultaneous determination of cyproheptadine HCl (CPH), its impurity B (dibenzosuberone) and CPH oxidative degradation product (10,11-dihydroxy-dibenzosuberone) in bulk powder and in pharmaceutical formulation. The RP-HPLC method depends on isocratic elution using C8 column and mobile phase consisting of 0.05 M KH2PO4 buffer:methanol (35:65, v/v, pH = 4.5) at a flow rate of 2 mL/min, and the eluant was monitored at 245 nm. Good resolution was obtained with tR values of 3.05, 7.54 and 6.17 min for CPH, impurity and oxidative degradate, respectively. The proposed method has been validated as per ICH guidelines using pure forms of CPH, its impurity and degradation product in pharmaceutical formulation with an accuracy of 100.48, 100.16 and 100.11, respectively. Additional spiking experiments yielded an accuracy of 100 ± 1.6%. Repeatability and intermediate precision results indicated acceptable low &lt;2% RSD values. Moreover, the developed method’s statistical results were favorably compared to the previously reported method results regarding both accuracy and precision. The developed method can be applied for analysis of the three components in quality control laboratories.
Revisiting the Performance of DNS Queries on a DNS Hierarchy Testbed over Dual-Stack
Authors: Adiwal Sanjay , Rajendran Balaji , Shetty D Pushparaj , Palaniappan Gopinath 
Published: October 2020

Abstract
The exponential growth of IoT devices and their need to use IPv6 addresses has the potential to create load stress on the existing DNS infrastructure and it is imperative that DNS servers to be deployed on IPv6 networks. The DNS query latency from a particular Internet vantage point for IPv4 and IPv6 network cannot be compared directly due to variations in the number of hops of query on IPv4 and IPv6 communication networks. Moreover, there is no assurance that DNS server in the hierarchy is hosted on a dual-stack. This work brings out the DNS query resolution latency over the IPv4 and IPv6 protocol stacks with better accuracy. The experiments are carried out by setting up a complete DNS hierarchy (ROOT, TLD, STLD, TTLD and recursive resolver) on dual IP stack (IPv4 and IPv6), enabling both forward and reverse lookup tree on a live testbed, ensuring a constant number of hops between the recursive resolver and each of the DNS servers in the hierarchy. This live testbed is a first of its kind and is made available for Internet researchers. The operational issues encountered during this deployment and service provisioning are discussed and documented in this paper. This paper also gives a clear illustration and provides reference guidelines for the DNS hierarchy setup, and also aims to bridge the knowledge gap required for deploying DNS over IPv6.
Impacts of Exotic Pasture Establishment on Dung Beetle Assemblages (Coleoptera: Scarabaeidae: Scarabaeinae) in the Brazilian Cerrado
Authors: Correa César M A , Puker Anderson , Abot Alfredo R 
Published: October 2020

Abstract
The Brazilian Cerrado is the second largest Neotropical biome and an important hotspot of biodiversity. However, land use change in this ecosystem is producing landscapes with modified natural environments and anthropogenic environments, such as exotic pastures. In this study, we evaluated how conversion of native Cerrado vegetation to exotic pastures affects the dung beetle assemblages (Coleoptera: Scarabaeidae: Scarabaeinae). We sampled dung beetles in four areas of Cerrado (sensu stricto) and in four areas of exotic pastures (Urochloa spp.) in Aquidauana, Mato Grosso do Sul, Brazil. In all, 7,544 individuals from 43 species of dung beetles were collected, and 19 species were found in both the Cerrado and exotic pastures. The abundance and species richness of dung beetles were higher in Cerrado remnants. Species composition differed between Cerrado and exotic pastures, where 11 species were classified as specialists of Cerrado, 10 species were considered specialists of exotic pastures, and 6 species were habitat generalists. Roller beetles were most negatively affected by exotic pasture establishment. We demonstrated that exotic pasture establishment has a negative impact on dung beetle assemblages in Brazilian Cerrado. The decline in abundance and richness of roller beetles has important implications for the understanding of ecosystem functioning because it can reduce the ecological functions performed by dung beetle assemblages in exotic pastures. Finally, the high number of dung beetle species shared between Cerrado and exotic pastures suggests that the Cerrado remnants is a fundamental requirement for the conservation of biodiversity of dung beetles in exotic pastures in the Brazilian Cerrado.
High Dietary Niche Overlap Between Non-native and Native Ant Species in Natural Ecosystems
Authors: Probert Anna F , Ward Darren F , Beggs Jacqueline R , Bury Sarah J , Hermans Syrie M , Lear Gavin , Stanley Margaret C 
Published: October 2020

AbstractAnts represent a highly diverse and ecologically important group of insects found in almost all terrestrial ecosystems. A subset of ant species have been widely transported around the globe and invade many natural ecosystems, often out-competing native counterparts and causing varying impacts on recipient ecosystems. Decisions to control non-native ant populations require an understanding of their interactions and related impacts on native communities. We employed stable isotope analysis and metabarcoding techniques to identify potential dietary niche overlap and identify gut contents of 10 ant species found in natural ecosystems in Aotearoa New Zealand. Additionally, we looked at co-occurrence to identify potential competitive interactions among native and non-native ant species. Ants fed mainly across two trophic levels, with high dietary overlap. Relative to other ant species sampled, two non-native ant species, Linepithema humile and Technomyrmex jocosus, were found to feed at the lowest trophic level. The largest isotopic niche overlap was observed between the native Monomorium antarcticum and the invasive Ochetellus glaber, with analyses revealing a negative co-occurrence pattern. Sequence data of ant gut content identified 51 molecular operational taxonomic units, representing 22 orders and 34 families, and primarily consisting of arthropod DNA. Although we generally found high dietary overlap among species, negative occurrence between a dominant, non-native species and a ubiquitous native species indicates that species-specific interactions could be negatively impacting native ecosystems. Our research progresses and informs the currently limited knowledge around establishing protocols for metabarcoding to investigate ant diet and interactions between native and non-native ant species.
Prognostic significance of the N1 classification pattern: a meta-analysis of different subclassification methods
Authors: Wang Zihuai , Yang Hanle , Hao Xiaohu , Zhou Jian , Chen Nan , Pu Qiang , Liu Lunxu 
Published: October 2020

Abstract

OBJECTIVES
The number of positive lymph node stations has been viewed as a subclassification in the N1 category in the new revision of tumour node metastasis (TNM) staging. However, the survival curve of these patients overlapped with that of some patients in the N2 categories. Our study focused on the prognostic significance of different subclassifications for N1 patients.

METHODS
We systematically searched PubMed, Ovid, Web of Science and the Cochrane Library on the topic of N1 lymph node dissection. Hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) were used to assess the prognostic significance of N1 metastases. I2 statistics was used to evaluate heterogeneity among the studies: If significant heterogeneity existed (P ≤ 0.10; I2 &gt;50%), a random effect model was adopted.

RESULTS
After a careful investigation, a total of 17 articles were included in the analysis. The results showed that patients with non-small-cell lung cancer with multistation N1 disease have worse survival compared with those with single-station N1 disease (HR 1.53, 95% CI 1.32–1.77; P &lt; 0.001; I2 = 5.1%). No significant difference was observed between groups when we assessed the number of positive lymph nodes (single or multiple) (HR 1.25, 95% CI 0.96–1.64; P = 0.097; I2 = 72.5%). Patients with positive hilar zone lymph nodes had poorer survival than those limited to the intrapulmonary zone (HR 1.80, 95% CI 1.57–2.07; P &lt; 0.001; I2 = 0%). A subgroup analysis conducted according to the different validated lymph node maps showed a stable result.

CONCLUSIONS
Our result confirmed the prognostic significance of the N1 subclassification based on station number. Meanwhile, location-based classifications, especially zone-based, were also identified as prognostically significant, which may need further confirmation and validation in the staged population.
‘Hypertension multiple’: Patients’ experiential knowledge concept of symptoms and care required, and its implications for public health
Authors: Mendoza J 
Published: October 2020

Abstract
Patients' conceptualisations of their disease do not always correspond to the biomedical definitions. Patients make sense of conditions by drawing on embodied experiences, beliefs circulating in their environments and information gathered from a variety of sources. Discrepancy between biomedical and patients' conceptualisations is problematic as it can affect treatment adherence, access to care, patient-provider communication and quality of patient experience. This is particularly the case for hypertension, an ‘invisible disease' that gives rise to various lay conceptions and practices. We examine how the disease is made ‘real' for Filipino hypertensive patients and the role their embodied experiences play in apprehending the chronicity of hypertension and in shaping care-related practices.
Drawing from interview and focus group data from hypertensive patients in low-income communities in the Philippines, and on Annemarie Mol's notion of ‘multiplicity', the ‘symptom' plays a key role in the ways in which participants self-manage ‘hypertension'. Hypertension is a ‘multiple' condition that is understood and enacted differently by people who rely on their own experiential knowledge and ‘symptoms' to define its nature and act accordingly to maintain health. Their ‘symptoms' may or may not correspond with the biomedical view of hypertension, leading to a non-chronic view of hypertension that informs the decision (not) to take maintenance medications regularly.
These findings have consequences for health communications and primary care. Failing to account for this ‘multiplicity' can also negatively impact experiences of care if patients feel that their embodied experiences are dismissed as less legitimate than biomedical indicators of the disease. Clinicians and public health officials must emphasize educational efforts that aim to address divergent views of noncommunicable diseases while respecting, listening to, and accounting for patients' experiential knowledge.