bluuebunny/crossref_metadata_2025_split huggingface dataset:
Varying richness need not imply non-random species co-occurrence: implications for specifying null models
Authors: Fayle Tom M. 
Published: November 2020

AbstractBackgroundNon-random species co-occurrence is of fundamental interest to ecologists. One approach to analysing non-random patterns is null modelling. This involves calculation of a metric for the observed dataset, and comparison to a distribution obtained by repeatedly randomising the data. Choice of randomisation algorithm, specifically whether null model species richness is fixed at that of the observed dataset, is likely to affect model results. This is particularly important in cases when there is high variation in species richness between sampling units in the observed data.MethodsHere I demonstrate the effects of accounting for variation in species richness. I use the C-score, a metric measuring species segregation as “checkerboard units”, applied to 289 datasets. First, I run null models in which sites are equally likely to be occupied (fixed-equiprobable algorithm). I do this both for the original datasets, and for the same datasets where occurrences are randomised with the species richness distribution fixed (pre-randomised datasets). Second, I run null models that fix site species richness to that observed (fixed-fixed algorithm).ResultsFor real datasets, using the fixed-equiprobable algorithm (sites are equally likely to be colonised), C-score standardised effect size (SES) was positively related to variability in species richness between sites within a dataset. This effect was also found for pre-randomised datasets, indicating that variability in species richness can be exclusively responsible for detection of non-random species co-occurrence. When using the fixed-fixed algorithm (richness is constrained to that of real sites), there was no relationship between SES and variability in species richness. There was also a reverse in the effect direction, with 94% of significant tests indicating a lower C-score than expected for the fixed-equiprobable algorithm, but 98% of significant tests indicating ahigherC-score than expected for the fixed-fixed algorithm.DiscussionI speculate that when variation in species richness is high, fewer checkerboard units are possible, regardless of segregation between species. Therefore, use of fixed-equiprobable algorithms in situations where real species richness is highly variable between sites within a dataset will yield significant results, even if species co-occur randomly within the constraints of the species richness distribution. Consequently, use of such tests makes the a priori assumption that high within-dataset variation in species richness indicates non-random species co-occurrence. I recommend using algorithms that explicitly take into account species richness distributions when one wants to eliminate the effect of richness variation in terms of producing significant but spurious positive co-occurrence results. Alternatively, non-null mechanistic models can be created, in which hypothesised species assembly processes must be explicitly stated and tested.
The oncogenic E3 ligase TRIP12 suppresses epithelial-mesenchymal transition (EMT) and metastasis-related processes through ZEB1/2
Authors: Lee Kwok Kin , Rajagopalan Deepa , Bhatia Shreshtha Sailesh , Chng Wee Joo , Jha Sudhakar 
Published: November 2020

ABSTRACTThyroid hormone receptor interactor 12 (TRIP12) is an E3 ligase most notably involved in the proteolytic degradation of the tumor suppressor p14ARF. Through this process, it is proposed that TRIP12 plays an oncogenic role in tumor initiation and growth. However, its role in other cancer processes such as metastasis is unknown. In this study, using publicly available cancer patient datasets, we found TRIP12 to be associated with distant metastasis-free survival in breast cancer, suggesting a contrary cancer process inhibitory role in metastasis. Following TRIP12 depletion in the MCF10A breast epithelial cell model, an epithelial-mesenchymal transition (EMT) shift occurred with concomitant changes in EMT cell adhesion markers identified through RNA-seq. In line with EMT changes, TRIP12-depleted cells lose polarity and dislodge from bulk cells at a higher frequency. Furthermore, ectopic TRIP12 expression sensitized cells to anoikis, a major barrier against metastasis. Mechanistically, TRIP12 suppresses EMT through inhibiting ZEB1/2 gene expression and ZEB1/2 depletion rescues EMT markers and cellular behavior. Overall, our study delineates TRIP12’s role in inhibition of EMT and metastasis-related processes, and implies a suppression role in breast cancer metastasis.
Deep brain stimulation modulates the dynamics of resting-state networks in patients with Parkinson’s Disease
Authors: Gomes Maria T. , Fernandes Henrique M. , Cabral Joana 
Published: November 2020

ABSTRACTDeep brain stimulation (DBS) of the subthalamic nucleus (STN) is increasingly used for the treatment of Parkinson’s Disease (PD), but despite its success, the neural mechanisms behind this surgical procedure remain partly unclear. As one working hypothesis, it was proposed that DBS works by restoring the balance of the brain’s resting-state networks (RSNs), which is reported to be disrupted in people with PD. Hence, to elucidate the effects that STN-DBS induces on disseminated networks, we analyzed an fMRI dataset of 20 PD patients at rest under DBS ON and OFF conditions. Moving beyond ‘static’ functional connectivity studies, we employ a recently developed fMRI analysis tool, the Leading Eigenvector Dynamic Analysis (LEiDA), to characterize the recurrence of brain-wide phase-locking patterns overlapping with known RSNs. Here, STN-DBS seems to increase the Default Mode Network (DMN) occurrence in individuals with PD. Since the DMN is usually disturbed in PD patients presenting deficits in cognition, our observation might be suggestive that STN-DBS contributes to a normalization of the PD-induced cognitive impairment.Moreover, we addressed the effects of DBS lead placement on RSNs balance, considering the overlap between the DBS-induced electric field and 3 STN subsections. We found that the Visual Network (VN) probability of occurrence increased proportionally to the electric field-limbic STN overlap. Our finding might be indicative that stimulation of the limbic STN is related to the stabilization of visual symptoms sometimes presented by PD patients, which are usually accompanied by VN disruption.Overall, this study offers new insights into the fine-grained temporal dynamics of brain states portraying the effects of STN-DBS in patients with PD, while at the same time trying to pave the way to improved planning strategies for this surgical procedure.
Integrated Analysis of Cell Shape and Movement in Moving Frame
Authors: Heryanto Yusri Dwi , Cheng Chin-Yi , Uchida Yutaka , Mimura Kazushi , Ishii Masaru , Yamada Ryo 
Published: November 2020

ABSTRACTThe cell movement and morphological change are two interrelated cellular processes. The integrated analysis is needed to explore the relationship between them. However, it has been challenging to investigate them as a whole. The cell trajectory can be described by its speed, curvature, and torsion. On the other hand, the 3-Dimensional (3D) cell shape can be studied by using a shape descriptor such as Spherical harmonic (SH) descriptor which is an extension of Fourier transform in 3D space.To integrate these shape-movement data, we propose a method to use a parallel-transport (PT) moving frame as the 3D-shape coordinate system. This moving frame is purely determined by the velocity vector. On this moving frame, the movement change will influence the coordinate system for shape analysis. By analyzing the change of the SH coefficients over time in the moving frame, we can observe the relationship between shape and movement.We illustrate the application of our approach using simulational and real datasets in this paper.
Community health worker knowledge, attitudes and practices towards COVID-19: learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique
Authors: Feldman Mitra , Krylova Vera Lacey , Farrow Poppy , Donovan Laura , Zandamela Edson , Rebelo Joaquim , Rodrigues Maria , Bulo Antonio , Ferraz Carlos , Gonzalez Juan Romero , Rodrigues Humberto , Roca-Feltrer Arantxa , Baker Kevin 
Published: November 2020

AbstractHealthcare workers (HCWs) are at the frontline of the Coronavirus Disease 2019 (COVID-19) pandemic response, yet there is a paucity of literature on their knowledge, attitudes and practices (KAP) in relation to the pandemic. Community Health Workers (CHWs) in Mozambique are known locally as agentes polivalentes elementares (APEs). While technical guidance surrounding COVID-19 is available to support APEs, communicating this information has been challenging due to restrictions on travel, face-to-face group meetings and training, imposed from May to August 2020. A digital health platform, upSCALE, that already supports 1,213 APEs and 299 supervisors across three provinces, is being used to support APEs on effective COVID-19 management by delivering COVID-19 sensitive SMS messages, training modules and a COVID-19 KAP survey.The KAP survey, conducted from June 2020 to August 2020, consisted of 10 questions. Of 1,065 active upSCALE APEs, 28 percent completed the survey. Results indicate that only a small proportion of APEs listed the correct COVID-19 symptoms, transmission routes and appropriate prevention measures (25 percent, 16 percent and 39 percent, respectively) specifically included in national health education materials. Misconceptions were mainly related to transmission routes, high risk individuals and asymptomatic patients. 84 percent said they followed all government prevention guidelines. The results from the KAP survey were used to support the rapid development and deployment of targeted COVID-19 awareness and education materials for the APEs. SMS messages were continually adjusted based on the KAP survey results and a series of seven COVID-19 training modules were developed and disseminated. A follow-up KAP survey is planned for November 2020.Adapting the existing upSCALE platform enabled a better understanding, in real time, of the KAP of APEs around COVID-19 management. Subsequently, supported improved delivery of tailored messages and education, vital for ensuring a successful COVID-19 response.
Evaluation of a home-based 7-day infection control strategy for healthcare workers following high-risk exposure to SARS-CoV-2: a cohort study
Authors: Benea Carla , Rendon Laura , Papenburg Jesse , Frenette Charles , Imcaoudene Ahmed , McDonald Emily G , Nguyen Quoc Dinh , Rajda Ewa , Tran Estelle , Vameghestahbanati Motahareh , Benedetti Andrea , Behr Marcel A , Smith Benjamin M 
Published: November 2020

ABSTRACTBackgroundEvidence-based infection control strategies are needed for healthcare workers (HCWs) following high-risk exposure to SARS-CoV-2. This study evaluated the negative predictive value (NPV) of a home-based 7-day infection control strategy.MethodsHCWs advised by their Infection Control or Occupational Health officer to self-isolate due to a high-risk SARS-CoV-2 exposure were enrolled between May-September 2020. The strategy consisted of symptom-triggered nasopharyngeal SARS-CoV-2 RNA testing from day 0-6 post exposure, followed by standardized home-based nasopharyngeal swab and saliva testing on day 7. The NPV of this strategy was calculated for i) clinical COVID-19 diagnosis from day 8-14 post exposure, and for ii) asymptomatic SARS-CoV-2 detected by standardized nasopharyngeal swab and saliva specimens collected at days 9-10 and 14 post exposure. Interim results are reported in the context of a second wave threatening this essential workforce.ResultsAmong 30 HCWs enrolled to date (age 31±9 years, 24 [80.0%] female), 3 were diagnosed with COVID-19 by day 14 post exposure (secondary attack rate 10.0%), with all cases detected by the 7-day infection control strategy: NPV for subsequent clinical COVID-19 or asymptomatic SARS-CoV-2 detection by day 14 was 100.0% (95%CI: 93.1-100.0%).InterpretationAmong HCWs with high-risk exposure to SARS-CoV-2, a home-based 7-day infection control strategy may have a high NPV for subsequent COVID-19 and asymptomatic SARS-CoV-2 detection. While ongoing data collection and data sharing are needed to improve the precision of the estimated NPV, we report interim results to inform infection control strategies in light of a second wave threatening this essential workforce.
Psychological resilience, coping behaviours, and social support among healthcare workers during the COVID-19 pandemic: A systematic review of quantitative studies
Authors: Labrague Leodoro J. 
Published: November 2020

AbstractAimTo appraise and synthesize studies examining resilience, coping behaviours, and social support among healthcare workers during the coronavirus pandemic.BackgroundA wide range of evidence has shown that healthcare workers, currently on the frontlines in the fight against COVID-19, are not spared from the psychological and mental health-related consequences of the pandemic. Studies synthesizing the role of coping behaviours, resilience, and social support in safeguarding the mental health of healthcare workers during the pandemic is largely unknown.EvaluationThis is a systematic review with a narrative synthesis. A total of 31 articles were included in the review.Key IssuesHealthcare workers utilized both problem-centred and emotion-centred coping to manage the stress-associated with the coronavirus pandemic. Coping behaviours, resilience, and social support were associated with positive mental and psychological health outcomes.ConclusionSubstantial evidence supports the effectiveness of coping behaviours, resilience, and social support to preserve psychological and mental health among healthcare workers during the COVID-19 pandemic.Implications for Nursing ManagementIn order to safeguard the mental health of healthcare workers during the pandemic, hospital and nursing administrators should implement proactive measures to sustain resilience in HCWs, build coping skills, and implement creative ways to foster social support in healthcare workers through theory-based interventions, supportive leadership, and fostering a resilient work environment.
Parental perceptions of COVID-19-like illness in their children
Authors: Hodson Ava , Woodland Lisa , Smith Louise E , Rubin G James 
Published: November 2020

AbstractObjectivesTo explore parents’ perceptions of COVID-19-like symptoms in their child and attitudes towards isolating from others in the household when unwell.Study DesignQualitative, semi-structured interviews.Methods30 semi-structured telephone interviews with parents of children between 4 and 18 years.ResultsWe found four themes relating to symptom attribution (‘normalising symptoms’, ‘err on the side of caution’, ‘experience of temperature’, ‘symptoms not normal for us’). In general, parents were more likely to attribute symptoms to COVID-19 if a temperature was present or the symptoms were perceived as ‘unusual’ for their family. Four themes relating to self-isolation (‘difficult to prevent contact with children’, ‘isolation would be no different to lockdown life’, ‘ability to get food and supplies’, ‘limited space’). Parents believed they would find isolation within the household difficult or impossible if they had dependent children, had limited space or could not shop for groceries.ConclusionsThe findings highlight complexities in symptom perception, attribution, and household isolation. We suggest that they can be overcome by a) providing better guidance on what symptoms require action, b) providing guidance as to how to prevent infection within the household, and c) by supporting families with grocery shopping through a potential second or third wave.
What support do frontline workers want? A qualitative study of health and social care workers’ experiences and views of psychosocial support during the COVID-19 pandemic
Authors: Billings Jo , Seif Nada Abou , Hegarty Siobhan , Ondruskova Tamara , Soulios Emilia , Bloomfield Michael , Greene Talya 
Published: November 2020

AbstractBackgroundThe COVID-19 pandemic has placed a significant burden on the mental health and wellbeing of frontline health and social care workers. The need to support frontline staff has been recognised. However, there is to date little research specifically on how best to support the mental health needs of frontline workers, and none on their own experiences and views about what might be most helpful.AimsWe set out to redress this research gap by qualitatively exploring UK frontline health and social care workers’ own experiences and views of psychosocial support during the pandemic.MethodFrontline health and social care workers were recruited purposively through social media and by snowball sampling via healthcare colleagues. Workers who volunteered to take part in the study were interviewed remotely following a semi-structured interview guide. Transcripts of the interviews were analysed by the research team following the principles of Reflexive Thematic Analysis.ResultsWe conducted 25 interviews with frontline workers from a variety of professional groups working in health and social care settings across the UK. Themes derived from our analysis showed that workers’ experiences and views about psychosocial support were complex. Peer support was many workers’ first line of support but could also be experienced as a burden. Workers were ambivalent about support shown by organisations, media and the public. Whilst workers valued psychological support services, there were many disparities in provision and barriers to access.ConclusionsThe results of this study show that frontline health and social care workers are likely to need a flexible system of support including peer, organisational and professional support. More research is needed to fully unpack the structural, systemic and individual barriers to accessing psychosocial support. Greater collaboration, consultation and co-production of support services and their evaluation is warranted.
SLAMF7 engagement super-activates macrophages in acute and chronic inflammation
Authors: Simmons Daimon P. , Nguyen Hung N. , Gomez-Rivas Emma , Jeong Yunju , Chen Antonia F. , Lange Jeffrey K. , Dyer George S. , Blazar Philip , Earp Brandon E. ,   Accelerating Medicines Partnership (AMP) RA/SLE Network, Rao Deepak A. , Kim Edy Y. , Brenner Michael B. 
Published: November 2020

AbstractMacrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a super-activated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression. Engaging this receptor drove an exuberant wave of inflammatory cytokine expression, and induction of TNF-α following SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients, but in gut macrophages from active Crohn’s disease patients and lung macrophages from severe COVID-19 patients. This suggests a central role for SLAMF7 in macrophage super-activation with broad implications in pathology.
CRISPRidentify: identification of CRISPR arrays using machine learning approach
Authors: Mitrofanov Alexander , Alkhnbashi Omer S. , Shmakov Sergey A. , Makarova Kira S. , Koonin Eugene V. , Backofen Rolf 
Published: November 2020

ABSTRACTCRISPR–Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR– Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are produced by processing of pre-crRNA, the transcript of CRISPR arrays, and guide Cas protein(s) to the cognate invading nucleic acids, enabling their destruction. Several bioinformatics tools have been developed to detect CRISPR arrays based solely on DNA sequences, but all these tools employ the same strategy of looking for repetitive patterns, which might correspond to CRISPR array repeats. The identified patterns are evaluated using a fixed, built-in scoring function, and arrays exceeding a cut-off value are reported. Here, we instead introduce a data-driven approach that uses machine learning to detect and differentiate true CRISPR arrays from false ones based on several features. Our CRISPR detection tool, CRISPRidentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false positive rate. In contrast to the existing tools, our approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as a practical measure of the likelihood that a given genomic region is a CRISPR array.
Ultra-precise quantification of mRNA targets across a broad dynamic range with nanoreactor beads
Authors: Loncarevic Ivan F. , Toepfer Susanne , Hubold Stephan , Klinger Susanne , Kanitz Lea , Ellinger Thomas , Steinmetzer Katrin , Ernst Thomas , Hochhaus Andreas , Ermantraut Eugen 
Published: November 2020

AbstractPrecise quantification of molecular targets in a biological sample across a wide dynamic range is a key requirement in many diagnostic procedures, such as monitoring response to therapy or detection of measurable residual disease. State of the art digital PCR assays provide for a dynamic range of four orders of magnitude. However digital assays are complex and require sophisticated microfluidic tools. Here we present an assay format that enables ultra-precise quantification of RNA targets in a single measurement across a dynamic range of more than seven orders of magnitude. The approach is based on hydrogel beads that provide for microfluidic free compartmentalization of the sample as they are used as digital nanoreactors for reverse transcription, PCR amplification and combined real time and digital detection of gene transcripts. We have applied these nanoreactors for establishing an assay for the detection and quantification of BCR-ABL1 fusion transcripts. The assay has been characterized for its accuracy and linear dynamic range. A comparison of the new method against the current clinical standard procedure with clinical samples from patients with chronic myeloid leukemia (CML) revealed good agreement between the results obtained with the respective method.