bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for cross-immunity can improve forecast accuracy during influenza epidemics
Authors: Sachak-Patwa Rahil , Byrne Helen M , Thompson Robin N 
Published: July 2020

AbstractPrevious exposure to influenza viruses confers partial cross-immunity against future infections with related strains. However, this is not always accounted for explicitly in mathematical models used for forecasting during influenza outbreaks. We show that, if an influenza outbreak is due to a strain that is similar to one that has emerged previously, then accounting for cross-immunity explicitly can improve the accuracy of real-time forecasts. To do this, we consider two infectious disease outbreak forecasting models. In the first (the “1-group model”), all individuals are assumed to be identical and partial cross-immunity is not accounted for. In the second (the “2-group model”), individuals who have previously been infected by a related strain are assumed to be less likely to experience severe disease, and therefore recover more quickly than immunologically naive individuals. We fit both models to case notification data from Japan during the 2009 H1N1 influenza pandemic, and then generate synthetic data for a future outbreak by assuming that the 2-group model represents the epidemiology of influenza infections more accurately. We use the 1-group model (as well as the 2-group model for comparison) to generate forecasts that would be obtained in real-time as the future outbreak is ongoing, using parameter values estimated from the 2009 epidemic as informative priors, motivated by the fact that without using prior information from 2009, the forecasts are highly uncertain. In the scenario that we consider, the 1-group model only produces accurate outbreak forecasts once the peak of the epidemic has passed, even when the values of important epidemiological parameters such as the lengths of the mean incubation and infectious periods are known exactly. As a result, it is necessary to use the more epidemiologically realistic 2-group model to generate accurate forecasts. Accounting for partial cross-immunity driven by exposures in previous outbreaks explicitly is expected to improve the accuracy of epidemiological modelling forecasts during influenza outbreaks.
Automated and accurate segmentation of leaf venation networks via deep learning
Authors: Xu H. , Blonder B. , Jodra M. , Malhi Y. , Fricker M.D. 
Published: July 2020

SummaryLeaf vein network geometry can predict levels of resource transport, defence, and mechanical support that operate at different spatial scales. However, it is challenging to quantify network architecture across scales, due to the difficulties both in segmenting networks from images, and in extracting multi-scale statistics from subsequent network graph representations.Here we develop deep learning algorithms using convolutional neural networks (CNNs) to automatically segment leaf vein networks. Thirty-eight CNNs were trained on subsets of manually-defined ground-truth regions from >700 leaves representing 50 southeast Asian plant families. Ensembles of 6 independently trained CNNs were used to segment networks from larger leaf regions (~100 mm2). Segmented networks were analysed using hierarchical loop decomposition to extract a range of statistics describing scale transitions in vein and areole geometry.The CNN approach gave a precision-recall harmonic mean of 94.5% ± 6%, outperforming other current network extraction methods, and accurately described the widths, angles, and connectivity of veins. Multi-scale statistics then enabled identification of previously-undescribed variation in network architecture across species.We provide a LeafVeinCNN software package to enable multi-scale quantification of leaf vein networks, facilitating comparison across species and exploration of the functional significance of different leaf vein architectures.
Cancer cells are uniquely susceptible to accumulation of MMBIR mutations
Authors: Osia Beth , Alsulaiman Thamer , Jackson Tyler , Kramara Juraj , Oliveira Suely , Malkova Anna 
Published: July 2020

AbstractMicrohomology-mediated break-induced replication (MMBIR) is a mechanism of polymerase template switching at microhomology, which can produce complex genomic rearrangements (CGRs), underlies neurological and metabolic diseases, and contributes to cancer development. Yet, the extent of MMBIR activity in genomes is poorly understood due to difficulty in directly identifying MMBIR events by whole genome sequencing (WGS). Here, by using our newly developed MMBSearch software, we directly detect MMBIR events in human genomes and report substantial differences in frequency and complexity of MMBIR events between normal and cancer cells. MMBIR events appear only as germline variants in normal human fibroblast cells but readily accumulatede novoacross several cancer types. Detailed analysis of MMBIR mutations in lung adenocarcinomas revealed MMBIR-initiated chromosome fusions that disrupted potential tumor suppressor genes and induced CGRs. Our findings document MMBIR as a trigger for widespread genomic instability and highlight MMBIR as a potential driver of tumor evolution.
Targeted single-cell RNA-seq identifies minority cell types of kidney distal nephron that regulate blood pressure and calcium balance
Authors: Chen Lihe , Chou Chun-Lin , Knepper Mark A. 
Published: July 2020

ABSTRACTA major objective in modern biology is generation of comprehensive atlases of various organs identifying all cell types and their expressed genes. In kidney, extensive data exists for proximal tubule and collecting duct cells, but not for non-abundant intermediate epithelial cell types. Here, we coupled a FACS-enrichment protocol with single-cell RNA-seq analysis to profile the transcriptomes of 9099 cells from the nephron region adjacent to the macula densa. Clusters containingSlc12a3+/Pvalb+andSlc12a3+/Pvalb-cells were identified as DCT1 and DCT2 cells. The DCT1 cells appear to be heterogeneously associated with variable expression ofSlc8a1, Calb1, andCkbamong other mRNAs. No DCT2-specific transcripts were found. The analysis also identified two distinct cell types in theSlc12a1+portion of Henle’s loop as well asNos1+/Avpr1a+macula densa cells. Thus, we identify unexpected cell diversity in the intermediate region of the nephron and create a web-based data resource for these cells.
RNA-binding protein FXR1 drives cMYC translation by mRNA circularization through eIF4F recruitment in ovarian cancer
Authors: George Jasmine , Li Yongsheng , Parashar Deepak , Tsaih Shirng-Wern , Gupta Prachi , Geethadevi Anjali , Kadembari Ishaque P. , Ghosh Chandrima , Sun Yunguang , Ramchandran Ramani , Rader Janet S. , Rui Hallgeir , Dey Madhusudan , Pradeep Sunila , Chaluvally-Raghavan Pradeep 
Published: July 2020

AbstractBackgroundThe RNA-binding protein FXR1 (fragile X-related protein 1) has been implicated as an important regulator of post-transcriptional changes of mRNAs. However, its role in mRNA circularization and recruitment of eukaryotic translation initiation factors for protein translation remains obscure. Here, we aimed to investigate the molecular mechanisms and potential clinical applications of FXR1 in ovarian cancer growth and progression.MethodsFXR1 copy number variation, mRNA expression, protein levels, and their association with prognosis were determined in clinical datasets. An orthotopic ovarian cancer model and bioluminescence imaging were used for preclinical evaluation of FXR1 in vivo. Reverse phase protein arrays (RPPA) and qPCR arrays were performed to identify FXR1’s key targets and downstream effects. SUnSET and polysome profiling were used to determine the translational effects of FXR1. Immunoprecipitation and immunofluorescence were performed to identify the interaction between FXR1 and cMYC mRNA and eIF4F complex. RNA-immunoprecipitation (RIP), RNA electrophoretic mobility shift assays (REMSA), proximity ligation assays (PLA), and biochemical assays were used to identify the specific site on cMYC mRNA to which FXR1 binds to promote mRNA circularization and translation.ResultsWe found that amplification and copy-gain of FXR1 increased the expression of FXR1 mRNA and FXR1 protein in ovarian cancer patients, and these events associated with poor prognosis. We demonstrated that FXR1 binds to AU-rich elements (ARE) within the 3’ untranslated region (3’UTR) of cMYC. As a consequence, FXR1 binding to cMYC 3’UTR leads to the circularization of mRNA and facilitated the recruitment of eukaryotic translation initiation factors (eIFs) to translation start site for improving protein synthesis.ConclusionWe found that FXR1 upregulates a known oncogene, cMYC, by binding to AU-rich elements within the 3’UTR, leading to the recruitment of the eIF4F complex for cMYC translation. Our findings uncover a novel mechanism of action of FXR1 in tumorigenesis and provides opportunities to use FXR1 and its downstream effectors as biomarkers or therapeutic targets in ovarian and other cancers.
Muscle cell type diversification facilitated by extensive gene duplications
Authors: Cole Alison G. , Kaul Sabrina , Jahnel Stefan M. , Steger Julia , Zimmerman Bob , Reischl Robert , Richards Gemma Sian , Rentzsch Fabian , Steinmetz Patrick , Technau Ulrich 
Published: July 2020

AbstractThe evolutionary mechanisms underlying the emergence of new cell types are still unclear. Here, we address the origin and diversification of muscle cells in the diploblastic sea anemoneNematostella vectensis. We discern two fast and two slow-contracting muscle cell populations inNematostelladiffering by extensive sets of paralogous genes. The regulatory gene set of the slow cnidarian muscles and the bilaterian cardiac muscle are remarkably similar. By contrast, the two fast muscles differ substantially from each other, while driving the same set of paralogous structural protein genes. Our data suggest that extensive gene duplications and co-option of individual effector modules may have played an important role in cell type diversification during metazoan evolution.One Sentence SummaryThe study of the simple sea anemone suggests a molecular mechanism for cell type evolution and morphological complexity.
Confirmation of interpersonal expectations is intrinsically rewarding
Authors: Reggev Niv , Chowdhary Anoushka , Mitchell Jason P. 
Published: July 2020

AbstractPeople want to interact successfully with other individuals, and they invest significant efforts in attempting to do so. Decades of research have demonstrated that to simplify the dauntingly complex task of interpersonal communication, perceivers use stereotypes and other sources of prior knowledge to predict the responses of individuals in their environment. Here, we show that these top-down expectations can also shape the subjective value of expectation-consistent and expectation-violating targets. Specifically, in two neuroimaging experiments (n= 58), we observed increased activation in brain regions associated with reward processing—including the nucleus accumbens—when perceivers observed information consistent with their social expectations. In two additional behavioral experiments (n= 704), we observed that perceivers were willing to forgo money to encounter an expectation-consistent target and avoid an expectation-violating target. Together, these findings suggest that perceivers value having their social expectations confirmed, much like food or monetary rewards.
Gaze dynamics of feature-based distractor inhibition under the prior-knowledge and expectation
Authors: Wen Wen , Zhang Yangming , Li Sheng 
Published: July 2020

AbstractPrior information about distractor facilitates selective attention to task-relevant items and helps the optimization of oculomotor planning. Particularly, feature-based attentional inhibition could be benefited from the pre-knowledge of critical features of the distractors. In the present study, we capitalized on gaze-position decoding to examine the dynamics of attentional deployment in a feature-based attentional task that involved two groups of dots (target/distractor dots) moving toward different directions. Specifically, this measurement revealed how pre-knowledge of the target’s or distractor’s direction modulated real-time feature-based attentional bias. In Experiment 1, participants were provided with target cues indicating the moving direction of target dots. The results showed that participants were biased towards the cued direction and tracked the target dots throughout the task period. In Experiment 2 and Experiment 3, participants were provided with cues that informed the moving direction of distractor dots. The results showed that participants would continuously monitor the distractor’s direction when the distractor cue varied on a trial-by-trial basis (Experiment 2). However, when the to-be-ignored distractor direction remained constant (Experiment 3), participants would strategically bias their attention to the distractor’s direction before the cue onset and reduce the cost of re-deployment of attention between trials. These results suggest that monitoring the distractor’s feature is a prerequisite for feature-based attentional inhibition and this process is facilitated by the predictability of the distractor’s feature.
Species-Specific Responses of Bird Song Output in the Presence of Drones
Authors: Wilson Andrew M. , Boyle Kenneth S. , Gilmore Jennifer L. , Kiefer Cody J. , Walker Matthew F. 
Published: July 2020

AbstractDrones are now widely used to study wildlife, but applications for studying bioacoustics have been limited. Drones can be used to collect data on bird vocalizations, but an ongoing concern is that noise from the drones could change bird vocalization behavior. To test this behavioral impact we conducted an experiment using 30 sound localization arrays to track the song output of seven songbird species before, during, and after a 3-minute flight of a small quadcopter drone hovering at 50 m above ground level. We analyzed 8,303 song bouts, of which 2,285 song bouts of 184 individual birds were within 50 meters of the array centers. We used linear mixed effect models to assess patterns in song output showed patterns that could be attributed to the drone’s presence. We found no evidence of any effect of the drone for five species: American RobinTurdus migratorius, Common YellowthroatGeothlypis trichas, Field SparrowSpizella pusilla, Song SparrowMelospiza melodia, and Indigo BuntingPasserina cyanea. However, we found a substantial decrease in Yellow WarblerSetophaga petechiasong detections during the 3-minute drone hover, such that there was an 81% drop in detections in the 3rdminute (Wald-test, p<0.001), compared with before the drone’s introduction. In contrast, the number of singing Northern CardinalCardinalis cardinalisincreased after the drone was introduced, and remained almost five-fold higher for 4-minutes after the drone departed (P<0.001). Further, we found an increase in cardinal contact/alarm calls when the drone was overhead, with the elevated calling-rate sustaining for 2 minutes after the drone had departed (P<0.001). Our study suggests that responses of songbirds to drones may be species-specific, an important consideration when proposing the use of drones in avian studies. We note that recent advances in drone technology have resulted in much quieter drones, which makes us hopeful that the impacts that we detected could be greatly reduced.
Measuring the operational and financial efficiency using a Malmquist data envelopment analysis: a case of Egyptian hospitals
Authors: Habib Ahmed Mohamed , Shahwan Tamer Mohamed 
Published: July 2020

PurposeThe efficient use of organizational resources is integral to the existence of prime firms. This study, using Malmquist data envelopment analysis (DEA), aims to assess in the level of operational and financial efficiency and its determinants for ensuring and sustaining excellent performance in 33 Egyptian private hospitals.Design/methodology/approachThis study adopted a Malmquist DEA approach to assess the changes in operational and financial efficiency in Egyptian hospitals. Tobit regression was also used to identify the significant variables affecting their efficiency. In addition, a sensitivity analysis is carried out for model validations.FindingsOut of 33 hospitals, 17 were found inefficient due to the decline in their technical efficiency. Moreover, the total value of the software programs and operational expenses and the total number of employees are common factors affecting both operational and financial efficiency. In addition, the number of physicians significantly affects the hospital's financial efficiency.Practical implicationsThe study sheds light on the value of using DEA to assess efficiency. DEA in the context of emerging economy such as Egypt's can be a useful tool for decision-makers and practitioners in identifying and addressing performance weaknesses and thus supports continuous improvement in performance.Originality/valueSeveral studies have adopted the DEA approach to assess the overall efficiency of hospitals in Europe and the United States. However, in the MENA region, these studies are uncommon. This study is thought to be one of the earliest attempts to assess hospitals' efficiency in Egypt.
The value of including employees: a pluralist perspective on sustainable HRM
Authors: Van Buren III Harry J. 
Published: July 2020

PurposeThe purpose of this paper is to advance a conceptualization of sustainable HRM that builds on scholarship focusing on the pluralistic nature of human resource management. The paper seeks to advance the promise of sustainable HRM as an alternative to HRM scholarship that adopts a unitarist frame of reference.Design/methodology/approachThe paper draws on a variety of HRM-related literatures to offer new insights about what a pluralist perspective on sustainable HRM from the perspective of employees would look like and what it would accomplish, and in so doing allow sustainable HRM to become socially sustainable.FindingsTaking a pluralistic perspective is essential for making the concept of sustainable HRM more distinct and robust. Sustainable HRM can offer a challenge to the dominant unitarist perspective on the employment relationship, focusing the attention of researchers on the extent to which employment practices benefit both employers and employees while contributing to social sustainability outside of the employment context.Originality/valueThis paper adds analyses of pluralism and unitarism to the current literature on sustainable HRM while also focusing attention on how sustainable HRM might be more robustly conceptualized and also more normative in its orientation.
Is it face time or structure and accountability that matter? Moving from a flipped to a flipped/hybrid classroom
Authors: Smith Kara Diane 
Published: July 2020

PurposeThis research examines whether a shift to a hybrid classroom, which replaces some face-to-face classroom time with online instruction, adversely affects student learning if the structure and incentives that are characteristic of a flipped classroom are already in place.Design/methodology/approachThis study features a quantitative analysis of individual student data collected over multiple sections of a single course with the same instructor. In all seven sections, over two semesters, principles of microeconomics used a flipped classroom format that features preclass video lectures, daily quizzes and highly interactive class time. In three of the seven sections, the time spent in class was reduced by one-third. For this experiment, student scores on the cumulative final exam evaluate student learning. Students took a survey at the end of the semester to provide feedback on time use during the course and to make observations about the class format.FindingsResults from this study suggest that despite accountability for the work done outside of class, students score 4.4% points lower on the final exam in the class format that features reduced face-to-face time. However, student comments also suggest that this is a worthwhile tradeoff as they balance work, internships and other nonacademic demands on their time. Student evaluations of the course and instructor are statistically unchanged.Practical implicationsEfficiency in educational delivery is an ongoing concern for students and faculty. This research demonstrates that a classroom that is both flipped and hybrid makes better use of student and faculty time, provides a richer learning experience and only modestly reduces student learning. It is notable that students report a preference for the hybrid classroom model, despite modestly lower levels of learning.Originality/valueWhile research has been done on flipped and hybrid classrooms separately, this is the first paper to isolate the effect of seat time within the flipped classroom context. This research addresses the flipped classroom design's ability to mitigate the documented reduction in student learning that often results from reduced class time or an increase in online learning.
The effect of competition and passive avoidant leadership style on the occurrence of workplace bullying
Authors: Sischka Philipp E. , Schmidt Alexander F. , Steffgen Georges 
Published: July 2020

PurposeThe present study aimed to investigate the main effect of competition on workplace bullying (WB) exposure and perpetration as well as its hypothesized moderation through passive avoidant leadership style. Specifically, the authors hypothesized that competition would have a stronger influence on WB when supervisors score higher on passive avoidant leadership style.Design/methodology/approachData were collected among employees (N = 1,260) on Amazon’s Mechanical Turk utilizing an online survey. WB exposure and perpetration were cross-sectionally assessed via self-labeling and behavioral experience self-reports.FindingsThe results partially corroborated the proposed model. Competition and passive avoidant leadership were predictors of WB exposure and perpetration (as determined by both assessment methods). Furthermore, passive avoidant leadership moderated the relationship between competition and self-labeled WB exposure. Passive avoidant leadership only moderated the relationship between competition and self-labeled WB perpetration but not the competition–WB perpetration link assessed with the behavioral experience method.Practical implicationsThis study shows that competition needs to be embedded within a leadership style sensitive to the detection of and taking action against WB phenomena.Originality/valueWhile other studies have mainly focused on work stressors as antecedents of WB exposure, this study looks at the motivators and facilitators of WB occurrence. Furthermore, not only WB exposure but also WB perpetration is considered here, with the latter being an underresearched topic. Moreover, the authors used two assessment methods in order to test the generalizability of the authors’ findings.