bluuebunny/crossref_metadata_2025 huggingface dataset:
Muribaculum gordoncarteri sp. nov., an anaerobic bacterium from the faeces of C57BL/6J mice
Authors: Miyake Sou , Ding Yichen , Soh Melissa , Low Adrian , Seedorf Henning
Published: July 2020

An anaerobic bacterial strain, named TLL-A4T, was isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of the 16S rRNA gene indicated that the strain belongs to the phylum Bacteroidetes and, more specifically, to the recently proposed

Muribaculaceae

(also known as S24-7 clade or Candidatus Homeothermaceae). Strain TLL-A4T’s 16S rRNA gene shared 92.8 % sequence identity with the type strain of the only published species of the genus

Muribaculum

,

Muribaculum intestinale

DSM 28989T. Genome-sequencing of TLL-A4T was performed to compare average amino acid identity (AAI) value and percentage of conserved proteins (POCP) between both strains. The AAI analysis revealed that strain TLL-A4T had high identity (69.8 %) with

M. intestinale

DSM 28989T, while the POCP was 56 %. These values indicate that strain TLL-A4T could be considered a member of the genus

Muribaculum

but not belonging to the species

M. intestinale

. Quinone analysis indicated MK10 (63 %) and MK11 (32 %) as major quinones in the membrane, while MK9 was only present as a minor component (5 %). The main cellular fatty acid was anteiso-C15 : 0 (42.8 %); summed feature 11 (17.5 %), C15 : 0 iso (13.4 %), C18 : 1 ω9c (5.6 %), C16.0 3-OH (4.5 %) and C15 : 0 (4.2 %) were detected in minor amounts. Analysis of enzyme activities using the API 32A and API 20A kits indicated major differences between strain TLL-A4T and

Muribaculum intestinale

DSM 28989T. Based on genotypic, phylogenetic and phenotypic differences, strain TLL-A4T is considered to represent a novel species of the genus

Muribaculum

, for which the name Muribaculum gordoncarteri sp. nov. is proposed. The type strain is TLL-A4T (=DSM 108194T=KCTC 15770T).
COVID-19, Race, and Redlining
Authors: Bertocchi Graziella , Dimico Arcangelo
Published: July 2020

Discussion on the disproportionate impact of COVID-19 on African Americans has been at center stage since the outbreak of the epidemic in the United States. To present day, however, lack of race-disaggregated individual data has prevented a rigorous assessment of the extent of this phenomenon and the reasons why blacks may be particularly vulnerable to the disease. Using individual and georeferenced death data collected daily by the Cook County Medical Examiner, we provide first evidence that race does affect COVID-19 outcomes. The data confirm that in Cook County blacks are overrepresented in terms of COVID-19 related deaths since—as of June 16, 2020—they constitute 35 percent of the dead, so that they are dying at a rate 1.3 times higher than their population share.

Furthermore, by combining the spatial distribution of mortality with the 1930s redlining maps for the Chicago area, we obtain a block group level panel dataset of weekly deaths over the period January 1, 2020-June 16, 2020, over which we establish that, after the outbreak of the epidemic, historically lower-graded neighborhoods display a sharper increase in mortality, driven by blacks, while no pre-treatment differences are detected. Thus, we uncover a persistence influence of the racial segregation induced by the discriminatory lending practices of the 1930s, by way of a diminished resilience of the black population to the shock represented by the COVID-19 outbreak. A heterogeneity analysis reveals that the main channels of transmission are socioeconomic status and household composition, whose influence is magnified in combination with a higher black share.

JEL Codes

I14, J15, N32, N92, R38.
The Effect of Refractive Blur in the Vividness of Mental Imagery
Authors: Suresh Tharan , Roy Anupama , Shaikh Atif , Rajkumar Joanne Lydia , Mathew Vivek , Prabhakar A.T.
Published: July 2020

Background

Visual mental imagery or “seeing with the mind’s eye” is an everyday phenomenon. Visual mental imagery and visual perception share common neural-networks. Hence deficits that affect the visual perception may also affect visual mental imagery.

Aim

We aimed to study the effect of refractive blur on the vividness of mental imagery.

Methods

Subjects were recruited from volunteers and divided into two groups; individuals with refractive errors–Ametropes(AM), and individuals without refractive errors – Emmetropes(EM). After filling in the Verbalizer-Visualizer-Questionnaire (VVQ), the subjects were asked to perform a mental imagery task with and without refractive blur. The participants were asked to generate a mental image of a specific object initially with eyes closed, eyes open and then with refractive blur in random order, and then judge the vividness of the mental image on a Likert scale ranging from 1 (low vividness) to 5 (good vividness). The EM participants had to wear a + 2D spectacles to produce refractive blur.

Results

A total of 162 participants were recruited to the study. Of these 73 were EM and 89 were AM. Of the AM, 30 had additional astigmatism. The mean VVQ score was 64.9(11.2). The mean refractive error was 1.8(1.3)D. Following the mental imagery task, at baseline with eyes closed, 138 (85.5%)subjects had vivid mental imagery close to visual perception(Likert scale:5). With the opening of the eyes, the vividness dropped by at least 1 point in the Likert scale in 139(85.8%). With the introduction of refractive blur, 153(94.4%) subjects had a drop in the vividness of the image by at least 1 point and 22(13.6%) subjects by at least 2 points.

Conclusion

Introduction of refractory blur results in the reduction of the vividness of mental imagery.
MRI Brain Templates of the Male Yucatan Minipig
Authors: Norris Carly , Lisinski Jonathan , McNeil Elizabeth , VanMeter John W. , VandeVord Pamela , LaConte Stephen M.
Published: July 2020

The pig is growing in popularity as an experimental animal because its gyrencephalic brain is similar to humans. Currently, however, there is a lack of appropriate brain templates to support functional and structural neuroimaging pipelines. The primary contribution of this work is an average volume from an iterative, non-linear registration of 70 male Yucatan minipig subjects whose ages ranged from five to seven months. In addition, several aspects of this study are unique, including the comparison of linear and non-linear template generation, the characterization of a large and homogeneous cohort, an analysis of effective resolution after averaging, and the evaluation of potential within template bias as well as a comparison with a template from another minipig species using a “left-out” validation set. We found that within our highly homogeneous co-hort, non-linear registration produced better templates, but only marginally so. Although our T1-weighted data were resolution limited, we preserved effective resolution across the multi-subject average, produced templates that have high gray-white matter contrast, and demonstrated superior registration accuracy compared to the only known alternative minipig template.
Multifractal roots of suprapostural dexterity
Authors: Kelty-Stephen Damian G. , Lee I-Chieh , Carver Nicole S. , Newell Karl M. , Mangalam Madhur
Published: July 2020

Visually guided postural control emerges in response to task constraints. Task constraints generate physiological fluctuations that foster the exploration of available sensory information at many scales. Temporally correlated fluctuations quantified using fractal and multifractal metrics have been shown to carry perceptual information across the body. The risk of temporally correlated fluctuations is that stable sway appears to depend on a healthy balance of standard deviation (SD): too much or too littleSDentails destabilization of posture. This study presses on the visual guidance of posture by prompting participants to quietly stand and fixate at distances within, less than, and beyond comfortable viewing distance. Manipulations of the visual precision demands associated with fixating nearer and farther than comfortable viewing distance reveals an adaptive relationship betweenSDand temporal correlations in postural fluctuations. Changing the viewing distance of the fixation target shows that increases in temporal correlations andSDpredict subsequent reductions in each other. These findings indicate that the balance ofSDwithin stable bounds may depend on a tendency for temporal correlations to self-correct across time. Notably, these relationships became stronger with greater distance from the most comfortable viewing and reaching distance, suggesting that this self-correcting relationship allows the visual layout to press the postural system into a poise for engaging with objects and events. Incorporating multifractal analysis showed that all effects attributable to monofractal evidence were better attributed to multifractal evidence of nonlinear interactions across scales. These results offer a glimpse of how current nonlinear dynamical models of self-correction may play out in biological goal-oriented behavior. We interpret these findings as part of the growing evidence that multifractal nonlinearity is a modeling strategy that resonates strongly with ecological-psychological approaches to perception and action.
Exposure to maternal high-fat diet induces extensive changes in the brain of adult offspring
Authors: Fernandes Darren J. , Spring Shoshana , Roy Anna R. , Qiu Lily R. , Yee Yohan , Nieman Brian J. , Lerch Jason P. , Palmert Mark R.
Published: July 2020

Maternal environmental exposures, such as high-fat diets, diabetes and obesity, can induce long term effects in offspring. These effects include increased risk of neurodevelopmental disorders (NDDs) including autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), depression and anxiety. The mechanisms underlying these late-life neurologic effects are unknown. In this article, we measured changes in the offspring brain and determined which brain regions are sensitive to maternal metabolic milieu and therefore may mediate NDD risk. We showed that mice exposed to maternal high-fat diet display extensive brain changes in adulthood despite being switched to low-fat diet at weaning. Brain regions impacted by early-life diet include the extended amygdalar system, which plays an important role in reward-seeking behaviour. Genes preferentially expressed in these regions have functions related to feeding behavior, while also being implicated in human NDDs, such as autism. Our data demonstrated that exposure to maternal high-fat diet in early-life leads to brain alterations that persist into adulthood, even after dietary modifications.
Agro-morphological, yield, and genotyping-by-sequencing data of selected wheat germplasm
Authors: Islam Madiha , Abdullah  , Zubaida Bibi , Shafqat Nosheen , Masood Rabia , Khan Uzma , Waseem Shahid , Waheed Mohammad Tahir , Haider Waseem , Tahir Jibran , Ahmed Ibrar , Naeem Muhammad , Ahmad Habib
Published: July 2020

Wheat (Triticum aestivum) is the most important staple food in Pakistan. Knowledge of its genetic diversity is critical for designing effective crop breeding programs. Here we report agro-morphological and yield data for 112 genotypes (including 7 duplicates) of wheat (Triticum aestivum) cultivars, advance lines, landraces and wild relatives, collected from several research institutes and breeders across Pakistan. We also report genotyping-by-sequencing (GBS) data for a selected sub-set of 52 genotypes. Sequencing was performed using Illumina HiSeq 2500 platform using the PE150 run. Data generated per sample ranged from 1.01 to 2.5 Gb; 90% of the short reads exhibited quality scores above 99.9%. TGACv1 wheat genome was used as a reference to map short reads from individual genotypes and to filter single nucleotide polymorphic loci (SNPs). On average, 364,074±54479 SNPs per genotype were recorded. The sequencing data has been submitted to the SRA database of NCBI (accession number SRP179096). The agro-morphological and yield data, along with the sequence data and SNPs will be invaluable resources for wheat breeding programs in future.
Lethality of SARS-CoV-2 infection in K18 human angiotensin converting enzyme 2 transgenic mice
Authors: Oladunni Fatai S. , Park Jun-Gyu , Tamayo Paula Pino , Gonzalez Olga , Akhter Anwari , Allué-Guardia Anna , Olmo-Fontánez Angélica , Gautam Shalini , Garcia-Vilanova Andreu , Ye Chengjin , Chiem Kevin , Headley Colwyn , Dwivedi Varun , Parodi Laura M. , Alfson Kendra J. , Staples Hilary M. , Schami Alyssa , Garcia Juan I. , Whigham Alison , Platt Roy Neal , Gazi Michal , Martinez Jesse , Chuba Colin , Earley Stephanie , Rodriguez Oscar H , Mdaki Stephanie Davis , Kavelish Katrina N , Escalona Renee , Hallam Cory R. A. , Christie Corbett , Patterson Jean L. , Anderson Tim J. C. , Carrion Ricardo , Dick Edward J. , Hall-Ursone Shannan , Schlesinger Larry S. , Kaushal Deepak , Giavedoni Luis D. , Alvarez Xavier , Turner Joanne , Martinez-Sobrido Luis , Torrelles Jordi B.
Published: July 2020

ABSTRACT

Vaccine and antiviral development against SARS-CoV-2 infection or COVID-19 disease currently lacks a validated small animal model. Here, we show that transgenic mice expressing human angiotensin converting enzyme 2 (hACE2) by the human cytokeratin 18 promoter (K18 hACE2) represent a susceptible rodent model. K18 hACE2-transgenic mice succumbed to SARS-CoV-2 infection by day 6, with virus detected in lung airway epithelium and brain. K18 ACE2-transgenic mice produced a modest TH1/2/17 cytokine storm in the lung and spleen that peaked by day 2, and an extended chemokine storm that was detected in both lungs and brain. This chemokine storm was also detected in the brain at day 4. K18 hACE2-transgenic mice are, therefore, highly susceptible to SARS-CoV-2 infection and represent a suitable animal model for the study of viral pathogenesis, and for identification and characterization of vaccines (prophylactic) and antivirals (therapeutics) for SARS-CoV-2 infection and associated severe COVID-19 disease.
Algorithms underlying flexible phototaxis in larval zebrafish
Authors: Chen Alex B. , Deb Diptodip , Bahl Armin , Engert Florian
Published: July 2020

To thrive, organisms must maintain physiological and environmental variables in optimal ranges. However, in a dynamic world, the optimal range of a variable might fluctuate depending on the organism’s state or environmental conditions. Given these fluctuations, how do biological control systems maintain optimal control of physiological and environmental variables? We explored this question by studying the phototactic behavior of larval zebrafish. We demonstrate, with behavioral experiments and computational modeling, that larval zebrafish use phototaxis to maintain environmental luminance at a set point that depends on luminance history. We further show that fish compute this set point using information from both eyes, and that the set point fluctuates on a timescale of seconds when environmental luminance changes. These results expand on previous studies, where phototaxis was found to be primarily positive, and suggest that larval zebrafish, rather than consistently turning towards the brighter areas, exert homeostatic control over the luminance of their surroundings. Furthermore, we show that fluctuations in the surrounding luminance feed back on the system to drive allostatic changes to the luminance set point. Our work has uncovered a novel principle underlying phototaxis in larval zebrafish and characterized a behavioral algorithm by which larval zebrafish exert control over a sensory variable.
Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens
Authors: de Andrade da Silva Maura Santos Reis , Tavares Orlando Carlos Huertas , Ribeiro Thiago Gonçalves , de Andrade da Silva Camilla Santos Reis , de Andrade da Silva Carolina Santos Reis , García-Mina José Maria , Baldani Vera Lúcia Divan , García Andrés Calderín , Berbara Ricardo Luiz Louro , da Conceição Jesus Ederson
Published: July 2020

Humic acids (HAs) stimulate the growth of several plant species by regulating their hormonal and redox metabolisms. Nevertheless, studies on the relationship of these substances with the plant-associated microbiota are almost nonexistent. Here, we hypothesized that the effect of HAs occurs in parallel with the regulation of the plant-associated bacterial community. Our results show the positive influence of HAs on the growth of rice and its stimulation of the root system. Metataxonomics revealed that the structure and composition of root bacterial communities were affected upon the application of HAs.ChitinophagaandMucilaginibacterwere the predominant genera in HA-treated roots. These bacteria produce enzymes that degrade compounds like those present in the wall of fungi, oomycetes, and nematode eggs.Pseudomonasand theGp 1group ofAcidobacteria,both siderophore-producers and plant-growth promoters were also enriched, although with lower abundances. Given these results, we suggest that plants recruit these microorganisms in response to the stress caused by the HA-root interaction. For the first time, our findings indicate that HA-stimulated plants adopt the ecological strategy of recruiting members of the bacterial community that are candidates for the suppression of pathogens and, therefore, involved in plant defense.
Double Domain Swapping in HumanγC andγD Crystallin Drives Early Stages of Aggregation
Authors: Mondal Balaka , Nagesh Jayashree , Reddy Govardhan
Published: July 2020

HumanγD (HγD) andγC (HγC) are double domained crystallin (Crys) proteins expressed in the nucleus of the eye lens. Structural perturbations in the protein often trigger aggregation, which eventually leads to cataract. To decipher the underlying molecular mechanism, it is important to characterize the partially unfolded conformations of Crys proteins. Using coarse grained protein models and molecular dynamics simulations, we studied the role of on-pathway folding intermediates in the early stages of aggregation. The multi-dimensional free energy surface revealed at least three different folding pathways with the population of partially structured intermediates. The two dominant pathways confirm sequential folding of the N-terminal [Ntd] and the C-terminal domains [Ctd], while the third, least favored pathway involves intermediates where both the domains are partially folded. A native like intermediate (I∗), featuring the folded domains and disrupted inter domain contacts, gets populated in all the three pathways.I∗forms domain swapped dimers by swapping the entire Ntds and Ctds with other monomers. Population of such oligomers can explain the increased resistance to unfolding resulting in hysteresis observed in the folding experiments of HγD Crys. An ensemble of double domain swapped dimers are also formed during refolding, where intermediates consisting of partially folded Ntds and Ctds swap secondary structures with other monomers. The double domain swapping model presented in our study provides structural insights into the early events of aggregation in Crys proteins and identifies the key secondary structural swapping elements, where introducing mutations will aid in regulating the overall aggregation propensity.

Abstract Figure

Graphical Abstract figure
Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy
Authors: Alteri Claudia , Cento Valeria , Piralla Antonio , Costabile Valentino , Tallarita Monica , Colagrossi Luna , Renica Silvia , Giardina Federica , Novazzi Federica , Gaiarsa Stefano , Matarazzo Elisa , Antonello Maria , Vismara Chiara , Fumagalli Roberto , Epis Oscar Massimiliano , Puoti Massimo , Perno Carlo Federico , Baldanti Fausto
Published: July 2020

From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.
Accounting for cross-immunity can improve forecast accuracy during influenza epidemics
Authors: Sachak-Patwa Rahil , Byrne Helen M , Thompson Robin N
Published: July 2020

Previous 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

Leaf 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

Microhomology-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

A 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

Background

The 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.

Methods

FXR1 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.

Results

We 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.

Conclusion

We 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

The 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 Summary

The 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

People 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

Prior 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

Drones 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

Purpose

The 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/approach

This 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.

Findings

Out 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 implications

The 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/value

Several 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

Purpose

The 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/approach

The 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.

Findings

Taking 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/value

This 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

Purpose

This 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/approach

This 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.

Findings

Results 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 implications

Efficiency 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/value

While 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

Purpose

The 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/approach

Data 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.

Findings

The 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 implications

This study shows that competition needs to be embedded within a leadership style sensitive to the detection of and taking action against WB phenomena.

Originality/value

While 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.
Social and programmatic interactions in a therapeutic community for women: an exponential random graph model analysis
Authors: Cao Qiuchang , Liao Li , Warren Keith Leverett
Published: July 2020

Purpose

To analyze networks of social interactions between the residents of a therapeutic community (TC) for women and the way, in which such interactions predict the discussion of issues that arise in treatment.

Design/methodology/approach

In total, 50 residents of a corrections-based TC for women were surveyed on the peers with whom they socialized informally, shared meals, shared letters from home and discussed issues that arose in treatment over a 12 h period. The data were analyzed using exponential random graph models (ERGM).

Findings

Reciprocity occurred in all networks while transitivity (a tendency of two residents who are connected to both connect to a third peer) occurred in all networks measuring informal social interactions. When controlling for reciprocity and transitivity, residents avoided spending social time or sharing meals with the same peers. There was no evidence of homophily by race, age or years of education. Homophily by entrance time and case manager occurred in social time. Case manager homophily occurred in the discussion of treatment issues but disappeared when controlling for social time and sharing letters from home.

Research limitations/implications

Social networks in this TC arise from factors endogenous to the TC itself. It should be possible to determine the characteristics of optimal social networks in TCs. External validity is limited.

Practical implications

It should be possible to intervene to optimize the social networks of TC residents.

Originality/value

This is the first ERGM analysis of both informal and formal interactions in a TC.
Cascading effects of climate variability on the breeding success of an edge population of an apex predator
Authors: Gangoso Laura , Viana Duarte S. , Dokter Adriaan M. , Shamoun‐Baranes Judy , Figuerola Jordi , Barbosa Sergio A. , Bouten Willem
Published: July 2020

Large‐scale environmental forces can influence biodiversity at different levels of biological organization. Climate, in particular, is often associated with species distributions and diversity gradients. However, its mechanistic link to population dynamics is still poorly understood.

Here, we unravelled the full mechanistic path by which a climatic driver, the Atlantic trade winds, determines the viability of a bird population.

We monitored the breeding population of Eleonora's falcons in the Canary Islands for over a decade (2007–2017) and integrated different methods and data to reconstruct how the availability of their prey (migratory birds) is regulated by trade winds. We tracked foraging movements of breeding adults using GPS, monitored departure of migratory birds using weather radar and simulated their migration trajectories using an individual‐based, spatially explicit model.

We demonstrate that regional easterly winds regulate the flux of migratory birds that is available to hunting falcons, determining food availability for their chicks and consequent breeding success. By reconstructing how migratory birds are pushed towards the Canary Islands by trade winds, we explain most of the variation (up to 86%) in annual productivity for over a decade.

This study unequivocally illustrates how a climatic driver can influence local‐scale demographic processes while providing novel evidence of wind as a major determinant of population fitness in a top predator.
Microbial community and transcriptional responses to increased temperatures in coral Pocillopora damicornis holobiont
Authors: Li Jie , Long Lijuan , Zou Yiyang , Zhang Si
Published: July 2020

A few studies have holistically examined successive changes in coral holobionts in response to increased temperatures. Here, responses of the coral host Pocillopora damicornis, its Symbiodiniaceae symbionts, and associated bacteria to increased water temperatures were investigated. High temperatures induced bleaching, but no coral mortality was observed. Transcriptome analyses showed that P. damicornis responded more quickly to elevated temperatures than its algal symbionts. Numerous genes putatively associated with apoptosis, exocytosis, and autophagy were upregulated in P. damicornis, suggesting that Symbiodiniaceae can be eliminated or expelled through these mechanisms when P. damicornis experiences heat stress. Furthermore, apoptosis in P. damicornis is presumably induced through tumour necrosis factor and p53 signalling and caspase pathways. The relative abundances of several coral disease‐associated bacteria increased at 32°C, which may affect immune responses in heat‐stressed corals and potentially accelerates the loss of algal symbionts. Additionally, consistency of Symbiodiniaceae community structures under heat stress suggests non‐selective loss of Symbiodiniaceae. We propose that heat stress elicits interrelated response mechanisms in all parts of the coral holobiont.