bluuebunny/crossref_metadata_2025 huggingface dataset:
Categorical encoding of voice in human superior temporal cortex
Authors: Rupp Kyle , Hect Jasmine , Remick Madison , Ghuman Avniel , Chandrasekaran Bharath , Holt Lori L. , Abel Taylor J.
Published: November 2021

The ability to recognize abstract features of voice during auditory perception is a complex, yet poorly understood, feat of human audition. For the listener, this occurs in near-automatic fasion to seamlessly extract complex cues from a highly variable auditory signal. Voice perception depends on specialized regions of auditory cortex, including superior temporal gyrus (STG) and superior temporal sulcus (STS). However, the nature of voice encoding at the cortical level remains poorly understoood. We leverage intracerebral recordings across human auditory cortex during presentation of voice and non-voice acoustic stimuli to examine voice encoding in auditory cortex, in eight patient-participants undergoing epilepsy surgery evaluation. We show that voice-selectivity increases along the auditory hierarchy from supratemporal plane (STP) to the STG and STS. Results show accurate decoding of vocalizations from human auditory cortical activity even in the complete absence of linguistic content. These findings show an early, less-selective temporal window of neural activity in the STG and STS followed by a sustained, strongly voice-selective window. We then developed encoding models that demonstrate divergence in the encoding of acoustic features along the auditory hierarchy, wherein STG/STS responses were best explained by voice category as opposed to the acoustic features of voice stimuli. This is in contrast to neural activity recorded from STP, in which responses were accounted for by acoustic features. These findings support a model of voice perception that engages categorical encoding mechanisms within STG and STS.

Significance Statement

Voice perception occurs via specialized networks in higher order auditory cortex, yet how voice features are encoded remains a central unanswered question. With human intracerebral recordings of auditory cortex, we provide evidence for categorical encoding of voice in STG and STS and occurs in the absence of linguistic content. This selectivity strengthens after an initial onset response and cannot be explained by simple acoustic features. Together, these data support the existence of sites within STG and STS that are specialized for voice perception.
A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13
Authors: Vialetto Elena , Yu Yanying , Collins Scott P. , Wandera Katharina G. , Barquist Lars , Beisel Chase L.
Published: November 2021

Immune systems must recognize and clear foreign invaders without eliciting autoimmunity. CRISPR-Cas immune systems in prokaryotes manage this task by following two criteria: extensive guide:target complementarity and a defined target-flanking motif. Here we report an additional requirement for RNA-targeting CRISPR-Cas13 systems: expression of the target transcript exceeding a threshold. This finding is based on targeting endogenous non-essential transcripts, which rarely elicited dormancy through collateral RNA degradation. Instead, eliciting dormancy required over-expressing targeted transcripts above a threshold. A genome-wide screen confirmed target expression levels as the principal determinant of cytotoxic autoimmunity and revealed that the threshold shifts with the guide:target pair. This expression threshold ensured defense against a lytic bacteriophage yet allowed tolerance of a targeted beneficial gene expressed from an invading plasmid. These findings establish target expression levels as a third criterion for immune activation by RNA-targeting CRISPR-Cas systems, buffering against autoimmunity and distinguishing pathogenic and benign invaders.

HIGHLIGHTS

Cas13-induced dormancy requires RNA target levels to exceed an expression threshold

The expression threshold can prevent cytotoxic self-targeting for endogenous transcripts

The threshold shifts depending on the CRISPR RNA guide:target pair

The threshold allows cells to distinguish pathogenic and benign infections
Modulation of PKM1/2 levels by steric blocking morpholinos alters the metabolic and pluripotent state of murine pluripotent stem cells
Authors: Dierolf Joshua G. , Hunter Hailey L.M. , Watson Andrew J. , Betts Dean H.
Published: November 2021

Cellular metabolism plays both an active and passive role in embryonic development, pluripotency, and cell-fate decisions. However, little is known regarding the role of metabolism in regulating the recently described “formative” pluripotent state. The pluripotent developmental continuum features a metabolic switch from a bivalent metabolism (both glycolysis and oxidative phosphorylation) in naïve cells, to predominantly glycolysis in primed cells. We investigated the role of pyruvate kinase muscle isoforms (PKM1/2) in naïve, formative, and primed mouse embryonic stem cells through modulation of PKM1/2 mRNA transcripts using steric blocking morpholinos that downregulate PKM2 and upregulate PKM1. We have examined these effects in naïve, formative, and primed cells by quantifying the effects of PKM1/2 modulation on pluripotent and metabolic transcripts and by measuring shifts in the population frequencies of cells expressing naïve and primed cell surface markers by flow cytometry. Our results demonstrate that modulating PKM1 and PKM2 levels alters the transition from the naïve state into a primed pluripotent state by enhancing the proportion of the affected cells seen in the “formative” state. Therefore, we conclude that PKM1/2 actively contributes to mechanisms that oversee early stem pluripotency and their progression towards a primed pluripotent state.
PerSVade: Personalized Structural Variation detection in your species of interest
Authors: Schikora-Tamarit Miquel Àngel , Gabaldón Toni
Published: November 2021

Structural variants (SVs) like translocations, deletions, and other rearrangements underlie genetic and phenotypic variation. SVs are often overlooked due to difficult detection from short-read sequencing. Most algorithms yield low recall on humans, but the performance in other organisms is unclear. Similarly, despite remarkable differences across species’ genomes, most approaches use parameters optimized for humans. To overcome this and enable species-tailored approaches, we developed perSVade (personalized Structural Variation Detection), a pipeline that identifies SVs in a way that is optimized for any input sample. Starting from short reads, perSVade uses simulations on the reference genome to choose the best SV calling parameters. The output includes the optimally-called SVs and the accuracy, useful to assess the confidence in the results. In addition, perSVade can call small variants and copy-number variations. In summary, perSVade automatically identifies several types of genomic variation from short reads using sample-optimized parameters. We validated that perSVade increases the SV calling accuracy on simulated variants for six diverse eukaryotes, and on datasets of validated human variants. Importantly, we found no universal set of “optimal” parameters, which underscores the need for species-specific parameter optimization. PerSVade will improve our understanding about the role of SVs in non-human organisms.
Competition for endothelial cell polarity drives vascular morphogenesis
Authors: Barbacena Pedro , Dominguez-Cejudo Maria , Fonseca Catarina G. , Gómez-González Manuel , Faure Laura M. , Zarkada Georgia , Pena Andreia A. , Pezzarossa Anna , Ramalho Daniela , Giarratano Ylenia , Ouarné Marie , Barata David , Fortunato Isabela , Misiková Lenka H. , Mauldin Ian , Carvalho Yulia , Trepat Xavier , Roca-Cusachs Pere , Eichmann Anne , Bernabeu Miguel O. , Franco Cláudio A.
Published: November 2021

Blood vessel formation generates unique vascular patterns in each individual. The principles governing the apparent stochasticity of this process remain to be elucidated. Using mathematical methods, we find that the transition between two fundamental vascular morphogenetic programs – sprouting angiogenesis and vascular remodeling – is established by a shift on collective front-rear polarity of endothelial cells. We demonstrate that the competition between biochemical (VEGFA) and mechanical (blood flow-induced shear stress) cues controls this collective polarity shift. Shear stress increases tension at focal adhesions overriding VEGFA-driven collective polarization, which relies on tension at adherens junctions. We propose that vascular morphogenetic cues compete to regulate individual cell polarity and migration through tension shifts that translates into tissue-level emergent behaviors, ultimately leading to uniquely organized vascular patterns.
An alternatively spliced TREM2 isoform lacking the ligand binding domain is expressed in human brain
Authors: Shaw Benjamin C. , Snider Henry C. , Turner Andrew K. , Zajac Diana J. , Simpson James F. , Estus Steven
Published: November 2021

Background

Genetic variants in TREM2 are strongly associated with Alzheimer’s Disease (AD) risk but alternative splicing in TREM2 transcripts has not been comprehensively described.

Objective

Recognizing that alternative splice variants can result in reduced gene expression and/or altered function, we sought to fully characterize splice variation in TREM2.

Methods

Human blood and anterior cingulate autopsy tissue from 61 donors were used for end-point and quantitative PCR and Western blotting to identify and quantify novel TREM2 isoforms.

Results

In addition to previously described transcripts lacking exon 3 or exon 4, or retaining part of intron 3, we identified novel isoforms lacking exon 2, along with isoforms lacking multiple exons. Isoforms lacking exon 2 were predominant at approximately 10% of TREM2 mRNA in the brain. Expression of TREM2 and frequency of exon 2 skipping did not differ between AD samples and non-AD controls (p = 0.1268 and p = 0.4909, respectively). Further, these novel splice isoforms were also observed across multiple tissues with similar frequency (range 5.3 – 13.0%). We found that the exon 2 skipped isoform D2-TREM2 is translated to protein and localizes similarly to full-length TREM2 protein, that both proteins are primarily retained in the Golgi complex, and that D2-TREM2 is expressed in AD and non-AD brain.

Conclusion

Since the TREM2 ligand binding domain is encoded by exon 2, and skipping this exon retains reading frame while conserving localization, we hypothesize that D2-TREM2 acts as an inhibitor of TREM2 and targeting TREM2 splicing may be a novel therapeutic pathway for AD.
Contractile force of transplanted cardiomyocytes contributes to heart function after injury
Authors: Stüdemann Tim , Rössinger Judith , Manthey Christoph , Geertz Birgit , Srikantharajah Rajiven , von Bibra Constantin , Shibamiya Aya , Köhne Maria , Wiehler Antonius , Wiegert J. Simon , Eschenhagen Thomas , Weinberger Florian
Published: November 2021

Transplantation of pluripotent stem cell-derived cardiomyocytes represents an innovative therapeutic strategy for heart failure. Studies in small and large animals have demonstrated functional recovery of left ventricular function after cardiomyocyte transplantation1–4, and first clinical studies are currently underway5. Yet, the mechanism of action underlying graft-induced benefit is unknown6. Here we demonstrate that transplanted cardiomyocytes actively contribute to heart function. We transplanted cardiomyocytes with an optogenetic off-on switch in a guinea pig cardiac injury model. Light-induced inhibition of engrafted cardiomyocyte contractility resulted in a rapid decrease of left ventricular function that was fully reversible with the offset of photostimulation. Hence, our optogenetic approach demonstrated that transplanted cardiomyocytes actively participate in heart function, supporting the hypothesis that the delivery of new force-generating myocardium can serve as a regenerative therapeutic strategy.
Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in wild-type controls
Authors: Soriano Sirena , Curry Kristen , Wang Qi , Chow Elsbeth , Treangen Todd , Villapol Sonia
Published: November 2021

Traumatic brain injury (TBI) causes neuroinflammation and neurodegeneration, both which increase the risk and accelerate the progression of Alzheimer’s disease (AD). The gut microbiome is an essential modulator of the immune system, impacting in the brain. AD has been related with reduced diversity and alterations in the community composition of the gut microbiota. This study aimed to determine whether the gut microbiota from AD mice exacerbates neurological deficits after TBI in control mice. We prepared fecal microbiota transplants from 18-24 months old 3xTg-AD (FMT-AD) and from healthy controls (FMT-young) mice. FMTs were administered orally to young control C57BL/6 (wild-type, WT) mice after they underwent controlled cortical impact (CCI) injury, as a model of TBI. Then, we characterized the microbiota composition of the fecal samples by full-length 16S rRNA gene sequencing analysis. We collected the blood, brain, and gut tissues for protein and immunohistochemical analysis. Our results showed that FMT-AD administration stimulates a higher relative abundance of the genus Muribaculum and a decrease in Lactobacillus johnsonii compared to FMT-young in WT mice. Furthermore, WT mice exhibited larger lesion, increased activated microglia/macrophages, and reduced motor recovery after FMT-AD compared to FMT-young one day after TBI. In summary, we observed gut microbiota from AD mice to have a detrimental effect and aggravate the neuroinflammatory response and neurological outcomes after TBI in young WT mice.
Identification of biological processes and signaling pathways in the stretched nucleus pulposus cells
Authors: Zhang Min , Wang Jing , Gu Hanming
Published: November 2021

Low back pain is mostly caused by disc degeneration, which is due to the alterations in the osmotic pressure of nucleus pulposus cells. However, the knowledge about the mechanism and therapies for disc degeneration is not fully understood. Here, our objective is to identify significantly changed genes and biological processes in the stretched nucleus pulposus cells. The GSE175710 dataset was originally produced by using the Illumina HiSeq 4000 (Rattus norvegicus). The KEGG and GO analyses indicated that “MAPK signaling”, “TNF signaling”, “IL17 signaling”, and the “NF-κB signaling pathway” are mostly affected in the stretched nucleus pulposus cells. Moreover, we identified several genes according to the PPI network such as Mmp9, Cxcl12, Col1a1, and Col3a1 in the stretched nucleus pulposus cells. Thus, our study provides further insights into the study of disc deterioration.
Quasi-universal scaling in mouse-brain neuronal activity stems from edge-of-instability critical dynamics
Authors: Morales Guillermo B. , Di Santo Serena , Muñoz Miguel A.
Published: November 2021

The brain is in a state of perpetual reverberant neural activity, even in the absence of specific tasks or stimuli. Shedding light on the origin and functional significance of such a dynamical state is essential to understanding how the brain transmits, processes, and stores information. An inspiring, albeit controversial, conjecture proposes that some statistical characteristics of empirically observed neuronal activity can be understood by assuming that brain networks operate in a dynamical regime near the edge of a phase transition. Moreover, the resulting critical behavior, with its concomitant scale invariance, is assumed to carry crucial functional advantages. Here, we present a data-driven analysis based on simultaneous high-throughput recordings of the activity of thousands of individual neurons in various regions of the mouse brain. To analyze these data, we synergistically combine cutting-edge methods for the study of brain activity (such as a phenomenological renormalization group approach and techniques that infer the general dynamical state of a neural population), while designing complementary tools. This strategy allows us to uncover strong signatures of scale invariance that is ”quasi-universal” across brain regions and reveal that all these areas operate, to a greater or lesser extent, near the edge of instability. Furthermore, this framework allows us to distinguish between quasi-universal background activity and non-universal input-related activity. Taken together, this study provides strong evidence that brain networks actually operate in a critical regime which, among other functional advantages, provides them with a scale-invariant substrate of activity covariances that can sustain optimal input representations.
Long-term potentiation at pyramidal cell to somatostatin interneuron synapses controls hippocampal network plasticity and memory
Authors: Asgarihafshejani Azam , Honoré Ève , Michon François-Xavier , Laplante Isabel , Lacaille Jean-Claude
Published: November 2021

Hippocampal somatostatin (SOM) cells are dendrite-projecting inhibitory interneurons. CA1 SOM cells receive major excitatory inputs from pyramidal cells (PC-SOM synapses) which show mGluR1a- and mTORC1-mediated long-term potentiation (LTP). PC-SOM synapse LTP contributes to CA1 network metaplasticity and memory consolidation, but whether it is sufficient to regulate these processes remains unknown. Here we used optogenetic stimulation of CA1 pyramidal cells and whole cell recordings in slices to show that optogenetic theta burst stimulation (TBSopto) produces LTP at PC-SOM synapses. At the network level, we found that TBSopto differentially regulates metaplasticity of pyramidal cell inputs: enhancing LTP at Schaffer collateral synapses and depressing LTP at temporo-ammonic synapses. At the behavioral level, we uncovered that in vivo TBSopto regulates learning-induced LTP at PC-SOM synapses, as well as contextual fear memory. Thus, LTP of PC-SOM synapses is a long-term feedback mechanism controlling pyramidal cell synaptic plasticity, sufficient to regulate memory consolidation.
Seed bio-priming with phosphate solubilizing bacteria strains to improve rice (Oryza sativa L. var. FARO 44) growth under ferruginous ultisol conditions
Authors: Ibrahim Musa Saheed , Ikhajiagbe Beckley
Published: November 2021

The research investigated the possibility of phosphate solubilizing bacteria (PSB) with plant growth-promoting (PGP) capabilities to improve growth properties of rice plant under ferruginous ultisol (FU) condition through bio-priming strategy. The PSB with PGP properties used in this research were Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 that were previously isolated and characterized following the 16S rRNA gene sequencing. Biosafety analysis of the PSB isolates was conducted using blood agar. The rice seeds were then bio-primed with the PSBs at 3, 12 and 24 hours priming durations and then sown in a composite FU soil sample. Differences in germination bioassay involving SEM, morphology, physiology and biomass parameters were investigated for 15 weeks after bio-priming. The composite FU soil used in the study had high pH, low bioavailable phosphorus, low water holding capacity and high iron levels which has led to a low growth properties of rice seeds without bio-priming in FU soil. Germination parameters was better in seeds bio-primed with the PSBs, especially at 12h priming duration as against seeds without priming. SEM showed more bacterial colonization in the PSB bio-primed seeds. Seed bio-priming of rice seed with Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 under FU soil condition significantly improved seed microbiome, rhizocolonization and soil nutrient properties, thereby enhancing growth properties of the rice plant. This suggest the ability of PSB to solubilize and mineralize soil phosphate and improve its availability and soil property for optimum plant usage in phosphate stressed and iron toxic soils.
Comparison of neuromuscular junction dynamics following ischemic and aged skeletal muscle
Authors: Aliya Berna , Mohiuddin Mahir , Choi Jeongmoon J. , Jeong Gunjae , Kang Innie , Castels Hannah , Jones Cade , Jang Young C.
Published: November 2021

Both aging and neuromuscular diseases lead to significant changes in the morphology and functionality of the neuromuscular synapse. Skeletal muscles display a remarkable regenerative capacity, however, are still susceptible to diseases of aging and peripheral nerve perturbations. In this study, we assessed how neuromuscular synapses differ in aged and injured skeletal muscle using an improved neuromuscular junction (NMJ) staining and imaging method. We found that both aged and ischemic skeletal muscle display Wallerian degeneration of the presynaptic motor axons and fragmentation of postsynaptic acetylcholine receptors (AChRs). Quantifiable measurements of various metrics of the NMJs provide a more concrete idea of the dynamics that are occurring in the muscle microenvironment. We questioned whether neuronal degradation precedes myofiber atrophy or vice versa. Previously, it was shown that a cellular crosstalk exists among the motor neurons, myofibers, vasculature, and mitochondria within the muscle microdomain. It is apparent that lack of blood flow to motor neurons in ischemic skeletal muscle disrupts the structure of NMJs, however it is unclear if the aging condition experiences similar dynamics. We demonstrated that both aged and ischemic skeletal muscle demonstrate similar patterns of degeneration, characterized by a smaller percentage overlap of presynaptic and postsynaptic sides, greater fragmentation of AChRs, and a smaller area of AChR clusters. Together, these results reveal high resolution, precise parallels between the aged and ischemic NMJs.

Impact Statement

The goal of this study was to assess changes in presynaptic motor neurons and postsynaptic acetylcholine receptors following an ischemic injury model and compare this with an aging model. This was accomplished by characterizing key components of NMJ morphology, including overlap and size of the receptors. There is currently limited research investigating the cellular communication between skeletal muscle fibers and motor neurons. Additionally, there is limited work comparing neuromuscular remodeling in aged and young models. With the substantial prevalence of neuromuscular disorders, especially in the aging population, it is essential to understand nerve-muscle interactions in order to promote increased mobility and improved quality of life in both injury and aging models.
Propagation of seminal toxins through binary expression gene drives can suppress polyandrous populations
Authors: Hurtado Juan , Revale Santiago , Matzkin Luciano M
Published: November 2021

Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this restriction may be relaxed by using a double gene drive design to spread a split binary expression system. One drive carries a dominant lethal/toxic effector alone and the other a transactivator factor, without which the effector will not act. Only after the drives reach sufficiently high frequencies would individuals have the chance to inherit both system components and the effector be expressed. We explore through mathematical modeling the potential of this design to spread dominant lethal/toxic alleles and suppress populations. We show that this system could be implemented to spread engineered seminal proteins designed to kill females, making it highly effective against polyandrous populations.
Ribonucleotide Reductase Regulatory Subunit M2 as a Driver of Glioblastoma TMZ-Resistance through Modulation of dNTP Production
Authors: Perrault Ella N , Shireman Jack M , Ali Eunus S , Preddy Isabelle , Lin Peiyu , Park Cheol , Tomes Luke , Zolp Andrew J , Budhiraja Shreya , Baisiwala Shivani , James C. David , Ben-Sahra Issam , Pott Sebastian , Basu Anindita , Ahmed Atique U
Published: November 2021

Glioblastoma (GBM) remains one of the most resistant and fatal forms of cancer. Previous studies have examined primary and recurrent GBM tumors, but it is difficult to study tumor evolution during therapy where resistance develops. To investigate this, we performed an in vivo single-cell RNA sequencing screen in a patient-derived xenograft (PDX) model. Primary GBM was modeled by mice treated with DMSO control, recurrent GBM was modeled by mice treated with temozolomide (TMZ), and during therapy GBM was modeled by mice euthanized after two of five TMZ treatments. Our analysis revealed the cellular population present during therapy to be distinct from primary and recurrent GBM. We found the Ribonucleotide Reductase gene family to exhibit a unique signature in our data due to an observed subunit switch to favor RRM2 during therapy. GBM cells were shown to rely on RRM2 during therapy causing RRM2-knockdown (KD) cells to be TMZ-sensitive. Using targeted metabolomics, we found RRM2-KDs to produce less dGTP and dCTP than control cells in response to TMZ (p<0.0001). Supplementing RRM2-KDs with deoxycytidine and deoxyguanosine rescued TMZ-sensitivity, suggesting an RRM2-driven mechanism of chemoresistance, established by regulating the production of these nucleotides. In vivo, tumor-bearing mice treated with the RRM2-inhibitor, Triapine, in combination with TMZ, survived longer than mice treated with TMZ alone (p<0.01), indicating promising clinical opportunities in targeting RRM2. Our data present a novel understanding of RRM2 activity, and its alteration during therapeutic stress as response to TMZ-induced DNA damage.
Prevalence and correlates of phenazine resistance in culturable bacteria from a dryland wheat field
Authors: Perry Elena K. , Newman Dianne K.
Published: November 2021

Phenazines are a class of bacterially-produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally-relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We find that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, but that there is also significant variability in susceptibility both within and across phyla. Phenazine-resistant strains are more likely to be isolated from the wheat rhizosphere, where PCA producers are also more abundant, compared to bulk soil. Furthermore, PCA toxicity is pH-dependent for most susceptible strains and broadly correlates with PCA reduction rates, suggesting that uptake and redox-cycling are important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities.

Importance

Microbial communities contribute to crop health in important ways. For example, phenazine metabolites are a class of redox-active molecules made by diverse soil bacteria that underpin the biocontrol of wheat and other crops. Their physiological functions are nuanced: in some contexts they are toxic, in others, beneficial. While much is known about phenazine production and the effect of phenazines on producing strains, our ability to predict how phenazines might shape the composition of environmental microbial communities is poorly constrained; that phenazine prevalence in the rhizosphere is predicted to increase in arid soils as the climate changes provides an impetus for further study. As a step towards gaining a predictive understanding of phenazine-linked microbial ecology, we document the effects of phenazines on diverse bacteria that were co-isolated from a wheat rhizosphere and identify conditions and phenotypes that correlate with how a strain will respond to phenazines.
Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons
Authors: Tzou Philip L. , Tao Kaiming , Kosakovsky Pond Sergei L. , Shafer Robert W.
Published: November 2021

As novel SARS-CoV-2 variants with different patterns of spike mutations have emerged, the susceptibility of these variants to neutralization by antibodies has been rapidly assessed. However, neutralization data are generated using different approaches and are scattered across different publications making it difficult for these data to be located and synthesized. The Stanford Coronavirus Resistance Database (CoV-RDB; https://covdb.stanford.edu) is designed to house comprehensively curated published data on the neutralizing susceptibility of SARS-CoV-2 variants and spike mutations to monoclonal antibodies (mAbs), convalescent plasma (CP), and vaccinee plasma (VP). As of October 2021, CoV-RDB contains 186 publications including 64 (34%) containing 7,328 neutralizing mAb susceptibility results, 96 (52%) containing 11,390 neutralizing CP susceptibility results, and 125 (68%) containing 20,872 neutralizing VP results. The database also records which spike mutations are selected during in vitro passage of SARS-CoV-2 in the presence of mAbs and which emerge in persons receiving mAbs as treatment. The CoV-RDB interface interactively displays neutralizing susceptibility data at different levels of granularity by filtering and/or aggregating query results according to one or more experimental conditions. The CoV-RDB website provides a companion sequence analysis program that outputs information about mutations present in a submitted sequence and that also assists users in determining the appropriate mutation-detection thresholds for identifying non-consensus amino acids. The most recent data underlying the CoV-RDB can be downloaded in its entirety from a Github repository in a documented machine-readable format.
Multivariate Characterization of Morpho-biometric Traits of Indigenous Helmeted Guinea Fowl (Numida meleagris) in Nigeria
Authors: Yakubu Abdulmojeed , Jegede Praise , Wheto Mathew , Shoyombo Ayoola J. , Adebambo Ayotunde O. , Popoola Mustapha A. , Osaiyuwu Osamede H. , Olafadehan Olurotimi A. , Alabi Olayinka O. , Ukim Comfort I. , Vincent Samuel T. , Mundi Harirat L. , Olayanju Adeniyi , Adebambo Olufunmilayo A.
Published: November 2021

This study was embarked upon to characterise phenotypically helmeted guinea fowls in three agro-ecologies in Nigeria using multivariate approach. Eighteen biometric characters, four morphological indices and eleven qualitative (phaneroptic) traits were investigated in a total of 569 adult birds (158 males and 411 females). Descriptive statistics, non-parametric Kruskal–Wallis H test followed by the Mann–Whitney U test for post hoc, Multiple Correspondence Analysis (MCA), General Linear Model, Canonical Discriminant Analysis, Categorical Principal Component Analysis and Decision Trees were employed to discern the effects of agro-ecological zone and sex on the morphostructural parameters. Agro-ecology had significant effect (P<0.05; P <0.01) on all the colour traits. In general, the most frequently observed colour phenotype of guinea fowl had pearl plumage colour (54.0%), pale red skin colour (94.2%), black shank colour (68.7%), brown eye colour (49.7%), white earlobe colour (54.8%) and brown helmet colour (72.6%). The frequencies of helmet shape and wattle size were significantly influenced (P <0.01) by agro-ecology and sex. Overall, birds from the Southern Guinea Savanna zone had significantly higher values (P <0.05) for most biometric traits compared to their Sudano-Sahelian and Tropical Rainforest counterparts. They were also more compact (120.83±1.61 vs. 113.96±0.97 vs. 111.33±1.19) and had lesser condition index (8.542±0.17 vs. 9.92±0.10 vs. 9.61±0.13) than their counterparts in the two other zones. The interaction between agro-ecology and sex had significant effect (P <0.05) on some quantitative variables. The MCA and discriminant analysis revealed considerable intermingling of the phaneroptic, biometric traits and body indices especially between the Sudano-Sahelian and Tropical Rainforest birds. Inspite of the high level of genetic admixture, the guinea fowl populations could best be distinguished using wing length, body length and eye colour. However, further complementary work on genomics will guide future selection and breeding programmes geared towards improving the productivity, survival and environmental adaptation of indigenous helmeted guinea fowls in the tropics.
Measuring the performance of the Indian banking industry: data envelopment window analysis approach
Authors: Akhtar Shakeb , Alam Mahfooz , Ansari Mohd Shamim
Published: November 2021

Purpose

This study aims to empirically evaluate the performance of commercial banks operating in India.

Design/methodology/approach

The efficiency of the commercial banks is evaluated using the data envelopment analysis (DEA) approach. We measure the technical, pure technical and scale efficiency of the sampled conventional banks using the input-oriented model. We employed an extended DEA window analysis approach based on a panel sample of 47 banks in the Indian scenario. The period of study is from 2009 to 2018.

Findings

The results obtained from CRS and VRS measures envisage that Indian banks have failed to manage their inputs efficiently and convert them into outputs. It implies that Indian banks do not operate at an optimum level. Moreover, the results show that public banks exhibit superior efficiency scores followed by private and foreign banks. Apart from the aggregate sector level, we also investigate the performance of Indian banks at the individual level for in-depth analysis. The individual bank-level analysis reports that the public sector banks (PSBs) are the most efficient followed by foreign banks, whereas, the least efficient are the private banks.

Research limitations/implications

The findings of our study have implications for government, financial institutions and policymakers to access the verve and flexibility of the Indian banking system. The government should consider restructuring inefficient banks to enhance overall performance. This can be considered by improvement in managerial efficiency, efficient allocation of scarce resources and appropriate scale of operation. However, the findings of the study should be interpreted in light of the period of study for the banks being operational (as we filter out banks that ceased to exist) in India and empirical methods employed. The results may vary if alternative measures are used.

Originality/value

The present paper investigates the efficiency of the Indian banking sector employing the Data Envelopment Window Analysis (DEWA) technique. To the best of our knowledge, the present study is perhaps the first one to employ the DEWA measure on the Indian banking industry to gauge their performance over time.
Designing platform ecosystems for collaboration, innovation and growth
Authors: Singal Ajay Kumar
Published: November 2021

Purpose

This paper explores the design dimensions that foster identity construction, legitimation, and growth of digitally mediated platform ecosystems.

Design/methodology/approach

A midrange theorizing approach was adopted to assimilate and induct the extant literature on ecosystems, platform business models and innovation, yielding testable propositions on ecosystem design for empirical testing.

Findings

The paper suggests that decentralized governance, partner engagement and shared context are three dimensions of criticality for designing a distinct platform ecosystem. These design dimensions nurture interactions, transactions, relationships between platform participants and external actors to make ecosystems authentic and legitimate. Decentralization is relevant for inducing flexibility and autonomy of participants on the platform. Engagement impacts the intensity of relationships the platform has with other firms in the ecosystem, while shared context is essential for creating knowledge and harnessing innovation on the platform.

Research limitations/implications

The paper identifies a set of three testable propositions on ecosystem design for further empirical analysis by ecosystem researchers.

Practical implications

To achieve future readiness, organizations must become resilient to the market environment. With that intent, traditional businesses are revising their operating models to become more collaborative, integrative and efficient. Adoption of digital initiatives for redesigning towards platform ecosystems will make traditional models more relevant as markets evolve. But as a new organization form, platform ecosystem faces the challenge of legitimacy. Author suggests that managers use the organization design lever to meet the challenge.

Originality/value

Emergence of platform-based businesses and transformation of existing models to platform ecosystems are impacting today's competitive environment. During initial phases of evolution, ecosystems aim for identity and legitimacy. The authors contribute to organizational aspects of the platform ecosystem design literature by identifying decentralization of governance, engagement and shared context as dimensions of criticality for future-ready platforms. Secondly, these dimensions are associated with identity and legitimation of platform ecosystems. Decentralization is relevant for supply-side producers of goods and services on the platform, engagement has impact on both supply and demand-side participants of platforms, and shared context is essential for knowledge creation and harnessing innovation.
Public participation in infrastructure projects: an integrative review and prospects for the future research
Authors: Xiao Han , Hao Shengyue
Published: November 2021

Purpose

In the past few decades, traditional project management theories mainly focused on quality, cost and schedule. However, with larger scale and wider influence of infrastructure projects, especially in megaprojects, social problems have gradually become pressing issues in the field of project governance. As the public is the main body of society, public participation has attracted the attention from both the academic field and industry field. Despite people are gradually realizing the significance of public participation, a deeper and more systematic understanding is still needed to be developed in this field. Therefore, this paper aims to conduct a systematic literature review on public participation in infrastructure projects. Based on existing literatures, this paper draws a knowledge map and develops a research framework in this field. Also, this paper tries to provide some theoretical and practical directions for the future.

Design/methodology/approach

In total, 142 papers from Web of Science Core collection were selected to be used in this systematic review. Quantitative analysis of this paper is concentrated on the knowledge map with bibliometric tools. Qualitative analysis is concentrated on identifying the research framework.

Findings

This paper reviewed existing literatures and the results are as below. Firstly, the results show a knowledge map containing knowledge domains, knowledge frontiers and knowledge evolution of research fields in public participation. Secondly, the results indicate a research framework in this field, including situational dimension, implementation dimension, individual dimension and influence dimension. Moreover, each dimension has several research topics, respectively. Finally, according to the results, the paper proposes practical suggestions for stakeholders and research directions for further study.

Originality/value

It is the first paper to draw a holistic knowledge map and build up a multilevel framework for public participation in the field of infrastructure projects. This paper bridges the gap in both quantitative and qualitative identification of existing literatures in this field. Besides, this paper proposes some practical suggestions and research directions for further study and development of public participation.
Gendered personality traits and entrepreneurial intentions: insights from information technology education
Authors: Sitaridis Ioannis , Kitsios Fotis C.
Published: November 2021

Purpose

Entrepreneurial intention of students is frequently used in entrepreneurship research as an indicator of creativity, innovativeness and entrepreneurial mindset. The entrepreneurship courses offered by engineering disciplines do not always have the expected outcomes, while differences are observed on students' entrepreneurial intention. These differences sometimes stem from the stereotypical beliefs about entrepreneurship, in favor of masculinity. Although these anachronistic perceptions gradually fade in the society, personality traits attributed to “traditional” gender schemas still have an impact on students' career choices, especially in academic fields considered “masculine,” such as information technology. The purpose of this paper is to examine the impact of gender-typed personality (GTP) on students' entrepreneurial intentions (EI) and identify differences between genders.

Design/methodology/approach

The impact of GTP traits on students' entrepreneurial intention is examined using gender schema theory and the theory of planned behavior (TPB) based on a sample of 321 university students of information technology. Structural equation models are used for the investigation of causal effects and group differences.

Findings

The results indicate significant interaction of GTP traits on the EI for both male and female students. However, no significant differences were found in the perception of gender schemas between males and females, which clearly suggests that the attribution of these traits to a specific gender nowadays is false.

Originality/value

The results offer convincing explanation of the differences observed in EI between the two genders and have both theoretical and practical implications for entrepreneurship education.
Games theory and strategic alliances: applications to British Russian partnership
Authors: Tlemsani Issam , Mohamed Hashim Mohamed Ashmel , Matthews Robin
Published: November 2021

Purpose

This conceptual paper examines the need for viable theoretical models of international learning alliances in the light of cooperative games and complexity in two distinguished educational settings. Game theory is used to demonstrate the need for the top managerial executives to acquire a detailed understanding of decision makers' behaviours and trigger the deployment of complex analytical methods. The paper scrutinizes Russia's pursued aggressive approach using shock therapy, also suggest the critical need to reform policy.

Design/methodology/approach

Combining the critical analysis of (1) cooperative games and (2) adaptive systems structures, a dependable model is derived, which sets the baseline for determining the role of costs and gains. The analysis is supported using a real-world example of an alliance between British University (theXandYalliance) and Russian University. It also emphasizes the importance of both internal and external pressure variables closely connected with the cooperative games, adaptive system and shock therapy.

Findings

Two features of alliances have been emphasized. The first is the importance of informal relationships in the evolution of partnerships and of cooperation. This is a well-known factor in the success of any relationship. Especially in international partnerships, empathy at the individual level is perhaps necessary to bypass the influence of historical and cultural differences that are barriers at the macro level, preconditions rather than consequences of successful policies and contractual arrangements at the level of organizations and governments. The second feature is interdependence at the cost–benefit level and in the domain of decisions. The cooperation of both partners is required to realize payoffs.

Practical implications

The implication of this paper is a guideline for regulators and policymakers designing worldwide alliances in higher education. In addition, this paper covers an interesting domain that could be of interest to organizations involved in forming strategic alliances, developing and re-engineering policies for strategic coalitions and setting future profitable payoff relationships within the contextual limitations ofXandY.

Originality/value

This paper creates new knowledge by concisely examining the meaning of strategic alliances in the context of the global education industry.
Overview of challenges faced by refugees following resettlement in Houston, Texas: a qualitative study at five refugee resettlement agencies
Authors: Kaplan Julika , Lazarescou Natalie , Huang Sally , Ali Sarah , Banu Sophia , Du Ye Beverly , Shrestha Srijana
Published: November 2021

Purpose

This paper aims to conduct a qualitative needs assessment to explore the effectiveness of Houston’s refugee resettlement efforts in the areas of employment, health care and education.

Design/methodology/approach

Using referral sampling, the authors identified refugee community leaders and staff members at the five refugee resettlement agencies in Houston. The authors conducted 29 qualitative interviews with these contacts from February–August 2017.

Findings

Recently resettled refugees may struggle to find and maintain employment in Houston due to difficulty accessing public transportation. Refugees seeking medical care in Houston often have difficulty navigating the complexities of the health-care system and communicating with their physicians due to language barriers. Finally, refugee children may have trouble adapting to Houston public schools, sometimes because they have limited experience with formal education. This study provided insights into the challenges Houston refugees face during resettlement and these barriers can be mitigated with policies designed specifically to address them.

Practical implications

The authors recommend decreasing public transportation fees for refugees, supporting programs that donate used vehicles to refugees, expanding access to English as a Second Language classes for refugee children and adults and giving refugees designated time to learn English upon arrival.

Originality/value

Houston welcomes more resettled refugees than any other American city. However, few studies have explored the barriers refugees face during the resettlement process.