bluuebunny/crossref_metadata_2025 huggingface dataset:
Challenges and adaptations for a cluster-randomized control trial targeting parents of pediatric cancer survivors with obesity during the COVID-19 pandemic
Authors: Buro Acadia W , Gray Heewon L , Ruble Kathy , Soca Lozano Sandra , Sauls Rachel , Albizu-Jacob Alexandra , Crowder Sylvia L , Mazzeo Suzanne E , Stern Marilyn
Published: November 2022

Although the COVID-19 pandemic has increased the importance of digital technology in clinical trial implementation, there is a dearth of literature reporting on challenges and strategies related to multi-site randomized controlled trials (RCTs) among pediatric cancer survivors during the pandemic. This paper discusses challenges faced in the implementation of the NOURISH-T+ trial so far (December 2019–March 2022) and describes adaptations made as a result of these disruptions in the areas of recruitment, data collection, and overall engagement. This reflection is based on a multisite cluster-RCT that aims to examine whether an intervention targeting parents as agents of change to promote healthy eating and physical activity in pediatric cancer survivors, NOURISH-T+ (Nourishing Our Understanding of Role modeling to Improve Support and Health for Healthy Transitions), reduces body mass and improves health behaviors compared to Brief NOURISH-T (Enhanced Usual Care/EUC). The COVID-19 pandemic has created and exacerbated challenges for our trial related to participant recruitment and engagement, technology access and literacy, and data collection and management, as well as COVID-related challenges (e.g., Zoom fatigue). Strategies used to address these challenges might prove helpful in future virtual or hybrid RCTs, including developing trust and rapport with participants, providing support through multiple routes of dissemination, and using data management applications (e.g., REDCap™) for automation and project management. Extra efforts to build families’ trust and rapport, offering multiple routes of support, and automating as many tasks as possible are critical to ensuring the continuation of high-quality clinical trials during the COVID-19 pandemic.
Multidisciplinary implementation of family-based treatment delivered by videoconferencing (FBT-V) for adolescent anorexia nervosa during the COVID-19 pandemic
Authors: Couturier Jennifer , Pellegrini Danielle , Grennan Laura , Nicula Maria , Miller Catherine , Agar Paul , Webb Cheryl , Anderson Kristen , Barwick Melanie , Dimitropoulos Gina , Findlay Sheri , Kimber Melissa , McVey Gail , Lock James
Published: November 2022

Family-Based Treatment (FBT)—the most widely supported treatment for pediatric eating disorders—transitioned to virtual delivery in many programs due to COVID-19. Using a blended implementation approach, we systematically examined therapist adherence to key components of FBT and fidelity to FBT by videoconferencing (FBT-V), preliminary patient outcomes, and team experiences with our FBT-V implementation approach as well as familial perceptions of FBT-V effectiveness. We examined our implementation approach across four pediatric eating disorder programs in Ontario, Canada, using mixed methods. Participants included therapists (n = 8), medical practitioners (n = 4), administrators (n = 6), and families (n = 5; 21 family members in total). We developed implementation teams at each site, provided FBT-V training, and offered clinical and implementation consultation. Therapists submitted video recordings of their first four FBT-V sessions for fidelity rating, and patient outcomes. Therapists self-reported readiness, attitudes, confidence, and adherence to FBT-V. Focus groups were conducted with each team and family after the first four sessions of FBT-V. Quantitative data were analyzed using repeated measures ANOVA. Qualitative data were analyzed using directed and summative content analysis. Therapists adhered to key FBT components and maintained FBT-V fidelity. Changes in therapists’ readiness, attitudes, and confidence in FBT-V over time were not significant. All patients gained weight. Focus groups revealed implementation facilitators/barriers, positives/negatives surrounding FBT-V training and consultation, suggestions for improvement, and effectiveness attributed to FBT-V. Our implementation approach appeared to be feasible and acceptable. Future research with a larger sample is required, furthering our understanding of this approach and exploring how organizational factors influence treatment fidelity.
The neuroprotective effects of estrogen and estrogenic compounds in spinal cord injury
Authors: Shvetcov Artur , Ruitenberg Marc J. , Delerue Fabien , Gold Wendy A. , Brown David A. , Finney Caitlin A.
Published: November 2022

Spinal cord injury (SCI) occurs when the spinal cord is damaged from either a traumatic event or disease. SCI is characterised by multiple injury phases that affect the transmission of sensory and motor signals and lead to temporary or long-term functional deficits. There are few treatments for SCI. Estrogens and estrogenic compounds, however, may effectively mitigate the effects of SCI and therefore represent viable treatment options. This review systematically examines the pre-clinical literature on estrogen and estrogenic compound neuroprotection after SCI. Several estrogens were examined by the included studies: estrogen, estradiol benzoate, Premarin, isopsoralen, genistein, and selective estrogen receptor modulators. Across these pharmacotherapies, we find significant evidence that estrogens indeed offer protection against myriad pathophysiological effects of SCI and lead to improvements in functional outcomes, including locomotion. A STRING functional network analysis of proteins modulated by estrogen after SCI demonstrated that estrogen simultaneously upregulates known neuroprotective pathways, such as HIF-1, and downregulates pro-inflammatory pathways, including IL-17. These findings highlight the strong therapeutic potential of estrogen and estrogenic compounds after SCI.
Identifying a minimal set of single nucleotide polymorphisms to classify the geographic origin of aP. falciparumsample from the pf3k database
Authors: Gustafson Kyle B. , Wenger Edward , Proctor Joshua L.
Published: November 2022

Genetic sequencing of malaria parasites has the potential to become an important tool in routine surveillance efforts for the control and eradication of malaria. For example, characterizing the epidemiological connectivity between different populations by assessing the genetic similarity of their parasites can offer insights for national malaria control programs and their strategic allocation of interventions. Despite the increase of whole-genome sequencing of malaria parasites, the development of a small set of single nucleotide polymorphisms (SNPs), often referred to as a barcode, or a panel of amplicons remains programmatically relevant for large-scale, local generation of genetic data. Here, we present an application of a machine-learning method to classify the geographic origin of a sampleandidentify a small set of region-specific SNPs. We demonstrate that this method can automatically identify sets of SNPs which complement the currently targeted loci from the malaria scientific community. More specifically, we find that many of these machine-learned SNPs are near known and well-studied loci such as regions and markers linked to drug resistance, while also identifying new areas of the genome where function is less characterized. The application of this technique can complement current approaches for selecting SNP locations and effectively scales with an increase in sample size.
Consumer feces impact coral health in guild-specific ways
Authors: Grupstra Carsten G.B. , Howe-Kerr Lauren I. , van der Meulen Jesse A. , Veglia Alex J. , Coy Samantha R. , Correa Adrienne M.S.
Published: November 2022

Microbiota from consumer feces can impact resource species in guild-specific ways. We tested the effect of fresh and heat-killed feces from corallivorous (coral-eating) and grazer/detritivorous fish on coral health and found that fresh grazer/detritivore feces, but not fresh corallivore feces, affected coral health in detrimental ways compared to heat-killed feces, suggesting that microbiota in grazer/detritivore feces were harmful. Bacterial diversity across 10 fish species suggests our experimental findings are generalizable to consumer guild: corallivore feces contained more coral-associated bacteria, and lower abundances of the coral pathogen,Vibrio coralliilyticus. These findings recontextualize the ecological roles of consumers on coral reefs: although herbivores support coral dominance through removal of algal competitors, they also disperse coral pathogens. Corallivore predation can wound corals, yet their feces contain potentially beneficial coral-associated bacteria, supporting the hypothesized role of corallivores in coral symbiont dispersal. Such consumer-mediated microbial dispersal as demonstrated here has broad implications for environmental management.
Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants
Authors: Leftwich Heidi K. , Vargas-Robles Daniela , Rojas-Correa Mayra , Yap Yan Rou , Bhattarai Shakti , Ward Doyle V. , Fujimori Gavin , Forconi Catherine S. , Yeboah Tracy , Carter Acara , Kastrinakis Alyssa , Asirwatham Alison M. , Bucci Vanni , Moormann Ann M. , Maldonado-Contreras Ana
Published: November 2022

The microbiome inherited at birth exerts marked effects on immune programming with long-term health consequences. Here, we demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition compared to healthy controls at the time of delivery. Accordingly, infants born to pregnant women with early SARS-CoV-2 infection exhibit a unique oral microbiota dominated byStreptococcusspecies. Together, we demonstrated that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infant’s microbiome-dependent immune programming.

One Sentence Summary

Pregnant patients with SARS-CoV-2 infection early in pregnancy and with active infection exhibit an altered vaginal and oral microbiota that is passed on to infants.
Automatically Identifying Childhood Health Outcomes on Twitter for Digital Epidemiology in Pregnancy
Authors: Klein Ari Z. , Gutiérrez Gómez José Agustín , Levine Lisa D. , Gonzalez-Hernandez Graciela
Published: November 2022

Data are limited regarding associations between pregnancy exposures and childhood outcomes. The objectives of this preliminary study were to (1) assess the availability of Twitter data during pregnancy for users who reported having a child with attention deficit/hyperactivity disorder (ADHD), autism spectrum disorders (ASD), delayed speech, or asthma, and (2) automate the detection of these outcomes. We annotated 9734 tweets that mentioned these outcomes, posted by users who had reported their pregnancy, and used them to train and evaluate the automatic classification of tweets that reported these outcomes in their children. A classifier based on a RoBERTa-Large pretrained model achieved the highest F1-score of 0.93 (precision = 0.92 and recall = 0.94). Manually and automatically, we identified 3806 total users who reported having a child with ADHD (678 users), ASD (1744 users), delayed speech (902 users), or asthma (1255 users), enabling the use of Twitter data for large-scale observational studies.
What is particular about microplastics? A meta-analysis of the toxicity of microplastics and suspended sediments
Authors: Ogonowski M. , Wagner M. , Rogell B. , Haave M. , Lusher A.
Published: November 2022

Microplastics (MP) are perceived as a threat to aquatic ecosystems but bear many similarities to suspended sediments which are often considered less harmful. It is, therefore pertinent to determine if and to what extent MPs are different from other particles occurring in aquatic ecosystems in terms of their adverse effects. We applied meta-regressions to hazard data extracted from the literature and harmonized the data to construct Species Sensitivity Distributions (SSDs) for both types of particles. The results demonstrate that the average toxicity of MPs is approximately one order of magnitude higher than that of suspended solids. However, the estimates were associated with large uncertainties and did not provide very strong evidence. In part, this is due to the general lack of comparable experimental studies and dose-dependent point estimates. We, therefore, argue that a precautionary approach should be used and MP in the 1–1000 µm size range should be considered moderately more hazardous to aquatic organisms capable of ingesting such particles. Organisms inhabiting oligotrophic habitats like coral reefs and alpine lakes, with naturally low levels of non-food particles are likely more vulnerable, and it is reasonable to assume that MP pose a relatively higher risk to aquatic life in such habitats.

Synopsis

A meta-analysis indicates that microplastics are one order of magnitude more toxic than suspended sediments/solids, an estimate surrounded by considerable uncertainty.

Graphical abstract
Multi-scale structural alterations of the thalamus and basal ganglia in focal epilepsy as demonstrated by 7T MRI
Authors: Haast Roy AM , Testud Benoit , Makhalova Julia , Dary Hugo , Cabane Alexandre , Le Troter Arnaud , Ranjeva Jean-Philippe , Bartolomei Fabrice , Guye Maxime
Published: November 2022

Focal epilepsy is characterized by repeated spontaneous seizures that originate from cortical epileptogenic zone networks (EZN). More recently, analysis of intracerebral recordings showed that subcortical structures, and in particular the thalamus, play an important role in facilitating and/or propagating epileptic activity. This supports previously reported structural alterations of these structures. Nonetheless, between-patient differences in EZN (e.g., temporal vs. non-temporal lobe epilepsy) as well as other clinical features (e.g., number of epileptogenic regions) might impact the magnitude as well as spatial distribution of subcortical structural changes. Here we used 7 Tesla MRI T1data to provide a comprehensive description of subcortical morphological (volume, tissue deformation, and shape) and longitudinal relaxation (T1) changes in focal epilepsy patients to evaluate the impact of the EZN and patient-specific clinical features. Our results showed widespread morphometric and T1changes. Focusing on the thalamus, atrophy varied across nuclei but appeared most prominent for the TLE group and the ipsilateral side, while shortening of T1was observed for the lateral thalamus, in particular. Multivariate analyses across thalamic nuclei and basal ganglia showed that volume acted as the dominant discriminator between patients and controls, while (posterolateral) thalamic T1measures looked promising to further differentiate patients based on EZN. In particular, the observed differences in T1changes between thalamic nuclei indicated differential involvement of thalamic nuclei based on EZN. Finally, the number of epileptogenic regions was found to best explain the observed variability between patients. To conclude, this work revealed multi-scale subcortical alterations in focal epilepsy as well as their dependence on several clinical characteristics. Our results provide a basis for further, in-depth investigations using (quantitative) MRI and SEEG data and warrant further personalization of intervention strategies, such as deep brain stimulation, for treating focal epilepsy patients.
Heterogeneities in infection outcomes across species: sex and tissue differences in virus susceptibility
Authors: Roberts Katherine E , Longdon Ben
Published: November 2022

Species vary in their susceptibility to pathogens, and this can alter the ability of a pathogen to infect a novel host. However, many factors can generate heterogeneity in infection outcomes, obscuring our ability to understand pathogen emergence. Such heterogeneities can alter the consistency of responses across individuals and host species. For example, sexual dimorphism in susceptibility means males are often intrinsically more susceptible than females (although this can vary by host and pathogen). Further, we know little about whether the tissues infected by a pathogen in one host are the same in another species, and how this relates to the harm a pathogen does to its host. Here, we first take a comparative approach to examine sex differences in susceptibility across 31 species of Drosophilidae infected with Drosophila C Virus (DCV). We found a strong positive inter-specific correlation in viral load between males and females, with a close to 1:1 relationship, suggesting that susceptibility to DCV across species is not sex specific. Next, we made comparisons of the tissue tropism of DCV across seven species of fly. We found differences in viral load between the tissues of the seven host species, but no evidence of tissues showing different patterns of susceptibility in different host species. We conclude that, in this system, patterns of viral infectivity across host species are robust between males and females, and susceptibility in a given host is general across tissue types.
Incorporating space in hierarchical capture mark recapture models: can we better capture variance?
Authors: Van Der Drift Anne – Merel , Leirs Herwig , Mariën Joachim , Sabuni Christopher , Mulungu Loth , Kirkpatrick Lucinda
Published: November 2022

Capture mark recapture (CMR) models allow the estimation of various components of animal populations, such as survival and recapture probabilities. In recent years, incorporating the spatial distribution of the devices used to detect an animals’ presence has become possible. By incorporating spatial information, we explicitly acknowledge the fact that there will be spatial structuring in the ecological processes which give rise to the capture data. Individual detection probability is not heterogeneous for a range of different reasons, for example the location of traps within an individual’s home range, the environmental context around the trap or the individual characteristics of an animal such as its age. Spatial capture recapture models incorporate this heterogeneity by including the spatial coordinates of traps, data which is often already collected in standard CMR approaches. Here, we compared how the inclusion of spatial data changed estimations of survival, detection probability, and to some extent the probability of seroconversion to a common arenavirus, using the multimammate mouse as our model system. We used a Bayesian framework to develop non spatial, partially spatial and fully spatial models alongside multievent CMR models. First, we used simulations to test whether certain parameters were sensitive to starting parameters, and whether models were able to return the expected values. Then we applied the non-spatial, partially spatial and fully spatial models to a real dataset. We found that bias and precision were similar for the three different model types, with simulations always returning estimates within the 95% credible intervals. When applying our models to the real data set, we found that the non-spatial model predicted a lower survival of individuals exposed to Morogoro virus (MORV) compared to unexposed individuals, yet in the spatial model survival between exposed and non-exposed individuals was the same. This suggests that the non-spatial model underestimated the survival of seropositive individuals, most likely due to an age effect. We suggest that spatial coordinates of traps should always be recorded when carrying out CMR and spatially explicit methods of analysis should be used whenever possible, particularly as incorporating spatial variation may more easily capture ecological processes without the need for additional data collection that can be challenging to acquire with wild animals.
Fitness and functional landscapes of theE. coliRNase III genernc
Authors: Weeks Ryan , Ostermeier Marc
Published: November 2022

How protein properties such as protein activity and protein essentiality affect the distribution of fitness effects (DFE) of mutations are important questions in protein evolution. Deep mutational scanning studies typically measure the effects of a comprehensive set of mutations on either protein activity or fitness. Our understanding of the underpinnings of the DFE would be enhanced by a comprehensive study of both for the same gene. Here, we compared the fitness effects and in vivo protein activity effects of ∼4,500 missense mutations in theE. coli rncgene. This gene encodes RNase III, a global regulator enzyme that cleaves diverse RNA substrates including precursor ribosomal RNA and various mRNAs including its own 5’ untranslated region (5’UTR). We find that RNase III’s ability to cleave dsRNA is the most important determinant of the fitness effects ofrncmutations. The DFE of RNase III was bimodal, with mutations centered around neutral and deleterious effects, consistent with previously reported DFE’s of enzymes with a singular physiological role. Fitness was buffered to small effects on RNase III activity. The enzyme’s RNase III domain (RIIID), which contains the RNase III signature motif and all active site residues, was more sensitive to mutation than its dsRNA binding domain (dsRBD), which is responsible for recognition and binding to dsRNA. Differential effects on fitness and functional scores for mutations at highly conserved residues G97, G99, and F188 suggest that these positions may be important for RNase III cleavage specificity.
Caveolae and Bin1 form ring-shaped platforms for T-tubule initiation
Authors: Lemerle Eline , Lainé Jeanne , Moulay Gilles , Bigot Anne , Labasse Clémence , Madelaine Angeline , Canette Alexis , Aubin-Tessier Perrine , Vallat Jean-Michel , Romero Norma , Bitoun Marc , Mouly Vincent , Marty Isabelle , Cadot Bruno , Picas Laura , Vassilopoulos Stéphane
Published: November 2022

Excitation-contraction coupling requires a highly specialized membrane structure, the triad, composed of a plasma membrane invagination, the T-tubule, surrounded by two sarcoplasmic reticulum terminal cisternae. Although the precise mechanisms governing T-tubule biogenesis and triad formation remain largely unknown, studies have shown that caveolae participate in T-tubule formation and mutations of several of their constituents induce muscle weakness and myopathies. Here, we demonstrate that, at the plasma membrane, caveolae composed of caveolin-3 and Bin1 assemble into ring-like structures from which emerge tubes enriched in the dihydropyridine receptor. Overexpression of Bin1 lead to the formation of both rings and tubes and we show that Bin1 forms scaffolds on which caveolae accumulate to form the initial T-tubule. Cav3 deficiency caused by either gene silencing or pathogenic mutations cause defective ring formation and perturbed Bin1-mediated tubulation that may explain defective T-tubule organization in mature muscles. Our results uncover new pathophysiological mechanisms that may prove relevant to myopathies caused by Cav3 or Bin1.
Genetic ablation of dentate hilar somatostatin-positive GABAergic interneurons is sufficient to induce cognitive impairment
Authors: Nagarajan Rajasekar , Lyu Jinrui , Kambali Maltesh , Wang Muxiao , Courtney Connor D. , Christian-Hinman Catherine A. , Rudolph Uwe
Published: November 2022

Aging is often associated with a decline in cognitive function. A reduction in the number of somatostatin-positive (SOM+) interneurons in the dentate gyrus (DG) has been described in cognitively impaired but not in unimpaired aged rodents. However, it remains unclear whether the reduction in SOM+ interneurons in the DG hilus is causal for age-related cognitive dysfunction. We hypothesized that hilar SOM+ interneurons play an essential role in maintaining cognitive function and that a reduction in the number of hilar SOM+ interneurons might be sufficient to induce cognitive dysfunction. Hilar SOM+ interneurons were ablated by expressing a diphtheria toxin transgene specifically in these interneurons, which resulted in a reduction in the number of SOM+/GAD-67+ neurons and dendritic spine density in the DG. C-fos and Iba-1 immunostainings were increased in DG and CA3 but not in CA1. Behavioral testing revealed a reduced recognition index in the novel object recognition test, a reduction in the percentage of correct alternations in the Y maze tests, and increased latencies and path lengths in the learning and the reversal learning phase of the Morris water maze. Our results show that partial genetic ablation of SOM+ hilar interneurons is sufficient to increase activity in DG and CA3, as has been described to occur with aging and to induce an impairment of learning and memory functions. Thus, partial ablation of hilar SOM+ interneurons may be a significant contributing factor to age-related cognitive dysfunction. These mice may also be useful as a cellularly defined model of hippocampal aging.
Disruption of HIF1Α translational control attenuates the HIF-dependent hypoxic response and solid tumour formationin vivo
Authors: Hunter Jill E , McHugh Oliver , Ecclestone Gabrielle B , Child Fraser , Mearns Hannah , Robson Georgia , Dadzie Molly , Rocha Sonia , Perkins Neil D , Kenneth Niall S
Published: November 2022

Adaptation to reduced oxygen availability is mediated by the hypoxia-inducible factor (HIF) family of transcription factors. The activity and availability of HIF proteins is primarily driven by the stability of the HIF alpha subunits. However, it is becoming increasingly apparent that preferential translation of HIF1α mRNA is also necessary for full activation of the HIF1-dependent hypoxic response. Consequently, the mechanisms controlling HIF1α translation are of equivalent importance to the proline hydroxylase-dependent degradation pathways. Here we investigate the role of the 5’UTR of the HIF1α mRNA in controlling preferential translation of endogenous HIF1α in hypoxic cells. CRISPR/Cas9-mediated genetic deletion of the 5’ UTR of HIF1α results in reduced HIF1α levels following hypoxia, without alteration in mRNA or protein stability. HIF1α mRNA lacking the 5’UTR was efficiently translated in adequately oxygenated cells but this was inhibited during hypoxia, consistent with the global block on protein synthesis. The HIF1α translational defect observed in cells missing the 5’UTR led to reduced viability in hypoxic conditionsin vitroand an impaired ability to form solid tumours in murine xenografts. Prevention of preferential HIF1α translation limits the duration and intensity of the HIF-dependent hypoxic response and disrupts the formation of solid tumours. Together these results demonstrate the importance of translation control over HIF1α and suggest that strategies to inhibit preferential HIF1α protein translation in hypoxic cancer cells will be an effective strategy to limit the growth of solid hypoxic tumours.
Autophagy limits inflammatory gene expression through targeting of nuclear p65/RelA by LC3 and p62 for lysosomal degradation
Authors: Brischetto Cristina , Mucka Patrick , Kaergel Eva , Scheidereit Claus
Published: November 2022

The interplay between NF-κB signaling and autophagy regulates inflammatory signaling in different cellular contexts and in response to different stimuli. The impairment of this crosstalk may play a role in chronic inflammation and in tumorigenesis. However, the molecular mechanism by which these two pathways interact to regulate the inflammatory response remains elusive. By using biochemical analysis and imaging techniques, we characterized the interaction of the endogenous autophagic marker LC3 and NF-κB/p65 in response to different stress conditions. Following irradiation or TNFα stimulation, nuclear accumulation of LC3 strongly co-localized with p65, suggesting that nuclear p65 is targeted for autophagic degradation. Mechanistically, we showed that the nuclear p65-LC3 interaction is mediated by ubiquitination of the same p65, which is recognized by the cargo receptor p62, resulting in its cytoplasmic export and lysosomal proteolysis. Accordingly, autophagy inhibition by depletion of the essential autophagy geneATG16L1selectively stabilizes nuclear p65, in turn enhancing NF-κB gene expression of pro-inflammatory cytokine. Our results revealed a novel molecular mechanism that modulates the NF-κB inflammatory response through nuclear sequestration of the NF-κB/p65 subunit by autophagy proteins. These findings are of importance for developing novel therapeutic strategies against chronic inflammatory diseases displaying defective autophagy and constitutive NF-κB activity.
The Longitudinal Analysis of Convergent Antibody VDJ Regions in SARS-CoV-2 Positive Patients Using RNA-seq
Authors: Liu Kate J. , Zelazowska Monika A. , McBride Kevin M.
Published: November 2022

The severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has infected over 600 million individuals and caused over 6.5 million deaths. To understand the immune response individuals have from the SARS-CoV-2 infection, we studied the immunoglobulins against the virus’s antigens. The diversified complementarity determining region 3 (CDR3) can be used to characterize an antibody. We downloaded four public RNA-seq data sets that were collected be-tween March 2020 and March 2022 from the Gene Expression Omnibus (GEO) in our longitudinal analysis. In total, there were 269 SARS-CoV-2 positive patients and 26 negative patients who served as a control group. Samples were grouped based on their SARS-CoV-2 variant type and/or the time they were collected. Among 629,137 immunoglobulin V(D)J sequences identified by reconstructing the V(D)J sequences, we found 1011 common V(D)Js (same V gene, J gene and CDR3 sequences in each SARS-CoV-2 positive group) shared by more than one patient in each group and no common V(D)Js were from the negative control group. In our clustering analysis, we identified 129 convergent clusters from the SARS-CoV-2 positive groups. One of these convergent clusters matched the protein sequence of crystal 3D structures of the antibodies against SARS-CoV-2 in the Protein Data Bank (PDB). In our longitudinal analysis between the Alpha and Omicron variant, we found 2.7% of common CDR3s were shared although the longitudinal profiling of common V(D)Js was variant specific. Although diverse immunoglobulin profiles were observed, the convergence of common V(D)Js suggests that there exists antibodies with similar antigenic specificities across patients in different groups over various stages of the pandemic.
Optimization strategies and artifacts of time-involved small-angle neutron scattering experiments
Authors: Mettus Denis , Chacon Alfonso , Bauer Andreas , Mühlbauer Sebastian , Pfleiderer Christian
Published: November 2022

Kinetic small-angle neutron scattering provides access to the microscopic properties of mesoscale systems under slow, periodic perturbations. By interlocking the phases of neutron pulse, sample modulation and detector signal, time-involved small-angle neutron scattering experiments (TISANE) allow one to exploit the neutron velocity spread and record data without major sacrifice in intensity at timescales down to microseconds. This article reviews the optimization strategies of TISANE that arise from specific aspects of the process of data acquisition and data analysis starting from the basic principles of operation. Typical artifacts of data recorded in TISANE due to the choice of time binning and neutron chopper pulse width are illustrated by virtue of the response of the skyrmion lattice in MnSi under periodic changes of the direction of the stabilizing magnetic field.
Multiscale magnetization in cobalt-doped ferrite nanocubes
Authors: Zákutná Dominika , Fischer Anne , Dresen Dominique , Nižňanský Daniel , Honecker Dirk , Disch Sabrina
Published: November 2022

The magnetization of cobalt ferrite nanocubes of similar size, but with varying Co/Fe ratio, is extensively characterized on atomistic and nanoscopic length scales. Combination of X-ray diffraction, Mössbauer spectroscopy, magnetization measurements and polarized small-angle neutron scattering (SANS) reveals that a lower amount of cobalt leads to an enhanced magnetization. At the same time, magnetic SANS confirms no or negligible near-surface spin disorder in these highly crystalline, homogeneously magnetized nanoparticles, resulting in an exceptionally hard magnetic material with high coercivity.
Competition between chalcogen and halogen bonding assessed through isostructural species
Authors: De Silva Viraj , Magueres Pierre Le , Averkiev Boris B. , Aakeröy Christer B.
Published: November 2022

The amino group of 2-amino-5-(4-halophenyl)-1,3,4-chalcogenadiazole has been replaced with bromo/iodo substituents to obtain a library of four compositionally related compounds. These are 2-iodo-5-(4-iodophenyl)-1,3,4-thiadiazole, C8H4I2N2S, 2-bromo-5-(4-bromophenyl)-1,3,4-selenadiazole, C8H4Br2N2Se, 2-bromo-5-(4-iodophenyl)-1,3,4-selenadiazole, C8H4BrIN2Se, and 2-bromo-5-(4-iodophenyl)-1,3,4-thiadiazole, C8H4BrIN2S. All were isostructural and contained bifurcated Ch...N (Ch is chalcogen) and X...X (X is halogen) interactions forming a zigzag packing motif. The noncovalent Ch...N interaction between the chalcogen-bond donor and the best-acceptor N atom appeared preferentially instead of a possible halogen bond to the same N atom. Hirshfeld surface analysis and energy framework calculations showed that, collectively, a bifurcated chalcogen bond was stronger than halogen bonding and this is more structurally influential in this system.
Geographic style maps for two-dimensional lattices
Authors: Bright Matthew , Cooper Andrew I. , Kurlin Vitaliy
Published: November 2022

This paper develops geographic style maps containing two-dimensional lattices in all known periodic crystals parameterized by recent complete invariants. Motivated by rigid crystal structures, lattices are considered up to rigid motion and uniform scaling. The resulting space of two-dimensional lattices is a square with identified edges or a punctured sphere. The new continuous maps show all Bravais classes as low-dimensional subspaces, visualize hundreds of thousands of lattices of real crystal structures from the Cambridge Structural Database, and motivate the development of continuous and invariant-based crystallography.
Value relevance of book values, earnings, and future earnings: evidence by time, life cycle stage, and market uncertainty
Authors: Boonlert-U-Thai Kriengkrai , Schaberl Philipp
Published: November 2022

Purpose

The purpose of this study is to investigate the role of book values, earnings, and future earnings in equity valuation by time, life cycle stage, and market uncertainty using samples of USA and Japanese companies.

Design/methodology/approach

This study employs Lubberink and Willett (2021) methodology in using log-linear models to estimate the value relevance of accounting numbers and follows Schaberl (2016) approach to measure %incremental value relevance. The study also includes future earnings in a basic valuation model (Ohlson, 1995) to explore the extent to which stock prices are forward looking.

Findings

This study finds a significant increase by time in the relative value relevance of a combined model with book values and earnings and a combined model with future earnings for both countries. However, the incremental value relevance of book values, earnings, and future earnings remain stable over time. The results by life cycle stage indicate that incremental value relevance of future earnings and earnings are more (less) pronounced for firms in the intro (mature) life cycle stage while the incremental value relevance of book values is highest for firms in the decline stage for both countries. The results by market uncertainty indicate that firms with high market uncertainty display higher incremental value relevance of book values for both countries. The results on future earnings are mixed as USA (Japan) firms with high (low) market uncertainty display more (less) incremental value relevance of future earnings.

Practical implications

The findings in this study enhance the merits of two basic financial statements (balance sheet and income statement) in a firm's equity valuation for potential investors and existing shareholders and document an additional role of future earnings information in reflecting a firm's stock price, which is beyond what book values and current earnings have already contributed.

Originality/value

This is the first study that uses log-linear models to estimate the value relevance of accounting numbers and investigates value relevance of accounting information in three views: time, life cycle stage, and market uncertainty.
Why, where and how are organizations using blockchain in their supply chains? Motivations, application areas and contingency factors
Authors: Ahmed Wafaa A.H. , MacCarthy Bart L. , Treiblmaier Horst
Published: November 2022

Purpose

Blockchain is increasingly being considered for applications in operations and supply chain management. However, evidence from practice is still scarce on why, where and how organizations seek to apply the technology in the supply chain across different industries. The study develops a comprehensive framework to enhance understanding of the application areas of blockchain technology in the supply chain, as well as organizations' motivations in seeking blockchain solutions and relevant contingency factors influencing applications.

Design/methodology/approach

The authors investigate 50 use cases of blockchain applications in the supply chain, covering six industries. Contingency theory is applied in conducting a qualitative textual and correlation analysis to identify and compare blockchain adoption motivations, application areas and contingency factors across different industries.

Findings

The analysis develops an evidence-based framework that captures ten principal motivations in seeking blockchain solutions, three main blockchain application areas along with important application sub-categories and five clusters of contingency factors that influence blockchain deployment and its uses in different industrial sectors.

Research limitations/implications

The study expands the limited cross-sectoral research on blockchain applications and motivations in the supply chain. Using contingency theory, it presents a comprehensive framework that captures the drivers and factors relating to blockchain adoption in the supply chain in a nomological network. The study lays the foundation for further theoretical perspectives and empirical research to investigate relevant sectoral characteristics and their importance for different types of blockchain application in the supply chain.

Practical implications

The study informs practitioners about potential supply chain application areas that can be enhanced through blockchain technology, taking account of the specific characteristics of their products, business and manufacturing processes, supply network configurations, industry standards, regulations and market demand.

Originality/value

The study is the first to provide cross-sectoral evidence on the relevance of organizations' motivations and numerous contingency factors on blockchain application areas in the supply chain.
Functional assembly of grassland plant species in native communities in Spain and recipient communities in California
Authors: Galán Díaz Javier , Vilà Montserrat , Parker Ingrid M. , de la Riva Enrique G.
Published: November 2022

A major aim in invasion ecology is to understand the role of exotic species in plant communities. Whereas most studies have explored the traits of exotic species in the context of the introduced community, functional comparisons of entire assemblages of species in their native and introduced communities have rarely been analysed. Taking advantage of the unidirectional invasion of plant species of European origin (i.e. colonizers) into California, this study aims to investigate the relative importance of plant traits, environmental factors and invasion status in biological invasions.

We compared the functional structure (i.e. trait composition and diversity) along resource availability gradients in recipient and native Mediterranean grassland communities in California and Spain, respectively. Traits were related to resource use in above‐ground and below‐ground organs and reproductive strategy. We also investigated how niche differences vary along environmental gradients between coexisting colonizer and native species assemblages within communities.

There were clear differences in the functional structure of Mediterranean grassland communities between regions, which were associated with the resource availability gradient. Paradoxically, the most acquisitive communities occurred in resource‐poor sites, highlighting that rapid acquisition and use of resources permit species to cope with environmental stress through stress avoidance. In Spain, colonizer species had greater specific leaf area than non‐colonizers. Yet, differences between colonizer and non‐colonizer species in Spain for other traits were mostly absent and did not change along the gradient. This might be a result of the greater native species richness as a consequence of the agricultural practices that have taken place in Europe for millennia and reflect that the entire species pool of grasslands is adapted to agricultural landscapes. In comparison, in California, colonizer species were more acquisitive in their use of resources than natives under favourable conditions, but functionally converged in resource‐limited sites.

Synthesis. These results underscore that the importance of niche differences between native and colonizer species as a community assembly mechanism is strongly subjected to the influence of habitat filtering. Trait comparisons are context dependent, and a correct interpretation of filtering processes in community assembly requires a regional perspective.
The neutrophil‐to‐lymphocyte ratio represents a systemic inflammation marker and reflects the relationship with 90‐day mortality in non‐cirrhotic chronic severe hepatitis
Authors: Dong Fu Chen , Tan Wen Ting , Wang Xian Bo , Zheng Xin , Huang Yan , Li Bei Ling , Meng Zhong Ji , Gao Yan Hang , Qian Zhi Ping , Liu Feng , Lu Xiao Bo , Shang Jia , Shi Yu , Zheng Yu Bao , Yan Hua Dong , Zhang Yan , Xu Bao Yan , Hou Yi Xin , Zhang Qun , Xiong Yan , Zou Cong Cong , Chen Jun , Huang Ze Bing , Jiang Xiu Hua , Luo Sen , Chen Yuan Yuan , Gao Na , Liu Chun Yan , Yuan Wei , Mei Xue , Li Jing , Li Tao , Zheng Rong Jiong , Zhou Xin Yi , Chen Jin Jun , Deng Guo Hong , Mei Xiang Xiao , Zhang Wei Tuo , Li Hai
Published: November 2022

Objectives

To investigate the relationship between systemic inflammatory response and short‐term mortality in patients with non‐cirrhotic chronic severe hepatitis (CSH) by using several indicators of inflammation including neutrophil‐to‐lymphocyte ratio (NLR), neutrophil (NEU), white blood cell (WBC), platelet‐to lymphocyte ratio (PLR), and monocyte‐to‐lymphocyte ratio (MLR).

Methods

Data were collected from two prospectively enrolled CATCH‐LIFE noncirrhotic cohorts. Cox regression analysis was used to investigate the association between systemic inflammatory biomarkers and 90‐day liver transplant (LT)‐free mortality. A generalized additive model (GAM) was used to illustrate the quantitative curve relationship between NLR and 90‐day LT‐free mortality. Kaplan–Meier method was used to estimate the 90‐year LT‐free survival.

Results

The prevalence of CSH was 20.5% (226/1103). The 28‐day and 90‐day LT‐free mortality rates were 17.7% and 26.1%, respectively, for patients with non‐cirrhotic CSH. Patients with no infection accounted for 75.0% of all CSH patients, and NLR was independently associated with 90‐day LT‐free mortality. NLR of 2.9 might be related to disease deterioration in CSH patients without infection.

Conclusions

NLR may be an independent risk factor for 90‐day LT‐free mortality in patients with non‐cirrhotic chronic liver disease. A NLR of 2.9 as the cut‐off value can be used to predict disease aggravation in CSH patients without infection.
Vitiligo and systemic sclerosis: Are they associated?– Lessons from a population‐based study
Authors: Kridin Khalaf , Lyakhovitsky Keren , Tzur‐Bitan Dana , Onn Erez , Lyakhovitsky Anna , Zoller Lilach , Cohen Arnon D.
Published: November 2022

Background

The epidemiological relationship of vitiligo with systemic sclerosis (SSc) remains to be precisely evaluated.

Objective

To investigate the bidirectional association between vitiligo and SSc.

Methods

A population‐based study was carried out to compare vitiligo patients (n = 20,851) with age‐, sex‐ and ethnicity‐matched control subjects (n = 102,475) regarding the incidence of new‐onset and the prevalence of preexisting SSc. Adjusted hazard ratios (HRs) and adjusted odds ratios (ORs) were calculated by the Cox regression and logistic regression, respectively.

Results

The incidence rate of new‐onset SSc was calculated at 2.4 (95% CI, 1.6–3.4) and 0.4 (95% CI, 0.3–0.6) cases per 10,000 person‐years among patients with vitiligo and controls, respectively. Patients with vitiligo had an increased risk of SSc (fully adjusted HR, 5.37; 95% CI, 3.03–9.54; p < 0.001). Correspondingly, a history of SSc predicted elevated odds of developing vitiligo (fully adjusted OR, 2.09; 95% CI, 1.23–3.55; p = 0.006). Relative to other patients with vitiligo, those with vitiligo and comorbid SSc were older and had a higher prevalence of ischaemic heart disease, hyperlipidaemia, and hypertension.

Conclusions

A robust bidirectional association exists between vitiligo and SSc. This knowledge is valuable for physicians managing patients with both conditions. Patients with vitiligo and comorbid SSc might be monitored for cardiovascular and metabolic comorbidities.
Erbu Zhuyu decoction improves endometrial angiogenesis via uterine natural killer cells and the PI3K/Akt/eNOS pathway a mouse model of embryo implantation dysfunction
Authors: Shen Mengmeng , Liu Yanfeng , Ma Xiaona , Zhu Qingwen
Published: November 2022

Background

We investigated the effect of Erbu Zhuyu decoction (EBZY) on angiogenesis via uterine natural killer (uNK) cells and the PI3K/Akt/eNOS pathway in embryo implantation dysfunction (EID) mice.

Methods

Pregnant mice were randomly divided into blank, model, EBZY, progynova, and aspirin groups. Uteri were excised on the 5th day of pregnancy for analysis.

Results

Mice in the model group showed pale uteri, a reduced implantation rate, and lower expression levels of phosphatidylinositol‐3‐kinase (PI3K), protein kinase B (Akt), endothelial nitric oxide synthase (eNOS) and nitric oxide (NO). Compared to the model group, implantation rates in the medium‐dose and high‐dose groups of EBZY were significantly higher (P < .05), PI3K and Akt mRNA expression levels in the low‐dose group were significantly higher (P < .05, P < .01), and the expression of p‐PI3K, p‐Akt, and p‐eNOS proteins in all treatment groups were significantly increased (P < .01, P < .05). The expression of NO was significantly increased in the low‐dose and high‐dose groups (P < .01, P < .05, respectively). The level of p‐Akt protein in the high‐dose group was significantly higher than those in the other treatment groups (P < .01, P < .05). There was no significant difference in the density of uNK cells (P > .05).

Conclusions

EBZY facilitated embryo implantation in EID mice by enhancing endometrial angiogenesis via activation of the PI3K/Akt/eNOS pathway, at least in part. There was no evidence to indicate that EBZY could adjust the expression of uNK.