bluuebunny/crossref_metadata_2025 huggingface dataset:
Hematological parameters to predict post-COVID-19 immune response among vaccinated and nonvaccinated individuals: a retrospective cross-sectional study
Authors: Khan Qaisar A. , Atta Tahira , Tango Tamara , Mumtaz Arif , Saravanan Priyadharshini , Vallabhaneni Sree H. , Shinwari Ismail K. , Vattikuti Bhavana , Jan Rukhsar , Verma Ravina , Sami Nayab , Farrukh Ameer M. , Levin-Carrion Yaxel
Published: April 2024

Background:

This study finds the changes in the hematological parameters of healthy individuals to predict the immune status against coronavirus disease 2019 (COVID-19) among COVID -19 vaccinated and nonvaccinated individuals.

Methods:

A comparative cross-sectional study among 210 healthy individuals was conducted. All individuals were divided into three groups, that is, IgG positive, IgG negative, and IgG and IgM positive, based on ELISA. Data analysis was done using SPSS version 25 for Windows.

Results:

A statistically significant effect was found among the three groups in terms of mean levels of hemoglobin (Hb), hematocrit (Hct), mean corpuscular hemoglobin concentration (MCHC), red blood cells (RBC), RDW-CV, lymphocyte, neutrophil, eosinophils, and basophil count. The study also showed that 52.8% (n=74) had neither taken vaccination nor had any history of previous COVID-19 infection but were IgG antibody positive.

Conclusion:

There was a statistically significant difference among hematological parameters between immune and nonimmune groups, and it can predict the COVID-19 immune status.
Tailoring epilepsy treatment: personalized micro-physiological systems illuminate individual drug responses
Authors: Shariff Sanobar , Kantawala Burhan , Xochitun Gopar Franco William , Dejene Ayele Nitsuh , Munyangaju Isabelle , Esam Alzain Fatima , Nazir Abubakar , Wojtara Madga , Uwishema Olivier
Published: April 2024

Introduction:

Approximately 50 million people worldwide have epilepsy, with many not achieving seizure freedom. Organ-on-chip technology, which mimics organ-level physiology, could revolutionize drug development for epilepsy by replacing animal models in preclinical studies. The authors’ goal is to determine if customized micro-physiological systems can lead to tailored drug treatments for epileptic patients.

Materials and methods:

A comprehensive literature search was conducted utilizing various databases, including PubMed, Ebscohost, Medline, and the National Library of Medicine, using a predetermined search strategy. The authors focused on articles that addressed the role of personalized micro-physiological systems in individual drug responses and articles that discussed different types of epilepsy, diagnosis, and current treatment options. Additionally, articles that explored the components and design considerations of micro-physiological systems were reviewed to identify challenges and opportunities in drug development for challenging epilepsy cases.

Results:

The micro-physiological system offers a more accurate and cost-effective alternative to traditional models for assessing drug effects, toxicities, and disease mechanisms. Nevertheless, designing patient-specific models presents critical considerations, including the integration of analytical biosensors and patient-derived cells, while addressing regulatory, material, and biological complexities. Material selection, standardization, integration of vascular systems, cost efficiency, real-time monitoring, and ethical considerations are also crucial to the successful use of this technology in drug development.

Conclusion:

The future of organ-on-chip technology holds great promise, with the potential to integrate artificial intelligence and machine learning for personalized treatment of epileptic patients.
Antibiotic Duration and UTI Outcomes in Recurrent UTI Patients
Authors: Shinnick Julia , Josephs Isabel , Suskin Johanna A. , Kurchena Kathryn , Pileika Lindsey , Darveau Spencer , Scarpaci Matthew M. , Carberry Cassandra
Published: April 2024

Importance

Little evidence is available to inform management of acute urinary tract infections (UTIs) in women with recurrent urinary tract infection (rUTI).

Objective

This study aimed to compare the proportion of acute UTIs with persistence/relapse or recurrence based on duration of treatment antibiotics (acute UTI guideline-consistent versus extended).

Study Design

A retrospective noninferiority study of women with rUTI was performed at an academic tertiary referral center from January 2016 to December 2020. Exposure was UTI treatment with acute UTI guideline-consistent versus extended antibiotics. Outcomes were persistent/relapsed UTI (subsequent culture with the same pathogen requiring additional antibiotics within 4 weeks), recurrent UTI (culture with different pathogen), or resolution. Sample size was calculated under the null hypothesis that the proportion of acute UTIs with persistence/relapse or recurrence after acute UTI guideline-consistent antibiotics would be within a 10% noninferiority margin of extended duration (α = 0.05, β = 0.20, 2-sided tests, P < 0.05 significant).

Results

We included 219 patients with 553 acute UTIs. The mean ± SD number of UTIs per patient was 2.53 ± 1.88, the mean ± SD age was 68.60 ± 16.29 years, and the mean ± SD body mass index was 29.73 ± 7 (calculated as weight in kilograms divided by height in meters squared). There were no differences in prior surgical procedures postvoid residual volume, pelvic floor disorders, or preventive treatments between groups. Two-hundred sixty UTIs (260 of 553 [47%]) were treated with acute UTI guideline-consistent antibiotics. Overall, 86 of 553 UTIs (15.6%) persisted/relapsed, and 29 of 553 (5.2%) recurred. The difference in the proportions of UTIs with persistence/relapse or recurrence excluded the noninferiority margin (4.4%; 95% confidence interval, −0.04 to 6.80%). In total, 115 of 553 UTIs (20.8%) had persistence/relapse or recurrence.

Conclusion

In this cohort of patients with rUTI experiencing acute UTIs, acute UTI guideline-consistent duration of antibiotics was noninferior.
Nocturnal Urinary Symptoms as Screening Tools for Obstructive Sleep Apnea
Authors: Burr Eliza F. , Myer Emily N.B. , Kikuchi Jacqueline Y. , Chen Chi Chiung Grace
Published: April 2024

Importance

Nocturnal lower urinary tract symptoms are part of obstructive sleep apnea (OSA), and urogynecology clinics may serve as OSA screening sites.

Objective

This study’s aim was to determine the accuracy of nocturia and nocturnal enuresis (NE) as screening tools for OSA in new patients at a urogynecology clinic.

Study Design

Using a retrospective study design, we gathered information regarding diagnostic OSA testing, continuous positive airflow pressure use, and lower urinary tract symptoms improvement from women in a urogynecology clinic who were previously screened for OSA using validated questionnaires. Nocturia and NE were tested for sensitivity and specificity using positive OSA diagnosis by polysomnography as the gold standard.

Results

Nocturia with a cutoff of ≥2 episodes per night had the best test characteristics—86.4% sensitivity (95% confidence interval [CI], 65.1–97.1) and 58.5% specificity (95% CI, 44.1–71.9) for an overall accuracy of 78.4% (95% CI, 67.0–89.8). Nocturnal enuresis with a cutoff of ≥1 episode per week had the best NE characteristics with 31.8% sensitivity (95% CI, 13.9–54.9) and 79.3% specificity (95% CI, 65.9–89.2) for an overall accuracy of 56.1% (95% CI, 41.2–71).

Conclusions

Lower urinary tract symptoms such as nocturia and NE are routinely assessed in urogynecology clinics, making them useful for OSA screening and referral. The present study found nocturia symptoms with ≥2 episodes per night to retain acceptable test characteristics in screening for OSA, whereas NE was found to have less acceptable test characteristics for OSA screening. Urogynecology clinics may utilize nocturia symptoms in clinical decision making for OSA referral.
Francis James Macdonald Farley. 13 October 1920—16 July 2018
Authors: Crease Robert P.
Published: April 2024

Francis Farley was a British experimental physicist who worked for much of his career at CERN. He was a clever designer and builder of particle beams, and a team leader and player who inspired, advised, amused and regaled others. In the middle of his career he worked on the first four experiments to measure
g
 − 2, one of the most important numbers in particle physics. Three of these were conducted while he was at CERN, and one at Brookhaven National Laboratory in New York. Later he studied the problem of extracting energy from water waves, attempting to build proof of concept models as well as to study the problems that might stand in the way of commercial application. Farley had the rare ability to synthesize both theoretical and experimental knowledge of a subject, to collaborate in solving problems and to pass on what he knew to others. He was also articulate about the wonder and awe that he found in science.
Probing the complexity of wood with computer vision: from pixels to properties
Authors: Lukovic Mirko , Ciernik Laure , Müller Gauthier , Kluser Dan , Pham Tuan , Burgert Ingo , Schubert Mark
Published: April 2024

We use data produced by industrial wood grading machines to train a machine learning model for predicting strength-related properties of wood lamellae from colour images of their surfaces. The focus was on samples of Norway spruce (
Picea abies
) wood, which display visible fibre pattern formations on their surfaces. We used a pre-trained machine learning model based on the residual network ResNet50 that we trained with over 15 000 high-definition images labelled with the indicating properties measured by the grading machine. With the help of augmentation techniques, we were able to achieve a coefficient of determination (
R
2
) value of just over 0.9. Considering the ever-increasing demand for construction-grade wood, we argue that computer vision should be considered a viable option for the automatic sorting and grading of wood lamellae in the future.
Allowing Wigner’s friend to sequentially measure incompatible observables
Authors: Utreras-Alarcón Aníbal , Cavalcanti Eric G. , Wiseman Howard M.
Published: April 2024

The Wigner’s friend thought experiment has gained a resurgence of interest in recent years thanks to no-go theorems that extend it to Bell-like scenarios. One of these, by us and co-workers, showcased the contradiction that arises between quantum theory and a set of assumptions, weaker than those in Bell’s theorem, which we named ‘Local Friendliness’. Using these assumptions, it is possible to arrive at a set of inequalities for a given scenario, and, in general, some of these inequalities will be harder to violate than the Bell inequalities for the same scenario. A crucial feature of the extended Wigner’s friend scenario in our aforementioned work was the ability of a superobserver to reverse the unitary evolution that gives rise to their friend’s measurement. Here, we present a new scenario where the superobserver can interact with the friend repeatedly in a single experimental instance, either by asking them directly for their result, thus ending that instance, or by reversing their measurement and instructing them to perform a new one. We show that, in these scenarios, the Local Friendliness inequalities will always be the same as Bell inequalities.
Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis
Authors: da Roza Patrick A. , Muller Héloïse , Sullivan Geraldine J. , Walker Roy S. K. , Goold Hugh D. , Willows Robert D. , Palenik Brian , Paulsen Ian T.
Published: April 2024

Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.
Surviving under Ice: Insights into gene expression changes during ice encasement in timothy (Phleum pratenseL.)
Authors: Pashapu Akhil Reddy , Dalmannsdottir Sigridur , Jørgensen Marit , Rognli Odd Arne , Kovi Mallikarjuna Rao
Published: April 2024

The predicted increase in frequency and duration of winter warming episodes (WWEs) at the higher northern latitudes is expected to negatively impact the forage production in this region. The formation of non-permeable ice cover due to WWEs creates hypoxic or anoxic conditions for plants leading to severe winter damages. Knowledge about molecular mechanisms underlying various winter stresses is crucial to develop cultivars with better winter survival under changing climatic conditions. In the current study, we aimed at identifying genes involved in ice encasement stress responses by RNAseq in the perennial forage grass timothy (Phleum pratenseL.) and study gene expression differentiation due to field survival using cultivars with diverse genetic backgrounds. The LD50estimates varied across cultivars and material. The expression of ethylene-responsive transcription factors, alcohol dehydrogenase, pyruvate decarboxylase, sucrose synthase, dehydrins, and heat shock proteins were highly upregulated under ice encasement conditions. Functional analysis of differentially expressed genes revealed that the upregulated genes were involved in glycolysis, pyruvate metabolism, carbon metabolism, and biosynthesis of amino acids while genes involved in photosynthesis, phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were downregulated. The results from the current study indicate a substantial overlap of ice encasement stress responses with those of hypoxia and freezing stresses. In addition, the potential strategies leading to higher ice encasement tolerance of timothy are outlined. Furthermore, differences in gene expression between field survivors and the original plant material, and differences between ice encasement responses of northern-adapted and southern-adapted cultivars are briefly discussed.
Exploring the Spatial Distribution of Persistent SARS-CoV-2 Mutations - Leveraging mobility data for targeted sampling
Authors: Spott Riccardo , Pletz Mathias W. , Fleischmann-Struzek Carolin , Kimmig Aurelia , Hadlich Christiane , Hauert Mathias , Lohde Mara , Jundzill Mateusz , Marquet Mike , Dickmann Petra , Schüchner Ruben , Hölzer Martin , Kühnert Denise , Brandt Christian
Published: April 2024

Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking lineage spread, we investigated the potential of combining mobile service data and fine-granular metadata (such as postal codes and genomic data) to advance integrated genomic surveillance of the pandemic in the federal state of Thuringia, Germany. We sequenced over 6,500 SARS-CoV-2 Alpha genomes (B.1.1.7) across seven months within Thuringia while collecting patients’ isolation dates and postal codes. Our dataset is complemented by over 66,000 publicly available German Alpha genomes and mobile service data for Thuringia. We identified the existence and spread of nine persistent mutation variants within the Alpha lineage, seven of which formed separate phylogenetic clusters with different spreading patterns in Thuringia. The remaining two are sub-clusters. Mobile service data can indicate these clusters’ spread and highlight a potential sampling bias, especially of low-prevalence variants. Thereby, mobile service data can be used either retrospectively to assess surveillance coverage and efficiency from already collected data or to actively guide part of a surveillance sampling process to districts where these variants are expected to emerge. The latter concept was successfully implemented as a proof-of-concept for a mobility-guided sampling strategy in response to the surveillance of Omicron sublineage BQ.1.1. The combination of mobile service data and SARS-CoV-2 surveillance by genome sequencing is a valuable tool for more targeted and responsive surveillance.
Bridge Capture permits cost-efficient, rapid and sensitive molecular precision diagnostics
Authors: Adamusová Simona , Korkiakoski Anttoni , Laine Nea , Musku Anna , Rantasalo Tuula , Kim Jorma , Blomster Juuso , Laine Jukka , Hirvonen Tatu , Pursiheimo Juha-Pekka , Tamminen Manu
Published: April 2024

Liquid biopsies are a less invasive alternative to tissue biopsies that have been the mainstay of cancer diagnostics to date. Recently, the quantification of mutations in circulating tumor DNA (ctDNA) by targeted next-generation sequencing (NGS) has been gaining popularity. Targeted NGS can be achieved through various library preparation methods, each with distinct advantages and limitations. Here we introduce Bridge Capture, a novel technology that goes beyond the advantages of market-leading liquid biopsy technologies, eliminating the need to compromise between scalability, cost-efficiency, sensitivity, or panel size. We compared Bridge Capture to leading commercial technologies currently available in cancer diagnostics; Archer™ LIQUIDPlex™ and AmpliSeq™ Cancer HotSpot Panel v2 for Illumina®. Of all methods, Bridge Capture detected the lowest mutant allele frequency (MAF) on matched contrived colorectal biospecimens mimicking ctDNA. Next, we demonstrated the capability of Bridge Capture to effectively utilize the sequencing capacity, permitting affordable and sensitive variant detection in smaller laboratories, while delivering significant cost savings for central laboratories. Additionally, we demonstrated the reproducibility of Bridge Capture by a high correlation between the results from two independent laboratories. These results highlight the method’s portability and suitability for kit use in entirely new settings. Moreover, we presented ease of automation and minimal hands-on time of Bridge Capture. Owing to its unique design, the Bridge Capture is compatible with the most commonly used NGS platforms. Taken together, Bridge Capture is cost efficient, simple, rapid and sensitive cancer diagnostics tool that significantly improves the detection of mutations in liquid biopsies.
CHAPAS-4 trial: second-line anchor drugs for children with HIV in Africa
Authors: Bwakura-Dangarembizi Mutsa , Szubert Alexander J , Mumbiro Vivian , Kityo Cissy M , Lugemwa Abbas , Doerholt Katja , Chabala Chishala , Nyathi Mary , Nduna Bwendo , Burger David , Shakeshaft Clare , Nathoo Kusum , Musiime Victor , Yawe Ibrahim , South Annabelle , Lungu Joyce , Ndebele Wedu , Mwamabazi Mwate , Griffiths Anna , Nazzinda Rashidah , Zimba Kevin , Zhang Yingying , Walker Simon , Turkova Anna , Walker A Sarah , Bamford Alasdair , Gibb Diana M ,   CHAPAS-4 Trial Team
Published: April 2024

Background

Children living with HIV requiring second-line antiretroviral therapy (ART) have limited options, an unmet need considering children require life-long ART.

Methods

Children from Uganda, Zambia, Zimbabwe were randomised to one of four second-line anchor drugs: dolutegravir(DTG), ritonavir-boosted darunavir(DRV/r), atazanavir(ATV/r), or lopinavir(LPV/r) in the factorial CHAPAS-4 trial (second randomisation to tenofovir alafenamide fumarate(TAF) or standard-of-care(SOC) backbone, reported elsewhere). Dosing followed WHO weight-bands. The primary endpoint was viral load(VL) <400copies/mL at week-96, analysed using logistic regression, hypothesising that DTG and DRV/r would be superior (threshold p=0.03) to LPV/r and ATV/r arms combined and ATV/r would be non-inferior to LPV/r(12% margin). Secondary endpoints included immunology and safety. Analyses were intention-to-treat.

Results

919 children, median(IQR) age 10(8-13) years, 54% male, baseline VL 17,573(5549,55700) copies/mL, CD4 669(413, 971) cells/mm3, weight-for-age Z-score -1.6(-2.4,-0.9), had spent median(IQR) 5.6(3.3,7.8) years on first-line ART. At week-96, DTG was superior (by 9.7%(95% CI 4.8%, 14.5%); p<0.0001) and DRV/r showed a trend to superiority(by 5.6%(0.3%, 11.0%); p=0.04) compared to LPV/r and ATV/r arms combined. ATV/r was non-inferior to LPV/r(+3.4%(-3.4%,+10.2%); p=0.33). CD4 counts increased with no differences between arms. Toxicity was lowest with DTG. All arms except LPV/r showed age-appropriate weight/height gains at week-96. DTG was not associated with excess absolute weight-gain(<1kg) vs. DRV/r or ATZ/r, irrespective of backbone randomisation.

Conclusions

DTG-based regimens are safe and cost-effective for second-line ART. DRV/r and ATV/r are also good options. Fixed-dose combinations of DTG, DRV/r or ATV/r with nucleoside/nucleotide-reverse-transcriptase-inhibitors(NRTIs) would increase access to robust, essential second-line options for children.(ISRCTN22964075)
Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis
Authors: Hernandez Damian J. , Pohlmann Gwendolyn B. , Afkhami Michelle E.
Published: April 2024

As environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency – how species regulate interactions to match changing environments – is crucial. However, generalizable molecular mechanisms underpinning context-dependency remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for the first time that gene family expansions undergird context-dependent regulation of species interactions. Gene families expanded in mycorrhizal fungi-associating plants display up to 200% more context-dependent gene expression and double the genetic variation associated with mycorrhizal benefits to plant fitness. Moreover, we discover these gene family expansions arise primarily from tandem duplications with >2-times more tandem duplications genome-wide, indicating gene family expansions continuously supply genetic variation allowing fine-tuning of context-dependency in species interactions throughout plant evolution.

One-Sentence Summary

Gene family expansions arising from tandem duplications underpin genetic regulation and fitness effects of context-dependency
Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements
Authors: Patty Benjamin J. , Hainer Sarah J.
Published: April 2024

Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and non-coding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
The chromatin-associated 53BP1 ortholog, HSR-9, regulates recombinational repair andXchromosome segregation in theCaenorhabditis elegansgerm line
Authors: Li Qianyan , Hariri Sara , Calidas Aashna , Kaur Arshdeep , Huey Erica , Engebrecht JoAnne
Published: April 2024

53BP1 plays a crucial role in regulating DNA damage repair pathway choice and checkpoint signaling in somatic cells; however, its role in meiosis has remained enigmatic. In this study, we demonstrate that theCaenorhabditis elegansortholog of 53BP1, HSR-9, associates with chromatin in both proliferating and meiotic germ cells. Notably, HSR-9 is enriched on theXchromosome pair in pachytene oogenic germ cells. HSR-9 is also present at kinetochores during both mitotic and meiotic divisions but does not appear to be essential for monitoring microtubule-kinetochore attachments or tension. Using cytological markers of different steps in recombinational repair, we found that HSR-9 influences the processing of a subset of meiotic double strand breaks into COSA-1-marked crossovers. Additionally, HSR-9 plays a role in meioticXchromosome segregation under conditions whereXchromosomes fail to pair, synapse, and recombine. Together, these results highlight that chromatin-associated HSR-9 has both conserved and unique functions in the regulation of meiotic chromosome behavior.

Article Summary

While 53BP1 is known for its crucial role in DNA damage signaling and repair in somatic cells, its role in meiosis is not well understood. Li, Hariri, et al., show thatC. elegans53BP1 not only functions in meiotic recombination and checkpoint signaling but also regulates the transmission of sex chromosomes when meiosis is perturbed. These results highlight the importance of 53BP1 inC. elegansmeiosis and suggest that 53BP1 has both conserved and organism-specific functions.
foxg1ais required for hair cell development and regeneration in the zebrafish lateral line
Authors: Bell Jon M , Biesemeyer Cole , Turner Emily M , Vanderbeck Maddie M , McGraw Hillary F
Published: April 2024

Mechanosensory hair cells located in the inner ear mediate the sensations of hearing and balance. If damaged, mammalian inner ear hair cells are unable to regenerate, resulting in permanent sensory deficits. Aquatic vertebrates like zebrafish(Danio rerio)have a specialized class of mechanosensory hair cells found in the lateral line system, allowing them to sense changes in water current. Unlike mammalian inner ear hair cells, lateral line hair cells can robustly regenerate following damage. In mammalian models, the transcription factor Foxg1 functions to promote normal development of the inner ear. Foxg1a is expressed in lateral line sensory organs in zebrafish larvae, but its function during lateral line development and regeneration has not been investigated. We find that loss of Foxg1a function results in reduced hair cell development and regeneration, as well as decreased cellular proliferation in the lateral line system. These data suggest that Foxg1 may be a valuable target for investigation of clinical hair cell regeneration.

Summary statement

Our work demonstrates a role for Foxg1a in developing and regenerating new sensory cells through proliferation.
Release the Krakencoder: A unified brain connectome translation and fusion tool
Authors: Jamison Keith W. , Gu Zijin , Wang Qinxin , Tozlu Ceren , Sabuncu Mert R. , Kuceyeski Amy
Published: April 2024

Brain connectivity can be estimated in many ways, depending on modality and processing strategy. Here we present the Krakencoder, a joint connectome mapping tool that simultaneously, bidirectionally translates between structural (SC) and functional connectivity (FC), and across different atlases and processing choices via a common latent representation. These mappings demonstrate unprecedented accuracy and individual-level identifiability; the mapping between SC and FC has identifiability 42-54% higher than existing models. The Krakencoder combines all connectome flavors via a shared low-dimensional latent space. This “fusion” representation i) better reflects familial relatedness, ii) preserves age- and sex-relevant information and iii) enhances cognition-relevant information. The Krakencoder can be applied without retraining to new, out-of-age-distribution data while still preserving inter-individual differences in the connectome predictions and familial relationships in the latent representations. The Krakencoder is a significant leap forward in capturing the relationship between multi-modal brain connectomes in an individualized, behaviorally- and demographically-relevant way.
Attention and control of posture: the effects of light touch on the center-of-pressure time series regularity and simple reaction time task
Authors: Brachman Anna , Michalska Justyna , Bacik Bogdan
Published: April 2024

The stabilizing influence of a light touch on a postural sway has been consistently shown in the literature, however there is still no consensus in what way attentional resources are used when adopting additional tactile information during controlling an upright posture. To better elucidate the underlying mechanisms we introduced conditions of both sensory deprivation (closing the eyes), additional feedback (light touch), which seems to distracts from postural control and verified it by introducing dual task paradigm (i.e. measuring simple reaction time to an unpredictable auditory stimulus). Twenty five healthy students randomly performed eight postural tasks, four with (RT) and four without simple reaction task (NoRT). Center of pressure displacements were measured on a force plate in two visual conditions: eyes open (EO), eyes closed (EC) and two sensory conditions: with light touch (LT), without light touch (NoLT). Before each measurement participants were asked to consider the postural task as the primary task. Although simple reaction time did not differ between postural conditions (p>0.05), additional tactile information in anteroposterior direction caused decreased postural sway velocity (p<0.001, η2=0.86) and decreased standard deviation (p<0.001, η2=0.91) in both, reaction and visual conditions relative to NoLT conditions. Interestingly, simple reaction task modified subjects behavior in NoLT conditions and caused slower COP velocity (p<0.001, η2=0.53) without changes in signal regularity. Results also showed a significant increase in irregularity during standing with LT (p<0.001, η2=0.86) in both vision and reaction conditions, suggesting that the signal was more random. Although there were no significant changes between length of the reaction time between postural conditions but there was strong effect of light touch on COP regularity, we can conclude that light touch is attention demanding but changes of flow of attention are very subtle in this simple postural tasks. Furthermore COP regularity analysis is sensitive to even such subtle changes.
Biophysical characterization of high-confidence, small human proteins
Authors: Whited A. M. , Jungreis Irwin , Allen Jeffre , Cleveland Christina , Mudge Jonathan M , Kellis Manolis , Rinn John , Hough Loren E
Published: April 2024

Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. Additionally, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from non-coding ones in otherwise ambiguous cases.
Trends and drivers of hypoxic thickness and volume in the Northern Gulf of Mexico: 1985-2018
Authors: Matli Venkata Rohith Reddy , Obenour Daniel
Published: April 2024

Hypoxia is a major environmental issue plaguing the commercially and ecologically important coastal waters of the Northern Gulf of Mexico. Several modeling studies have explored this phenomenon, but primarily focus on the areal extent of the mid-summer hypoxic zone. Research into the variability and drivers of hypoxic volume and thickness is also important in evaluating the seasonal progression of hypoxia and its impact on coastal resources. In this study, we compile data from multiple monitoring programs and develop a geospatial model capable of estimating hypoxic thickness and volume across the summer season. We adopt a space-time geostatistical framework and introduce a rank-based inverse normal transformation to simulate more realistic distributions of hypoxic layer thickness. Our findings indicate that, on average, there is a seasonal lag in peak hypoxic volume and thickness compared to hypoxic area. We assess long-term trends in different hypoxia metrics (area, thickness, and volume), and while most metrics did not exhibit significant trends, mid-summer hypoxic thickness is found to have increased at a rate of 5.9 cm/year (p<0.05) over the past three decades. In addition, spring nitrogen load is found to be the major driver of all hypoxia metrics, when considered along with other riverine inputs and meteorological factors in multiple regression models. Hypoxic volume, which was also often influenced by east-west wind velocities, was found to be more predictable than hypoxic thickness.
Why is usefulness rarely useful
Authors: Wang Fangyi , Feldmann Mitchell J. , Runcie Daniel E.
Published: April 2024

Mate selection plays an important role in breeding programs. The usefulness criterion was proposed as a criterion for mate selection, combining information on both the mean and standard deviation of the potential offspring, particularly in clonally propagated outbred species where large family sizes are possible. Predicting mean values of offspring of a cross is generally easier than predicting the standard deviation, especially in outbred species where the linkage of alleles is often unknown and phasing is required. In this study, we developed a method for estimating phasing accuracy from unphased genotype data on possible parental lines and evaluated whether the accuracy was sufficient to predict family standard deviations of possible crosses using a set of simulations spanning a wide range of genetic architectures and genotypes from a real strawberry breeding population. We find that despite highly accurate computational phasing, predicting family standard deviations and using predicted values of the usefulness criterion per possible cross confers little benefit relative to simply selecting parents based on predicted family means. Therefore even in this species, which is clonally propagated, outbred, and produces large families, we find the usefulness criterion unlikely to be useful.
A Critical Analysis of UK Media Characterisations of Long Covid in Children and Young People
Authors: Connor Chloe , Kranert Michael , Mckelvie Sara , Clutterbuck Donna , Mcfarland Sammie , Alwan Nisreen A
Published: April 2024

Long Covid is the continuation or development of symptoms related to a SARSCoV2 infection. Those with Long Covid may face epistemic injustice, where they are unjustifiably viewed as unreliable evaluators of their own illness experiences. Media articles both reflect and influence perception and subsequently how people regard children and young people (CYP) with Long Covid, and may contribute to epistemic injustice.

We aimed to explore how the UK media characterises Long Covid in CYP through examining three key actor groups: parents, healthcare professionals, and CYP with Long Covid, through the lens of epistemic injustice. A systematic search strategy resulted in the inclusion of 103 UK media articles. We used an adapted corpus-assisted Critical Discourse Analysis in tandem with thematic analysis. Specifically, we utilised search terms to locate concordances of key actor groups.

In the corpus, parents highlighted minimisation of Long Covid, barriers to care, and experiences of personal attacks. Mothers were presented as also having Long Covid. Fathers were not mentioned once. Healthcare professionals emphasised the rarity of Long Covid in CYP, avoided pathologizing Long Covid, and overemphasised psychological components. CYP rarely were consulted in media articles but were presented as formerly very able. Manifestations of Long Covid in CYP were validated or invalidated in relation to adults.

Media characterisations contributed to epistemic injustice. The disempowering portrayal of parents promote stigma and barriers to care. Healthcare professionals’ narratives often contributed to negative healthcare experiences and enacted testimonial injustice, where CYP and parent’s credibility was diminished due to unfair identity prejudice, in their invalidation of Long Covid. Media characterisations reveal and maintain a lack of societal framework for understanding Long Covid in CYP. The findings of this study illustrate the discursive practices employed by journalists that contribute to experiences of epistemic injustice. Based on our findings, we propose recommendations for journalists.
A self-cooling self-humidifying mosquito carrier backpack for transporting live adult mosquitoes on foot over long distances under challenging field conditions
Authors: Kavishe Deogratius R , Msoffe Rogath V , Malika Goodluck Z , Walsh Katrina A , Duggan Lily M , Tarimo Lucia J , Butler Fidelma , Kaindoa Emmanuel W. , Ngowo Halfan S , Killeen Gerry F
Published: April 2024

It is often necessary to use motorized transport to move live mosquitoes from distant field collection points into a central insectary, so that their behavioural and/or physiological phenotypes can be assessed under carefully controlled conditions. However, a survey of heritable insecticide susceptibility traits among wild-caughtAnopheles arabiensismosquitoes, collected across an extensive study area composed largely of wilderness in southern Tanzania, necessitated that live mosquitoes were carried on foot over distances up to 25 km per day because most of the area was impassable by car, motorcycle or even bicycle during the rains. A self-cooling, self-humidifying carrier backpack was therefore developed that allows live adult mosquito specimens to be transported across rugged miombo woodland and floodplain terrain throughout the year. This wettable backpack was fabricated from stitched Tanzaniankitengecotton fabric and PVC-coated fiberglass netting that allows easy circulation of air in and out. An outer cover flap made of cotton towelling embedded inside a kitenge envelope overhangs the fiberglass netting upper body of the bag, to protect mosquitoes from direct sunlight, and can be soaked with water to maintain low temperature and high humidity inside. Mean survival of insectary-reared femaleAnopheles arabiensistransported through 9 different mobile camps inside the 509 km2Ifakara-Lupiro-Mang’ula Wildlife Management Area (ILUMA WMA), over up to 143km and 25 days, was indistinguishable from those left in the field insectary over the same period. Although considerable variance was observed between different batches of mosquitoes from the insectary and between individual cups of mosquitoes, the different levels and positions inside the backpack had no influence on survival. Temperature and humidity inside the backpack were maintained at standard insectary condition throughout, despite much more extreme conditions immediately outside. When the backpack was applied to collecting wildAn. arabiensisandAnopheles quadriannulatusacross a much larger study area of >4000 km2, encompassing the ILUMA WMA, some nearby villages and adjacent parts of Nyerere National Park (NNP), it achieved a mean survival rate of 58.2% [95% confidence interval 47.5 to 68.2]. Encouragingly, no difference in survival was observed between ILUMA WMA and NNP even though transport back from NNP involves much longer distances, sometimes involving lengthy journeys by car or boat. Overall, this mosquito carrier backpack prototype appears to represent a viable and effective method for transporting live wild-caught mosquitoes on foot across otherwise impassable terrain under challenging weather conditions with minimal detrimental impact on their survival.
REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators
Authors: Srivastava Shriyansh , Vishnu A.M. , Thakur Rakesh , Srivastava Ashutosh
Published: April 2024

ABSTRACT

REV-ERBβ is a nuclear receptor (NR) with heme as an endogenous ligand that regulates its transcriptional activity. With key role in cellular functions such as glucose metabolism, immune response, and dysregulation in pathologies such as Type-2 diabetes mellitus and obesity, small molecule agonists and antagonists targeting REV-ERBs have been discovered. However, due to lack of crystal structures in complex with these compounds, the structural and dynamical basis of these activities still remains elusive and hinders rational design of molecules targeting REV-ERB. Using molecular dynamics simulations and docking studies, we have characterized the dynamics of REV-ERBβ ligand-binding domain (LBD) in different conformational states. The presence of heme in the binding pocket within LBD was found to stabilize its dynamics as well as nuclear co-repressor (NCoR) peptide binding. We further show that the binding of antagonist destabilizes the NCoR peptide binding to LBD mediated by loss of interactions with residues at the NCoR-REV-ERBβ interface. These findings could be utilized to design molecular scaffolds with better activity and selectivity against REV-ERBβ.
Effect of Emoji on Autonomic Nervous System: Evidence from EDA and RSA studies
Authors: Patel Deeksha , Dixit Abhinav , Bhagat Om Lata
Published: April 2024

Background

Facial expression, gesture, and posture play an important role in perceiving emotions during communication. In virtual communication platforms, users have devised and learned to use a variety of expressive emojis along with text messages to express certain emotions. The effect of emojis on human psychology and associated autonomic responses is still vague.

Methods

A total of 100 healthy individuals (50 males and 50 females) aged between 18-40 years were recruited. Electrodermal activity (skin conductance level (SCL) and skin conductance response (SCR) amplitude) and Respiratory Sinus Arrhythmia (RSA) were assessed during the Emotional Stroop Task (EST). EST having expressive emojis superimposed with the congruent and incongruent words was used.

Result

Mean SCL and SCR amplitude was significantly increased during EST in incongruent and congruent blocks as compared to neutral block (respectively: 14.64 ± 6.73, 12.99 ± 6.26 vs. 7.75 ± 4.93 μS, p < 0.001 and 0.182 ± 0.168, 0.158 ± 0.134 vs. 0.021 ± 0.015 μS, p < 0.001). RSA was significantly decreased in incongruent and congruent blocks as compared to neutral blocks (respectively: 36.47 ± 10.53, 39.40 ± 10.15 vs. 48.66 ± 10.27 msec2, p < 0.001). We found an increased sympathetic activity and parasympathetic withdrawal while performing the task.

Conclusion

The results of this study suggested that emojis are adequate stimuli to elicit autonomic responses and change both sympathetic (EDA) as well as parasympathetic responses (RSA). Males and females showed similar autonomic arousal for emoji but the baseline emotional status was different for both genders.
WITHDRAWN: Modified one-step conservative surgery for placenta accreta spectrum versus caesarean hysterectomy: The CMNT PAS prospective comparative Non-Randomized pilot study
Authors: Abouda Hassine S , Aloui Haithem , Marzouk Sofiene B , Frikha Hatem , Hammami Rami , Makdoud Khaoula , Minjli Sana , Chennoufi Badis , Karoui Abir , Maghrebi Hayen
Published: April 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to [Since its posting, we have identified significant statistical errors resulting from a mix-up between data from the pilot study and the main study. Given these inaccuracies, we believe it is in the best interest of the scientific community to withdraw the manuscript. We have since corrected these errors in a revised version of the manuscript]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
CFI-1/ARID3 functions unilaterally to restrict gap junction formation inC. elegans
Authors: Wu Zan , Pang Lin , Ding Mei
Published: April 2024

Electrical coupling is vital to neural communication, facilitating synchronized activity among neurons. Despite its significance, the precise mechanisms governing the establishment of gap junction connections between specific neurons remain elusive. Here, we identified that the PVC interneuron inCaenorhabditis elegansforms gap junction connections with the PVR interneuron. The transcriptional regulator CFI-1/ARID3 is specifically expressed in the PVC but not PVR interneuron. Reducingcfi-1expression in the PVC interneuron leads to enhanced gap junction formation in the PVR neuron, while ectopic expression ofcfi-1in the PVR neuron restores the proper level of gap junction connections in the PVC neuron, along with the normal touch response. These findings unveil the pivotal role of CFI-1/ARID3 in bidirectionally regulating the formation of gap junctions within a specific neuronal pair, shedding light on the intricate molecular mechanisms governing neuronal connectivityin vivo.

SUMMARY STATEMENT

Proper electrical coupling could be achieved by either of the partner cells; however distinctive influence on neuron circuits maybe achieved.