bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lectin-Seq: a method to profile lectin-microbe interactions in native communities
Authors: McPherson Robert L. , Isabella Christine R. , Walker Rebecca L. , Sergio Dallis , Gaca Tony , Raman Smrithi , Nguyen Le Thanh Tu , Wesener Darryl A. , Halim Melanie , Wuo Michael , Dugan Amanda , Kerby Robert , Ghosh Soumi , Rey Federico E. , Vlamakis Hera , Alm Eric J. , Xavier Ramnik J. , Kiessling Laura L. 
Published: December 2022

AbstractSoluble human lectins are critical components of innate immunity. Genetic models suggest lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins’ roles in regulating microbiota requires understanding which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using mannose-binding lectin (MBL) and intelectin-1 (hItln1). The microbial interactomes of MBL and hItln1 differ in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1’s interaction profile encompasses a broad range of lower-abundance species. Thus, human lectins have evolved to recognize distinct species of commensals, suggesting they directly influence microbiome composition. Lectin-Seq offers a new means of annotating microbial communities.One-Sentence SummarySoluble human lectins bind distinct bacterial species in fecal microbiota.
The feedback loop of thetransformergene results in proper feminization under multiple sex determination signals in the ant,Vollenhovia emeryi
Authors: Miyakawa Misato Okamoto , Miyakawa Hitoshi 
Published: December 2022

AbstractOrganisms that reproduce sexually have evolved highly sophisticated mechanisms to generate two sexes. Some hymenopterans (such as ants, bees, and wasps) have a complementary sex-determination system in which heterozygosity at one CSD locus induces female development, whereas hemi- or homozygosity at the locus induces male development. This system can generate a high cost of inbreeding, as individuals that are homozygous at the locus become sterile, diploid males. On the other hand, some hymenopterans have evolved a multi-locus, complementary, sex-determination system in which heterozygosity in at least one CSD locus induces female development. This system effectively reduces the proportion of sterile diploid males; however, how multiple primary signals pass through a molecular cascade to regulate the terminal sex-determination gene has remained unclear. To clarify this matter, we investigated the molecular cascade in the ant,Vollenhovia emeryi, with two CSD loci. Here we show thattransformer(tra) is necessary for proper feminization. Expression and functional analysis showed that individuals heterozygous in at least one of the two CSD loci develop into females. Individuals heterozygous at only a single CSD locus do not develop into sexual intermediates, because the signal derived from the heterozygous CSD is amplified by a positive-feedback splicing loop oftra. Our data also demonstrate thattracontrols splicing ofdoublesex(dsx), which is involved in sexual differentiation. We suggest a cascade model to arrive at a binary determination of sex under multiple primary signals.
Paradoxical improvement of cognitive control in older adults under dual-task walking conditions is associated with more flexible reallocation of neural resources: A Mobile Brain-Body Imaging (MoBI) study
Authors: Patelaki Eleni , Foxe John J. , Mantel Emma P. , Kassis George , Freedman Edward G. 
Published: December 2022

AbstractCombining walking with a demanding cognitive task is traditionally expected to elicit decrements in gait and/or cognitive task performance. However, it was recently shown that, in a cohort of young adults, most participants ‘paradoxically’ improved performance when walking was added to performance of a Go/NoGo response inhibition task. The present study aims to extend these previous findings to an older adult cohort, to investigate whether this paradoxical improvement when dual-tasking is observed in healthy older adults. Mobile Brain/Body Imaging (MoBI) was used to record electroencephalographic (EEG) activity, three-dimensional (3D) gait kinematics and behavioral responses in the Go/NoGo task, during sitting or walking on a treadmill, in 34 young adults and 37 older adults. Increased response accuracy during walking, independent of age, was found to correlate with slower responses to stimuli and with walking-related EEG amplitude modulations over latencies and topographies related to the cognitive component of inhibition. On the other hand, aging, independent of response accuracy during walking, was found to correlate with slower treadmill walking speeds and attenuation in walking-related EEG amplitude modulations over latencies and topographies associated with the motor component of inhibition. Older adults whose response accuracy improved during walking manifested neural signatures of both behavioral improvement and aging, suggesting that their flexibility in reallocating neural resources while walking might be maintained for the cognitive but not for the motor inhibitory component. These distinct neural signatures of aging and behavior can potentially be used to identify ‘super-agers’, or individuals at risk for cognitive decline due to aging or neurodegenerative disease.
Age-associated downregulation of glutamate and GABA neurotransmission-related gene expression in the rostral ventrolateral medulla of male Fischer 344 rats
Authors: Balivada Sivasai , Tapia Geronimo P. , Pawar Hitesh N. , Khan Arshad M. , Kenney Michael J. 
Published: December 2022

AbstractThe rostral ventrolateral medulla (RVLM), a part of the medullary reticular formation, plays a major role in several physiological responses, including cardiovascular and sympathetic nervous system functions. Although aging causes disturbances in the responses of these physiological systems, RVLM involvement in these age-related changes is not clear. Previous work using high-throughput gene expression analysis of the RVLM in aged animals suggested that chemical neurotransmission-related genes might be downregulated with advancing age. Since RVLM function involves a balance of signals from inhibitory and excitatory inputs, which is largely mediated by gamma-aminobutyric acid (GABA) and excitatory amino acid (EAA) neurotransmission, we hypothesized that aging is associated with altered excitatory and/or inhibitory neurotransmission-related gene expression in the RVLM. To test this hypothesis, we micropunched an RVLM-containing area from young (3–5 months), middle-aged (12–14 months), and aged (22– 26 months) Fischer 344 male rats. RNA purified from these micropunches was analyzed using GABA and Glutamate RT2Profiler PCR arrays (n= 8–10). Each profiler array has primers for 84 GABA and glutamate neurotransmission related genes. In addition, the expression of selected genes was validated at the RNA level using TaqMan®based-qPCR and at the protein level using western blotting. All the genes that displayed significant differential expression (1.5-fold,p< .05, FDR < .05) were identified to be downregulated in the RVLM of aged and middle-aged rats compared to young rats. This downregulation did not appear to be a result of RVLM tissue sampling differences among the age groups, since a separate validation of our sampling method, which involved careful mapping of micropunched regions to a standardized brain atlas, revealed no spatial differences in sampled sites among age groups. Among the downregulated genes, the percentage of glutamate neurotransmission-related genes was higher than GABA neurotransmission-related genes. The Solute carrier family 1 member 6 (Slc1a6) gene showed the highest fold downregulation at the RNA level in the RVLM of aged compared to young rats, and its protein product, Excitatory amino acid transporter 4 (EAAT4), showed a downregulatory trend in the RVLM of aged and middle-aged rats. These results suggest that molecular constituents of both GABA and glutamate neurotransmission might be altered in the RVLM of aged and middle-aged rats, and the changes in glutamate neurotransmission might be more prominent. Investigating age-associated anatomical and functional changes in RVLM GABA and glutamate neurotransmission might provide a foundation for understanding the effects of aging on physiological function.
Quantifying physiological trait variation with automated hyperspectral imaging in rice
Authors: Ting To-Chia , Souza Augusto , Imel Rachel K. , Guadagno Carmela R. , Hoagland Chris , Yang Yang , Wang Diane R. 
Published: December 2022

ABSTRACTAdvancements in hyperspectral imaging (HSI) and establishment of dedicated plant phenotyping facilities have enabled researchers to gather large quantities of plant spectral images with the aim of inferring target phenotypes non-destructively. However, large volumes of data that result from HSI and corequisite specialized methods for analysis may prevent plant scientists from taking full advantage of these systems. Here, we explore estimation of physiological traits in 23 rice accessions using an automated HSI system. Under contrasting nitrogen conditions, HSI data are used to classify treatment groups with ≥ 83% accuracy by utilizing support vector machines. Out of the 14 physiological traits collected, leaf-level nitrogen content (N, %) and carbon to nitrogen ratio(C:N)could also be predicted from the hyperspectral imaging data with normalized root mean square error of predictions smaller than 14% (R2of 0.88 forNand 0.75 forC:N).This study demonstrates the potential of using an automated HSI system to analyze genotypic variation for physiological traits in a diverse panel of rice; to help lower barriers of application of hyperspectral imaging in the greater plant science research community, analysis scripts used in this study are carefully documented and made publicly available.HIGHLIGHTData from an automated hyperspectral imaging system are used to classify nitrogen treatment and predict leaf-level nitrogen content and carbon to nitrogen ratio during vegetative growth in rice.
Multi-modal multi-resolution atlas of the human neonatal cerebral cortex based on microstructural similarity
Authors: Li Mingyang , Xu Xinyi , Cao Zuozhen , Chen Ruike , Zhao Ruoke , Zhao Zhiyong , Dang Xixi , Oishi Kenichi , Wu Dan 
Published: December 2022

AbstractThe neonatal period is a critical window for the development of the human brain and may hold implications for the long-term development of cognition and disorders. Multi-modal connectome studies have revealed many important findings underlying the adult brain but related studies were rare in the early human brain. One potential challenge is the lack of an appropriate and unbiased parcellation that combines structural and functional information in this population. Using 348 multi-modal MRI datasets from the developing human connectome project, we found that the information fused from the structural, diffusion, and functional MRI was relatively stable across MRI features and showed high reproducibility at the group level. Therefore, we generated automated multi-resolution parcellations (300 - 500 parcels) based on the similarity across multi-modal features using a gradient-based parcellation algorithm. In addition, to acquire a parcellation with high interpretability, we provided a manually delineated parcellation (210 parcels), which was approximately symmetric, and the adjacent areas around each boundary were statistically different in terms of the integrated similarity metric and at least one kind of original features. Overall, the present study provided multi-resolution and neonate-specific parcellations of the cerebral cortex based on multi-modal MRI properties, which may facilitate future studies of the human connectome in the early development period.
Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening
Authors: Ryan Gerard E. , Shearer Freya M. , McCaw James M. , McVernon Jodie , Golding Nick 
Published: December 2022

ABSTRACTThe availability of COVID-19 vaccines promised a reduction in the severity of disease and relief from the strict public health and social measures (PHSMs) imposed in many countries to limit spread and burden of COVID-19. We were asked to define vaccine coverage thresholds for Australia’s transition to easing restrictions and reopening international borders. Using evidence of vaccine effectiveness against the then-circulating Delta variant, we used a mathematical model to determine coverage targets. The absence of any COVID-19 infections in many sub-national jurisdictions in Australia posed particular methodological challenges. We used a novel metric called Transmission Potential (TP) as a proxy measure of the population-level effective reproduction number. We estimated TP of the Delta variant under a range of PHSMs, test-trace-isolate-quarantine (TTIQ) efficiencies, vaccination coverage thresholds, and age-based vaccine allocation strategies. We found that high coverage across all ages (≥70%) combined with ongoing TTIQ and minimal PHSMs was sufficient to avoid lockdowns. At lesser coverage (≤60%) rapid case escalation risked overwhelming of the health sector or the need to reimpose stricter restrictions. Maintaining low case numbers was most beneficial for health and the economy, and at higher coverage levels (≥80%) further easing of restrictions was deemed possible. These results directly informed easing of COVID-19 restrictions in Australia.
Prevalence of salivary anti-SARS-CoV-2 IgG antibodies in vaccinated children
Authors: Badano María Noel , Duarte Alejandra , Salamone Gabriela , Sabbione Florencia , Pereson Matias , Chuit Roberto , Baré Patricia 
Published: December 2022

ABSTRACTVaccination against COVID-19 has mitigated the impact of SARS-CoV-2 infection, decreasing the probability of progression to severe disease and death in vaccinated people.Parallel to the development and administration of COVID-19 vaccines, the immune response induced by the different vaccine platforms has been investigated, mainly, in the adult population. However, since the approval of the vaccines for use in pediatric individuals was a posteriori, vaccination began later in this population. This, added to the difficulty in obtaining blood samples from pediatric individuals, has led to less knowledge about the humoral immune response following vaccination in children.In this work, we analyzed the humoral response induced by vaccination in children through a non-invasive approach such as the measurement of specific salivary antibodies. Our results showed a high prevalence of specific salivary antibodies (81%), with the highest levels of antibodies being observed in those children who had three doses, a greater number of exposures and a shorter interval time between the last exposure to SARS-CoV-2 antigens and saliva collection. These results agree with those reported for the systemic humoral immune response in vaccinated adults, suggesting the administration of booster doses in children to maintain high antibody levels.Therefore, determination of salivary antibodies against SARS-CoV-2 could be a non-invasive tool for disease surveillance, vaccination follow-up and to assist vaccination strategies against COVID-19.
Dynamic Biobanking for Advancing Breast Cancer Research
Authors: Abdollahyan Maryam , Gadaleta Emanuela , Asif Millahat , Oscanoa Jorge , Barrow-McGee Rachel , Jones Samantha , Jones Louise , Chelala Claude 
Published: December 2022

AbstractLongitudinal patient biospecimens and data advance breast cancer research through enabling precision medicine approaches for identifying risk, early diagnosis, improved disease management and targeted therapy. Cancer biobanks must evolve to provide not only access to high-quality annotated biospecimens and rich associated data, but also the tools required to harness these data. We present the Breast Cancer Now Tissue Bank centre at the Barts Cancer Institute as an exemplar of a dynamic biobanking ecosystem that hosts and links longitudinal biospecimens and multimodal data including electronic health records, genomic and imaging data, offered alongside integrated data sharing and analytics tools. We demonstrate how such an ecosystem can inform precision medicine efforts in breast cancer research.SummaryWe present the infrastructure established for the Breast Cancer Now Tissue Bank centre at the Barts Cancer Institute as an exemplar of a dynamic biobank that supports precision medicine for breast cancer through providing access to integrated data and tools, and could serve as a blueprint for future cancer biobanks.
Prevalence and antimicrobial sensitivity patterns of uropathogens, in Tikur Anbessa specialized hospital emergency department Addis Ababa, Ethiopia
Authors: Boru Yared , Shelton Dominick , Azazh Aklilu , Engida Hywet , Kifle Fitsum , Debebe Finot 
Published: December 2022

AbstractBackgroundEmpirical treatment of infections remains a major contributing factor to the emergence of pathogens that are resistant to antibiotics. The study aimed to assess the prevalence and anti-microbial sensitivity patterns of uropathogens in the emergency center of Tikur Anbessa Hospital, Ethiopia.MethodsUrine sample data collected over two years from January 2015 to January 2016 at Tikur Anbessa Hospital’s laboratory were retrospectively analyzed for bacterial pathogens, and their antimicrobial susceptibility. Antimicrobial sensitivity tests were done using the disc diffusion technique as per the standard of the Kirby-Bauer method.ResultOf the total 220 samples that were collected, 50 (22.7%) were culture-positive. Male to female data ratio was 1:1.1. Escherichia coli was the dominant isolate (50%) followed by Enterococcus species (12%), Enterobacter species (12%), and Klebsiella species (8%). Overall resistance rates to Cotrimoxazole, Ampicillin, Augmentin, and Ceftriaxone were 90.4%, 88.8%, 82.5%, and 79.3%, respectively. The sensitivity rates for Chloramphenicol, Amikacin, Vancomycin, Meropenem, Cefoxitin, and Nitrofurantoin ranged from 72% - 100%. The antibiogram of isolates showed that 43 (86%) isolates were resistant to two or more antimicrobials, and 49 (98%) were resistant to at least one antibiotic.Conclusion and recommendationUrinary tract infections are mostly caused by Gram-negative bacteria predominantly in females and Escherichia coli are the most common isolates. Resistance rates to Cotrimoxazole, Ampicillin, Augmentin, and Ceftriaxone were high. Chloramphenicol, Amikacin, Vancomycin, Meropenem, Cefoxitin, and Nitrofurantoin are considered appropriate antimicrobials for the empirical treatment of urinary tract infections in the emergency department. Yet, using antibiotics indiscriminately for patients with complicated UTIs may increase the resistance rate and also lead to treatment failure, hence the prescriptions should be revised following the culture and sensitivity results
Cannabinoids Exposure Levels and its Relation to Anxiety Symptoms and Sleep Disturbances: A Scoping Review Protocol
Authors: Perez-Carreño Juan Guillermo , Vaddiparti Krishna , Castaneda Elizabeth , Garcia Gabriela A. , Gupta Pranav Sai , Lopez-Quintero Catalina 
Published: December 2022

AbstractAt least 60% of individuals with anxiety disorders report sleep disturbances. Shared physiological mechanisms might explain their co-occurrence. Scientific literature related to medical cannabis, a promising therapeutical candidate for these conditions, increased about 15 times in the last 10 years. However, assessments of cannabinoid exposure, anxiety, and sleep are inconsistent across studies, and the quality of the evidence is not often evaluated. We developed a Scoping Review to examine the current knowledge on these gaps related to cannabinoid use for anxiety and sleep disturbances.This protocol provides detailed information on how the scoping review will be conducted. It shows the inclusion criteria for studies on the topic of interest as well as the search strategies for the following databases: PubMed, EMBASE, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, CINAHL, LILACS, and PsycINFO. We present the methodological aspects for screening, data extraction, and data charting. In addition, we proposed to evaluate the quality of the evidence by applying critical appraisal tools according to the study designs.Adherence to this protocol will allow the research team to effectively and reliably synthesize research evidence on the effect of cannabinoids on anxiety symptoms and sleep disturbances.
Omicron-associated mortality for principal causes other than COVID-19, including mortality with a confirmed SARS-CoV-2 infection, and ICU admissions with an Omicron infection in adults aged over 60 years in France
Authors: Goldstein Edward 
Published: December 2022

AbstractBackgroundWith the emergence of the Omicron variant, an increasing proportion of SARS-CoV-2 associated deaths have a principal cause of death other than COVID-19. In France, between Nov. 1, 2021 --July 31, 2022, in addition to 33,353 deaths with the principal cause of COVID-19, there were 9,638 deaths with a confirmed SARS-CoV-2 infection with a principal cause of death other than COVID-19 (as well as SARS-CoV-2-associated deaths with an undetected SARS-CoV-2 infection).MethodsWe examined the relation between mortality for COVID-19, mortality for other causes, and ICU admissions with a SARS-CoV-2-infection in adults aged over 60y in France.ResultsThe number of deaths with principal causes other than COVID-19 in France between July 2021-June 2022 was greater than the corresponding number between July 2020-June 2021 by 20,860 (95% CI (11241,30421)) after adjusting for pre-pandemic trends in mortality (compared to the increase of 3,078 in the number of deaths with a SARS-CoV-2 infection with principal causes other than COVID-19 between the two time periods). During the period of Omicron circulation (Nov. 1, 2021 - Nov. 13, 2022), there was a strong association between the rates of ICU admission with a SARS-CoV-2 infection in adults aged over 60y and (a) rates of COVID-19 deaths (correlation=0.96 (0.92,0.97)); (b) rates of mortality with principal causes other than COVID-19 (correlation=0.89 (0.82,0.94)). Proportions of ICU admissions for causes other than COVID-19 among all ICU admissions with a SARS-CoV-2 infection in older adults were lower during the periods when rates of COVID-19 disease in the community were higher.ConclusionsThe significant increase in mortality with principal causes other than COVID-19, as well as the decreases in the proportions of ICU admissions for causes other than COVID-19 among all ICU admissions with a SARS-CoV-2 infection in older adults during the periods when rates of COVID-19 disease in the community were higher suggest under-detection of Omicron infections in associated complications that did not manifest themselves as COVID-19, which is related to the treatment of SARS-CoV-2 infection in those complications.