bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots
Authors: Ding Yan , Owen Mallory , Le Jennie , Batalov Sergey , Chau Kevin , Kwon Yong Hyun , Van Der Kraan Lucita , Bezares-Orin Zaira , Zhu Zhanyang , Veeraraghavan Narayanan , Nahas Shareef , Bainbridge Matthew , Gleeson Joe , Baer Rebecca J. , Bandoli Gretchen , Chambers Christina , Kingsmore Stephen F. 
Published: February 2023

AbstractUniversal newborn screening (NBS) is a highly successful public health intervention. Archived dried bloodspots (DBS) collected for NBS represent a rich resource for population genomic studies. To fully harness this resource in such studies, DBS must yield high-quality genomic DNA (gDNA) for whole genome sequencing (WGS). In this pilot study, we hypothesized that gDNA of sufficient quality and quantity for WGS could be extracted from archived DBS up to 20 years old without PCR (Polymerase Chain Reaction) amplification. We describe simple methods for gDNA extraction and WGS library preparation from several types of DBS. We tested these methods in DBS from 25 individuals who had previously undergone diagnostic, clinical WGS and 29 randomly selected DBS cards collected for NBS from the California State Biobank. While gDNA from DBS had significantly less yield than from EDTA blood from the same individuals, it was of sufficient quality and quantity for WGS without PCR. All samples DBS yielded WGS that met quality control metrics for high-confidence variant calling. Twenty-eight variants of various types that had been reported clinically in 19 samples were recapitulated in WGS from DBS. There were no significant effects of age or paper type on WGS quality. Archived DBS appear to be a suitable sample type for WGS in population genomic studies.
QuilA® adjuvanted Coxevac® sustains Th1-CD8+-type immunity and increases protection in Coxiella burnetii-challenged goats
Authors: Tomaiuolo Sara , Jansen Wiebke , Soares Martins Susana , Devriendt Bert , Cox Eric , Mori Marcella 
Published: February 2023

AbstractCoxevac® is the EMA-approved veterinary vaccine for the protection of cattle and goats against Q fever, a zoonotic bacterial disease due to Coxiella burnetii. Since Coxevac® reduces bacterial shedding and clinical symptoms but does not prevent infection, novel, ready-to-use vaccine formulations are needed to increase its immunogenicity. Here, a goat vaccination-challenge model was used to evaluate the impact of the commercially available saponin-based QuilA® adjuvant on Coxevac® immunity. Upon challenge, the QuilA®-Coxevac® group showed a stronger immune response reflected in a higher magnitude of total IgG and an increase in circulating and splenic CD8+ T-cells compared to the Coxevac® and challenged-control groups. The QuilA®-Coxevac® group was characterized by a targeted Th1-type response (IFNγ, IP10) associated with increased transcripts of CD8+ and NK cells in spleens and γδ T cells in bronchial lymph nodes. Coxevac® vaccinated animals presented an intermediate expression of Th1-related genes, while the challenged-control group showed an immune response characterized by pro-inflammatory (IL1β, TNFα, IL12), Th2 (IL4 and IL13), Th17 (IL17A) and other immunoregulatory cytokines (IL6, IL10). An intriguing role was observed for γδ T cells, which were of TBX21- and SOX4-types in the QuilA®-Coxevac® and challenged control group, respectively. Overall, the addition of QuilA® resulted in a sustained Th1-type activation associated with an increased vaccine-induced bacterial clearance of 33.3% as compared to Coxevac® only. QuilA® could be proposed as a readily-applied veterinary solution to improve Coxevac® efficacy against C. burnetii infection in field settings.
The Streptococcus pyogenes vaccine landscape
Authors: Walkinshaw Donald R. , Wright Meghan E. E. , Mullin Anne E. , Excler Jean-Louis , Kim Jerome H. , Steer Andrew C. 
Published: February 2023

AbstractRecent efforts have re-invigorated the Streptococcus pyogenes (Group A Streptococcus) vaccine development field, though scientific, regulatory and commercial barriers persist, and the vaccine pipeline remains sparse. There is an ongoing need to accelerate all aspects of development to address the large global burden of disease caused by the pathogen. Building on over 100 years of S. pyogenes vaccine development, there are currently eight candidates on a product development track, including four M protein-based candidates and four candidates designed around non-M protein antigens. These candidates have demonstrated proof of concept for protection against S. pyogenes in preclinical models, one has demonstrated safety and immunogenicity in a Phase 1 trial and at least four others are poised to soon enter clinical trials. To maintain momentum, the Strep A Vaccine Global Consortium (SAVAC) was established to bring together experts to accelerate global S. pyogenes vaccine development. This article highlights the past, present and future of S. pyogenes vaccine development and emphasizes key priorities, and the role of SAVAC, in advancing the field.
Carbohydrate fatty acid monosulphate: oil-in-water adjuvant enhances SARS-CoV-2 RBD nanoparticle-induced immunogenicity and protection in mice
Authors: Nanishi Etsuro , Borriello Francesco , Seo Hyuk-Soo , O’Meara Timothy R. , McGrath Marisa E. , Saito Yoshine , Chen Jing , Diray-Arce Joann , Song Kijun , Xu Andrew Z. , Barman Soumik , Menon Manisha , Dong Danica , Caradonna Timothy M. , Feldman Jared , Hauser Blake M. , Schmidt Aaron G. , Baden Lindsey R. , Ernst Robert K. , Dillen Carly , Yu Jingyou , Chang Aiquan , Hilgers Luuk , Platenburg Peter Paul , Dhe-Paganon Sirano , Barouch Dan H. , Ozonoff Al , Zanoni Ivan , Frieman Matthew B. , Dowling David J. , Levy Ofer 
Published: February 2023

AbstractDevelopment of SARS-CoV-2 vaccines that protect vulnerable populations is a public health priority. Here, we took a systematic and iterative approach by testing several adjuvants and SARS-CoV-2 antigens to identify a combination that elicits antibodies and protection in young and aged mice. While demonstrating superior immunogenicity to soluble receptor-binding domain (RBD), RBD displayed as a protein nanoparticle (RBD-NP) generated limited antibody responses. Comparison of multiple adjuvants including AddaVax, AddaS03, and AS01B in young and aged mice demonstrated that an oil-in-water emulsion containing carbohydrate fatty acid monosulphate derivative (CMS:O/W) most effectively enhanced RBD-NP-induced cross-neutralizing antibodies and protection across age groups. CMS:O/W enhanced antigen retention in the draining lymph node, induced injection site, and lymph node cytokines, with CMS inducing MyD88-dependent Th1 cytokine polarization. Furthermore, CMS and O/W synergistically induced chemokine production from human PBMCs. Overall, CMS:O/W adjuvant may enhance immunogenicity and protection of vulnerable populations against SARS-CoV-2 and other infectious pathogens.
Symplectic superposition solutions for free in-plane vibration of orthotropic rectangular plates with general boundary conditions
Authors: Hu Zhaoyang , Du Jingyu , Liu Mingfeng , Li Yihao , Wang Zixuan , Zheng Xinran , Quoc Bui Tinh , Li Rui 
Published: February 2023

AbstractThis work reports new analytic free in-plane vibration solutions for orthotropic non-Lévy-type rectangular plates, i.e., those without two opposite edges simply supported, by the symplectic superposition method (SSM), which has never been applied to in-plane elasticity problems in any existing works. Such analytic solutions are not accessible through conventional analytic methods as seeking analytic solutions that meet both the governing partial differential equations and various non-Lévy-type boundary conditions is an acknowledged challenge in mechanical analysis of plates. The clamped and free plates are considered as two most representative cases of non-Lévy-type plates. The SSM is implemented in the Hamiltonian system-based symplectic space, where the separation of variables and the symplectic eigen expansion prove to be well-grounded. These two mathematical treatments are adopted to first gain the analytic solutions of two elementary problems. The final analytic free in-plane vibration solutions are obtained by superposition of the two elementary problems. Comprehensive new natural frequencies and vibration modes are studied and validated by reference solutions from the finite element method or other approaches. The rigorous solution procedure, fast convergence, and highly accurate results render the present framework capable of serving as benchmarks for future comparison and applicable to analytic investigation of more plate problems.
Adjusting time-of-day and depth of fishing provides an economically viable solution to seabird bycatch in an albacore tuna longline fishery
Authors: Gilman Eric , Evans Tom , Pollard Iain , Chaloupka Milani 
Published: February 2023

AbstractMarine megafauna exposed to fisheries bycatch belong to some of the most threatened taxonomic groups and include apex and mesopredators that contribute to ecosystem regulation. Fisheries bycatch is a major threat to the conservation of albatrosses, large petrels and other pelagic seabirds. Using data sourced from a fisheries electronic monitoring system, we assessed the effects of the time-of-day and relative depth of fishing on seabird and target species catch rates for a Pacific Ocean pelagic longline fishery that targets albacore tuna with an apparently high albatross bycatch rate. Using a Bayesian inference workflow with a spatially-explicit generalized additive mixed model for albacore tuna and generalized linear mixed regression models both for combined albatrosses and combined seabirds, we found that time-of-day and fishing depth did not significantly affect the target species catch rate while night-time deep setting had > 99% lower albatross and total seabird catch rates compared to both deep and shallow partial day-time sets. This provides the first evidence that night-time setting in combination with fishing deep reduces seabird catch risk and may be commercially viable in this and similar albacore tuna longline fisheries. Findings support evidence-informed interventions to reduce the mortality of threatened seabird bycatch species in pelagic longline fisheries.
Performance of novice versus experienced surgeons for dental implant placement with freehand, static guided and dynamic navigation approaches
Authors: Wang Xiaotong , Shujaat Sohaib , Meeus Jan , Shaheen Eman , Legrand Paul , Lahoud Pierre , Gerhardt Maurício do Nascimento , Jacobs Reinhilde 
Published: February 2023

AbstractLack of evidence exists related to the investigation of the accuracy and efficacy of novice versus experienced practitioners for dental implant placement. Hence, the following in vitro study was conducted to assess the accuracy of implant positioning and self-efficacy of novice compared to experienced surgeons for placing implant using freehand (FH), pilot drill-based partial guidance (PPG) and dynamic navigation (DN) approaches. The findings revealed that DN significantly improved the angular accuracy of implant placement compared with FH (P < 0.001) and PPG approaches (P < 0.001). The time required with DN was significantly longer than FH and PPG (P < 0.001), however, it was similar for both novice and experienced practitioners. The surgeon’s self-confidence questionnaire suggested that novice practitioners scored higher with both guided approaches, whereas experienced practitioners achieved higher scoring with PPG and FH compared to DN. In conclusion, implant placement executed under the guidance of DN showed high accuracy irrespective of the practitioner’s experience. The application of DN could be regarded as a beneficial tool for novices who offered high confidence of using the navigation system with the same level of accuracy and surgical time as that of experienced practitioners.
Usability of a mobile application for health professionals in home care services: a user-centered approach
Authors: Manzano-Monfort Griselda , Paluzie Guillermo , Díaz-Gegúndez Mercedes , Chabrera Carolina 
Published: February 2023

AbstractThe use of mobile devices by healthcare professionals has led to rapid growth in the development of mobile healthcare applications designed to improve healthcare services. This study was conducted to assess the acceptability and usability of a mobile application for health professionals in relation to their work in hospitalization at home. A mixed methods approach was used. Acceptance, included the satisfaction of the professionals, attitudes toward using the application, and intention or willingness to continue using the application. Usability tests were performed in laboratory analyzing five controlled clinical tasks, and the interaction of the participants with the mobile application was based on the six basic facial expressions published by the American Psychological Association. Perceived satisfaction was assessed using the computer system usability questionnaire. Thirty-two participants completed the task scenarios and questionnaire. More than 90 per cent of participants were able to complete the tasks with only some difficult with vital signs. Satisfaction had a score of 6.18/7 (SD: 0.76), and recommendation of the mobile application had a score of 6.21/7 (SD: 0.81). This study showed a significant usability and acceptability of this mobile application, in terms of effectiveness, efficiency, and satisfaction.
Association of p-phenylenediamine exposure with alterations of pulmonary function, pruritus and health-related quality of life in hair dye factory workers: a cross-sectional study
Authors: Zhang Ming , Zhang Meibian , Zeng Qiang , Lin Dafeng , Zhang Naixing 
Published: February 2023

AbstractP-Phenylenediamine (PPD) is a common component of hair dye, which can cause skin contact allergy and asthma with impaired pulmonary function. However, the adverse effects of occupational exposure to different dose PPD was rarely mentioned. We recruited 124 workers from a hair dye factory to explore the association of occupational PPD exposure on pulmonary function, pruritus and health related quality of life (HRQL). We categorized exposure to PPD into 3 levels: lower exposure group (< 0.00001 mg/m3); middle exposure group (0.00001–0.00033 mg/m3); higher exposure group (0.00033–0.047 mg/m3). The HRQL and subjective pruritus of the workers were assessed by the short form 36 health survey (SF-36) and Visual analogue scale (VAS) of pruritus, respectively. In the high PPD-exposed group, the percentage of FEV1 (FEV1%) was lower in higher exposure group compared with lower exposure group. The FEV1/FVC was also lower in comparison to the higher exposure and middle exposure groups (p < 0.05). PPD levels were negatively correlated with vitality and mental health (p < 0.01). The structural equation model showed the positive effects of PPD on VAS level (β = 0.213,p < 0.001), and indicated partly negtive effects of PPD on total score of SF-36 (β = − 0.465,p = 0.002), respectively. Our results indicate that occupational exposure to PPD might be associated with pulmonary function impairment, poor HRQL, and subjective pruritus of the workers.
Diagnosis of Fusarium oxysporum f. sp. ciceris causing Fusarium wilt of chickpea using loop-mediated isothermal amplification (LAMP) and conventional end-point PCR
Authors: Achari Saidi R. , Mann Ross C. , Sharma Mamta , Edwards Jacqueline 
Published: February 2023

AbstractFusarium oxysporum (Fo) is ubiquitous in soil and forms a species complex of pathogenic and putatively non-pathogenic strains. Pathogenic strains cause disease in over 150 plant species. Fusarium oxysporum f. sp. ciceris (Foc) is a major fungal pathogen causing Fusarium wilt in chickpeas (Cicer arietinum). In some countries such as Australia, Foc is a high-priority pest of biosecurity concern. Specific, sensitive, robust and rapid diagnostic assays are essential for effective disease management on the farm and serve as an effective biosecurity control measure. We developed and validated a novel and highly specific PCR and a LAMP assay for detecting the Indian Foc race 1 based on a putative effector gene uniquely present in its genome. These assays were assessed against 39 Fo formae speciales and found to be specific, only amplifying the target species, in a portable real-time fluorometer (Genie III) and qPCR machine in under 13 min with an anneal derivative temperature ranging from 87.7 to 88.3 °C. The LAMP assay is sensitive to low levels of target DNA (> 0.009 ng/µl). The expected PCR product size is 143 bp. The LAMP assay developed in this study was simple, fast, sensitive and specific and could be explored for other Foc races due to the uniqueness of this marker to the Foc genome.
Use of the speckle imaging sub-pixel correlation analysis in revealing a mechanism of microbial colony growth
Authors: Balmages Ilya , Liepins Janis , Auzins Ernests Tomass , Bliznuks Dmitrijs , Baranovics Edgars , Lihacova Ilze , Lihachev Alexey 
Published: February 2023

AbstractThe microbial colony growth is driven by the activity of the cells located on the edges of the colony. However, this process is not visible unless specific staining or cross-sectioning of the colony is done. Speckle imaging technology is a non-invasive method that allows visualization of the zones of increased microbial activity within the colony. In this study, the laser speckle imaging technique was used to record the growth of the microbial colonies. This method was tested on three different microorganisms: Vibrio natriegens, Escherichia coli, and Staphylococcus aureus. The results showed that the speckle analysis system is not only able to record the growth of the microbial colony but also to visualize the microbial growth activity in different parts of the colony. The developed speckle imaging technique visualizes the zone of “the highest microbial activity” migrating from the center to the periphery of the colony. The results confirm the accuracy of the previous models of colony growth and provide algorithms for analysis of microbial activity within the colony.
Total and regional appendicular skeletal muscle mass prediction from dual-energy X-ray absorptiometry body composition models
Authors: McCarthy Cassidy , Tinsley Grant M. , Bosy-Westphal Anja , Müller Manfred J. , Shepherd John , Gallagher Dympna , Heymsfield Steven B. 
Published: February 2023

AbstractSarcopenia, sarcopenic obesity, frailty, and cachexia have in common skeletal muscle (SM) as a main component of their pathophysiology. The reference method for SM mass measurement is whole-body magnetic resonance imaging (MRI), although dual-energy X-ray absorptiometry (DXA) appendicular lean mass (ALM) serves as an affordable and practical SM surrogate. Empirical equations, developed on relatively small and diverse samples, are now used to predict total body SM from ALM and other covariates; prediction models for extremity SM mass are lacking. The aim of the current study was to develop and validate total body, arm, and leg SM mass prediction equations based on a large sample (N = 475) of adults evaluated with whole-body MRI and DXA for SM and ALM, respectively. Initial models were fit using ordinary least squares stepwise selection procedures; covariates beyond extremity lean mass made only small contributions to the final models that were developed using Deming regression. All three developed final models (total, arm, and leg) had high R2s (0.88–0.93; all p < 0.001) and small root-mean square errors (1.74, 0.41, and 0.95 kg) with no bias in the validation sample (N = 95). The new total body SM prediction model (SM = 1.12 × ALM – 0.63) showed good performance, with some bias, against previously reported DXA-ALM prediction models. These new total body and extremity SM prediction models, developed and validated in a large sample, afford an important and practical opportunity to evaluate SM mass in research and clinical settings.
DUSP1 mediates BCG induced apoptosis and inflammatory response in THP-1 cells via MAPKs/NF-κB signaling pathway
Authors: Liu Zhanyou , Wang Jianhong , Dai Fan , Zhang Dongtao , Li Wu 
Published: February 2023

AbstractTuberculosis (TB) is a zoonotic infectious disease caused by Mycobacterium tuberculosis (Mtb). Apoptosis and necrosis caused by the interaction between the host and the pathogen, as well as the host’s inflammatory response, play an important role in the pathogenesis of TB. Dual-specificity phosphatase 1 (DUSP1) plays a vital role in regulating the host immune responses. However, the role of DUSP1 in the regulation of THP-1 macrophage apoptosis induced by attenuated Mycobacterium bovis Bacillus Calmette-Guérin (BCG) infection remains unclear. In the present study, we report that infection with BCG significantly induces macrophage apoptosis and induces the production of DUSP1, TNF-α and IL-1β. DUSP1 knockdown significantly inhibited BCG-induced macrophage apoptosis and activation of MAPKs/NF-κB signaling pathway. In addition, DUSP1 knockdown suppressed BCG-induced inflammation in vivo. Taken together, this study demonstrates that DUSP1, as a regulator of MAPKs/NF-κB signaling pathway, plays a novel role in BCG-induced macrophage apoptosis and inflammatory response.
Multi-center retrospective cohort study applying deep learning to electrocardiograms to identify left heart valvular dysfunction
Authors: Vaid Akhil , Argulian Edgar , Lerakis Stamatios , Beaulieu-Jones Brett K. , Krittanawong Chayakrit , Klang Eyal , Lampert Joshua , Reddy Vivek Y. , Narula Jagat , Nadkarni Girish N. , Glicksberg Benjamin S. 
Published: February 2023

Abstract
Background
Aortic Stenosis and Mitral Regurgitation are common valvular conditions representing a hidden burden of disease within the population. The aim of this study was to develop and validate deep learning-based screening and diagnostic tools that can help guide clinical decision making.

Methods
In this multi-center retrospective cohort study, we acquired Transthoracic Echocardiogram reports from five Mount Sinai hospitals within New York City representing a demographically diverse cohort of patients. We developed a Natural Language Processing pipeline to extract ground-truth labels about valvular status and paired these to Electrocardiograms (ECGs). We developed and externally validated deep learning models capable of detecting valvular disease, in addition to considering scenarios of clinical deployment.

Results
We use 617,338 ECGs paired to transthoracic echocardiograms from 123,096 patients to develop a deep learning model for detection of Mitral Regurgitation. Area Under Receiver Operating Characteristic curve (AUROC) is 0.88 (95% CI:0.88–0.89) in internal testing, and 0.81 (95% CI:0.80–0.82) in external validation. To develop a model for detection of Aortic Stenosis, we use 617,338 Echo-ECG pairs for 128,628 patients. AUROC is 0.89 (95% CI: 0.88-0.89) in internal testing, going to 0.86 (95% CI: 0.85-0.87) in external validation. The model’s performance increases leading up to the time of the diagnostic echo, and it performs well in validation against requirement of Transcatheter Aortic Valve Replacement procedures.

Conclusions
Deep learning based tools can increase the amount of information extracted from ubiquitous investigations such as the ECG. Such tools are inexpensive, can help in earlier disease detection, and potentially improve prognosis.
Visible-light-driven reductive dearomatization ofN-arylformyl indoles in EDA complexes with a thiophenolviaa HAT pathway
Authors: Cai Yi-Ping , Ma Meng-Yue , Xu Xiao , Song Qin-Hua 
Published: February 2023

A visible light-driven dearomatization of an N-(o-haloarylformyl)indole in an electron donor–acceptor (EDA) complex with a thiophenol. The radical reaction is terminated by a concerted hydrogen atom transfer (HAT).