bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly-stable generation of vector beams through a common-path interferometer and a DMD
Authors: Perez-Garcia Benjamin , Mecillas-Hernández Francisco I , Rosales-Guzmán Carmelo 
Published: June 2022

Abstract
Complex vector modes of light, non-separable in their spatial and polarisation degrees of freedom, are revolutionising a wide variety of research fields. It is therefore not surprising that the generation techniques have evolved quite dramatically since their inception. At present it is common to use computer-controlled devices, among which digital micromirror devices have become popular. Some of the reason for this are their low-cost, their polarisation-insensitive and their high-refresh rates. As such, in this manuscript we put forward a novel technique characterised by its high stability, which is achieved through a common-path interferometer. We demonstrate the capabilities of this technique experimentally, first by generating arbitrary vector modes on a higher-order Poincaré sphere, secondly, by generating vector modes in different coordinates systems and finally, by generating various vector modes simultaneously. Our technique will find applications in fields such as optical manipulations, optical communications, optical metrology, among others.
Magnesium- and intermetallic alloys-based hydrides for energy storage: modelling, synthesis and properties
Authors: Pasquini Luca , Sakaki Kouji , Akiba Etsuo , Allendorf Mark D , Alvares Ebert , Ares Josè R , Babai Dotan , Baricco Marcello , Bellosta von Colbe Josè , Bereznitsky Matvey , Buckley Craig E , Cho Young Whan , Cuevas Fermin , de Rango Patricia , Dematteis Erika Michela , Denys Roman V , Dornheim Martin , Fernández J F , Hariyadi Arif , Hauback Bjørn C , Heo Tae Wook , Hirscher Michael , Humphries Terry D , Huot Jacques , Jacob Isaac , Jensen Torben R , Jerabek Paul , Kang Shin Young , Keilbart Nathan , Kim Hyunjeong , Latroche Michel , Leardini F , Li Haiwen , Ling Sanliang , Lototskyy Mykhaylo V , Mullen Ryan , Orimo Shin-ichi , Paskevicius Mark , Pistidda Claudio , Polanski Marek , Puszkiel Julián , Rabkin Eugen , Sahlberg Martin , Sartori Sabrina , Santhosh Archa , Sato Toyoto , Shneck Roni Z , Sørby Magnus H , Shang Yuanyuan , Stavila Vitalie , Suh Jin-Yoo , Suwarno Suwarno , Thi Thu Le , Wan Liwen F , Webb Colin J , Witman Matthew , Wan ChuBin , Wood Brandon C , Yartys Volodymyr A 
Published: June 2022

Abstract
Hydrides based on magnesium and intermetallic compounds provide a viable solution to the challenge of energy storage from renewable sources, thanks to their ability to absorb and desorb hydrogen in a reversible way with a proper tuning of pressure and temperature conditions. Therefore, they are expected to play an important role in the clean energy transition and in the deployment of hydrogen as an efficient energy vector. This review, by experts of Task 40 ‘Energy Storage and Conversion based on Hydrogen’ of the Hydrogen Technology Collaboration Programme of the International Energy Agency, reports on the latest activities of the working group ‘Magnesium- and Intermetallic alloys-based Hydrides for Energy Storage’. The following topics are covered by the review: multiscale modelling of hydrides and hydrogen sorption mechanisms; synthesis and processing techniques; catalysts for hydrogen sorption in Mg; Mg-based nanostructures and new compounds; hydrides based on intermetallic TiFe alloys, high entropy alloys, Laves phases, and Pd-containing alloys. Finally, an outlook is presented on current worldwide investments and future research directions for hydrogen-based energy storage.
Hepatitis C viral clearance with coadministration of crushed sofosbuvir/velpatasvir and high-dose pantoprazole after liver transplantation
Authors: Pluckrose Dawn M , Szczepanik Amanda , Bova Sarah E , Freedman Sari R 
Published: June 2022

Abstract

Purpose
Direct-acting antivirals (DAAs) allow for successful transplantation of livers from hepatitis C nucleic acid test (NAT)–positive donors to negative recipients. However, limited data exist to support crushing DAAs in patients with multiple absorption concerns or significant drug interactions.

Summary
Crushed sofosbuvir/velpatasvir has been successfully used in nontransplant patients with dysphagia, but data in transplant patients with absorption concerns are limited. A 31-year-old hepatitis C–negative female underwent liver transplantation from a hepatitis C NAT–positive donor. Her postoperative course was complicated by a mucormycosis infection, gastrointestinal bleed, and necrotizing pancreatitis requiring treatment with liposomal amphotericin B and pantoprazole 80 mg twice daily. Surgical interventions included an above-the-knee amputation and ileostomy. Hepatitis C treatment was initially delayed because of concern for reduced absorption with crushed DAA administration through the nasogastric (NG) tube, high ileostomy output, gastrointestinal bleed, pancreatitis, and a known drug interaction with pantoprazole. One month after transplantation, the patient’s bilirubin level remained elevated and hepatitis C treatment was initiated with sofosbuvir/velpatasvir. Crushed sofosbuvir/velpatasvir was mixed with 30 mL of water and administered through the NG tube daily. Hepatitis C viral loads were obtained weekly during treatment to monitor efficacy. Although the patient died before evaluation of sustained virological response at 12 weeks, hepatitis C viral clearance was observed within 4 weeks of initiating treatment.

Conclusion
A liver transplant patient exhibited viral clearance of hepatitis C following administration of crushed sofosbuvir/velpatasvir in the setting of multiple absorption concerns.
Functions and applications of glycolipid-hydrolyzing microbial glycosidases
Authors: Ishibashi Yohei 
Published: June 2022

ABSTRACT
Glycolipids are important components of cell membranes in several organisms. The major glycolipids in mammals are glycosphingolipids (GSLs), which are composed of ceramides. In mammals, GSLs are degraded stepwise from the non-reducing end of the oligosaccharides via exo-type glycosidases. However, endoglycoceramidase (EGCase), an endo-type glycosidase found in actinomycetes, is a unique enzyme that directly acts on the glycosidic linkage between oligosaccharides and ceramides to generate intact oligosaccharides and ceramides. Three molecular species of EGCase, namely EGCase I, EGCase II, and endogalactosylceramidase, have been identified based on their substrate specificity. EGCrP1 and EGCrP2, which are homologs of EGCase in pathogenic fungi, were identified as the first fungal glucosylceramide- and sterylglucoside-hydrolyzing glycosidases, respectively. These enzymes are promising targets for antifungal drugs against pathogenic fungi. This review describes the functions and properties of these microbial glycolipid-degrading enzymes, the molecular basis of their differential substrate specificity, and their applications.
meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data
Authors: Wu Qiong , Zheng Xubin , Leung Kwong-Sak , Wong Man-Hon , Tsui Stephen Kwok-Wing , Cheng Lixin 
Published: June 2022

AbstractMotivationHepatocellular carcinoma (HCC) is a primary malignancy with a poor prognosis. Recently, multi-omics molecular-level measurement enables HCC diagnosis and prognosis prediction, which is crucial for early intervention of personalized therapy to diminish mortality. Here, we introduce a novel strategy utilizing DNA methylation and RNA expression data to achieve a multi-omics gene pair signature (GPS) for HCC discrimination.ResultsThe immune genes with negative correlations between expression and promoter methylation are enriched in the highly connected cancer-related pathway network, which are considered as the candidates for HCC detection. After that, we separately construct a methylation GPS (mGPS) and an expression GPS (eGPS), and then assemble them as a meGPS with five gene pairs, in which the significant methylation and expression changes occur between HCC tumor and non-tumor groups. Reliable performance has been validated by independent tissue (age, gender and etiology) and blood datasets. This study proposes a procedure for multi-omics GPS identification and develops a novel HCC signature using both methylome and transcriptome data, suggesting potential molecular targets for the detection and therapy of HCC.Availability and implementationModels are available at https://github.com/bioinformaticStudy/meGPS.git.Supplementary informationSupplementary data are available at Bioinformatics online.
OverProt: secondary structure consensus for protein families
Authors: Midlik Adam , Hutařová Vařeková Ivana , Hutař Jan , Chareshneu Aliaksei , Berka Karel , Svobodová Radka 
Published: June 2022

AbstractSummaryEvery protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and β-connectivity.Availability and implementationOverProt Server is freely available at https://overprot.ncbr.muni.cz.Supplementary informationSupplementary data are available at Bioinformatics online.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage—Connecticut, August 2021–September 2021
Authors: Bart Stephen M , Curtiss Christina C , Earnest Rebecca , Lobe-Costonis Rachel , Peterson Hanna , McWilliams Caroline , Billig Kendall , Hadler James L , Grubaugh Nathan D , Arcelus Victor J , Sosa Lynn E 
Published: June 2022

Abstract

Background
During August 2021–September 2021, a Connecticut college experienced a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant outbreak despite high (99%) vaccination coverage, indoor masking policies, and twice-weekly testing. The Connecticut Department of Public Health investigated characteristics associated with infection and phylogenetic relationships among cases.

Methods
A case was a SARS-CoV-2 infection diagnosed by a viral test during August 2021–September 2021 in a student. College staff provided enrollment and case information. An anonymous online student survey collected demographics, SARS-CoV-2 case and vaccination history, and activities preceding the outbreak. Multivariate logistic regression identified characteristics associated with infection. Phylogenetic analyses compared 115 student viral genome sequences with contemporaneous community genomes.

Results
Overall, 199 of 1788 students (11%) had laboratory-confirmed SARS-CoV-2 infection; most were fully vaccinated (194 of 199, 97%). Attack rates were highest among sophomores (72 of 414, 17%) and unvaccinated students (5 of 18, 28%). Attending in-person classes with an infectious student was not associated with infection (adjusted odds ratio [aOR], 1.0; 95% confidence interval [CI], .5–2.2). Compared with uninfected students, infected students were more likely to be sophomores (aOR, 3.3; 95% CI, 1.1–10.7), attend social gatherings before the outbreak (aOR, 2.8; 95% CI, 1.3–6.4), and complete a vaccine series ≥180 days prior (aOR, 5.5; 95% CI, 1.8–16.2). Phylogenetic analyses suggested a common viral source for most cases.

Conclusions
SARS-CoV-2 infection in this highly vaccinated college population was associated with unmasked off-campus social gatherings, not in-person classes. Students should stay up to date on vaccination to reduce infection.
Maternal and Perinatal Outcomes Associated With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy, Florida, 2020–2021: A Retrospective Cohort Study
Authors: Doyle Timothy J , Kiros Gebre egziabhe , Schmitt-Matzen Emily N , Propper Randy , Thompson Angela , Phillips-Bell Ghasi S 
Published: June 2022

Abstract

Background
The objective was to estimate risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pregnancy and assess adverse maternal and perinatal outcomes.

Methods
We used a population-based, retrospective cohort of all pregnancies with a live birth or fetal death in Florida from 1 March 2020 to 30 April 2021. Coronavirus disease 2019 (COVID-19) case reports were matched to vital registries. Outcomes assessed were risk of infection in pregnancy, preterm birth, maternal or neonatal admission to an intensive care unit (ICU), perinatal or fetal death, and maternal death. Modified Poisson and multinomial logistic regression models were used to derive relative risk estimates.

Results
Of 234 492 women with a live birth or fetal death during the study period, 12 976 (5.5%) were identified with COVID-19 during pregnancy. Risk factors for COVID-19 in pregnancy included Hispanic ethnicity (relative risk [RR] = 1.89), Black race (RR = 1.34), being unmarried (RR = 1.04), and being overweight or obese pre-pregnancy (RR = 1.08–1.32). COVID-19 during pregnancy was associated with preterm birth (RR = 1.31), Cesarean delivery (RR = 1.04), and neonatal (RR = 1.17) and maternal (RR = 3.10) ICU admission; no association was found with increased risk of perinatal (RR = 0.72) or fetal death (RR = 0.86). Women infected during any trimester showed increased risk of preterm birth. Fourteen maternal deaths were identified among COVID-19 cases; of those who died, 12 were obese. The death rate per 10 000 was 22.09 among obese and 1.22 among non-obese gravida with COVID-19 during pregnancy (RR = 18.99, P = .001).

Conclusions
Obesity is a risk factor for SARS-CoV-2 infection in pregnancy and for more severe COVID-19 illness among pregnant women. SARS-CoV-2 infection is associated with preterm birth.
Messenger RNA Coronavirus Disease 2019 (COVID-19) Vaccination With BNT162b2 Increased Risk of Bell’s Palsy: A Nested Case-Control and Self-Controlled Case Series Study
Authors: Wan Eric Yuk Fai , Chui Celine Sze Ling , Ng Vanessa Wai Sei , Wang Yuan , Yan Vincent Ka Chun , Lam Ivan Chun Hang , Fan Min , Lai Francisco Tsz Tsun , Chan Esther Wai Yin , Li Xue , Wong Carlos King Ho , Chung Raccoon Ka Cheong , Cowling Benjamin John , Fong Wing Chi , Lau Alexander Yuk Lun , Mok Vincent Chung Tong , Chan Frank Ling Fung , Lee Cheuk Kwong , Chan Lot Sze Tao , Lo Dawin , Lau Kui Kai , Hung Ivan Fan Ngai , Lau Chak Sing , Leung Gabriel Matthew , Wong Ian Chi Kei 
Published: June 2022

AbstractBackgroundObservable symptoms of Bell’s palsy following vaccinations arouse concern over the safety profiles of novel coronavirus disease 2019 (COVID-19) vaccines. However, there are only inconclusive findings on Bell’s palsy following messenger (mRNA) COVID-19 vaccination. This study aims to update the previous analyses on the risk of Bell’s palsy following mRNA (BNT162b2) COVID-19 vaccination.MethodsThis study included cases aged ≥16 years with a new diagnosis of Bell’s palsy within 28 days after BNT162b2 vaccinations from the population-based electronic health records in Hong Kong. Nested case-control and self-controlled case series (SCCS) analyses were used, where the association between Bell’s palsy and BNT162b2 was evaluated using conditional logistic and Poisson regression, respectively.ResultsTotally 54 individuals were newly diagnosed with Bell’s palsy after BNT162b2 vaccinations. The incidence of Bell’s palsy was 1.58 (95% confidence interval [CI], 1.19–2.07) per 100 000 doses administered. The nested case-control analysis showed significant association between BNT162b2 vaccinations and Bell’s palsy (adjusted odds ratio [aOR], 1.543; 95% CI, 1.123–2.121), with up to 1.112 excess events per 100 000 people who received 2 doses of BNT162b2. An increased risk of Bell’s palsy was observed during the first 14 days after the second dose of BNT162b2 in both nested case-control (aOR, 2.325; 95% CI, 1.414–3.821) and SCCS analysis (adjusted incidence rate ratio, 2.44; 95% CI, 1.32–4.50).ConclusionsThere was an overall increased risk of Bell’s palsy following BNT162b2 vaccination, particularly within the first 14 days after the second dose, but the absolute risk was very low.
Administrators’ Perception of School Social Work
Authors: Stalnecker Deirdre , Tan Kevin , Alvarez Michelle E 
Published: June 2022

Abstract
This study addresses a gap in the literature by examining K–12 administrators’ perceptions of school social workers’ usage of student data. Before the start of the 2020–2021 school year, school social workers from a national organization invited their administrators via email to complete a survey, producing 48 responses. Administrators perceived that the top tasks of school social workers were in the areas of crisis intervention, community resource referrals, and student consultations for teachers and staff. Administrators also indicated that the data most frequently reported to them by school social workers were attendance-related information, and they were not aware of other educational-related data reported by school social workers. Administrators shared that, while they would prefer formal reporting, school social workers were more likely to report data through informal conversations. Overall, this article underscores the need for school social workers to examine their data use practices with K–12 administrators to better advocate for student needs and place greater emphasis on their data use practices in promoting systematic changes. Data use is a powerful tool in demonstrating the relationship between school social work and student outcomes.
Evaluating (weighted) dynamic treatment effects by double machine learning
Authors: Bodory Hugo , Huber Martin , Lafférs Lukáš 
Published: June 2022

Summary
We consider evaluating the causal effects of dynamic treatments, i.e., of mul-tiple treatment sequences in various periods, based on double machine learning to control for observed, time-varying covariates in a data-driven way under a selection-on-observables assumption. To this end, we make use of so-called Neyman-orthogonal score functions, which imply the robustness of treatment effect estimation to moderate (local) misspecifications of the dynamic outcome and treatment models. This robustness property permits approximating outcome and treatment models by double machine learning even under high-dimensional covariates. In addition to effect estimation for the total population, we consider weighted estimation that permits assessing dynamic treatment effects in specific subgroups, e.g., among those treated in the first treatment period. We demonstrate that the estimators are asymptotically normal and $\sqrt{n}$-consistent under specific regularity conditions and investigate their finite sample properties in a simulation study. Finally, we apply the methods to the Job Corps study.
On the prospect of achieving accurate joint estimation of selection with population history
Authors: Johri Parul , Eyre-Walker Adam , Gutenkunst Ryan N , Lohmueller Kirk E , Jensen Jeffrey D 
Published: June 2022

Abstract
As both natural selection and population history can affect genome-wide patterns of variation, disentangling the contributions of each has remained as a major challenge in population genetics. We here discuss historical and recent progress towards this goal—highlighting theoretical and computational challenges that remain to be addressed, as well as inherent difficulties in dealing with model complexity and model violations—and offer thoughts on potentially fruitful next steps.
Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut
Authors: Arab Mohammad M , Brown Patrick J , Abdollahi-Arpanahi Rostam , Sohrabi Seyed Sajad , Askari Hossein , Aliniaeifard Sasan , Mokhtassi-Bidgoli Ali , Mesgaran Mohsen B , Leslie Charles A , Marrano Annarita , Neale David B , Vahdati Kourosh 
Published: June 2022

Abstract
Uncovering the genetic basis of photosynthetic trait variation under drought stress is essential for breeding climate-resilient walnut cultivars. To this end, we examined photosynthetic capacity in a diverse panel of 150 walnut families (1500 seedlings) from various agro-climatic zones in their habitats and grown in a common garden experiment. Photosynthetic traits were measured under well-watered (WW), water-stressed (WS) and recovery (WR) conditions. We performed genome-wide association studies (GWAS) using three genomic datasets: genotyping by sequencing data (∼43 K SNPs) on both mother trees (MGBS) and progeny (PGBS) and the Axiom™ Juglans regia 700 K SNP array data (∼295 K SNPs) on mother trees (MArray). We identified 578 unique genomic regions linked with at least one trait in a specific treatment, 874 predicted genes that fell within 20 kb of a significant or suggestive SNP in at least two of the three GWAS datasets (MArray, MGBS, and PGBS), and 67 genes that fell within 20 kb of a significant SNP in all three GWAS datasets. Functional annotation identified several candidate pathways and genes that play crucial roles in photosynthesis, amino acid and carbohydrate metabolism, and signal transduction. Further network analysis identified 15 hub genes under WW, WS and WR conditions including GAPB, PSAN, CRR1, NTRC, DGD1, CYP38, and PETC which are involved in the photosynthetic responses. These findings shed light on possible strategies for improving walnut productivity under drought stress.
Scaling of Jumping Performance in Click Beetles (Coleoptera: Elateridae)
Authors: Bolmin Ophelia , McElrath Thomas C , Wissa Aimy , Alleyne Marianne 
Published: June 2022

Synopsis
Click beetles (Coleoptera: Elateridae) are known for their unique clicking mechanism that generates a powerful legless jump. From an inverted position, click beetles jump by rapidly accelerating their center of mass (COM) upwards. Prior studies on the click beetle jump have focused on relatively small species (body length ranging from 7 to 24 mm) and have assumed that the COM follows a ballistics trajectory during the airborne phase. In this study, we record the jump and the morphology of 38 specimens from diverse click beetle genera (body length varying from 7 to 37 mm) to investigate how body length and jumping performance scale across the mass range. The experimental results are used to test the ballistics motion assumption. We derive the first morphometric scaling laws for click beetles and provide evidence that the click beetle body scales isometrically with increasing body mass. Linear and nonlinear statistical models are developed to study the jumping kinematics. Modeling results show that mass is not a predictor of jump height, take-off angle, velocity at take-off, and maximum acceleration. The ballistics motion assumption is strongly supported. This work provides a modeling framework to reconstruct complete morphological data sets and predict the jumping performance of click beetles from various shapes and sizes.