bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing
Authors: Chen Fang , Wang Xingyan , Jang Seon-Kyeong , Quach Bryan C. , Weissenkampen J. Dylan , Khunsriraksakul Chachrit , Yang Lina , Sauteraud Renan , Albert Christine M. , Allred Nicholette D. D. , Arnett Donna K. , Ashley-Koch Allison E. , Barnes Kathleen C. , Barr R. Graham , Becker Diane M. , Bielak Lawrence F. , Bis Joshua C. , Blangero John , Boorgula Meher Preethi , Chasman Daniel I. , Chavan Sameer , Chen Yii-Der I. , Chuang Lee-Ming , Correa Adolfo , Curran Joanne E. , David Sean P. , Fuentes Lisa de las , Deka Ranjan , Duggirala Ravindranath , Faul Jessica D. , Garrett Melanie E. , Gharib Sina A. , Guo Xiuqing , Hall Michael E. , Hawley Nicola L. , He Jiang , Hobbs Brian D. , Hokanson John E. , Hsiung Chao A. , Hwang Shih-Jen , Hyde Thomas M. , Irvin Marguerite R. , Jaffe Andrew E. , Johnson Eric O. , Kaplan Robert , Kardia Sharon L. R. , Kaufman Joel D. , Kelly Tanika N. , Kleinman Joel E. , Kooperberg Charles , Lee I-Te , Levy Daniel , Lutz Sharon M. , Manichaikul Ani W. , Martin Lisa W. , Marx Olivia , McGarvey Stephen T. , Minster Ryan L. , Moll Matthew , Moussa Karine A. , Naseri Take , North Kari E. , Oelsner Elizabeth C. , Peralta Juan M. , Peyser Patricia A. , Psaty Bruce M. , Rafaels Nicholas , Raffield Laura M. , Reupena Muagututi’a Sefuiva , Rich Stephen S. , Rotter Jerome I. , Schwartz David A. , Shadyab Aladdin H. , Sheu Wayne H-H. , Sims Mario , Smith Jennifer A. , Sun Xiao , Taylor Kent D. , Telen Marilyn J. , Watson Harold , Weeks Daniel E. , Weir David R. , Yanek Lisa R. , Young Kendra A. , Young Kristin L. , Zhao Wei , Hancock Dana B. , Jiang Bibo , Vrieze Scott , Liu Dajiang J. 
Published: January 2023

AbstractMost transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.
Prediction model for myocardial injury after non-cardiac surgery using machine learning
Authors: Oh Ah Ran , Park Jungchan , Shin Seo Jeong , Choi Byungjin , Lee Jong-Hwan , Lee Seung-Hwa , Yang Kwangmo 
Published: January 2023

AbstractMyocardial injury after non-cardiac surgery (MINS) is strongly associated with postoperative outcomes. We developed a prediction model for MINS and have provided it online. Between January 2010 and June 2019, a total of 6811 patients underwent non-cardiac surgery with normal preoperative level of cardiac troponin (cTn). We used machine learning techniques with an extreme gradient boosting algorithm to evaluate the effects of variables on MINS development. We generated two prediction models based on the top 12 and 6 variables. MINS was observed in 1499 (22.0%) patients. The top 12 variables in descending order according to the effects on MINS are preoperative cTn level, intraoperative inotropic drug infusion, operation duration, emergency operation, operation type, age, high-risk surgery, body mass index, chronic kidney disease, coronary artery disease, intraoperative red blood cell transfusion, and current alcoholic use. The prediction models are available at https://sjshin.shinyapps.io/mins_occur_prediction/. The estimated thresholds were 0.47 in 12-variable models and 0.53 in 6-variable models. The areas under the receiver operating characteristic curves are 0.78 (95% confidence interval [CI] 0.77–0.78) and 0.77 (95% CI 0.77–0.78), respectively, with an accuracy of 0.97 for both models. Using machine learning techniques, we demonstrated prediction models for MINS. These models require further verification in other populations.
Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation
Authors: Kubo Shintaroh , Bui Khanh Huy 
Published: January 2023

AbstractIntraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific to the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e., “tubulin code”, for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the landing behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.
A fully automatic method for segmentation of soccer playing fields
Authors: Cuevas Carlos , Berjón Daniel , García Narciso 
Published: January 2023

AbstractThis paper proposes a strategy to segment the playing field in soccer images, suitable for integration in many soccer image analysis applications. The combination of a green chromaticity-based analysis and an analysis of the chromatic distortion using full-color information, both at the pixel-level, allows segmenting the green areas of the images. Then, a fully automatic post-processing block at the region-level discards the green areas that do not belong to the playing field. The strategy has been evaluated with hundreds of annotated images from matches in several stadiums with different grass shades and light conditions. The results obtained have been of great quality in all the images, even in those with the most complex lighting conditions (e.g., high contrast between sunlit and shadowed areas). In addition, these results have improved those obtained with leading state-of-the-art playing field segmentation strategies.
Green roofs and pollinators, useful green spots for some wild bee species (Hymenoptera: Anthophila), but not so much for hoverflies (Diptera: Syrphidae)
Authors: Jacobs Jeffrey , Beenaerts Natalie , Artois Tom 
Published: January 2023

AbstractUrbanisation has become one of the major anthropogenic drivers behind insect decline in abundance, biomass and species richness over the past decades. As a result, bees and other pollinators' natural habitats are reduced and degraded. Green roofs are frequently recommended as ways to counter the negative impacts of urbanisation on nature and enhance the amount of green space in cities. In this study we evaluated the pollinator (more specifically wild bees and hoverflies) diversity, abundance and species richness on twenty green roofs in Antwerp, Belgium. We analysed the influence of roof characteristics (age, surface area, height, percent cover of green space surrounding each site) on species richness or abundance of pollinators. In total we found 40 different wild bee species on the green roofs. None of the physical roof characteristics appear to explain differences in wild bees species richness and abundance. Neither could we attribute the difference in roof vegetation cover, i.e. roofs build-up with only Sedum species and roofs with a combined cover of Sedum, herbs and grasses, to differences in diversity, abundance, or species richness. We found a positive trend, although not significant, in community weighted mean body size for wild bees with an increase in green roof surface area. Roof wild bee communities were identified as social polylectic individuals, with a preference for ground nesting. Only eleven individuals from eight different hoverfly species were found. Our results show that green roofs can be a suitable habitat for wild bee species living in urban areas regardless of the roofs’ characteristics, but hoverflies have more difficulties conquering these urban green spaces.
Near-infrared to red-light emission and carrier dynamics in full series multilayer GaTe1−xSex (0≤x≤1) with structural evolution
Authors: Muhimmah Luthviyah Choirotul , Peng Yu-Hong , Yu Feng-Han , Ho Ching-Hwa 
Published: January 2023

AbstractTwo-dimensional layered gallium monochalcogenide (GaX, where X = S, Se, Te) semiconductors possess great potential for use in optoelectronic and photonic applications, owing to their direct band edge. In this work, the structural and optical properties of full-series multilayer GaTe1−xSex for x = 0 to x = 1 are examined. The experimental results show that the whole series of GaTe1−xSex layers may contain one hexagonal (H) phase from GaTe to GaSe, whereas the monoclinic (M) phase predominates at 0 ≤ x ≤ 0.4. For x ≥ 0.5, the H-phase dominates the GaTe1−xSex series. The micro-photoluminescence (μPL) results indicate that the photon emission energy of M-phase GaTe1−xSex increases as the Se content increases from 1.652 eV (M-GaTe) to 1.779 eV (M-GaTe0.6Se0.4), whereas that of H-phase GaTe1−xSex decreases from 1.998 eV (H-GaSe) to 1.588 eV (H-GaTe) in the red to near-infrared (NIR) region. Micro-time-resolved photoluminescence (TRPL) and area-fluorescence lifetime mapping (AFLM) of the few-layer GaTe1−xSex series indicates that the decay lifetime of the band-edge emission of the M phase is faster than that of the H phase in the mixed alloys of layered GaTe1−xSex (0 ≤ x ≤ 0.4). On the other hand, for H-phase GaTe1−xSex, the decay lifetime of the band-edge emission also increases as the Se content increases, owing to the surface effect. The dark resistivity of GaTe1−xSex for 0.5 ≤ x ≤ 1 (i.e., predominantly H phase) is greater than that of the other instance of majority M-phase GaTe1−xSex for 0 ≤ x ≤ 0.4, owing to the larger bandgaps. The predominantly H phase GaTe1−xSex (0.5 ≤ x ≤ 1) also shows a greater photoconductive response under visible-light illumination because of the greater contribution from surface states. The superior light-emission and photodetection capability of the GaTe1−xSex multilayers (0 ≤ x ≤ 1) means that they can be used for future optoelectronic devices.
Designing diversified renewable energy systems to balance multisector performance
Authors: Gonzalez Jose M. , Tomlinson James E. , Martínez Ceseña Eduardo A. , Basheer Mohammed , Obuobie Emmanuel , Padi Philip T. , Addo Salifu , Baisie Rasheed , Etichia Mikiyas , Hurford Anthony , Bottacin-Busolin Andrea , Matthews John , Dalton James , Smith D. Mark , Sheffield Justin , Panteli Mathaios , Harou Julien J. 
Published: January 2023

AbstractRenewable energy system development and improved operation can mitigate climate change. In many regions, hydropower is called to counterbalance the temporal variability of intermittent renewables like solar and wind. However, using hydropower to integrate these renewables can affect aquatic ecosystems and increase cross-sectoral water conflicts. We develop and apply an artificial intelligence-assisted multisector design framework in Ghana, which shows how hydropower’s flexibility alone could enable expanding intermittent renewables by 38% but would increase sub-daily Volta River flow variability by up to 22 times compared to historical baseload hydropower operations. This would damage river ecosystems and reduce agricultural sector revenues by US$169 million per year. A diversified investment strategy identified using the proposed framework, including intermittent renewables, bioenergy, transmission lines and strategic hydropower re-operation could reduce sub-daily flow variability and enhance agricultural performance while meeting future national energy service goals and reducing CO2 emissions. The tool supports national climate planning instruments such as nationally determined contributions (NDCs) by steering towards diversified and efficient power systems and highlighting their sectoral and emission trade-offs and synergies.
Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks
Authors: Appadurai Vivek , Bybjerg-Grauholm Jonas , Krebs Morten Dybdahl , Rosengren Anders , Buil Alfonso , Ingason Andrés , Mors Ole , Børglum Anders D. , Hougaard David M. , Nordentoft Merete , Mortensen Preben B. , Delaneau Olivier , Werge Thomas , Schork Andrew J. 
Published: January 2023

AbstractSample recruitment for research consortia, biobanks, and personal genomics companies span years, necessitating genotyping in batches, using different technologies. As marker content on genotyping arrays varies, integrating such datasets is non-trivial and its impact on haplotype estimation (phasing) and whole genome imputation, necessary steps for complex trait analysis, remains under-evaluated. Using the iPSYCH dataset, comprising 130,438 individuals, genotyped in two stages, on different arrays, we evaluated phasing and imputation performance across multiple phasing methods and data integration protocols. While phasing accuracy varied by choice of method and data integration protocol, imputation accuracy varied mostly between data integration protocols. We demonstrate an attenuation in imputation accuracy within samples of non-European origin, highlighting challenges to studying complex traits in diverse populations. Finally, imputation errors can bias association tests, reduce predictive utility of polygenic scores. Carefully optimized data integration strategies enhance accuracy and replicability of complex trait analyses in complex biobanks.
The HDAC inhibitor zabadinostat is a systemic regulator of adaptive immunity
Authors: Liu Geng , Barczak Wojciech , Lee Lian Ni , Shrestha Amit , Provine Nicholas M. , Albayrak Gulsah , Zhu Hong , Hutchings Claire , Klenerman Paul , La Thangue Nicholas B. 
Published: January 2023

AbstractProtein acetylation plays a key role in regulating cellular processes and is subject to aberrant control in diverse pathologies. Although histone deacetylase (HDAC) inhibitors are approved drugs for certain cancers, it is not known whether they can be deployed in other therapeutic contexts. We have explored the clinical HDAC inhibitor, zabadinostat/CXD101, and found that it is a stand-alone regulator of the adaptive immune response. Zabadinostat treatment increased expression of MHC class I and II genes in a variety of cells, including dendritic cells (DCs) and healthy tissue. Remarkably, zabadinostat enhanced the activity of DCs, and CD4 and CD8 T lymphocytes. Using an antigenic peptide presented to the immune system by MHC class I, zabadinostat caused an increase in antigen-specific CD8 T lymphocytes. Further, mice immunised with covid19 spike protein and treated with zabadinostat exhibit enhanced covid19 neutralising antibodies and an increased level of T lymphocytes. The enhanced humoral response reflected increased activity of T follicular helper (Tfh) cells and germinal centre (GC) B cells. Our results argue strongly that zabadinostat has potential to augment diverse therapeutic agents that act through the immune system.
In-vivo or in-vitro stone attenuation: what is more valuable for the prediction of renal stone composition in non-contrast-enhanced abdominal computed tomography?
Authors: Ilki Yavuz , Bulbul Emre , Gultekin Mehmet Hamza , Erozenci Ahmet , Tutar Onur , Citgez Sinharib , Onal Bulent 
Published: January 2023

Abstract
Objectives To compare the efficacy of in-vivo and in-vitro stone
attenuation in the prediction of stone composition using non-contrast-enhanced abdominal
computed tomography (NCCT).
Methods This study included a total of 104 patients with renal
stones who received percutaneous nephrolithotomy treatment for renal stones between December
2016 and December 2019 and underwent NCCT before the procedure. Preoperative (in-vivo) and
postoperative (in-vitro) kidney stone attenuations were compared using the NCCT images of the
patients. Renal stone fragments were analysed with the infrared spectrophotometer
method.
Results The mean age of the 104 patients was 49.5 (interquartile
range: 37–61) years. According to the receiver operating characteristics analysis, the cut-off
values for the prediction of uric acid stones were determined to be 556 HU for the in-vivo and
774 HU for the in-vitro attenuation measurement. Sensitivity and specificity were 100% and
96.6%, respectively, for the in-vivo and 90.9 and 91%, respectively, for the in-vitro images.
The cut-off values for the prediction of calcium stones were determined to be 824 HU and 1065
HU for the in-vivo and in-vitro attenuation measurements, respectively. Sensitivity and
specificity were 97.3 and 96% for the in-vivo and 96 and 96% for the in-vitro images.
Conclusions In-vivo stone attenuation measurement in NCCT was
slightly superior to in-vitro measurement due to the reduction in the composition and size of
the stone. Our findings show that NCCT in-vivo stone attenuation might differentiate uric acid
and calcium stones from the other stone types.
Design, Synthesis and Biological Evaluation of Imidazole-Substituted/Fused Aryl Derivatives Targeting Tubulin Polymerization as Anticancer Agents
Authors: Goel Kapil Kumar , Kharb Rajeev , Rajput Satyendra Kumar 
Published: January 2023

AbstractThe development of new pharmacologically active molecules targeting tubulin polymerization has recently attracted great interest in research groups. In efforts to develop new potent anticancer compounds, imidazole-tethered/fused pharmacologically active aryl derivatives possessing different substitution patterns targeting tubulin polymerization have been rationally designed and synthesized. The target molecules (P1-5 and KG1-5) were synthesized by multistep syntheses involving the reaction of intermediate 2-aminophenyl-tethered imidazoles with appropriate reactants in the presence of p-TsOH under different conditions. The synthesized compounds displayed moderate to good cytotoxicity, comparable to that of colchicine, against four cancer cell lines (MCF-7, MD-MBA-231, A549, and HCT-116). Compounds P2 and P5, with an imidazoloquinoxaline moiety, emerged as potential leads with cytotoxicity profiles against these cell lines similar to colchicine. Compounds P2 and P5 arrested cell division at the G2/M phase and prevented cancerous cell growth through induced apoptosis. These results favored the hypothesis that the compounds might act by binding to the colchicine binding site, which was further confirmed with the help of a tubulin polymerization inhibition assay. The results encourage the further exploration of imidazoloquinoxalines as promising leads that deserve advanced clinical investigation.
Anosmia in COVID-19 Patients: Can We Predict the Severity of Chest Manifestations?
Authors: Hendawy Ehsan , El-Anwar Mohammad Waheed , Elghamry Reda M. , Abdallah Amany M. , Ibrahim Amin M. 
Published: January 2023

Abstract
Introduction Anosmia is one of the common symptoms of COVID-19, the link between severity of chest infection and anosmia was investigated by few studies.
Objectives To find an association between anosmia and severity of chest infection.
Methods An analysis of patients admitted to isolation hospital of our university with confirmed polymerase chain reaction positive testing for COVID-19, between March 2021 until September 2021. We called all patients who reported anosmia during their time of illness and asked them about anosmia. We examined their chest CT. A statistical analysis was done.
Results A total of 140 patients completed the study; 65% were female and 56.4% had complete anosmia. Anosmia was significantly associated with loss of taste. Smell returned in 92.5% of anosmic patients. Duration of smell loss was ∼ 2 weeks in 40.5%. The most common symptoms associated with anosmia were running nose, sore throat, fever, and cough. Loss of smell was significantly associated with mild chest disease. 73.4% of anosmic patients had mild chest infection, 21.5% of them had moderate infection, and 5.1% had severe chest infection.
Conclusion The pattern of anosmia in COVID-19 patients has some common similarities in general; the way it starts, the associated symptoms, the time until smell returns and, the most important, the severity of chest infection. As anosmia is significantly associated with mild chest infection. the presence of anosmia could be an independent predictor of good COVID-19 outcome as reflected by a lower disease severity and less frequent ICU admissions.
Exact thresholds for global existence to the nonlinear beam equations with and without a damping
Authors: Yuan Yiyin , Tian Shuai , Qing Jun , Zhu Shihui 
Published: January 2023

In this paper, we study the Cauchy problem for focusing nonlinear beam equations with and without a damping term. By constructing two pairs of invariant flows, we obtain the exact thresholds for the global existence and blow-up to the above equations in the sense that both thresholds are explicitly expressed by the L2-norm of the fourth-order nonlinear elliptic equation without any damping.
A multilingual learner corpus for less commonly taught languages
Authors: Sommer-Farias Bruna , Novikov Aleksey , Picoral Adriana , Centanin-Bertho Mariana , Staples Shelley 
Published: January 2023

Abstract
This article provides a detailed account of the framework, pedagogical and research applications of the Multilingual Academic Corpus of Assignments – Writing and Speech (MACAWS).1 MACAWS is a monitor learner corpus of written and oral assignments produced by foreign language learners in the context of their language learning classrooms. Currently the corpus focuses on two less commonly taught languages rarely represented in learner corpora, Portuguese and Russian, and contains 124,054 words in Russian and 536,168 in Portuguese, being updated each semester as new texts are added to the corpus. The online interface is designed for ease of use by teachers and students. Our novel interactive data-driven learning (iDDL) tool allows embedding of concordance lines into websites and learning management systems (LMS), facilitating student interaction with concordance lines. Researchers can gain access to an offline corpus for greater flexibility.