bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring DFT+U parameter space with a Bayesian calibration assisted by Markov chain Monte Carlo sampling
Authors: Tavadze Pedram , Boucher Reese , Avendaño-Franco Guillermo , Kocan Keenan X. , Singh Sobhit , Dovale-Farelo Viviana , Ibarra-Hernández Wilfredo , Johnson Matthew B. , Mebane David S. , Romero Aldo H. 
Published: November 2021

AbstractThe density-functional theory is widely used to predict the physical properties of materials. However, it usually fails for strongly correlated materials. A popular solution is to use the Hubbard correction to treat strongly correlated electronic states. Unfortunately, the values of the Hubbard U and J parameters are initially unknown, and they can vary from one material to another. In this semi-empirical study, we explore the U and J parameter space of a group of iron-based compounds to simultaneously improve the prediction of physical properties (volume, magnetic moment, and bandgap). We used a Bayesian calibration assisted by Markov chain Monte Carlo sampling for three different exchange-correlation functionals (LDA, PBE, and PBEsol). We found that LDA requires the largest U correction. PBE has the smallest standard deviation and its U and J parameters are the most transferable to other iron-based compounds. Lastly, PBE predicts lattice parameters reasonably well without the Hubbard correction.
Visible-light driven regioselective synthesis, characterization and binding studies of 2-aroyl-3-methyl-6,7-dihydro-5H-thiazolo[3,2-a]pyrimidines with DNA and BSA using biophysical and computational techniques
Authors: Aggarwal Ranjana , Jain Naman , Sharma Shilpa , Kumar Prince , Dubey Gyan Prakash , Chugh Heerak , Chandra Ramesh 
Published: November 2021

AbstractIn recent times, fused azaheterocycles emerged as impressive therapeutic agents. Binding studies of such azaheterocycles with biomolecules is an important subject for pharmaceutical and biochemical studies aiming at the design and development of new drugs. Fused heterocyclic scaffolds, such as thiazolopyrmidines have long been used in the pharmaceutical industry for the treatment of various diseases. In this study, we have accomplished a regioselective synthesis of 2-aroyl-3-methyl-6,7-dihydro-5H-thiazolo[3,2-a]pyrimidines by the reaction of tetrahydropyrimidine-2(H)-thione with α-bromo-1,3-diketones, generated in situ from 1,3-diketones and NBS, using visible light as an inexpensive, green and renewable energy source under mild reaction conditions with wide-ranging substrate scope. The regioisomer was characterized unambiguously by 2D-NMR [1H-13C] HMBC and [1H-13C] HMQC spectroscopy. In silico toxicity data analysis showed the low toxicity risks of the synthesized compounds. Computational molecular docking studies were carried out to examine the interaction of thiazolo[3,2-a]pyrimidines with calf-thymus DNA (ct-DNA) and Bovine Serum Albumin (BSA). Moreover, different spectroscopic approaches viz. steady-state fluorescence, competitive displacement assay, UV–visible and circular dichroism (CD) along with viscosity measurements were employed to investigate the binding mechanisms of thiazolo[3,2-a]pyrimidines with DNA and BSA. The results thus obtained revealed that thiazolo[3,2-a]pyrimidines offer groove bindings with DNA and showed moderate bindings with BSA.
Sildenafil improves hippocampal brain injuries and restores neuronal development after neonatal hypoxia–ischemia in male rat pups
Authors: Yazdani Armin , Howidi Belal , Shi Meng Zhu , Tugarinov Nicol , Khoja Zehra , Wintermark Pia 
Published: November 2021

AbstractThe hippocampus is a fundamental structure of the brain that plays an important role in neurodevelopment and is very sensitive to hypoxia–ischemia (HI). The purpose of this study was to investigate the effects of sildenafil on neonatal hippocampal brain injuries resulting from HI, and on neuronal development in this context. HI was induced in male Long–Evans rat pups at postnatal day 10 (P10) by a left common carotid ligation followed by a 2-h exposure to 8% oxygen. Rat pups were randomized to vehicle or sildenafil given orally twice daily for 7 days starting 12 h after HI. Hematoxylin and eosin staining was performed at P30 to measure the surface of the hippocampus; immunohistochemistry was performed to stain neurons, oligodendrocytes, and glial cells in the hippocampus. Western blots of the hippocampus were performed at P12, P17, and P30 to study the expression of neuronal markers and mTOR pathway. HI caused significant hippocampal atrophy and a significant reduction of the number of mature neurons, and induced reactive astrocytosis and microgliosis in the hippocampus. HI increased apoptosis and caused significant dysregulation of the normal neuronal development program. Treatment with sildenafil preserved the gross morphology of the hippocampus, reverted the number of mature neurons to levels comparable to sham rats, significantly increased both the immature and mature oligodendrocytes, and significantly reduced the number of microglia and astrocytes. Sildenafil also decreased apoptosis and reestablished the normal progression of post-natal neuronal development. The PI3K/Akt/mTOR pathway, whose activity was decreased after HI in the hippocampus, and restored after sildenafil treatment, may be involved. Sildenafil may have both neuroprotective and neurorestorative properties in the neonatal hippocampus following HI.
Association between social psychological status and efavirenz and nevirapine plasma concentration among HIV patients in Kenya
Authors: Ngayo Musa Otieno , Oluka Margaret , Bulimo Wallace Dimbuson , Okalebo Faith Apolot 
Published: November 2021

AbstractHIV-related stigma, lack of disclosure and social support are still hindrances to HIV testing, care, and prevention. We assessed the association of these social-psychological statuses with nevirapine (NVP) and efavirenz (EFV) plasma concentrations among HIV patients in Kenya. Blood samples were obtained from 254 and 312 consenting HIV patients on NVP- and EFV-based first-line antiretroviral therapy (ART), respectively, and a detailed structured questionnaire was administered. The ARV plasma concentration was measured by liquid chromatography-tandem mass spectrometry (LC–MS/MS). There were 68.1% and 65.4% of the patients on NVP and EFV, respectively, who did not feel guilty for being HIV positive. The disclosure rates were approximately 96.1% and 94.6% of patients on NVP and EFV, respectively. Approximately 85% and 78.2% of patients on NVP and EFV, respectively, received social support as much as needed. There were 54.3% and 14.2% compared to 31.7% and 4.5% patients on NVP and EFV, respectively, with supratherapeutic and suboptimal plasma concentrations. Multivariate quantile regression analysis showed that feeling guilty for being HIV positive was associated with increased 954 ng/mL NVP plasma concentrations (95% CI 192.7 to 2156.6; p = 0.014) but not associated with EFV plasma concentrations (adjusted β = 347.7, 95% CI = − 153.4 to 848.7; p = 0.173). Feeling worthless for being HIV positive was associated with increased NVP plasma concentrations (adjusted β = 852, 95% CI = 64.3 to 1639.7; p = 0.034) and not with EFV plasma concentrations (adjusted β = − 143.3, 95% CI = − 759.2 to 472.5; p = 0.647). Being certain of telling the primary sexual partner about HIV-positive status was associated with increased EFV plasma concentrations (adjusted β 363, 95% CI, 97.9 to 628.1; p = 0.007) but not with NVP plasma concentrations (adjusted β = 341.5, 95% CI = − 1357 to 2040; p = 0.692). Disclosing HIV status to neighbors was associated with increased NVP plasma concentrations (adjusted β = 1731, 95% CI = 376 to 3086; p = 0.012) but not with EFV plasma concentrations (adjusted β = − 251, 95% CI = − 1714.1 to 1212.1; p = 0.736). Obtaining transportation to the hospital whenever needed was associated with a reduction in NVP plasma concentrations (adjusted β = − 1143.3, 95% CI = − 1914.3 to − 372.4; p = 0.004) but not with EFV plasma concentrations (adjusted β = − 6.6, 95% CI = − 377.8 to 364.7; p = 0.972). HIV stigma, lack disclosure and inadequate social support are still experienced by HIV-infected patients in Kenya. A significant proportion of patients receiving the NVP-based regimen had supra- and subtherapeutic plasma concentrations compared to EFV. Social-psychological factors negatively impact adherence and are associated with increased NVP plasma concentration compared to EFV.
Integrative Bioinformatics approaches to therapeutic gene target selection in various cancers for Nitroglycerin
Authors: Chinnappan Jayaprakash , Ramu Akilandeswari , V. Vidhya Rajalakshmi , S. Akil Kavya 
Published: November 2021

AbstractIntegrative Bioinformatics analysis helps to explore various mechanisms of Nitroglycerin activity in different types of cancers and help predict target genes through which Nitroglycerin affect cancers. Many publicly available databases and tools were used for our study. First step in this study is identification of Interconnected Genes. Using Pubchem and SwissTargetPrediction Direct Target Genes (activator, inhibitor, agonist and suppressor) of Nitroglycerin were identified. PPI network was constructed to identify different types of cancers that the 12 direct target genes affected and the Closeness Coefficient of the direct target genes so identified. Pathway analysis was performed to ascertain biomolecules functions for the direct target genes using CluePedia App. Mutation Analysis revealed Mutated Genes and types of cancers that are affected by the mutated genes. While the PPI network construction revealed the types of cancer that are affected by 12 target genes this step reveals the types of cancers affected by mutated cancers only. Only mutated genes were chosen for further study. These mutated genes were input into STRING to perform NW Analysis. NW Analysis revealed Interconnected Genes within the mutated genes as identified above. Second Step in this study is to predict and identify Upregulated and Downregulated genes. Data Sets for the identified cancers from the above procedure were obtained from GEO Database. DEG Analysis on the above Data sets was performed to predict Upregulated and Downregulated genes. A comparison of interconnected genes identified in step 1 with Upregulated and Downregulated genes obtained in step 2 revealed Co-Expressed Genes among Interconnected Genes. NW Analysis using STRING was performed on Co-Expressed Genes to ascertain Closeness Coefficient of Co-Expressed genes. Gene Ontology was performed on Co-Expressed Genes to ascertain their Functions. Pathway Analysis was performed on Co-Expressed Genes to identify the Types of Cancers that are influenced by co-expressed genes. The four types of cancers identified in Mutation analysis in step 1 were the same as the ones that were identified in this pathway analysis. This further corroborates the 4 types of cancers identified in Mutation analysis. Survival Analysis was done on the co-expressed genes as identified above using Survexpress. BIOMARKERS for Nitroglycerin were identified for four types of cancers through Survival Analysis. The four types of cancers are Bladder cancer, Endometrial cancer, Melanoma and Non-small cell lung cancer.
Rotavirus spike protein ΔVP8* as a novel carrier protein for conjugate vaccine platform with demonstrated antigenic potential for use as bivalent vaccine
Authors: Park Wook-Jin , Yoon Yeon-Kyung , Park Ji-Sun , Pansuriya Ruchirkumar , Seok Yeong-Jae , Ganapathy Ravi 
Published: November 2021

AbstractConjugate vaccine platform is a promising strategy to overcome the poor immunogenicity of bacterial polysaccharide antigens in infants and children. A carrier protein in conjugate vaccines works not only as an immune stimulator to polysaccharide, but also as an immunogen; with the latter generally not considered as a measured outcome in real world. Here, we probed the potential of a conjugate vaccine platform to induce enhanced immunogenicity of a truncated rotavirus spike protein ΔVP8*. ΔVP8* was covalently conjugated to Vi capsular polysaccharide (Vi) of Salmonella Typhi to develop a bivalent vaccine, termed Vi-ΔVP8*. Our results demonstrated that the Vi-ΔVP8* vaccine can induce specific immune responses against both antigens in immunized mice. The conjugate vaccine elicits high antibody titers and functional antibodies against S. Typhi and Rotavirus (RV) when compared to immunization with a single antigen. Together, these results indicate that Vi-ΔVP8* is a potent and immunogenic vaccine candidate, thus strengthening the potential of conjugate vaccine platform with enhanced immune responses to carrier protein, including ΔVP8*.
Diversification and post-glacial range expansion of giant North American camel spiders in genus Eremocosta (Solifugae: Eremobatidae)
Authors: Santibáñez-López Carlos E. , Cushing Paula E. , Powell Alexsis M. , Graham Matthew R. 
Published: November 2021

AbstractSpecies of camel spiders in the family Eremobatidae are an important component of arthropod communities in arid ecosystems throughout North America. Recently, research demonstrated that the evolutionary history and biogeography of the family are poorly understood. Herein we explore the biogeographic history of this group of arachnids using genome-wide single nucleotide polymorphism (SNP) data, morphology, and distribution modelling to study the eremobatid genusEremocosta, which contains exceptionally large species distributed throughout North American deserts. Relationships among sampled species were resolved with strong support and they appear to have diversified within distinct desert regions along an east-to-west progression beginning in the Chihuahuan Desert. The unexpected phylogenetic position of some samples suggests that the genus may contain additional, morphologically cryptic species. Geometric morphometric analyses reveal a largely conserved cheliceral morphology amongEremocostaspp. Phylogeographic analyses indicate that the distribution ofE. titaniawas substantially reduced during the last glacial maximum and the species only recently colonized much of the Mojave Desert. Results from this study underscore the power of genome-wide data for unlocking the genetic potential of museum specimens, which is especially promising for organisms like camel spiders that are notoriously difficult to collect.
Perforated flexible catheters improve joint fluid aspiration in shoulder cadavers
Authors: Hecker Andreas , Waltenspül Manuel , Ernstbrunner Lukas , Sutter Reto , Wieser Karl , Bouaicha Samy 
Published: November 2021

AbstractA fluoroscopically controlled anterior approach in supine position is often used for arthrocentesis of the shoulder, but can lead to a high rate of dry aspirations. The aim of this study was to compare the aspiration performance of rigid needles and flexible catheters used with this approach. We hypothesized that a flexible catheter can significantly improve the amount of the obtained fluid. The glenohumeral joint of ten human cadaveric shoulder specimens were sequentially filled with 5, 10, 20 and 30 mL of contrast agent. For each volume the maximum aspirated amount of contrast agent with 4 different aspiration devices (20 gauge needle, 16 gauge needle, 16 gauge flexible catheter and 16 gauge perforated flexible catheter) were compared. All aspirations were done in supine cadaver position from anterior under fluoroscopic control. The aspirated amount of fluid was significantly higher using the 16 gauge perforated flexible catheter (p = 0.002–0.028) compared with all other devices when 5, 10 and 20 mL of contrast agent were in the joint. This perforated flexible catheter aspirated 80–96% of the available fluid while the standard 20 gauge needle aspirated 40–60%. Using a 16 gauge perforated flexible catheter in a supine anterior arthrocentesis technique results in aspiration of most of the fluid in human cadaveric shoulder specimens, while standard needles aspirate only about 50% of it. This can be clinically relevant when there is very little synovial fluid available and might reduce the number of insufficient aspirations.
Implication of thyroid function in periodontitis: a nationwide population-based study
Authors: Song Eyun , Park Min Jeong , Kim Jung A. , Roh Eun , Yu Ji Hee , Kim Nam Hoon , Yoo Hye Jin , Seo Ji A. , Kim Sin Gon , Kim Nan Hee , Baik Sei Hyun , Choi Kyung Mook 
Published: November 2021

AbstractPossible links between periodontitis and various cardiometabolic and autoimmune diseases have been advocated on the basis of chronic inflammation or oxidative stress. However, the association between periodontitis and thyroid dysfunction is under-researched. Participants without previous thyroid disease or ongoing thyroid-related medication were included from a nationwide population-level survey. Participants were categorized into tertiles of thyroid stimulating hormone (TSH) levels (first tertile < 1.76 mIU/L; second tertile 1.76–2.83 mIU/L; third tertile > 2.83 mIU/L), and periodontal condition was assessed using the Community Periodontal Index. Of the total of 5468 participants, 1423 had periodontitis (26%). A significant difference in the weighted prevalence of periodontitis according to TSH tertiles was observed, with the highest prevalence in the first tertile (26.5%) and the lowest prevalence in the third tertile (20.9%, p = 0.003). Subjects in the first TSH tertile had higher odds for periodontitis than those in the third tertile (OR 1.36, 95% CI 1.10–1.68; p for trend = 0.005) after adjusting for covariates. This association was consistent across subgroups and within sensitivity analyses among subjects without specific factors affecting thyroid function or diseases reported to be related to periodontitis. The present study demonstrated that low TSH levels were associated with significantly higher odds for periodontitis.
Robust seed germination prediction using deep learning and RGB image data
Authors: Nehoshtan Yuval , Carmon Elad , Yaniv Omer , Ayal Sharon , Rotem Or 
Published: November 2021

AbstractAchieving seed germination quality standards poses a real challenge to seed companies as they are compelled to abide by strict certification rules, while having only partial seed separation solutions at their disposal. This discrepancy results with wasteful disqualification of seed lots holding considerable amounts of good seeds and further translates to financial losses and supply chain insecurity. Here, we present the first-ever generic germination prediction technology that is based on deep learning and RGB image data and facilitates seed classification by seed germinability and usability, two facets of germination fate. We show technology competence to render dozens of disqualified seed lots of seven vegetable crops, representing different genetics and production pipelines, industrially appropriate, and to adequately classify lots by utilizing available crop-level image data, instead of lot-specific data. These achievements constitute a major milestone in the deployment of this technology for industrial seed sorting by germination fate for multiple crops.
Hydrometallurgical process development to recycle valuable metals from spent SCR deNOX catalyst
Authors: Jeon Jong Hyuk , Cueva Sola Ana Belen , Lee Jin-Young , Jyothi Rajesh Kumar 
Published: November 2021

AbstractSpent catalyst, containing vanadium and tungsten oxide in a TiO2 glass fiber matrix, pose a risk of environmental contamination due to the high toxicity of its metal oxides if leached into the soil when disposed in landfills. Due to the increasing demand of metals and the continuous depletion of primary resources there is an growing necessity for recycling and reprocessing of spent catalysts and other secondary metal sources for environmental and economical reasons. Study of spent SCR catalyst soda roasting process with dissolved NaOH compared with the usual NaOH dry roasting and its influence in the subsequent water leaching. After optimization, the ideal parameters are roasting using a 0.4 ratio of NaOH/spent SCR catalyst in solution for 2 h at 973 K and de-ionized water leaching for 30 min, at 298 K with a pulp density of 30%. The research results show an important reduction of the roasting temperature and leaching time during the processing of spent SCR catalyst obtaining a 95.4% W and 80.2% V leaching efficiency liquor. Silicon compounds are one of the main impurities leached alongside the valuable metals and in this work, the silicon compounds leached are reduced significantly with the aim of avoiding the de-silication post-processing of the leach liquor. The main advantage of the proposed process is the increase of the leaching efficiency of vanadium and tungsten with a minimization of silicon impurities in a shorter time regardless of the leaching temperature.
Measurement of various intensities of physical activities and categorization of “Locomotive” and “Household” activities provide a subject-specific detailed assessment
Authors: Inaba Ryuichiro , Yamakawa Satoshi , Kanamoto Takashi , Ukimoto Sho , Sato Seira , Ogasawara Issei , Konda Shoji , Yokoyama Teruki , Ueda Yuko , Onuki Takashi , Nakata Ken 
Published: November 2021

AbstractThis study aimed to compare the physical activity (PA) measured by a wearable sensor device (WSD) and the step count measurement, and to investigate the association between PAs and lifestyle. Data of 301 participants were collected from March 2019 to March 2021. Step counts, sedentary behavior, performance time of light/moderate/vigorous PA, METs × hour of “Locomotive” and “Household” categorized activities, and energy expenditure (EE) were measured by the WSD, respectively. Furthermore, the participants were classified into student, standing worker, and sitting worker groups. Data were analyzed using the Steel–Dwass and Pearson correlation coefficient tests. The correlation between the performance time of each PA and step count was weak, except for moderate PA. “Household” EE and step count also had a weak correlation. In the comparison of lifestyle, there was a significant difference in the mean performance time of each type of PA between the groups. Additionally, the standing worker and sitting worker groups had a significant difference in METs × hour of "Household" activities, indicating that the difference between the occupations is reflected in “Household” activities. The WSD measurement can be used to evaluate detailed individual PA, whereas the step count measurement showed weakness in the PA estimation.
PLZF and its fusion proteins are pomalidomide-dependent CRBN neosubstrates
Authors: Shimizu Nobuyuki , Asatsuma-Okumura Tomoko , Yamamoto Junichi , Yamaguchi Yuki , Handa Hiroshi , Ito Takumi 
Published: November 2021

AbstractPomalidomide and lenalidomide are immunomodulatory agents that were derived from thalidomide. Cereblon (CRBN) is a common direct target of thalidomide and related compounds and works as a Cullin Ring 4 E3 ubiquitin ligase (CRL4) with DDB1, CUL4, and ROC1. The substrate specificity of CRL4CRBN is modulated by thalidomide-related compounds. While lenalidomide is approved for the treatment of several diseases including multiple myeloma, 5q- syndrome, mantle cell lymphoma, and follicular lymphoma, pomalidomide is approved only for the treatment of lenalidomide-resistant multiple myeloma. Here we show that PLZF/ZBTB16 and its fusion proteins are pomalidomide-dependent neosubstrates of CRL4CRBN. PLZF joins to RARα or potentially other partner genes, and the translocation causes leukemias, such as acute promyelocytic leukemia and T-cell acute lymphoblastic leukemia. We demonstrate that pomalidomide treatment induces PLZF-RARα degradation, resulting in antiproliferation of leukemic cells expressing PLZF-RARα. This study highlights a potential therapeutic role of pomalidomide as a degrader of leukemogenic fusion proteins.