bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Neoproterozoic source rock potential in SE Pakistan and adjacent Bikaner–Nagaur Basin India
Authors: Yasin Qamar , Baklouti Syrine , Sohail Ghulam Mohyuddin , Asif Muhammad , Xufei Gong 
Published: June 2022

AbstractDiscoveries of heavy crude oil in the Neoproterozoic rocks (Infracambrian rock sequence) from the Bikaner-Nagaur Basin of India emphasize the significance of studying and exploring the Neoproterozoic source rock potential in the southeastern part of Pakistan. This study evaluates the potential of the source rock in the Infracambrian rock sequence (Salt Range Formation) based on surface geochemical surveys, Rock–Eval pyrolysis, source biomarkers, geophysical characterization, and seismic inversion using machine learning for maturity index estimation. Core samples of Infracambrian rock were extracted for Rock–Eval pyrolysis and biomarker characterization. Additionally, 81 geomicrobial soil and gas samples were collected from the surface to explore the petroleum system and potential source rocks in the subsurface. Advanced interpretation techniques were used to investigate the origin and concentration of hydrocarbon gases at the surface, including Rock–Eval pyrolysis, thermal maturity, source biomarkers, and the environment of deposition of organic matter. The results show that the investigated samples are characterized by restricted marine clay devoid of sedimentary carbonate facies with thermal maturity in the early stage of the oil generation window. The seismic inverted maturity index profile demonstrates a reasonable correlation of thermal maturity with the biomarkers and Rock–Eval pyrolysis. Further scrutiny of the surface geochemical samples confirms the presence of higher concentrations of thermogenic C2–C4 hydrocarbons in the vicinity of anticlinal structures, suggesting the existence of an effective migration path along deep-seated faults to the surface. This study concludes that the Infracambrian rocks on the eastern flank of Pakistan are thicker, thermally mature, and have deep-seated structural closures, indicating a greater probability of heavy and light oil in this area than in the Bikaner–Nagaur Basin, India.
The influence of CeF3 on radiation hardness and luminescence properties of Gd2O3–B2O3 glass scintillator
Authors: Kaewnuam E. , Wantana N. , Ruangtaweep Y. , Cadatal-Raduban M. , Yamanoi K. , Kim H. J. , Kidkhunthod P. , Kaewkhao J. 
Published: June 2022

AbstractThe effect of CeF3 concentration and γ-irradiation on the physical, optical and luminescence properties of Gd2O3–B2O3–CeF3 glasses were studied in this work. Before irradiation, the addition of CeF3 in glass degraded the network connectivity observed from FTIR and possibly created the non-bridging oxygen (NBO) in glass structure. This NBO caused the reduction of Ce3+/Ce4+ ratio in XANES, the red-shift in transmission spectra and the raise of refractive index with addition of CeF3 content. Such red-shift also was influenced by 4f–5d transition of Ce3+ dopant. This ion generated the strongest photoluminescence (PL) and radioluminescence (RL) in 0.3 mol% CeF3-doped glass with nanoseconds decay time. The irradiation with γ-rays damaged the glass structure, broke the chemical bonds, and created color center in the glass network. The non-bridging oxygen hole center (NBOHC), that absorbed photons in the visible light region, caused the darkening, color change and increment of refractive index. These irradiation effects on glass were mitigated by the addition of CeF3 that the electron donation of Ce3+ decreased the number of NBOHC. The Ce3+/Ce4+ ratio in most glasses after irradiation then reduced compared to them before irradiation, resulting to the decrease in PL and RL intensity. Our results confirm that CeF3 can enhance the radiation hardness of glass and the 0.3 mol% CeF3-doped glass is a promising glass scintillator.
Genetic diversity of Prosopis juliflora in the state of Qatar and its valuable use against postharvest pathogen of mango fruits
Authors: Saleh Iman , Ahmed Talaat , Halboosi Ream , Abu-Dieyeh Mohammed 
Published: June 2022

AbstractMango (Mangifera indica) is the second most internationally traded tropical fruit in the world. The fruit has high nutritional value. Its susceptibility to postharvest diseases and chill injuries increases its storage cost and put stress on exploring natural products that can increase its shelf-life. Our team has previously described Prosopis juliflora water-soluble leaf ethanolic (PJ-WS-LE) extract with fungicidal effectiveness against spoiling fungi. The present study explores P. juliflora genetic diversity in the state of Qatar and the antifungal effectiveness of the leaf extract of plants collected from different locations. The study also evaluates PJ-WS-LE extract efficacy against Alternaria. alternata and Colletotrichum gloeosporioides inoculated in mango samples and the power of the extract as coating material. P. juliflora samples collected from six different locations showed genetic and antimicrobial effectiveness similarities. They showed also similarity to the sequence representing P. juliflora 18S ribosomal RNA partial sequence, accession number JX139107.1 originated from India. PJ-WS-LE extract (8 mg/ml) has 80% efficacy in controlling A. alternata in mango and it lowers C. gloeosporioides disease severity by 53.4%. PJ-WS-LE extract (8 mg/ml) embedded in 1% chitosan maintained mango quality for 5 weeks. In vivo results of PJ-WS-LE extract highlights the potentials of the extract as chemical fungicides replacement.
Simulation-based evaluation of two insect trapping grids for delimitation surveys
Authors: Fang Hui , Caton Barney P. , Manoukis Nicholas C. , Pallipparambil Godshen R. 
Published: June 2022

AbstractIn the United States of America, delimitation trapping surveys with square grids have been used for decades for exotic insects without rigorous evaluation. We used simulations to investigate the effectiveness of two representative designs: an 8-km grid for Acrolepiopsis assectella (leek moth) and a 14.5-km grid for Ceratitis capitata (Mediterranean fruit fly, “Medfly”). We investigated grid compositions and design factors, measuring performance as the mean probability of pest capture over all traps, p(capture), and designed improved grids for both species. For the standard designs, p(capture) was 0.86 for leek moth and 0.71 for Medfly, with the latter performing better due to greater lure and trap attractiveness. For both designs, 86 percent or more of mean p(capture) came from core area captures. Egress testing indicated that both grids were oversized. An improved grid for leek moths would use 177 traps in a 4.8-km diameter circle, which had mean p(capture) = 0.73 and reduced the cost by 80 percent. The best Medfly grid was a 4.8-km diameter circle with 232 traps, which gave mean p(capture) of 0.66 and reduced the cost by 86 percent. Simulation may be used to improve trapping survey plans, often saving significantly on costs while maintaining survey performance.
Milk microbiomes of three great ape species vary among host species and over time
Authors: Bornbusch Sally L. , Keady Mia M. , Power Michael L. , Muletz-Wolz Carly R. 
Published: June 2022

AbstractIn mammalian neonates, milk consumption provides nutrients, growth factors, immune molecules, and microbes. Milk microbiomes are increasingly recognized for their roles in seeding infant gut microbiomes and priming immune development. However, milk microbiome variation within and among individuals remains under investigation. We used 16S rRNA gene sequencing to investigate factors shaping milk microbiomes in three captive great ape species:Gorilla gorilla gorilla(individuals, N = 4; samples, n = 29),Pongo abelii(N = 2; n = 16), andPongo pygmaeus(N = 1; n = 9). We demonstrate variation among host species, over lactation, and between housing facilities. In phylogenetic community composition, milk microbiomes were distinct among the three ape species. We found only a few shared, abundant bacterial taxa and suggest that they likely serve functional roles. The diversity and community composition of milk microbiomes showed gradual changes over time in gorillas and the Bornean orangutan, which was detectable with our comprehensive sampling over lactation stages (> 300-day span). In gorillas, milk microbiomes differed between housing facilities, but were similar between dams within a facility. These results support the strong influence of evolutionary history in shaping milk microbiomes, but also indicate that more proximate cues from mother, offspring, and the environment affect the distribution of rarer microbial taxa.
A Nurr1 ligand C-DIM12 attenuates brain inflammation and improves functional recovery after intracerebral hemorrhage in mice
Authors: Kinoshita Keita , Yoshimizu Ayaka , Ichihara Yusei , Ushida Keisuke , Kotani Shunsuke , Kurauchi Yuki , Seki Takahiro , Katsuki Hiroshi 
Published: June 2022

AbstractWe have previously reported that amodiaquine, a compound that binds to the ligand-binding domain of a nuclear receptor Nurr1, attenuates inflammatory responses and neurological deficits after intracerebral hemorrhage (ICH) in mice. 1,1-Bis(3′-indolyl)-1-(p-chlorophenyl)methane (C-DIM12) is another Nurr1 ligand that recognizes a domain of Nurr1 different from the ligand-binding domain. In the present study, mice were treated daily with C-DIM12 (50 or 100 mg/kg, p.o.) or amodiaquine (40 mg/kg, i.p.), or twice daily with 1400 W (20 mg/kg, i.p.), an inducible nitric oxide synthase (iNOS) inhibitor, from 3 h after ICH induction by microinjection of collagenase into the striatum. C-DIM12 improved the recovery of neurological function and prevented neuron loss in the hematoma, while suppressed activation of microglia/macrophages and expression of inflammatory mediators interleukin-6 and CC chemokine ligand 2. In addition, C-DIM12 as well as amodiaquine preserved axonal structures in the internal capsule and axonal transport function. We also found that C-DIM12 and amodiaquine suppressed the increases of iNOS mRNA expression after ICH. Moreover, 1400 W improved neurological function and prevented neuron loss, activation of microglia/macrophages and axonal transport dysfunction. These results suggest that suppression of iNOS induction contributes to several features of the therapeutic effects of Nurr1 ligands.
Prospective bidirectional associations between depression and chronic kidney diseases
Authors: Zheng Xiaowei , Wu Wenyan , Shen Suwen 
Published: June 2022

AbstractPrevious studies had reported the mutual relation between depression and chronic kidney diseases (CKD). This study aimed to investigate potential bidirectional relationships between depression and CKD. Participants more than 45 years from the China Health and Retirement Longitudinal Study (CHARLS) were included in present study. In study I, we tended to assess the association between baseline depression with the risk of subsequent CKD. In study II, we aimed to examine whether the onset of CKD could predict the development of depression. Multivariate logistic regression models were used to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs) in study I and study II, respectively. In study I, 301 (6.16%) respondents experienced CKD in participants without depression, and 233 (8.48%) respondents experienced CKD in participants with depression. Participants with depression had higher risk of developing CKD with the corresponding ORs (95% CIs) was 1.38(1.08–1.76). In study II, 1333 (22.29%) subjects in the non-CKD group and 97 (27.17%) in CKD group developed depressive symptoms. Individuals with CKD had higher risk of developing depression than those without CKD, with the multivariate ORs (95% CIs) was 1.48(1.23–1.78). Significant bidirectional relationships remained in both sensitivity and subgroup analyses. Findings demonstrate bidirectional relationships between depression and CKD. Individuals with depression were associated with increasing risk of CKD; in addition, CKD patients had higher risk of developing depression.
Decision-making of citizen scientists when recording species observations
Authors: Bowler Diana E. , Bhandari Netra , Repke Lydia , Beuthner Christoph , Callaghan Corey T. , Eichenberg David , Henle Klaus , Klenke Reinhard , Richter Anett , Jansen Florian , Bruelheide Helge , Bonn Aletta 
Published: June 2022

AbstractCitizen scientists play an increasingly important role in biodiversity monitoring. Most of the data, however, are unstructured—collected by diverse methods that are not documented with the data. Insufficient understanding of the data collection processes presents a major barrier to the use of citizen science data in biodiversity research. We developed a questionnaire to ask citizen scientists about their decision-making before, during and after collecting and reporting species observations, using Germany as a case study. We quantified the greatest sources of variability among respondents and assessed whether motivations and experience related to any aspect of data collection. Our questionnaire was answered by almost 900 people, with varying taxonomic foci and expertise. Respondents were most often motivated by improving species knowledge and supporting conservation, but there were no linkages between motivations and data collection methods. By contrast, variables related to experience and knowledge, such as membership of a natural history society, were linked with a greater propensity to conduct planned searches, during which typically all species were reported. Our findings have implications for how citizen science data are analysed in statistical models; highlight the importance of natural history societies and provide pointers to where citizen science projects might be further developed.
Identification of ultra-rare genetic variants in pediatric acute onset neuropsychiatric syndrome (PANS) by exome and whole genome sequencing
Authors: Trifiletti Rosario , Lachman Herbert M. , Manusama Olivia , Zheng Deyou , Spalice Alberto , Chiurazzi Pietro , Schornagel Allan , Serban Andreea M. , van Wijck Rogier , Cunningham Janet L. , Swagemakers Sigrid , van der Spek Peter J. 
Published: June 2022

AbstractAbrupt onset of severe neuropsychiatric symptoms including obsessive–compulsive disorder, tics, anxiety, mood swings, irritability, and restricted eating is described in children with Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS). Symptom onset is often temporally associated with infections, suggesting an underlying autoimmune/autoinflammatory etiology, although direct evidence is often lacking. The pathological mechanisms are likely heterogeneous, but we hypothesize convergence on one or more biological pathways. Consequently, we conducted whole exome sequencing (WES) on a U.S. cohort of 386 cases, and whole genome sequencing (WGS) on ten cases from the European Union who were selected because of severe PANS. We focused on identifying potentially deleterious genetic variants that were de novo or ultra-rare (MAF) < 0.001. Candidate mutations were found in 11 genes (PPM1D, SGCE, PLCG2, NLRC4, CACNA1B, SHANK3, CHK2, GRIN2A, RAG1, GABRG2, and SYNGAP1) in 21 cases, which included two or more unrelated subjects with ultra-rare variants in four genes. These genes converge into two broad functional categories. One regulates peripheral immune responses and microglia (PPM1D, CHK2, NLRC4, RAG1, PLCG2). The other is expressed primarily at neuronal synapses (SHANK3, SYNGAP1, GRIN2A, GABRG2, CACNA1B, SGCE). Mutations in these neuronal genes are also described in autism spectrum disorder and myoclonus-dystonia. In fact, 12/21 cases developed PANS superimposed on a preexisting neurodevelopmental disorder. Genes in both categories are also highly expressed in the enteric nervous system and the choroid plexus. Thus, genetic variation in PANS candidate genes may function by disrupting peripheral and central immune functions, neurotransmission, and/or the blood-CSF/brain barriers following stressors such as infection.
Peptidoglycan compositional analysis of Mycobacterium smegmatis using high-resolution LC–MS
Authors: Rimal Binayak , Senzani Sibusiso , Ealand Christopher , Lamichhane Gyanu , Kana Bavesh , Kim Sung Joon 
Published: June 2022

AbstractPeptidoglycan (PG) is the exoskeleton of bacterial cells and is required for their viability, growth, and cell division. Unlike most bacteria, mycobacteria possess an atypical PG characterized by a high degree of unique linkages and chemical modifications which most likely serve as important determinants of virulence and pathogenesis in mycobacterial diseases. Despite this important role, the chemical composition and molecular architecture of mycobacterial PG have yet to be fully determined. Here we determined the chemical composition of PG from Mycobacterium smegmatis using high-resolution liquid chromatography-mass spectrometry. Purified cell walls from the stationary phase were digested with mutanolysin and compositional analysis was performed on 130 muropeptide ions that were identified using an in silico PG library. The relative abundance for each muropeptide ion was measured by integrating the extracted-ion chromatogram. The percentage of crosslink per PG subunit was measured at 45%. While both 3→3 and 4→3 transpeptide cross-linkages were found in PG dimers, a high abundance of 3→3 linkages was found associated with the trimers. Approximately 43% of disaccharides in the PG of M. smegmatis showed modifications by acetylation or deacetylation. A significant number of PG trimers are found with a loss of 41.00 amu that is consistent with N-deacetylation, whereas the dimers show a gain of 42.01 amu corresponding to O-acetylation of the PG disaccharides. This suggests a possible role of PG acetylation in the regulation of cell wall homeostasis in M. smegmatis. Collectively, these data report important novel insights into the ultrastructure of mycobacterial PG.
Impaired differentiation potential of CD34-positive cells derived from mouse hair follicles after long-term culture
Authors: Ouji Yukiteru , Misu Masayasu , Kitamura Tomotaka , Okuzaki Daisuke , Yoshikawa Masahide 
Published: June 2022

AbstractHair follicle epithelial stem cells (HFSCs), which exist in the bulge region, have important functions for homeostasis of skin as well as hair follicle morphogenesis. Although several methods for isolation of HFSCs using a variety of stem cell markers have been reported, few investigations regarding culture methods or techniques to yield long-term maintenance of HFSCs in vitro have been conducted. In the present study, we screened different types of commercially available culture medium for culturing HFSCs. Among those tested, one type was shown capable of supporting the expression of stem cell markers in cultured HFSCs. However, both the differentiation potential and in vivo hair follicle-inducing ability of HFSCs serially passaged using that optimal medium were found to be impaired, probably because of altered responsiveness to Wnt signaling. The changes noted in HFSCs subjected to a long-term culture suggested that the Wnt signaling-related environment must be finely controlled for maintenance of the cells.
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia
Authors: Shu Lili , Wang Miaoyue , Xu Hui , Qiu Zhiheng , Li Tianlai 
Published: June 2022

AbstractThe genes associated with fruiting body formation of Sparasis latifolia are valuable for improving mushroom breeding. To investigate this process, 4.8 × 108 RNA-Seq reads were acquired from three stages: hyphal knot (SM), primordium (SP), and primordium differentiation (SPD). The de novo assembly generated a total of 48,549 unigenes, of which 71.53% (34,728) unigenes could be annotated by at least one of the KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and KOG (Eukaryotic Orthologous Group) databases. KEGG and KOG analyses respectively mapped 32,765 unigenes to 202 pathways and 19,408 unigenes to 25 categories. KEGG pathway enrichment analysis of DEGs (differentially expressed genes) indicated primordium initiation was significantly related to 66 pathways, such as “Ribosome”, “metabolism of xenobiotics by cytochrome P450”, and “glutathione metabolism” (among others). The MAPK and mTOR signal transduction pathways underwent significant adjustments during the SM to SP transition. Further, our research revealed the PI3K-Akt signaling pathway related to cell proliferation could play crucial functions during the development of SP and SPD. These findings provide crucial candidate genes and pathways related to primordium differentiation and development in S. latifolia, and advances our knowledge about mushroom morphogenesis.
The IDentif.AI-x pandemic readiness platform: Rapid prioritization of optimized COVID-19 combination therapy regimens
Authors: Blasiak Agata , Truong Anh T. L. , Remus Alexandria , Hooi Lissa , Seah Shirley Gek Kheng , Wang Peter , Chye De Hoe , Lim Angeline Pei Chiew , Ng Kim Tien , Teo Swee Teng , Tan Yee-Joo , Allen David Michael , Chai Louis Yi Ann , Chng Wee Joo , Lin Raymond T. P. , Lye David C. B. , Wong John Eu-Li , Tan Gek-Yen Gladys , Chan Conrad En Zuo , Chow Edward Kai-Hua , Ho Dean 
Published: June 2022

AbstractIDentif.AI-x, a clinically actionable artificial intelligence platform, was used to rapidly pinpoint and prioritize optimal combination therapies against COVID-19 by pairing a prospective, experimental validation of multi-drug efficacy on a SARS-CoV-2 live virus and Vero E6 assay with a quadratic optimization workflow. A starting pool of 12 candidate drugs developed in collaboration with a community of infectious disease clinicians was first narrowed down to a six-drug pool and then interrogated in 50 combination regimens at three dosing levels per drug, representing 729 possible combinations. IDentif.AI-x revealed EIDD-1931 to be a strong candidate upon which multiple drug combinations can be derived, and pinpointed a number of clinically actionable drug interactions, which were further reconfirmed in SARS-CoV-2 variants B.1.351 (Beta) and B.1.617.2 (Delta). IDentif.AI-x prioritized promising drug combinations for clinical translation and can be immediately adjusted and re-executed with a new pool of promising therapies in an actionable path towards rapidly optimizing combination therapy following pandemic emergence.
Variational autoencoders learn transferrable representations of metabolomics data
Authors: Gomari Daniel P. , Schweickart Annalise , Cerchietti Leandro , Paietta Elisabeth , Fernandez Hugo , Al-Amin Hassen , Suhre Karsten , Krumsiek Jan 
Published: June 2022

AbstractDimensionality reduction approaches are commonly used for the deconvolution of high-dimensional metabolomics datasets into underlying core metabolic processes. However, current state-of-the-art methods are widely incapable of detecting nonlinearities in metabolomics data. Variational Autoencoders (VAEs) are a deep learning method designed to learn nonlinear latent representations which generalize to unseen data. Here, we trained a VAE on a large-scale metabolomics population cohort of human blood samples consisting of over 4500 individuals. We analyzed the pathway composition of the latent space using a global feature importance score, which demonstrated that latent dimensions represent distinct cellular processes. To demonstrate model generalizability, we generated latent representations of unseen metabolomics datasets on type 2 diabetes, acute myeloid leukemia, and schizophrenia and found significant correlations with clinical patient groups. Notably, the VAE representations showed stronger effects than latent dimensions derived by linear and non-linear principal component analysis. Taken together, we demonstrate that the VAE is a powerful method that learns biologically meaningful, nonlinear, and transferrable latent representations of metabolomics data.