bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus
Authors: Khunsriraksakul Chachrit , Li Qinmengge , Markus Havell , Patrick Matthew T. , Sauteraud Renan , McGuire Daniel , Wang Xingyan , Wang Chen , Wang Lida , Chen Siyuan , Shenoy Ganesh , Li Bingshan , Zhong Xue , Olsen Nancy J. , Carrel Laura , Tsoi Lam C. , Jiang Bibo , Liu Dajiang J. 
Published: February 2023

AbstractSystemic lupus erythematosus is a heritable autoimmune disease that predominantly affects young women. To improve our understanding of genetic etiology, we conduct multi-ancestry and multi-trait meta-analysis of genome-wide association studies, encompassing 12 systemic lupus erythematosus cohorts from 3 different ancestries and 10 genetically correlated autoimmune diseases, and identify 16 novel loci. We also perform transcriptome-wide association studies, computational drug repurposing analysis, and cell type enrichment analysis. We discover putative drug classes, including a histone deacetylase inhibitor that could be repurposed to treat lupus. We also identify multiple cell types enriched with putative target genes, such as non-classical monocytes and B cells, which may be targeted for future therapeutics. Using this newly assembled result, we further construct polygenic risk score models and demonstrate that integrating polygenic risk score with clinical lab biomarkers improves the diagnostic accuracy of systemic lupus erythematosus using the Vanderbilt BioVU and Michigan Genomics Initiative biobanks.
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses
Authors: Hirz Taghreed , Mei Shenglin , Sarkar Hirak , Kfoury Youmna , Wu Shulin , Verhoeven Bronte M. , Subtelny Alexander O. , Zlatev Dimitar V. , Wszolek Matthew W. , Salari Keyan , Murray Evan , Chen Fei , Macosko Evan Z. , Wu Chin-Lee , Scadden David T. , Dahl Douglas M. , Baryawno Ninib , Saylor Philip J. , Kharchenko Peter V. , Sykes David B. 
Published: February 2023

AbstractThe treatment of low-risk primary prostate cancer entails active surveillance only, while high-risk disease requires multimodal treatment including surgery, radiation therapy, and hormonal therapy. Recurrence and development of metastatic disease remains a clinical problem, without a clear understanding of what drives immune escape and tumor progression. Here, we comprehensively describe the tumor microenvironment of localized prostate cancer in comparison with adjacent normal samples and healthy controls. Single-cell RNA sequencing and high-resolution spatial transcriptomic analyses reveal tumor context dependent changes in gene expression. Our data indicate that an immune suppressive tumor microenvironment associates with suppressive myeloid populations and exhausted T-cells, in addition to high stromal angiogenic activity. We infer cell-to-cell relationships from high throughput ligand-receptor interaction measurements within undissociated tissue sections. Our work thus provides a highly detailed and comprehensive resource of the prostate tumor microenvironment as well as tumor-stromal cell interactions.
Up-conversion emission in transition metal and lanthanide co-doped systems: dimer sensitization revisited
Authors: Avram Daniel , Colbea Claudiu , Patrascu Andrei A. , Istrate Marian Cosmin , Teodorescu Valentin , Tiseanu Carmen 
Published: February 2023

AbstractLanthanide (Ln) co-doped transition metal (TM) upconversion (UC) co-doped systems are being intensively investigated for their exciting applications in photonics, bioimaging, and luminescence thermometry. The presence of TM, such as Mo6 + /W6 +, Mn2 +, or Fe3 + determines significant changes in Ln UC emission, such as intensity enhancement, colour modulation, and even the alteration of the photon order. The current mechanism assumes a ground-state absorption/excited-state absorption (ESA/GSA) in TM-Yb dimer followed by direct energy transfer to Er/Tm excited states. We revisit this mechanism by addressing two issues that remain ignored: a dynamical approach to the investigation of the upconversion mechanism and the intrinsic chemical complexity of co-doped TM, Ln systems. To this aim, we employ a pulsed, excitation variable laser across a complete set of UC measurements, such as the emission and excitation spectra and emission decays and analyze multiple grains with transmission electron microscopy (TEM). In the Mo co-doped garnet, the results sustain the co-existence of Mo-free garnet and Mo oxide impurity. In this Mo oxide, the Er upconversion emission properties are fully explained by a relatively efficient sequential Yb to Er upconversion process, with no contribution from Yb-Mo dimer sensitization.
A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance
Authors: Jaganathan Deepa , Rajakani Raja , Doddamani Dadakhalandar , Saravanan Divya , Pulipati Shalini , Hari Sundar G Vivek , Sellamuthu Gothandapani , Jayabalan Shilpha , Kumari Kumkum , Parthasarathy Pavithra , S. Punitha , Ramalingam Sivaprakash , Shivaprasad Padubidri V. , Venkataraman Gayatri 
Published: February 2023

AbstractPlant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the ‘A10234287911’ allele may promote better processing vis-à-vis the structure conferred by ‘G10234287911’ allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.
Mechanisms of amyloid-β34 generation indicate a pivotal role for BACE1 in amyloid homeostasis
Authors: Ulku Irem , Liebsch Filip , Akerman S. Can , Schulz Jana F. , Kulic Luka , Hock Christoph , Pietrzik Claus , Di Spiezio Alessandro , Thinakaran Gopal , Saftig Paul , Multhaup Gerhard 
Published: February 2023

AbstractThe beta‑site amyloid precursor protein (APP) cleaving enzyme (BACE1) was discovered due to its “amyloidogenic” activity which contributes to the production of amyloid-beta (Aβ) peptides. However, BACE1 also possesses an “amyloidolytic” activity, whereby it degrades longer Aβ peptides into a non‑toxic Aβ34 intermediate. Here, we examine conditions that shift the equilibrium between BACE1 amyloidogenic and amyloidolytic activities by altering BACE1/APP ratios. In Alzheimer disease brain tissue, we found an association between elevated levels of BACE1 and Aβ34. In mice, the deletion of one BACE1 gene copy reduced BACE1 amyloidolytic activity by ~ 50%. In cells, a stepwise increase of BACE1 but not APP expression promoted amyloidolytic cleavage resulting in dose-dependently increased Aβ34 levels. At the cellular level, a mislocalization of surplus BACE1 caused a reduction in Aβ34 levels. To align the role of γ-secretase in this pathway, we silenced Presenilin (PS) expression and identified PS2-γ-secretase as the main γ-secretase that generates Aβ40 and Aβ42 peptides serving as substrates for BACE1’s amyloidolytic cleavage to generate Aβ34.
Dynamic response characteristics and damage rule of graphite ore rock under different strain rates
Authors: Ye Haiwang , Li Xingwang , Lei Tao , Li Lifeng , Wang Qizhou , Li Ning 
Published: February 2023

AbstractIn the process of mining graphite mine, rock mass is often subjected to dynamic loads such as blasting or mechanical crushing, which involves dynamic responses of different strain rates, and blasting and crushing effect are affected by the rock dynamic properties and damage specials. The dynamic response characteristics and damage rule of graphite ore rock under different strain rates are very important but rarely studied in the past. To study these issues and provide support for graphite ore rock mining, the dynamic compression tests of graphite ore rock under five kinds of impact pressures were designed and carried out by using the Split Hopkinson Pressure Bar (SHPB) test system, combining with the high-speed photography system and crushing screening tests. The dynamic characteristics, crushing process, crushing mode, crushing form and fragmentation distribution of the graphite ore rock under different strain rates were analyzed. The results show that the dynamic characteristics of the graphite ore rock have obvious strain rate effect. The hardening coefficient (DIF) is positively correlated with the cubic root of strain rate, and the softening factor (K) is negatively correlated with the cubic root of strain rate. Shear failure mainly occurs in the graphite ore rock under impact load, and the crushing process can be divided into five stages, they are compaction, crack initiation, crack expansion and penetration, fragmentation collision and fragmentation fall. In addition, the crushed blocks are mainly triangular pyramid (or cone-like) fine granular and powder. The broken fragments of the graphite ore rock are in accord with the fractal geometry characteristics. That is, the average broken particle size (dS) decreases linearly with the increase of strain rate, and the fractal dimension (Da) increases weakly with the increase of strain rate. Based on D-P fracture criterion and Weibull distribution model, the dynamic damage constitutive model of the graphite ore rock was established, and the correlation between strain rate and Weibull distribution parameters (m and F0) was used to reasonably modify the damage constitutive model. The modified damage constitutive model curve is in good agreement with the experimental curve, which can basically reflect the strain rate effect of the dynamic characteristics of the graphite ore rock and the evolution characteristics of the dynamic stress–strain curve at different stage.
Synchrotron-based operando X-ray diffraction and X-ray absorption spectroscopy study of LiCo0.5Fe0.5PO4 mixed d-metal olivine cathode
Authors: Hamdalla Taymour A. , Aboraia Abdelaziz M. , Shapovalov V. V. , Guda A. A. , Kosova N. V. , Podgornova O. A. , Darwish A. A. A. , Al-Ghamdi S. A. , Alfadhli S. , Alatawi Aadel M. , Soldatov Alexander 
Published: February 2023

AbstractLithium-ion batteries based on high-voltage cathode materials, such as LiCoPO4, despite being promising in terms of specific power, still suffer from poor cycle life due to the lower stability of common non-aqueous electrolytes at higher voltages. One way to overcome this issue might be decreasing the working potential of the battery by doping LiCoPO4 by Fe, thus reducing electrolyte degradation upon cycling. However, such modification requires a deep understanding of the structural behavior of cathode material upon lithiation/delithiation. Here we used a combination of operando synchrotron-based XRD and XAS to investigate the dynamics of d-metal local atomic structure and charge state upon cycling of LiCo0.5Fe0.5PO4 mixed d-metal olivine cathode material. Principal components analysis (PCA) of XAS data allowed the extraction of spectra of individual phases in the material and their concentrations. For both Co and Fe two components were extracted, they correspond to fully lithiated and delithiated phases of LixMPO4 (where M = Fe, Co). Thus, we were able to track the phase transitions in the material upon charge and discharge and quantitatively analyze the M2+/M3+ electrochemical conversion rate for both Fe and Co. Rietveld's refinement of XRD data allowed us to analyze the changes in the lattice of cathode material and their reversibility upon (de)lithiation during cycling. The calculation of DFT and Bader charge analysis expects the oxygen redox procedure combined with d-metals redox, which supplements iron charge variations and dominates at high voltages when x < 0.75 in LixCoFePO4.
Combating lead and cadmium exposure with an orally administered chitosan-based chelating polymer
Authors: Howard Jordyn Ann , Kuznietsova Halyna , Dziubenko Natalia , Aigle Axel , Natuzzi Marco , Thomas Eloise , Lysenko Vladimir , David Laurent , Brichart Thomas , Lux François , Tillement Olivier 
Published: February 2023

AbstractHeavy metals present a threat to human health, even at minimal concentrations within the body. One source of exposure is due to the consumption of low-level contaminated foodstuff and water. Lead and cadmium have been shown to be absorbed by and accumulate within organs like the kidneys and liver, and they have also been associated to many diseases including cardiovascular disease and kidney dysfunction as well as developmental disorders and neurodegenerative diseases. Since this contamination of lead and cadmium is found worldwide, limiting the exposure is complicated and novel strategies are required to prevent the absorption and accumulation of these metals by forcing their elimination. In this study, a DOTAGA-functionalized chitosan polymer is evaluated for this preventative strategy. It shows promising results when orally administered in mice to force the elimination and negate the toxic effects of lead and cadmium found within foodstuff.
Limbic progesterone receptors regulate spatial memory
Authors: Joshi Suchitra , Williams Cedric L. , Kapur Jaideep 
Published: February 2023

AbstractProgesterone and its receptors (PRs) participate in mating and reproduction, but their role in spatial declarative memory is not understood. Male mice expressed PRs, predominately in excitatory neurons, in brain regions that support spatial memory, such as the hippocampus and entorhinal cortex (EC). Furthermore, segesterone, a specific PR agonist, activates neurons in both the EC and hippocampus. We assessed the contribution of PRs in promoting spatial and non-spatial cognitive learning in male mice by examining the performance of mice lacking this receptor (PRKO), in novel object recognition, object placement, Y-maze alternation, and Morris-Water Maze (MWM) tasks. In the recognition test, the PRKO mice preferred the familiar object over the novel object. A similar preference for the familiar object was also seen following the EC-specific deletion of PRs. PRKO mice were also unable to recognize the change in object position. We confirmed deficits in spatial memory of PRKO mice by testing them on the Y-maze forced alternation and MWM tasks; PR deletion affected animal’s performance in both these tasks. In contrast to spatial tasks, PR removal did not alter the response to fear conditioning. These studies provide novel insights into the role of PRs in facilitating spatial, declarative memory in males, which may help with finding reproductive partners.
Rare variant aggregation in 148,508 exomes identifies genes associated with proxy dementia
Authors: Wightman Douglas P. , Savage Jeanne E. , de Leeuw Christiaan A. , Jansen Iris E. , Posthuma Danielle 
Published: February 2023

AbstractProxy phenotypes allow for the utilization of genetic data from large population cohorts to analyze late-onset diseases by using parental diagnoses as a proxy for genetic disease risk. Proxy phenotypes based on parental diagnosis status have been used in previous studies to identify common variants associated with Alzheimer’s disease. As of yet, proxy phenotypes have not been used to identify genes associated with Alzheimer’s disease through rare variants. Here we show that a proxy Alzheimer’s disease/dementia phenotype can capture known Alzheimer’s disease risk genes through rare variant aggregation. We generated a proxy Alzheimer’s disease/dementia phenotype for 148,508 unrelated individuals of European ancestry in the UK biobank in order to perform exome-wide rare variant aggregation analyses to identify genes associated with proxy Alzheimer’s disease/dementia. We identified four genes significantly associated with the proxy phenotype, three of which were significantly associated with proxy Alzheimer’s disease/dementia in an independent replication cohort consisting of 197,506 unrelated individuals of European ancestry in the UK biobank. All three of the replicated genes have been previously associated with clinically diagnosed Alzheimer’s disease (SORL1, TREM2, and TOMM40/APOE). We show that proxy Alzheimer’s disease/dementia can be used to identify genes associated with Alzheimer’s disease through rare variant aggregation.
Benefits of the microalgae Spirulina and Schizochytrium in fish nutrition: a meta-analysis
Authors: Trevi S. , Uren Webster T. , Consuegra S. , Garcia de Leaniz C. 
Published: February 2023

AbstractUse of microalgae in fish nutrition can relieve pressure on wild fish stocks, but there is no systematic quantitative evaluation of microalgae benefits. We conducted a metanalysis on the nutritional benefits ofSpirulinaandSchizochytriumas replacements of fishmeal and fish or plant oil, respectively. We reviewed 50 peer-reviewed studies involving 26 finfish species and 144 control vs microalgae replacement comparisons. Inclusion ofSpirulinain the fish diet significantly improved growth compared to controls (SMD = 1.21; 95% CI 0.71–1.70), while inclusion ofSchizochytriummaintained the content of omega-3 PUFA of the fish fillet compared to fish fed on fish or plant oils (SMD = 0.62; 95% CI − 0.51–1.76). Benefits were apparent at replacement levels as low as 0.025% in the case ofSpirulinaand 10% in the case ofSchizochytriumoil. Dose-dependent effects were found forSpirulinareplacement on growth, but not forSchizochytriumon omega-3 fillet content. Subgroup analysis and meta-regression revealed that ~ 24–27% of variation in effect sizes can be accounted by variation between fish families, the rest likely reflecting variation in experimental conditions. Overall, the evidence indicates thatSpirulinaandSchizochytriumreplacement in aquafeeds can be used to improve fish growth and maintain fillet quality, respectively, but considerable uncertainty exists on the predicted responses. To reduce uncertainty and facilitate the transition towards more sustainable aquafeeds, we recommend that feeding trials using microalgae are conducted under commercially relevant conditions and that greater care is taken to report full results to account for sources of heterogeneity.
Evaluation of solar photovoltaic carport canopy with electric vehicle charging potential
Authors: Fakour Hoda , Imani Moslem , Lo Shang-Lien , Yuan Mei-Hua , Chen Chih-Kuei , Mobasser Shariat , Muangthai Isara 
Published: February 2023

AbstractWhile sustainable mobility and decarbonization of transportation sector are among the most comprehensive solutions to the problem of climate change, electric vehicles (EV) are becoming increasingly popular as the future mode of transport. In this study, the integration of a solar carport canopy to a potential EV charging station is analyzed using various operating conditions. A detailed analysis has been provided for the carport located in southern Taiwan, Kaohsiung city, where electricity generation, emission impacts, and financial analysis of the solar EV charging station are discussed. The results of a case study showed a potential of 140 MWh/year of solar energy yield, which could provide solar electricity of more than 3000 vehicles per month with 1-h parking time, generating 94% lower total carbon dioxide emission than the electricity produced from traditional grid methods. Taken into account the impact of carbon tax implementation on driver economics, the results demonstrated the viability of such photovoltaic (PV)-based charging stations, particularly for possible higher carbon tax scenarios in the future. The presented results can be implemented on a larger scale, offering guidelines and tools for constructing solar-powered EV charging station infrastructure.
Ghrelin signaling in the cerebellar cortex enhances GABAergic transmission onto Purkinje cells
Authors: Hirono Moritoshi , Nakata Masanori 
Published: February 2023

AbstractGhrelin, an orexigenic peptide ligand for growth hormone secretagogue receptor 1a (GHS-R1a), occurs not only in the stomach but also in the brain, and modulates neuronal activity and synaptic efficacy. Previous studies showed that GHS-R1a exists in the cerebellum, and ghrelin facilitates spontaneous firing of Purkinje cells (PCs). However, the effects of ghrelin on cerebellar GABAergic transmission have yet to be elucidated. We found that ghrelin enhanced GABAergic transmission between molecular layer interneurons (MLIs) and PCs using electrophysiological recordings in mouse cerebellar slices. This finding was consistent with the possibility that blocking synaptic transmission enhanced the ghrelin-induced facilitation of PC firing. Ghrelin profoundly increased the frequency of spontaneous inhibitory postsynaptic currents (IPSCs) in PCs without affecting miniature or stimulation-evoked IPSCs, whereas it significantly facilitated spontaneous firing of MLIs. This facilitation of MLI spiking disappeared during treatments with blockers of GHS-R1a, type 1 transient receptor potential canonical (TRPC1) channels and KCNQ channels. These results suggest that both activating TRPC1 channels and inhibiting KCNQ channels occur downstream the ghrelin-GHS-R1a signaling pathway probably in somatodendritic sites of MLIs. Thus, ghrelin can control PC firing directly and indirectly via its modulation of GABAergic transmission, thereby impacting activity in cerebellar circuitry.
Deposition of carbon from methane on manganese sources
Authors: Dalaker Halvor , Gjøvik Jonas E. , Ringdalen Eli 
Published: February 2023

AbstractCarbon has been deposited on HCFeMn slag from methane-containing gas with and without CO2, creating C-MnO composites and giving a hydrogen-rich off-gas as a by-product. The maximum deposited amount corresponds to 38 ± 6% of the carbon required for reduction of all manganese in the slag to metallic Mn. This was achieved at 1100 °C with a H2-concentration in the off gas of 76%. Temperature was an important parameter. At 790 °C, no deposited carbon was detected, at temperatures ≥ 1000 °C, deposition increased with temperature. A lower gas-flow leads to more methane decomposition. Experiments with CO2 in the process gas gave less deposited carbon than other experiments. This could be caused by dilution of methane or chemical reactions involving CO2, or a combination. Investigations of fines formation indicate that the deposited carbon sticks well to the HCFeMn-slag, and would not fall off easily during transport and handling. This demonstrates that biogas can potentially be a non-fossil source of carbon in manganese production.