bluuebunny/crossref_metadata_2025_split huggingface dataset:
The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase
Authors: Blueggel Mike , Kroening Alexander , Kracht Matthias , van den Boom Johannes , Dabisch Matthias , Goehring Anna , Kaschani Farnusch , Kaiser Markus , Bayer Peter , Meyer Hemmo , Beuck Christine 
Published: June 2023

AbstractThe AAA+ ATPase p97/VCP together with different sets of substrate-delivery adapters and accessory cofactor proteins unfolds ubiquitinated substrates to facilitate degradation by the proteasome. The UBXD1 cofactor is connected to p97-associated multisystem proteinopathy but its biochemical function and structural organization on p97 has remained largely elusive. Using a combination of crosslinking mass spectrometry and biochemical assays, we identify an extended UBX (eUBX) module in UBXD1 related to a lariat in another cofactor, ASPL. Of note, the UBXD1-eUBX intramolecularly associates with the PUB domain in UBXD1 close to the substrate exit pore of p97. The UBXD1 PUB domain can also bind the proteasomal shuttling factor HR23b via its UBL domain. We further show that the eUBX domain has ubiquitin binding activity and that UBXD1 associates with an active p97-adapter complex during substrate unfolding. Our findings suggest that the UBXD1-eUBX module receives unfolded ubiquitinated substrates after they exit the p97 channel and before hand-over to the proteasome. The interplay of full-length UBXD1 and HR23b and their function in the context of an active p97:UBXD1 unfolding complex remains to be studied in future work.
INSurVeyor: improving insertion calling from short read sequencing data
Authors: Rajaby Ramesh , Liu Dong-Xu , Au Chun Hang , Cheung Yuen-Ting , Lau Amy Yuet Ting , Yang Qing-Yong , Sung Wing-Kin 
Published: June 2023

AbstractInsertions are one of the major types of structural variations and are defined as the addition of 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold. First, we introduce INSurVeyor, a fast, sensitive and precise method that detects insertions from next-generation sequencing paired-end data. Using publicly available benchmark datasets (both human and non-human), we show that INSurVeyor is not only more sensitive than any individual caller we tested, but also more sensitive than all of them combined. Furthermore, for most types of insertions, INSurVeyor is almost as sensitive as long reads callers. Second, we provide state-of-the-art catalogues of insertions for 1047 Arabidopsis Thaliana genomes from the 1001 Genomes Project and 3202 human genomes from the 1000 Genomes Project, both generated with INSurVeyor. We show that they are more complete and precise than existing resources, and important insertions are missed by existing methods.
Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana
Authors: Berthelier Jérémy , Furci Leonardo , Asai Shuta , Sadykova Munissa , Shimazaki Tomoe , Shirasu Ken , Saze Hidetoshi 
Published: June 2023

AbstractTransposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.
Broad host susceptibility of North American amphibian species to Batrachochytrium salamandrivorans suggests high invasion potential and biodiversity risk
Authors: Gray Matthew J. , Carter Edward Davis , Piovia-Scott Jonah , Cusaac J. Patrick W. , Peterson Anna C. , Whetstone Ross D. , Hertz Andreas , Muniz-Torres Aura Y. , Bletz Molly C. , Woodhams Douglas C. , Romansic John M. , Sutton William B. , Sheley Wesley , Pessier Allan , McCusker Catherine D. , Wilber Mark Q. , Miller Debra L. 
Published: June 2023

AbstractBatrachochytrium salamandrivorans(Bsal) is a fungal pathogen of amphibians that is emerging in Europe and could be introduced to North America through international trade or other pathways. To evaluate the risk ofBsalinvasion to amphibian biodiversity, we performed dose-response experiments on 35 North American species from 10 families, including larvae from five species. We discovered thatBsalcaused infection in 74% and mortality in 35% of species tested. Both salamanders and frogs became infected and developedBsalchytridiomycosis. Based on our host susceptibility results, environmental suitability conditions forBsal, and geographic ranges of salamanders in the United States, predicted biodiversity loss is expected to be greatest in the Appalachian Region and along the West Coast. Indices of infection and disease susceptibility suggest that North American amphibian species span a spectrum of vulnerability toBsalchytridiomycosis and most amphibian communities will include an assemblage of resistant, carrier, and amplification species. Predicted salamander losses could exceed 80 species in the United States and 140 species in North America.
Acetolysis of waste polyethylene terephthalate for upcycling and life-cycle assessment study
Authors: Peng Yuantao , Yang Jie , Deng Chenqiang , Deng Jin , Shen Li , Fu Yao 
Published: June 2023

AbstractTo reduce environmental pollution and reliance on fossil resources, polyethylene terephthalate as the most consumed synthetic polyester needs to be recycled effectively. However, the existing recycling methods cannot process colored or blended polyethylene terephthalate materials for upcycling. Here we report a new efficient method for acetolysis of waste polyethylene terephthalate into terephthalic acid and ethylene glycol diacetate in acetic acid. Since acetic acid can dissolve or decompose other components such as dyes, additives, blends, etc., Terephthalic acid can be crystallized out in a high-purity form. In addition, Ethylene glycol diacetate can be hydrolyzed to ethylene glycol or directly polymerized with terephthalic acid to form polyethylene terephthalate, completing the closed-loop recycling. Life cycle assessment shows that, compared with the existing commercialized chemical recycling methods, acetolysis offers a low-carbon pathway to achieve the full upcycling of waste polyethylene terephthalate.
Point singularity array with metasurfaces
Authors: Lim Soon Wei Daniel , Park Joon-Suh , Kazakov Dmitry , Spägele Christina M. , Dorrah Ahmed H. , Meretska Maryna L. , Capasso Federico 
Published: June 2023

AbstractPhase singularities are loci of darkness surrounded by monochromatic light in a scalar field, with applications in optical trapping, super-resolution imaging, and structured light-matter interactions. Although 1D singular structures, like optical vortices, are common due to their robust topological properties, uncommon 0D (point) and 2D (sheet) singularities can be generated by wavefront-shaping devices like metasurfaces. With the design flexibility of metasurfaces, we deterministically position ten identical point singularities using a single illumination source. The phasefront is inverse-designed using phase-gradient maximization with an automatically-differentiable propagator and produces tight longitudinal intensity confinement. The array is experimentally realized with a TiO2 metasurface. One possible application is blue-detuned neutral atom trap arrays, for which this field would enforce 3D confinement and a potential depth around 0.22 mK per watt of incident laser power. We show that metasurface-enabled point singularity engineering may significantly simplify and miniaturize the optical architecture for super-resolution microscopes and dark traps.
Lanthanide-doped MoS2 with enhanced oxygen reduction activity and biperiodic chemical trends
Authors: Hao Yu , Wang Liping , Huang Liang-Feng 
Published: June 2023

AbstractMolybdenum disulfide has broad applications in catalysis, optoelectronics, and solid lubrication, where lanthanide (Ln) doping can be used to tune its physicochemical properties. The reduction of oxygen is an electrochemical process important in determining fuel cell efficiency, or a possible environmental-degradation mechanism for nanodevices and coatings consisting of Ln-doped MoS2. Here, by combining density-functional theory calculations and current-potential polarization curve simulations, we show that the dopant-induced high oxygen reduction activity at Ln-MoS2/water interfaces scales as a biperiodic function of Ln type. A defect-state pairing mechanism, which selectively stabilizes the hydroxyl and hydroperoxyl adsorbates on Ln-MoS2, is proposed for the activity enhancement, and the biperiodic chemical trend in activity is found originating from the similar trends in intraatomic 4f–5d6s orbital hybridization and interatomic Ln–S bonding. A generic orbital-chemistry mechanism is described for explaining the simultaneous biperiodic trends observed in many electronic, thermodynamic, and kinetic properties.
A materials data framework and dataset for elastomeric foam impact mitigating materials
Authors: Landauer Alexander K. , Kafka Orion L. , Moser Newell H. , Foster Ian , Blaiszik Ben , Forster Aaron M. 
Published: June 2023

AbstractThe availability of materials data for impact-mitigating materials has lagged behind applications-based data. For example, data describing on-field helmeted impacts are available, whereas material behaviors for the constituent impact-mitigating materials used in helmet designs lack open datasets. Here, we describe a new FAIR (findable, accessible, interoperable, reusable) data framework with structural and mechanical response data for one example elastic impact protection foam. The continuum-scale behavior of foams emerges from the interplay of polymer properties, internal gas, and geometric structure. This behavior is rate and temperature sensitive, therefore, describing structure-property characteristics requires data collected across several types of instruments. Data included are from structure imaging via micro-computed tomography, finite deformation mechanical measurements from universal test systems with full-field displacement and strain, and visco-thermo-elastic properties from dynamic mechanical analysis. These data facilitate modeling and design efforts in foam mechanics, e.g., homogenization, direct numerical simulation, or phenomenological fitting. The data framework is implemented using data services and software from the Materials Data Facility of the Center for Hierarchical Materials Design.
Geochemical and remote sensing integrated with satellite gravity data of Darhib and Atshan talc deposits, South Eastern Desert, Egypt
Authors: Lasheen El Saeed R. , Mohamed Waheed H. , Elyaseer Mahmoud H. , Rashwan Mohamed A. , Azer Mokhles K. 
Published: June 2023

AbstractThe current contribution conducted new geochemical, remote sensing integrated with gravity detailed studies of talc deposits to identify the talc protolith as well as its extension, depth, and structures. There are two examined areas, distributed from north to south, Atshan and Darhib and both belong to the southern sector of the Egyptian Eastern Desert. They occur as individual lenses or pocket bodies in ultramafic-metavolcanics following NNW-SSE and E-W shear zones. Geochemically, among the investigated talc, Atshan samples have high contents of SiO2 (av. 60.73 wt.%), and higher concentrations of transition elements such as Co (av. 53.92 ppm), Cr (781 ppm), Ni (av. 1303.6 ppm), V (av. 16.67 ppm), and Zn (av. 55.7 ppm). Notably, the examined talc deposits contain low contents of CaO (av. 0.32 wt.%), TiO2 (av. 0.04 wt.%), SiO2/MgO (av. 2.15), and Al2O3 (av. 0.72 wt.%), which is comparable with ophiolitic peridotite and forearc setting. False color composite (FCC), principal component analysis (PCA), minimum noise fraction (MNF), and band ratio (BR) have been used to distinguish talc deposits in the investigated areas. Two new proposed band ratios were created to separate talc deposits. FCC band ratios (2/4, 4/7, 6/5) and (4 + 3/5, 5/7, 2 + 1/3) have been derived to focus on talc deposits in two case studies, Atshan and Darhib areas. The application of regional, residual, horizontal gradient (HG), and analytical signal (AS) techniques to gravity data are used in interpreting the structural directions of the study area. The analysis of this technique displays several notable faults trending in NW–SE, NE–SW, NNW–SSE, and E–W directions. Two techniques of gravity depth calculation were applied in the study areas, namely source parameter image (SPI), and Euler deconvolution (EU). The analysis of these techniques reflects that the depth of subsurface sources ranges between 383 and 3560 m. Talc deposits may be attributed to greenschist facies metamorphism or to a magmatic solution that is (associated with granitic intrusions) interacted with the surrounding volcanic rocks forming metasomatic minerals.
Genetically predicted circulating serum homocysteine levels on osteoporosis: a two-sample mendelian randomization study
Authors: Wang ChenYu , Zhang Xiang , Qiu Bo 
Published: June 2023

AbstractTo investigate the causal relationship between circulating serum homocysteine (Hcy) levels and osteoporosis (OP). Using public datasets gathered from independently published genome-wide association studies (GWAS), Mendelian randomization (MR) analysis was done to investigate the causal influence of Hcy on OP. SNPs were selected from a meta-analysis of GWAS on Hcy concentrations in 44,147 individuals of European ancestry. Meanwhile, SNPs of individuals of European descent for OP were extracted from the Genetic Factors of Osteoporosis Consortium (GEFOS) UK Biobank. The odds ratio (OR) of inverse variance weighted (IVW) approaches was established as the primary outcome. Moreover, weighted median (WM) and MR-Egger regressions were included in the sensitivity analysis. There were no causal effects of Hcy on forearm bone mineral density and lumbar bone mineral density according to IVW, MR-Egger, and WM analyses (all p > 0.05). In the IVW, we discovered the causality between genetically predicted Hcy and heel bone mineral density (H-BMD) with an OR of 0.96 [95% confidence interval (CI) = 0.927–0.990, p = 0.011]. In the additional sensitivity analysis, WM regression (OR = 0.97, 95% CI = 0.995–1.076, p = 0.084) and MR-Egger regression (OR = 0.98, 95% CI = 0.918–1.049, p = 0.609) yielded values that were comparable in direction but less precise. The MR-Egger intercept, funnel plot, and IVW all indicate the absence of any discernible directional pleiotropy. The leave-one-out analysis revealed that a single SNP did not influence the results of the MR analysis. In conclusion, our MR investigation revealed evidence of a causal relationship between circulating serum Hcy levels and H-BMD, but not OP in the European population. However, larger sample sizes are needed in the future to get more reliable conclusions.
Acute exposure to organophosphorus pesticide metabolites compromises buffalo sperm function and impairs fertility
Authors: Chhillar Shivani , Batra Vipul , Kumaresan Arumugam , Kumar Rakesh , Pal Ankit , Datta Tirtha Kumar 
Published: June 2023

AbstractAgrichemicals such as organophosphorus pesticides’ metabolites (OPPMs) are more hazardous and pervasive than their parent pesticides. Parental germline exposure to such xenobiotics leads to an elevated susceptibility towards reproductive failures e.g. sub- or in-fertility. This study sought to examine the effects of low-dose, acute OPPM exposure on mammalian sperm function using buffalo as the model organism. The buffalo spermatozoa were briefly (2 h) exposed to metabolites of the three most prevalent organophosphorus pesticides (OPPs) viz. Omethoate (from Dimethoate), paraoxon-methyl (from methyl/ethyl parathion) and 3, 5, 6-trichloro-2-pyridinol (from chlorpyrifos). Exposure to OPPMs resulted in compromised structural and functional integrity (dose-dependent) of the buffalo spermatozoa typified by elevated membrane damage, increased lipid peroxidation, precocious capacitation and tyrosine phosphorylation, perturbed mitochondrial activity and function and (P < 0.05). This led to a decline in the in vitro fertilizing ability (P < 0.01) of the exposed spermatozoa, as indicated by reduced cleavage and blastocyst formation rates. Preliminary data indicate that acute exposure to OPPMs, akin to their parent pesticides, induces biomolecular and physiological changes in spermatozoa that compromise their health and function ultimately affecting their fertility. This is the first study demonstrating the in vitro spermatotoxic effects of multiple OPPMs on male gamete functional integrity.
Impact of Covid-19 pandemic lockdown on the urban litter and clean environment index
Authors: Darabi Khadijeh , Hayati Ramin , Morovati Maryam , Alinejad Navid , Hassani Ghasem 
Published: June 2023

AbstractChanging the level of pollution in the urban environment is one of the consequences of Covid-19. Litter are one of the most important urban pollutants affected by the Covid-19 pandemic. In this research, the pollution level of urban areas during the Covid-19 pandemic was investigated by studying the urban environment. To this end, the protocol of observation and counting was used and litter were studied in two groups including common litter and Covid-19 related litter in Yasuj, Iran. The results were interpreted based on the clean environment index (CEI). The time of observation was selected based on the peak of the disease and the decline in the incidence rate. The results showed that on average, at the peak of the disease, the density of the litter was reduced by 19% compared to the low lockdown related to Covid-19. The CEI on average was 4.76 at the peak of the disease that was interpreted in the clean status, while the CEI on average was 5.94 at the low lockdown related to Covid-19 so interpreted in the moderate status. Among urban land uses, recreational areas with a difference of more than 60% showed the greatest impact caused by Covid-19, while in commercial areas this difference was less than 3%. The effect of Covid-19 related litter on the calculated index was 73% in the worst case and 0.8% in the lowest case. Although Covid-19 decreased the number of litter in urban areas, the emergence of Covid-19 lockdown related litter was a cause for concern and led to increasing the CEI.
Ecological risk assessment of aquatic organisms induced by heavy metals in the estuarine waters of the Pearl River
Authors: Tang Zhihua , Liu Xinyu , Niu Xiaojun , Yin Hua , Liu Minru , Zhang Dongqing , Guo Huafang 
Published: June 2023

AbstractWith the rapid economic development of China's coastal areas and the growth of industry and population, the problem of heavy metal contamination in estuarine waters is increasing in sensitivity and seriousness. In order to accurately and quantitatively describe the current status of heavy metal contamination and identify sensitive aquatic organisms with high ecological risks, five heavy metals in eight estuaries of the Pearl River were monitored at monthly intervals from January to December in 2020, and the ecological risks of aquatic organisms induced by heavy metals were evaluated using Risk quotients (RQ) and species sensitivity distributions (SSD) methods. The results showed that the concentrations of As, Cu, Pb, Hg and Zn in estuaries of the Pearl River were (0.65–9.25) μg/L, (0.07–11.57) μg/L, (0.05–9.09) μg/L, (< 0.40) μg/L and (0.67–86.12) μg/L, respectively. With the exception of Hg in Jiaomen water, the other heavy metals in each sampling site met or exceed the water quality standard of Grade II. The aquatic ecological risks of As, Pb and Hg were generally low in the waters of the Pearl River estuary, but individual aquatic organisms are subject to elevated ecological risks due to Cu and Zn. The content of Zn has a lethal effect on the crustaceans Temora Stylifera, and the content of Cu has a serious impact on the mollusks Corbicula Fluminea and has a certain impact on the crustaceans Corophium sp. and the fish Sparus aurata. Heavy metal levels and joint ecological risks (msPAF) in the Humen, Jiaomen, Hongqimen, and Hengmen estuaries were slightly higher than in other estuaries, and the Yamen estuary had the lowest contration of heavy metals and ecological risk. Research findings can serve as a basis for formulating water quality standards for heavy metals and for protecting aquatic biodiversity in the Pearl River Estuary.
Quantum neural networks with multi-qubit potentials
Authors: Ban Yue , Torrontegui E. , Casanova J. 
Published: June 2023

AbstractWe propose quantum neural networks that include multi-qubit interactions in the neural potential leading to a reduction of the network depth without losing approximative power. We show that the presence of multi-qubit potentials in the quantum perceptrons enables more efficient information processing tasks such as XOR gate implementation and prime numbers search, while it also provides a depth reduction to construct distinct entangling quantum gates like CNOT, Toffoli, and Fredkin. This simplification in the network architecture paves the way to address the connectivity challenge to scale up a quantum neural network while facilitating its training.
Prehospital stroke-scale machine-learning model predicts the need for surgical intervention
Authors: Yoshida Yoichi , Hayashi Yosuke , Shimada Tadanaga , Hattori Noriyuki , Tomita Keisuke , Miura Rie E. , Yamao Yasuo , Tateishi Shino , Iwadate Yasuo , Nakada Taka-aki 
Published: June 2023

AbstractWhile the development of prehospital diagnosis scales has been reported in various regions, we have also developed a scale to predict stroke type using machine learning. In the present study, we aimed to assess for the first time a scale that predicts the need for surgical intervention across stroke types, including subarachnoid haemorrhage and intracerebral haemorrhage. A multicentre retrospective study was conducted within a secondary medical care area. Twenty-three items, including vitals and neurological symptoms, were analysed in adult patients suspected of having a stroke by paramedics. The primary outcome was a binary classification model for predicting surgical intervention based on eXtreme Gradient Boosting (XGBoost). Of the 1143 patients enrolled, 765 (70%) were used as the training cohort, and 378 (30%) were used as the test cohort. The XGBoost model predicted stroke requiring surgical intervention with high accuracy in the test cohort, with an area under the receiver operating characteristic curve of 0.802 (sensitivity 0.748, specificity 0.853). We found that simple survey items, such as the level of consciousness, vital signs, sudden headache, and speech abnormalities were the most significant variables for accurate prediction. This algorithm can be useful for prehospital stroke management, which is crucial for better patient outcomes.