bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipase regulation of cellular fatty acid homeostasis as a Parkinson’s disease therapeutic strategy
Authors: Fanning Saranna , Cirka Haley , Thies Jennifer L. , Jeong Jooyoung , Niemi Sarah M. , Yoon Joon , Ho Gary P. H. , Pacheco Julian A. , Dettmer Ulf , Liu Lei , Clish Clary B. , Hodgetts Kevin J. , Hutchinson John N. , Muratore Christina R. , Caldwell Guy A. , Caldwell Kim A. , Selkoe Dennis 
Published: June 2022

AbstractSynucleinopathy (Parkinson’s disease (PD); Lewy body dementia) disease-modifying treatments represent a huge unmet medical need. Although the PD-causing protein α-synuclein (αS) interacts with lipids and fatty acids (FA) physiologically and pathologically, targeting FA homeostasis for therapeutics is in its infancy. We identified the PD-relevant target stearoyl-coA desaturase: inhibiting monounsaturated FA synthesis reversed PD phenotypes. However, lipid degradation also generates FA pools. Here, we identify the rate-limiting lipase enzyme, LIPE, as a candidate target. Decreasing LIPE in human neural cells reduced αS inclusions. Patient αS triplication vs. corrected neurons had increased pSer129 and insoluble αS and decreased αS tetramer:monomer ratios. LIPE inhibition rescued all these and the abnormal unfolded protein response. LIPE inhibitors decreased pSer129 and restored tetramer:monomer equilibrium in αS E46K-expressing human neurons. LIPE reduction in vivo alleviated αS-induced dopaminergic neurodegeneration in Caenorhabditis elegans. Co-regulating FA synthesis and degradation proved additive in rescuing PD phenotypes, signifying co-targeting as a therapeutic strategy.
Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model
Authors: Mendik Péter , Kerestély Márk , Kamp Sebestyén , Deritei Dávid , Kunšič Nina , Vassy Zsolt , Csermely Péter , Veres Daniel V. 
Published: June 2022

AbstractRegulation of translocating proteins is crucial in defining cellular behaviour. Epithelial-mesenchymal transition (EMT) is important in cellular processes, such as cancer progression. Several orchestrators of EMT, such as key transcription factors, are known to translocate. We show that translocating proteins become enriched in EMT-signalling. To simulate the compartment-specific functions of translocating proteins we created a compartmentalized Boolean network model. This model successfully reproduced known biological traits of EMT and as a novel feature it also captured organelle-specific functions of proteins. Our results predicted that glycogen synthase kinase-3 beta (GSK3B) compartment-specifically alters the fate of EMT, amongst others the activation of nuclear GSK3B halts transforming growth factor beta-1 (TGFB) induced EMT. Moreover, our results recapitulated that the nuclear activation of glioma associated oncogene transcription factors (GLI) is needed to achieve a complete EMT. Compartmentalized network models will be useful to uncover novel control mechanisms of biological processes. Our algorithmic procedures can be automatically rerun on the https://translocaboole.linkgroup.hu website, which provides a framework for similar future studies.
Third-party punishment by preverbal infants
Authors: Kanakogi Yasuhiro , Miyazaki Michiko , Takahashi Hideyuki , Yamamoto Hiroki , Kobayashi Tessei , Hiraki Kazuo 
Published: June 2022

AbstractThird-party punishment of antisocial others is unique to humans and seems to be universal across cultures. However, its emergence in ontogeny remains unknown. We developed a participatory cognitive paradigm using gaze-contingency techniques, in which infants can use their gaze to affect agents displayed on a monitor. In this paradigm, fixation on an agent triggers the event of a stone crushing the agent. Throughout five experiments (total N = 120), we show that eight-month-old infants punished antisocial others. Specifically, infants increased their selective looks at the aggressor after watching aggressive interactions. Additionally, three control experiments excluded alternative interpretations of their selective gaze, suggesting that punishment-related decision-making influenced looking behaviour. These findings indicate that a disposition for third-party punishment of antisocial others emerges in early infancy and emphasize the importance of third-party punishment for human cooperation. This behavioural tendency may be a human trait acquired over the course of evolution.
Programmable gear-based mechanical metamaterials
Authors: Fang Xin , Wen Jihong , Cheng Li , Yu Dianlong , Zhang Hongjia , Gumbsch Peter 
Published: June 2022

AbstractElastic properties of classical bulk materials can hardly be changed or adjusted in operando, while such tunable elasticity is highly desired for robots and smart machinery. Although possible in reconfigurable metamaterials, continuous tunability in existing designs is plagued by issues such as structural instability, weak robustness, plastic failure and slow response. Here we report a metamaterial design paradigm using gears with encoded stiffness gradients as the constituent elements and organizing gear clusters for versatile functionalities. The design enables continuously tunable elastic properties while preserving stability and robust manoeuvrability, even under a heavy load. Such gear-based metamaterials enable excellent properties such as continuous modulation of Young’s modulus by two orders of magnitude, shape morphing between ultrasoft and solid states, and fast response. This allows for metamaterial customization and brings fully programmable materials and adaptive robots within reach.
Auto-generating databases of Yield Strength and Grain Size using ChemDataExtractor
Authors: Kumar Pankaj , Kabra Saurabh , Cole Jacqueline M. 
Published: June 2022

AbstractThe emerging field of material-based data science requires information-rich databases to generate useful results which are currently sparse in the stress engineering domain. To this end, this study uses the’materials-aware’ text-mining toolkit, ChemDataExtractor, to auto-generate databases of yield-strength and grain-size values by extracting such information from the literature. The precision of the extracted data is 83.0% for yield strength and 78.8% for grain size. The automatically-extracted data were organised into four databases: a Yield Strength, Grain Size, Engineering-Ready Yield Strength and Combined database. For further validation of the databases, the Combined database was used to plot the Hall-Petch relationship for, the alloy, AZ31, and similar results to the literature were found, demonstrating how one can make use of these automatically-extracted datasets.
Indoor heat measurement data from low-income households in rural and urban South Asia
Authors: Tasgaonkar Premsagar , Zade Dipak , Ehsan Sana , Gorti Ganesh , Mamnun Nabir , Siderius Christian , Singh Tanya 
Published: June 2022

AbstractRising temperatures are causing distress across the world, and for those most vulnerable, it is a silent killer. Information about indoor air temperature in residential dwellings is of interest for a range of reasons, such as health, thermal comfort and coping practices. However, there have been only few studies that measure indoor heat exposure, and contrast these to outdoor temperatures in rural-urban areas, of which none are in South Asia. We aim to close this knowledge gap with our indoor and outdoor heat measurement dataset, covering five low-income sites in South Asia. Two sites are in rural areas (Maharashtra, India), while three sites focus on urban areas (Dhaka, Delhi and Faisalabad). Data are based on 206 indoor temperature data loggers and complemented by data from five outdoor automated weather stations. The data-set can be used to examine temperature and humidity variation in low-socioeconomic status households in rural and urban areas and to better understand factors aggravating heat stress. This is important to plan and implement actions for combating heat stress.
A cross-verified database of notable people, 3500BC-2018AD
Authors: Laouenan Morgane , Bhargava Palaash , Eyméoud Jean-Benoît , Gergaud Olivier , Plique Guillaume , Wasmer Etienne 
Published: June 2022

AbstractA new strand of literature aims at building the most comprehensive and accurate database of notable individuals. We collect a massive amount of data from various editions of and . Using deduplication techniques over these partially overlapping sources, we cross-verify each retrieved information. For some variables, adds 15% more information when missing in . We find very few errors in the part of the database that contains the most documented individuals but nontrivial error rates in the bottom of the notability distribution, due to sparse information and classification errors or ambiguity. Our strategy results in a cross-verified database of 2.29 million individuals (an elite of 1/43,000 of human being having ever lived), including a third who are not present in the English edition of . Data collection is driven by specific social science questions on gender, economic growth, urban and cultural development. We document an Anglo-Saxon bias present in the English edition of , and document when it matters and when not.
A Chinese multi-modal neuroimaging data release for increasing diversity of human brain mapping
Authors: Gao Peng , Dong Hao-Ming , Liu Si-Man , Fan Xue-Ru , Jiang Chao , Wang Yin-Shan , Margulies Daniel , Li Hai-Fang , Zuo Xi-Nian 
Published: June 2022

AbstractThe big-data use is becoming a standard practice in the neuroimaging field through data-sharing initiatives. It is important for the community to realize that such open science effort must protect personal, especially facial information when raw neuroimaging data are shared. An ideal tool for the face anonymization should not disturb subsequent brain tissue extraction and further morphological measurements. Using the high-resolution head images from magnetic resonance imaging (MRI) of 215 healthy Chinese, we discovered and validated a template effect on the face anonymization. Improved facial anonymization was achieved when the Chinese head templates but not the Western templates were applied to obscure the faces of Chinese brain images. This finding has critical implications for international brain imaging data-sharing. To facilitate the further investigation of potential culture-related impacts on and increase diversity of data-sharing for the human brain mapping, we released the 215 Chinese multi-modal MRI data into a database for imaging Chinese young brains, namely’I See your Brains (ISYB)’, to the public via the Science Data Bank (https://doi.org/10.11922/sciencedb.00740).
Experimental characterization of colloidal silica gel for water conformance control in oil reservoirs
Authors: Ghaffari Zahra , Rezvani Hosein , Khalilnezhad Ali , Cortes Farid B. , Riazi Masoud 
Published: June 2022

AbstractHigh water production in oil fields is an area of concern due to economic issues and borehole/wellhead damages. Colloidal gels can be a good alternative to polymers to address this as they can tolerate harsh oil reservoir conditions. A series of bottle tests with different silica and NaCl concentrations were first conducted. The gelation time, cation valence, rheology, and viscosity were investigated to characterize the gels. The applicability of solid gels in porous media was finally inspected in a dual-patterned glass micromodel. Bottle test results showed that increasing NaCl concentration at a constant silica concentration can convert solid gels into two-phase gels and then viscous suspensions. Na+ replacement with Mg2+ resulted a distinctive behaviour probably due to higher coagulating ability of Mg2+. Rheology and viscosity results agreed with gelation times: gel with shortest gelation time had the highest viscosity and storage/loss modulus but was not the most elastic one. Water injection into glass micromodel half-saturated with crude oil and solid gel proved that the gel is strong against pressure gradients applied by injected phase which is promising for water conformance controls. The diverted injected phase recorded an oil recovery of 53% which was not feasible without blocking the water zone.
iTRAQ-based quantitative proteomic analysis provides insight into the drought-stress response in maize seedlings
Authors: Ren Wen , Shi Zi , Zhou Miaoyi , Zhao Bingbing , Li Hanshuai , Wang Jiarong , Liu Ya , Zhao Jiuran 
Published: June 2022

AbstractDrought is a major abiotic stress that harms plant cell physiology and limits the growth and productivity of crops. Maize (Zea maysL.), one of the most drought-susceptible crops, is a major food source for humans and an important resource for industrial bioenergy production; therefore, understanding the mechanisms of the drought response is essential for maize improvement. Using isotopic tagging relative quantitation (iTRAQ)-based protein labeling technology, we detected the proteomic changes in maize leaves under drought stress. Among the 3063 proteins that were identified, the abundance of 214 and 148 proteins increased and decreased, respectively, after three days of drought treatment. These differentially abundant proteins (DAPs) were mainly involved in cell redox homeostasis, cell wall organization, photosynthesis, abscisic acid biosynthesis, and stress-response processes. Furthermore, some of the DAP abundances still differed from the control six days after the drought treatment, most of which were molecular chaperones, heat shock proteins, metabolism-related enzymes, hydrolases, and transmembrane signal receptors. The expression level of some DAPs returned to normal when the water supply was restored, but for others it did not. A significant correlation between the protein and transcript levels was observed following an RT-qPCR analysis. Finally, our research provides insights into the overall mechanism of drought-stress tolerance, and important information for breeding of drought-tolerant maize.
Development of a DNA barcode library of plants in the Thai Herbal Pharmacopoeia and Monographs for authentication of herbal products
Authors: Urumarudappa Santhosh Kumar J. , Tungphatthong Chayapol , Jaipaew Jirayut , Pornputtapong Natapol , Pakdeesattayapong Duangkamol , Vimolmangkang Sornkanok , Sukrong Suchada 
Published: June 2022

AbstractTraditional herbal medicine has long been practiced as a method of health care in many countries worldwide. The usage of herbal products has been increasing and is expected to continue to do so in the future. However, admixture and adulteration are concerns regarding the quality of herbal medicine, including its safety and efficacy. We aimed to develop a reference DNA barcode library of plants listed in the Thai Herbal Pharmacopoeia (THP) and Monographs of Selected Thai Materia Medica (TMM) (n = 101 plant species) using four core barcode regions, namely, the ITS2, matK, rbcL and trnH-psbA intergenic spacer regions, for authentication of the plant origin of raw materials and herbal products. Checking sequences from samples obtained from local markets and the Thai Food and Drug Administration (Thai FDA) against our digital reference DNA barcode system revealed the authenticity of eighteen out of twenty tested samples as claimed on their labels. Two samples, no. 3 and 13, were not Cyanthillium cinereum (L.) H.Rob. and Pueraria candollei Wall. ex Benth. as claimed, respectively. They were recognized as Emilia sonchifolia (L.) DC. and Butea superba (Roxb.), respectively. Hence, it is important for the Thai FDA or regulatory agencies to immediately initiate strict enforcement for the development of pharmacopoeial standards as well as revisions or modifications of available regulatory guidelines and to implement close monitoring for the quality control of herbal products in terms of authentication before they enter the herbal market. The centralized digital reference DNA barcode database developed here could play a very important role in monitoring or checking the authenticity of medicinal plants.
Hybrid data-driven resilience assessment and enhancement of distribution system for cyclone susceptible zones
Authors: Sonal  , Ghosh Debomita 
Published: June 2022

AbstractThe sprawl of distribution system towards the need of smart grid, demands better sustenance and adaptation strategies to deal with high-impact low-frequency (HILF) events. One of the predominant causes of HILF events are natural calamities. Therefore, the resilience assessment of the distribution system is inevitable. The contributions majorly focuses on hybrid data driven approach using micro-phasor measurement unit (μ-PMU), for dynamic voltage, current phasors monitoring, and unmanned aerial vehicle (UAV) confirms structural vulnerability of nodes within network. Mesh grid approach, which analyses cyclone trajectory affecting the network, supplemented identification of most vulnerable part within network. However, priorities of vulnerable nodes are corroborated using complex network (CN) theory. This hybrid data driven approach and spatial parameters are used to estimate appropriate mitigation strategies against HILF scenarios. Hence, resilience analysis based on location parameters and dynamic network conditions are further analyzed based on degree of correlation of location dependent resilience with latitude, elevation, and probable water level. Based on susceptible vulnerable nodes, identification of optimum alleviation schemes is adopted and justified using resilience trapezoid. To validate efficacy of the proposed approach, the analysis is tested on IEEE 33-bus distribution network subjected to 5 cyclone prone geographical coordinates for 20 years cyclone data.
Next-generation sequencing in advanced Chinese melanoma reveals therapeutic targets and prognostic biomarkers for immunotherapy
Authors: Huang Fuxue , Li Jingjing , Wen Xizhi , Zhu Baoyan , Liu Wei , Wang Jiuhong , Jiang Hang , Ding Ya , Li Dandan , Zhang Xiaoshi 
Published: June 2022

AbstractLimited studies have interrogated the genomic landscape of Chinese melanoma in which acral and mucosal melanoma are the mainstay. In this study, we carried out a retrospective analysis on 81 Chinese melanoma patients (15 acral, 25 mucosal and 41 cutaneous melanoma). With the identification of 1114 mutations spanning 248 genes, we summarized that the mutation spectrum varied significantly by subtypes. Acral melanoma and mucosal melanoma had significantly more CNVs. MYC amplification was one of the most commonly detected CNVs, other frequent CNVs in mucosal melanoma included NBN and KDR, which were associated with the poor survival of melanoma patients. A generally low TMB, with a median of only 5.1 mut/Mb, was observed in three groups including cutaneous melanoma. Additionally, over 50% variants in DNA damage repair pathway were detected in all three subtypes, most of which were HRD related genes. Patients with alterations of HRD related genes had a longer survival time after immunotherapy. This study revealed a molecular profiling of Chinese patients with advanced melanoma, and proposed the high variant rate in DDR pathway as a biomarker of immunotherapy, which might provide therapeutic targets and guidance in making clinical decision for different Chinese melanoma.
An exploratory study of resting-state functional connectivity of amygdala subregions in posttraumatic stress disorder following trauma in adulthood
Authors: Leite Leticia , Esper Nathalia Bianchini , Junior José Roberto M. Lopes , Lara Diogo Rizzato , Buchweitz Augusto 
Published: June 2022

AbstractWe carried out an exploratory study aimed at identifying differences in resting-state functional connectivity for the amygdala and its subregions, right and left basolateral, centromedial and superficial nuclei, in patients with Posttraumatic Stress Disorder (PTSD), relative to controls. The study included 10 participants with PTSD following trauma in adulthood (9 females), and 10 controls (9 females). The results suggest PTSD was associated with a decreased (negative) functional connectivity between the superficial amygdala and posterior brain regions relative to controls. The differences were observed between right superficial amygdala and right fusiform gyrus, and between left superficial amygdala and left lingual and left middle occipital gyri. The results suggest that among PTSD patients, the worse the PTSD symptoms, the lower the connectivity. The results corroborate the fMRI literature that shows PTSD is associated with weaker amygdala functional connectivity with areas of the brain involved in sensory and perceptual processes. The results also suggest that though the patients traumatic experience occured in adulthood, the presence of early traumatic experiences were associated with negative connectivity between the centromedial amygdala and sensory and perceptual regions. We argue that the understanding of the mechanisms of PTSD symptoms, its behaviors and the effects on quality of life of patients may benefit from the investigation of brain function that underpins sensory and perceptual symptoms associated with the disorder.
ICAM-1 related long noncoding RNA is associated with progression of IgA nephropathy and fibrotic changes in proximal tubular cells
Authors: Wen Lu , Zhao Zhanzheng , Li Fanghua , Ji Fengping , Wen Jianguo 
Published: June 2022

AbstractIntercellular adhesion molecule 1 (ICAM-1) related long noncoding RNA (ICR) is on the antisense strand of ICAM-1 and regulates ICAM-1 expression. ICAM-1 is involved in renal tubulointerstitial injury; however, the expression and clinical implication of ICR are not determined in IgA nephropathy (IgAN). We compared renal ICR levels in 337 IgAN patients with those of 89 biopsy controls, and a markedly increased ICR level was observed in IgAN patients. By Cox proportional hazards models, higher levels of renal ICR were independently associated with disease progression event defined as end-stage renal disease or ≥ 40% decline in estimated glomerular filtration rate. Patients in the highest tertile of renal ICR had a 3.5-fold higher risk for disease progression compared with those in the lowest tertile. The addition of renal ICR to a model with traditional risk factors improved risk prediction of disease progression (net reclassification index: 0.31 [95% CI 0.01–0.50]; integrated discrimination index: 0.10 [95% CI 0.04–0.16]). Inhibition of ICR by transfection with plasmids containing ICR shRNA significantly reduced expression of collagen I and α-SMA, and phosphorylation of Akt and mTOR in TGF-β1- treated HK-2 cells. Our findings suggest that renal ICR might be an independent predictor of IgAN progression and contribute to renal fibrosis.