bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distributed implantation of a flexible microelectrode array for neural recording
Authors: Wei Chunrong , Wang Yang , Pei Weihua , Han Xinyong , Lin Longnian , Liu Zhiduo , Ming Gege , Chen Ruru , Wu Pingping , Yang Xiaowei , Zheng Li , Wang Yijun 
Published: May 2022

AbstractFlexible multichannel electrode arrays (fMEAs) with multiple filaments can be flexibly implanted in various patterns. It is necessary to develop a method for implanting the fMEA in different locations and at various depths based on the recording demands. This study proposed a strategy for reducing the microelectrode volume with integrated packaging. An implantation system was developed specifically for semiautomatic distributed implantation. The feasibility and convenience of the fMEA and implantation platform were verified in rodents. The acute and chronic recording results provied the effectiveness of the packaging and implantation methods. These methods could provide a novel strategy for developing fMEAs with more filaments and recording sites to measure functional interactions across multiple brain regions.
Examining the variability of neurocognitive functioning in individuals at clinical high risk for psychosis: a meta-analysis
Authors: Catalan Ana , Radua Joaquim , McCutcheon Robert , Aymerich Claudia , Pedruzo Borja , González-Torres Miguel Ángel , Baldwin Helen , Stone William S. , Giuliano Anthony J. , McGuire Philip , Fusar-Poli Paolo 
Published: May 2022

AbstractThis study aims to meta-analytically characterize the presence and magnitude of within-group variability across neurocognitive functioning in young people at Clinical High-Risk for psychosis (CHR-P) and comparison groups. Multistep, PRISMA/MOOSE-compliant systematic review (PROSPERO-CRD42020192826) of the Web of Science database, Cochrane Central Register of Reviews and Ovid/PsycINFO and trial registries up to July 1, 2020. The risk of bias was assessed using a modified version of the NOS for cohort and cross-sectional studies. Original studies reporting neurocognitive functioning in individuals at CHR-P compared to healthy controls (HC) or first-episode psychosis (FEP) patients were included. The primary outcome was the random-effect meta-analytic variability ratios (VR). Secondary outcomes included the coefficient of variation ratios (CVR). Seventy-eight studies were included, relating to 5162 CHR-P individuals, 2865 HC and 486 FEP. The CHR-P group demonstrated higher variability compared to HC (in descending order of magnitude) in visual memory (VR: 1.41, 95% CI 1.02–1.94), executive functioning (VR: 1.31, 95% CI 1.18–1.45), verbal learning (VR: 1.29, 95% CI 1.15–1.45), premorbid IQ (VR: 1.27, 95% CI 1.09–1.49), processing speed (VR: 1.26, 95% CI 1.07–1.48), visual learning (VR: 1.20, 95% CI 1.07–1.34), and reasoning and problem solving (VR: 1.17, 95% CI 1.03–1.34). In the CVR analyses the variability in CHR-P population remains in the previous neurocognitive domains and emerged in attention/vigilance, working memory, social cognition, and visuospatial ability. The CHR-P group transitioning to psychosis showed greater VR in executive functioning compared to those not developing psychosis and compared to FEP groups. Clinical high risk for psychosis subjects shows increased variability in neurocognitive performance compared to HC. The main limitation of this study is the validity of the VR and CVR as an index of variability which has received debate. This finding should be explored by further individual-participant data research and support precision medicine approaches.
snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology
Authors: Huang Zheng-hao , Du Yu-ping , Wen Jing-tao , Lu Bing-feng , Zhao Yang 
Published: May 2022

AbstractSmall nucleolar RNAs (snoRNAs), a type of non-coding RNA, are widely present in the nucleoli of eukaryotic cells and play an important role in rRNA modification. With the recent increase in research on snoRNAs, new evidence has emerged indicating that snoRNAs also participate in tRNA and mRNA modification. Studies suggest that numerous snoRNAs, including tumor-promoting and tumor-suppressing snoRNAs, are not only dysregulated in tumors but also show associations with clinical prognosis. In this review, we summarize the reported functions of snoRNAs and the possible mechanisms underlying their role in tumorigenesis and cancer development to guide the snoRNA-based clinical diagnosis and treatment of cancer in the future.
Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
Authors: Fröhlich Klemens , Brombacher Eva , Fahrner Matthias , Vogele Daniel , Kook Lucas , Pinter Niko , Bronsert Peter , Timme-Bronsert Sylvia , Schmidt Alexander , Bärenfaller Katja , Kreutz Clemens , Schilling Oliver 
Published: May 2022

AbstractNumerous software tools exist for data-independent acquisition (DIA) analysis of clinical samples, necessitating their comprehensive benchmarking. We present a benchmark dataset comprising real-world inter-patient heterogeneity, which we use for in-depth benchmarking of DIA data analysis workflows for clinical settings. Combining spectral libraries, DIA software, sparsity reduction, normalization, and statistical tests results in 1428 distinct data analysis workflows, which we evaluate based on their ability to correctly identify differentially abundant proteins. From our dataset, we derive bootstrap datasets of varying sample sizes and use the whole range of bootstrap datasets to robustly evaluate each workflow. We find that all DIA software suites benefit from using a gas-phase fractionated spectral library, irrespective of the library refinement used. Gas-phase fractionation-based libraries perform best against two out of three reference protein lists. Among all investigated statistical tests non-parametric permutation-based statistical tests consistently perform best.
Mechanical loading of intraluminal pressure mediates wound angiogenesis by regulating the TOCA family of F-BAR proteins
Authors: Yuge Shinya , Nishiyama Koichi , Arima Yuichiro , Hanada Yasuyuki , Oguri-Nakamura Eri , Hanada Sanshiro , Ishii Tomohiro , Wakayama Yuki , Hasegawa Urara , Tsujita Kazuya , Yokokawa Ryuji , Miura Takashi , Itoh Toshiki , Tsujita Kenichi , Mochizuki Naoki , Fukuhara Shigetomo 
Published: May 2022

AbstractAngiogenesis is regulated in coordinated fashion by chemical and mechanical cues acting on endothelial cells (ECs). However, the mechanobiological mechanisms of angiogenesis remain unknown. Herein, we demonstrate a crucial role of blood flow-driven intraluminal pressure (IP) in regulating wound angiogenesis. During wound angiogenesis, blood flow-driven IP loading inhibits elongation of injured blood vessels located at sites upstream from blood flow, while downstream injured vessels actively elongate. In downstream injured vessels, F-BAR proteins, TOCA1 and CIP4, localize at leading edge of ECs to promote N-WASP-dependent Arp2/3 complex-mediated actin polymerization and front-rear polarization for vessel elongation. In contrast, IP loading expands upstream injured vessels and stretches ECs, preventing leading edge localization of TOCA1 and CIP4 to inhibit directed EC migration and vessel elongation. These data indicate that the TOCA family of F-BAR proteins are key actin regulatory proteins required for directed EC migration and sense mechanical cell stretching to regulate wound angiogenesis.
Diurnal changes in the efficiency of information transmission at a sensory synapse
Authors: Moya-Díaz José , James Ben , Esposti Federico , Johnston Jamie , Lagnado Leon 
Published: May 2022

AbstractNeuromodulators adapt sensory circuits to changes in the external world or the animal’s internal state and synapses are key control sites for such plasticity. Less clear is how neuromodulation alters the amount of information transmitted through the circuit. We investigated this question in the context of the diurnal regulation of visual processing in the retina of zebrafish, focusing on ribbon synapses of bipolar cells. We demonstrate that contrast-sensitivity peaks in the afternoon accompanied by a four-fold increase in the average Shannon information transmitted from an active zone. This increase reflects higher synaptic gain, lower spontaneous “noise” and reduced variability of evoked responses. Simultaneously, an increase in the probability of multivesicular events with larger information content increases the efficiency of transmission (bits per vesicle) by factors of 1.5-2.7. This study demonstrates the multiplicity of mechanisms by which a neuromodulator can adjust the synaptic transfer of sensory information.
Dual-resolving of positional and geometric isomers of C=C bonds via bifunctional photocycloaddition-photoisomerization reaction system
Authors: Feng Guifang , Gao Ming , Wang Liwei , Chen Jiayi , Hou Menglu , Wan Qiongqiong , Lin Yun , Xu Guoyong , Qi Xiaotian , Chen Suming 
Published: May 2022

AbstractThe biological functions of lipids largely depend on their chemical structures. The position and configuration of C=C bonds are two of the essential attributes that determine the structures of unsaturated lipids. However, simultaneous identification of both attributes remains challenging. Here, we develop a bifunctional visible-light-activated photocycloaddition-photoisomerization reaction system, which enables the dual-resolving of the positional and geometric isomerism of C=C bonds in lipids when combines with liquid chromatography-mass spectrometry. The dual-pathway reaction mechanism is demonstrated by experiments and density functional theory calculations. Based on this bifunctional reaction system, a workflow of deep structural lipidomics is established, and allows the revealing of unique patterns of cis-trans-isomers in bacteria, as well as the tracking of C=C positional isomers changes in mouse brain ischemia. This study not only offers a powerful tool for deep lipid structural biology, but also provides a paradigm for developing the multifunctional visible-light-induced reaction.
Understanding the complementarities of surface-enhanced infrared and Raman spectroscopies in CO adsorption and electrochemical reduction
Authors: Chang Xiaoxia , Vijay Sudarshan , Zhao Yaran , Oliveira Nicholas J. , Chan Karen , Xu Bingjun 
Published: May 2022

AbstractIn situ/operando surface enhanced infrared and Raman spectroscopies are widely employed in electrocatalysis research to extract mechanistic information and establish structure-activity relations. However, these two spectroscopic techniques are more frequently employed in isolation than in combination, owing to the assumption that they provide largely overlapping information regarding reaction intermediates. Here we show that surface enhanced infrared and Raman spectroscopies tend to probe different subpopulations of adsorbates on weakly adsorbing surfaces while providing similar information on strongly binding surfaces by conducting both techniques on the same electrode surfaces, i.e., platinum, palladium, gold and oxide-derived copper, in tandem. Complementary density functional theory computations confirm that the infrared and Raman intensities do not necessarily track each other when carbon monoxide is adsorbed on different sites, given the lack of scaling between the derivatives of the dipole moment and the polarizability. Through a comparison of adsorbed carbon monoxide and water adsorption energies, we suggest that differences in the infrared vs. Raman responses amongst metal surfaces could stem from the competitive adsorption of water on weak binding metals. We further determined that only copper sites capable of adsorbing carbon monoxide in an atop configuration visible to the surface enhanced infrared spectroscopy are active in the electrochemical carbon monoxide reduction reaction.
Monte Carlo study of the pseudogap and superconductivity emerging from quantum magnetic fluctuations
Authors: Jiang Weilun , Liu Yuzhi , Klein Avraham , Wang Yuxuan , Sun Kai , Chubukov Andrey V. , Meng Zi Yang 
Published: May 2022

AbstractThe origin of the pseudogap behavior, found in many high-Tc superconductors, remains one of the greatest puzzles in condensed matter physics. One possible mechanism is fermionic incoherence, which near a quantum critical point allows pair formation but suppresses superconductivity. Employing quantum Monte Carlo simulations of a model of itinerant fermions coupled to ferromagnetic spin fluctuations, represented by a quantum rotor, we report numerical evidence of pseudogap behavior, emerging from pairing fluctuations in a quantum-critical non-Fermi liquid. Specifically, we observe enhanced pairing fluctuations and a partial gap opening in the fermionic spectrum. However, the system remains non-superconducting until reaching a much lower temperature. In the pseudogap regime the system displays a “gap-filling" rather than “gap-closing" behavior, similar to the one observed in cuprate superconductors. Our results present direct evidence of the pseudogap state, driven by superconducting fluctuations.
Constructing chemical stable 4-carboxyl-quinoline linked covalent organic frameworks via Doebner reaction for nanofiltration
Authors: Yang Yongliang , Yu Ling , Chu Tiancheng , Niu Hongyun , Wang Jun , Cai Yaqi 
Published: May 2022

AbstractCovalent linkages are the key component of covalent organic frameworks (COFs). The development of stable and functional linkages is essential to expand the COFs family and broaden their application prospects. In this work, we report the synthesis of crystalline and chemical stable 4-carboxyl-quinoline linked COFs (QL-COFs) via Doebner reactions in both one-pot (OP) and post-synthetic modification (PSM) methods. Both methods can be universally applied to most of the reported imine COFs family via bottom-up construction or linkage conversion. Owing to the contractive pore size, more hydrophilic structure and better chemical stability than the conventional imine COFs endowed by 4-carboxyl-quinoline linkage, QL-COFs are supposed to possess a wider application range. We further demonstrate the nanofiltration membrane (NFM) based on QL-COF exhibited a desirable separation capacity with high rejection for small dye molecules (> 90%), high water permeance (850 L m−2 h−1 MPa−1) and tolerance of extreme conditions (1 M HCl/NaOH), which were benefitted from the enhanced properties of QL-COFs. Additionally, efficient ion sieving properties were also achieved by QL-COF membrane. We anticipate that this work opens up a way for the construction of robust and functional COFs materials for practical applications.
Direct synthesis of highly stretchable ceramic nanofibrous aerogels via 3D reaction electrospinning
Authors: Cheng Xiaota , Liu Yi-Tao , Si Yang , Yu Jianyong , Ding Bin 
Published: May 2022

AbstractCeramic aerogels are attractive for many applications due to their ultralow density, high porosity, and multifunctionality but are limited by the typical trade-off relationship between mechanical properties and thermal stability when used in extreme environments. In this work, we design and synthesize ceramic nanofibrous aerogels with three-dimensional (3D) interwoven crimped-nanofibre structures that endow the aerogels with superior mechanical performances and high thermal stability. These ceramic aerogels are synthesized by a direct and facile route, 3D reaction electrospinning. They display robust structural stability with structure-derived mechanical ultra-stretchability up to 100% tensile strain and superior restoring capacity up to 40% tensile strain, 95% bending strain and 60% compressive strain, high thermal stability from −196 to 1400 °C, repeatable stretchability at working temperatures up to 1300 °C, and a low thermal conductivity of 0.0228 W m−1 K−1 in air. This work would enable the innovative design of high-performance ceramic aerogels for various applications.
Accelerated identification of equilibrium structures of multicomponent inorganic crystals using machine learning potentials
Authors: Kang Sungwoo , Jeong Wonseok , Hong Changho , Hwang Seungwoo , Yoon Youngchae , Han Seungwu 
Published: May 2022

AbstractThe discovery of multicomponent inorganic compounds can provide direct solutions to scientific and engineering challenges, yet the vast uncharted material space dwarfs synthesis throughput. While the crystal structure prediction (CSP) may mitigate this frustration, the exponential complexity of CSP and expensive density functional theory (DFT) calculations prohibit material exploration at scale. Herein, we introduce SPINNER, a structure-prediction framework based on random and evolutionary searches. Harnessing speed and accuracy of neural network potentials (NNPs), the program navigates configurational spaces 102–103 times faster than DFT-based methods. Furthermore, SPINNER incorporates algorithms tuned for NNPs, achieving performances exceeding conventional algorithms. In blind tests on 60 ternary compositions, SPINNER identifies experimental (or theoretically more stable) phases for ~80% of materials. When benchmarked against data-mining or DFT-based evolutionary predictions, SPINNER identifies more stable phases in many cases. By developing a reliable and fast structure-prediction framework, this work paves the way to large-scale, open exploration of undiscovered inorganic crystals.
A smart ball sensor fabricated by laser kirigami of graphene for personalized long-term grip strength monitoring
Authors: Zhang Huiqing , Ding Xin , Zhang Xiongwen , Xu Feng 
Published: May 2022

AbstractGrip strength is an important indicator of health conditions and needs to be monitored for health management. However, different populations (e.g., babies and rehabilitation patients) have different hand sizes and different levels of grip strengths, requiring a personalized sensor to monitor grip strength. In this paper, we developed a smart ball sensor by laser kirigami of graphene for personalized grip strength monitoring. To realize the rational utilization of space, a transparent pill shell embedding all electronic accessories is installed in the center of the ball sensor with a spiral-sensing unit fabricated by laser kirigami of graphene on the surface. Furthermore, we assessed the influence of contact area between hand and ball on grip strength using finite-element analysis (FEA), which was then considered in our results readout. The grip strength can be continuously read by a mobile phone in a wireless manner. The smart ball sensor demonstrated a high performance in vitro against gold-standard method in diseased and healthy subjects. It would be a powerful tool for personalized long-term monitoring of grip strength, especially suitable for specific populations such as babies and sensitive enough for samll grip strength.
Parkinson’s disease clinical milestones and mortality
Authors: Gonzalez Maria Camila , Dalen Ingvild , Maple-Grødem Jodi , Tysnes Ole-Bjørn , Alves Guido 
Published: May 2022

AbstractIdentification of factors predicting and driving mortality in PD is important for patient information, disease management, and design of future clinical trials. This study included newly diagnosed PD patients and normal controls (NC) from a population-based study with repeated assessments over a 10-year period. We used the Kaplan–Meier method to estimate survival, Cox proportional hazards regression models to identify baseline risk factors of mortality, and Cox regression models with time-dependent covariates to evaluate the impact of four clinical milestones of advanced PD (visual hallucinations, recurrent falls, dementia, and nursing home placement) on mortality risk. During the 10-year study, 65 (34.2%) of 190 patients and 25 (12.3%) of 203 NC died, with an unadjusted hazard ratio (HR) of 2.85 (95% CI 1.80–4.52) and a HR of 2.48 (95% CI 1.55–3.95) when adjusted for confounders, including comorbidities. Higher age, more severe motor impairment, and postural instability-gait difficulty (PIGD) phenotype were independent baseline predictors of mortality. Each clinical milestone alone more than doubled the risk of death and had a cumulative effect on mortality, with a HR of 10.83 (95% CI 4.39–26.73) in those experiencing all four milestones. PD patients have an increased mortality risk that is disease-related and becomes evident early during the course of the disease. While motor severity and PIGD phenotype were early risk factors of mortality, clinical milestones signaled a substantially increased risk of death later during the disease course, highlighting their potential significance in clinical disease staging and prognosis.
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes
Authors: Malhan Deeksha , Basti Alireza , Relógio Angela 
Published: May 2022

AbstractEmerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin’s lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTLKO), SNW1 (in NR1D1KO), and HNRNPC (in PER2KO), which led to a differential pattern of KO-specific AS events. All HCT116KO cells showed a rhythmicity loss of a crucial spliceosome gene U2AF1, which was also not rhythmic in higher progression stage CRC and HL cancer cells. AS analysis revealed an increase in alternative first exon events specific to PER2 and NR1D1 KO in HCT116 cells, and a KO-specific change in expression and rhythmicity pattern of AS transcripts related to cancer hallmarks genes including FGFR2 in HCT116_ARNTLKO, CD44 in HCT116_NR1D1KO, and MET in HCT116_PER2KO. KO-specific changes in rhythmic properties of known spliced variants of these genes (e.g. FGFR2 IIIb/FGFR2 IIIc) correlated with epithelial-mesenchymal-transition signalling. Altogether, our bioinformatic analysis highlights a role for the circadian clock in the regulation of AS, and reveals a potential impact of clock disruption in aberrant splicing in cancer hallmark genes.