bluuebunny/crossref_metadata_2025_split huggingface dataset:
A significant, functional and replicable risk KTN1 variant block for schizophrenia
Authors: Mao Qiao , Lin Xiandong , Yin Qin , Liu Ping , Zhang Yong , Qu Shihao , Xu Jianying , Cheng Wenhong , Luo Xinqun , Kang Longli , Taximaimaiti Reyisha , Zheng Chengchou , Zhang Huihao , Wang Xiaoping , Ren Honggang , Cao Yuping , Lin Jie , Luo Xingguang 
Published: March 2023

AbstractCortical and subcortical structural alteration has been extensively reported in schizophrenia, including the unusual expansion of gray matter volumes (GMVs) of basal ganglia (BG), especially putamen. Previous genome-wide association studies pinpointed kinectin 1 gene (KTN1) as the most significant gene regulating the GMV of putamen. In this study, the role of KTN1 variants in risk and pathogenesis of schizophrenia was explored. A dense set of SNPs (n = 849) covering entire KTN1 was analyzed in three independent European- or African-American samples (n = 6704) and one mixed European and Asian Psychiatric Genomics Consortium sample (n = 56,418 cases vs. 78,818 controls), to identify replicable SNP-schizophrenia associations. The regulatory effects of schizophrenia-associated variants on the KTN1 mRNA expression in 16 cortical or subcortical regions in two European cohorts (n = 138 and 210, respectively), the total intracranial volume (ICV) in 46 European cohorts (n = 18,713), the GMVs of seven subcortical structures in 50 European cohorts (n = 38,258), and the surface areas (SA) and thickness (TH) of whole cortex and 34 cortical regions in 50 European cohorts (n = 33,992) and eight non-European cohorts (n = 2944) were carefully explored. We found that across entire KTN1, only 26 SNPs within the same block (r2 > 0.85) were associated with schizophrenia across ≥ 2 independent samples (7.5 × 10–5 ≤ p ≤ 0.048). The schizophrenia-risk alleles, which increased significantly risk for schizophrenia in Europeans (q < 0.05), were all minor alleles (f < 0.5), consistently increased (1) the KTN1 mRNA expression in 12 brain regions significantly (5.9 × 10–12 ≤ p ≤ 0.050; q < 0.05), (2) the ICV significantly (6.1 × 10–4 ≤ p ≤ 0.008; q < 0.05), (3) the SA of whole (9.6 × 10–3 ≤ p ≤ 0.047) and two regional cortices potentially (2.5 × 10–3 ≤ p ≤ 0.042; q > 0.05), and (4) the TH of eight regional cortices potentially (0.006 ≤ p ≤ 0.050; q > 0.05), and consistently decreased (1) the BG GMVs significantly (1.8 × 10–19 ≤ p ≤ 0.050; q < 0.05), especially putamen GMV (1.8 × 10–19 ≤ p ≤ 1.0 × 10–4; q < 0.05, (2) the SA of four regional cortices potentially (0.010 ≤ p ≤ 0.048), and (3) the TH of four regional cortices potentially (0.015 ≤ p ≤ 0.049) in Europeans. We concluded that we identified a significant, functional, and robust risk variant block covering entire KTN1 that might play a critical role in the risk and pathogenesis of schizophrenia.
Preparation of gypsum with high purity and whiteness from phosphogypsum for CO2 mineral sequestration
Authors: Zhang Man , Fan Xing 
Published: March 2023

AbstractPhosphogypsum (PG) is a solid waste product generated during wet-process phosphoric acid production. Various impurities considerably reduce the purity, whiteness, and application range of PG. This article analyzes the physical properties of PG in detail and systematically examines the content and distribution of impurities. Based on the obtained results, a simple process for the efficient removal of almost all impurities in the PG is proposed. The purity and whiteness of the purified gypsum (CaSO4) significantly increased to 99% and 92%, respectively. The migration of impurities and the material balance of this process were then analyzed. Most importantly, the purified gypsum showed high CO2 sequestration efficiency for CO2 mineral sequestration, through which a high value-added CaCO3 product was obtained.
Clinical parameters predictors of malignant transformation of recurrent parotid pleomorphic adenoma
Authors: Pei Yu , Li Wenlu 
Published: March 2023

AbstractMalignant transformation (MT) in recurrent parotid pleomorphic adenomas (PAs) is rare; therefore its occurrence lacks reliable predictive factors. Our goal was to clarify the predictors for MT of recurrent parotid PAs based on preoperative clinical parameters. Patients with a clinical diagnosis of recurrent parotid PA were retrospectively enrolled. The association between clinicopathologic variables and MT of PA was assessed using univariate and multivariate analyses. MT occurred in 11.8% of the 467 patients. In univariate analysis, three or more previous recurrences, newly developed facial nerve paralysis, difficulty in mouth opening, tumors with the largest tumor diameter ≥ 2.4 cm, and abnormal neck lymph node enlargement were associated with MT occurrence. Further, multivariate analysis showed that three or more previous recurrences, newly developed facial nerve paralysis, difficulty in mouth opening, and abnormal neck lymph node enlargement were independently related to MT. MT of recurrent PA was not uncommon. Clinical signs of malignancy included newly developed facial nerve paralysis, difficulty in mouth opening, three or more previous recurrences, and abnormal neck lymph node enlargement.
Group refractive index via auto-differentiation and neural networks
Authors: Alagappan G. , Png C. E. 
Published: March 2023

AbstractIn this article, using principles of automatic differentiation, we demonstrate a generic deep learning representation of group refractive index for photonic channel waveguides. It enables evaluation of group refractive indices in a split of second, without any traditional numerical calculations. Traditionally, the group refractive index is calculated by a repetition of the optical mode calculations via a parametric wavelength sweep of finite difference (or element) calculations. To the direct contrary, in this work, we show that the group refractive index can be quasi-instantaneously obtained from the auto-gradients of the neural networks that models the effective refractive index. We embed the wavelength dependence of the effective index in the deep learning model by applying the scaling property of the Maxwell’s equations and this eliminates the problems caused by the curse of dimensionality. This work portrays a very clear illustration on how physics-based derived optical quantities can be calculated instantly from the underlying deep learning models of the parent quantities using automatic differentiation.
Quantum causality emerging in a delayed-choice quantum Cheshire Cat experiment with neutrons
Authors: Wagner Richard , Kersten Wenzel , Lemmel Hartmut , Sponar Stephan , Hasegawa Yuji 
Published: March 2023

AbstractWe report an experiment with neutrons in a silicon perfect crystal interferometer, that realizes a quantum Cheshire Cat in a delayed choice setting. In our setup the quantum Cheshire Cat is established by spatially separating the particle and its property (i.e. the neutron and its spin) into the two different paths of the interferometer. The condition for a delayed choice setting is achieved by postponing the choice of path assignment for the quantum Cheshire Cat, i.e. which path is taken by the particle and which by its property, until the point in time when the neutron wave function has already split and entered the interferometer. The results of the experiment suggest not only the fact that the neutrons and its spin are separated and take different paths in the interferometer, but also quantum-mechanical causality is implied, insomuch that the behavior of a quantum system is affected by the choice of the selection at a later point in time.
Identification of two early blood biomarkers ACHE and CLEC12A for improved risk stratification of critically ill COVID-19 patients
Authors: Kattner Simone , Müller Jan , Glanz Karolina , Manoochehri Mehdi , Sylvester Caroline , Vainshtein Yevhen , Berger Marc Moritz , Brenner Thorsten , Sohn Kai 
Published: March 2023

AbstractIn order to identify biomarkers for earlier prediction of COVID-19 outcome, we collected blood samples from patients with fatal outcomes (non-survivors) and with positive clinical outcomes (survivors) at ICU admission and after seven days. COVID-19 survivors and non-survivors showed significantly different transcript levels for 93 genes in whole blood already at ICU admission as revealed by RNA-Seq. These differences became even more pronounced at day 7, resulting in 290 differentially expressed genes. Many identified genes play a role in the differentiation of hematopoietic cells. For validation, we designed an RT-qPCR assay for C-type lectin domain family 12 member A (CLEC12A) and acetylcholinesterase (ACHE), two transcripts that showed highest potential to discriminate between survivors and non-survivors at both time points. Using our combined RT-qPCR assay we examined 33 samples to accurately predict patient survival with an AUROC curve of 0.931 (95% CI = 0.814–1.000) already at ICU admission. CLEC12A and ACHE showed improved prediction of patient outcomes compared to standard clinical biomarkers including CRP and PCT in combination (AUROC = 0.403, 95% CI = 0.108–0.697) or SOFA score (AUROC = 0.701 95% CI = 0.451–0.951) at day 0. Therefore, analyzing CLEC12A and ACHE gene expression from blood may provide a promising approach for early risk stratification of severely ill COVID-19 patients.
Post-fumigation sub-lethal activities of phosphine and ethyl formate on survivorship, fertility and female sex pheromone production of Callosobruchus chinensis (L.)
Authors: Chiluwal Kashinath , Lee Byung Ho , Kwon Tae Hyung , Kim Junheon , Park Chung Gyoo 
Published: March 2023

AbstractPhosphine (PH3) and ethyl formate (EF), the two popular fumigant disinfectants of stored product insect pests, are primarily evaluated for their knock down effects without considering their post-fumigation sub-lethal activities. The sub-lethal activities (adult survivorship, fecundity, sterility and female sex pheromone production) of the fumigants were evaluated on a field-to-storage insect pest adzuki bean beetle, Callosobruchus chinensis (L.). The adults’ survivorship and female fecundity, both were dose-dependently affected by sub-lethal PH3 and EF fumigation exposures. Hatchability of the eggs laid by fumigated female adults were also significantly affected. Gas-chromatography mass-spectrometry analysis of solid-phase micro-extraction from virgin fumigated C. cinensis females revealed that the PH3 LC25 (the lethal concentration required to kill the 25% of the population) fumigated female C. chinensis released significantly less amount of the pheromone components. In contrast, EF LC25 exposure did not affect the pheromone release. This study unveils the facts that the EF and PH3 fumigation have detrimental bioactivities against C. chinensis. Notably, this suggests to consider the sub-lethal EF and PH3 fumigation rather than the dose required to instantly kill all the C. chinensis individuals for disinfestation of stored adzuki bean.
Functional interaction between Vangl2 and N-cadherin regulates planar cell polarization of the developing neural tube and cochlear sensory epithelium
Authors: Nagaoka Tadahiro , Katsuno Tatsuya , Fujimura Kyoka , Tsuchida Kunihiro , Kishi Masashi 
Published: March 2023

AbstractAlthough the core constituents of the Wnt/planar cell polarity (PCP) signaling have been extensively studied, their downstream molecules and protein–protein interactions have not yet been fully elucidated. Here, we show genetic and molecular evidence that the PCP factor, Vangl2, functionally interacts with the cell–cell adhesion molecule, N-cadherin (also known as Cdh2), for typical PCP-dependent neural development. Vangl2 and N-cadherin physically interact in the neural plates undergoing convergent extension. Unlike monogenic heterozygotes, digenic heterozygous mice with Vangl2 and Cdh2 mutants exhibited defects in neural tube closure and cochlear hair cell orientation. Despite this genetic interaction, neuroepithelial cells derived from the digenic heterozygotes did not show additive changes from the monogenic heterozygotes of Vangl2 in the RhoA–ROCK–Mypt1 and c-Jun N-terminal kinase (JNK)–Jun pathways of Wnt/PCP signaling. Thus, cooperation between Vangl2 and N-cadherin is at least partly via direct molecular interaction; it is essential for the planar polarized development of neural tissues but not significantly associated with RhoA or JNK pathways.
Reliable cell retention of mammalian suspension cells in microfluidic cultivation chambers
Authors: Schmitz Julian , Stute Birgit , Täuber Sarah , Kohlheyer Dietrich , von Lieres Eric , Grünberger Alexander 
Published: March 2023

AbstractMicrofluidic cultivation, with its high level of environmental control and spatio-temporal resolution of cellular behavior, is a well-established tool in today’s microfluidics. Yet, reliable retention of (randomly) motile cells inside designated cultivation compartments still represents a limitation, which prohibits systematic single-cell growth studies. To overcome this obstacle, current approaches rely on complex multilayer chips or on-chip valves, which makes their application for a broad community of users infeasible. Here, we present an easy-to-implement cell retention concept to withhold cells inside microfluidic cultivation chambers. By introducing a blocking structure into a cultivation chamber’s entrance and nearly closing it, cells can be manually pushed into the chamber during loading procedures but are unable to leave it autonomously in subsequent long-term cultivation. CFD simulations as well as trace substance experiments confirm sufficient nutrient supply within the chamber. Through preventing recurring cell loss, growth data obtained from Chinese hamster ovary cultivation on colony level perfectly match data determined from single-cell data, which eventually allows reliable high throughput studies of single-cell growth. Due to its transferability to other chamber-based approaches, we strongly believe that our concept is also applicable for a broad range of cellular taxis studies or analyses of directed migration in basic or biomedical research.
A framework for multi-sensor satellite data to evaluate crop production losses: the case study of 2022 Pakistan floods
Authors: Qamer Faisal Mueen , Abbas Sawaid , Ahmad Bashir , Hussain Abid , Salman Aneel , Muhammad Sher , Nawaz Muhammad , Shrestha Sravan , Iqbal Bilal , Thapa Sunil 
Published: March 2023

AbstractIn August 2022, one of the most severe floods in the history of Pakistan was triggered due to the exceptionally high monsoon rainfall. It has affected ~ 33 million people across the country. The agricultural losses in the most productive Indus plains aggravated the risk of food insecurity in the country. As part of the loss and damage (L&D) assessment methodologies, we developed an approach for evaluating crop-specific post-disaster production losses based on multi-sensor satellite data. An integrated assessment was performed using various indicators derived from pre- and post-flood images of Sentinel-1 (flood extent mapping), Sentinel-2 (crop cover), and GPM (rainfall intensity measurements) to evaluate crop-specific losses. The results showed that 2.5 million ha (18% of Sindh’s total area) was inundated out of which 1.1 million ha was cropland. The remainder of crop damage came from the extreme rainfall downpour, flash floods and management deficiencies. Thus approximately 57% (2.8 million ha) of the cropland was affected out of the 4.9 million ha of agricultural area in Sindh. The analysis indicated expected production losses of 88% (3.1 million bales), 80% (1.8 million tons), and 61% (10.5 million tons) for cotton, rice, and sugarcane. This assessment provided useful tools to evaluate the L&D of agricultural production and to develop evidence-based policies enabling post-flood recovery, rehabilitation of people and restoration of livelihood.
Suppression of CEBPδ recovers exhaustion in anti-metastatic immune cells
Authors: Yin Chenxue , Kato Masayoshi , Tomita Takeshi , Han Yibing , Hiratsuka Sachie 
Published: March 2023

AbstractThe pre-metastatic microenvironment consists of pro-metastatic and anti-metastatic immune cells in the early stages of cancer, when the primary tumor begins to proliferate. Redundantly, pro-inflammatory immune cells predominated during tumor growth. Although it is well known that pre-metastatic innate immune cells and immune cells fighting primary tumor cells become exhausted, the mechanism by which this occurs is unknown. We discovered that anti-metastatic NK cells were mobilized from the liver to the lung during primary tumor progression and that the transcription factor CEBPδ, which was upregulated in a tumor-stimulated liver environment, inhibited NK cell attachment to the fibrinogen-rich bed in pulmonary vessels and sensitization to the environmental mRNA activator. CEBPδ-siRNA treated anti-metastatic NK cells regenerated the binding proteins that support sitting in fibrinogen-rich soil, such as vitronectin and thrombospondin, increasing fibrinogen attachment. Furthermore, CEBPδ knockdown restored an RNA-binding protein, ZC3H12D, which captured extracellular mRNA to increase tumoricidal activity. Refreshed NK cells using CEBPδ-siRNA with anti-metastatic abilities would work at metastatic risk areas in the pre-metastatic phase, resulting in a reduction in lung metastasis. Furthermore, tissue-specific siRNA-based therapy in lymphocyte exhaustion may be beneficial in the treatment of early metastases.
The distribution of submerged macrophytes in response to intense solar radiation and salinity reveals hydrogen peroxide as an abiotic stress indicator
Authors: Asaeda Takashi , Rashid Md Harun , Liping Xia , Vamsi-Krishna Lekkala , Barnuevo Abner , Takeuchi Chihiro , Rahman Mizanur 
Published: March 2023

AbstractThe feasible condition for submerged macrophyte growth is hard to understand as many environmental factors contribute to establishing macrophyte distribution with different intensities generating excess reactive oxygen species (ROS). Among various kinds of ROS, hydrogen peroxide (H2O2) is relatively stable and can be measured accurately. Thus, for the quantification of submerged macrophyte species, H2O2 can be used to evaluate their distribution in a lake. Submerged macrophytes, such as Potamogeton anguillanus, were abundant in Lake Shinji. The largest biomass distribution was around 1.35 m deep, under low solar radiation intensity, and nearly no biomass was found less than 0.3 m deep, where solar radiation was high. Tissue H2O2 concentrations varied in response to the diurnal photosynthetically active radiation (PAR) intensity, which was followed by antioxidant activities, though slightly delayed. Laboratory experiments were conducted with different PAR intensities or salinity concentrations. A stable level of H2O2 was maintained up to about 200 μmol m−2 s−1 of PAR for 30 days, followed by a gradual increase as PAR increased. The H2O2 concentration increased with higher salinity. A change in Chlorophyll a (Chl-a) concentration is associated with an altering H2O2 concentration, following a unique negative relationship with H2O2 concentration. If H2O2 exceeded 45 μmol/gFW, the homeostasis collapsed, and H2O2 and Chl-a significantly declined afterward. The above findings indicate that H2O2 has a negative effect on the physiological condition of the plant. The increase in H2O2 concentration was prevented by antioxidant activities, which elevated with increasing H2O2 concentration.
A CAD system for automatic dysplasia grading on H&E cervical whole-slide images
Authors: Oliveira Sara P. , Montezuma Diana , Moreira Ana , Oliveira Domingos , Neto Pedro C. , Monteiro Ana , Monteiro João , Ribeiro Liliana , Gonçalves Sofia , Pinto Isabel M. , Cardoso Jaime S. 
Published: March 2023

AbstractCervical cancer is the fourth most common female cancer worldwide and the fourth leading cause of cancer-related death in women. Nonetheless, it is also among the most successfully preventable and treatable types of cancer, provided it is early identified and properly managed. As such, the detection of pre-cancerous lesions is crucial. These lesions are detected in the squamous epithelium of the uterine cervix and are graded as low- or high-grade intraepithelial squamous lesions, known as LSIL and HSIL, respectively. Due to their complex nature, this classification can become very subjective. Therefore, the development of machine learning models, particularly directly on whole-slide images (WSI), can assist pathologists in this task. In this work, we propose a weakly-supervised methodology for grading cervical dysplasia, using different levels of training supervision, in an effort to gather a bigger dataset without the need of having all samples fully annotated. The framework comprises an epithelium segmentation step followed by a dysplasia classifier (non-neoplastic, LSIL, HSIL), making the slide assessment completely automatic, without the need for manual identification of epithelial areas. The proposed classification approach achieved a balanced accuracy of 71.07% and sensitivity of 72.18%, at the slide-level testing on 600 independent samples, which are publicly available upon reasonable request.
Effect of bedding dip angle and dynamic load on spatial variation of microscopic failure stress of shale
Authors: Wang Miaomiao , Shao Xiaozhou , Pan Xiaohua 
Published: March 2023

AbstractPhysico-mechanical properties of shale are important parameters in evaluating the stability of potential wellbore and the design of hydraulic fracturing, which are primarily affected by their non-uniform spatial distribution of the microscopic physical–mechanical properties at particle scale. A series of constant strain rate experiments and stress-cycling experiments on shale specimens with different bedding dip angles were conducted to have a comprehensive understanding of the effect of the non-uniform distribution of microscopic failure stress on macroscopic physico-mechanical properties. According to the experimental results and Weibull distribution, we find that bedding dip angle and the dynamic load applying type affect the spatial distributions of microscopic failure stress. The values of crack damage stress (σcd), σcd/σucs (peak stress), εcd (strain at crack damage stress), Poissons' ratio (ν), elastic strain energy (Ue) and dissipated energy (Uirr) of the specimens with more uniform distribution of microscopic failure stress are overall higher, while εucs (peak strain)/εcd and elastic modulus (E) are lower. The dynamic load enables the spatial distributions of microscopic failure stress trend to be more homogeneous prior to the final failure with the increment of σcd/σucs, ν, Ue and Uirr and the decrement of E.
Exponential increase of transition rates in metastable systems driven by non-Gaussian noise
Authors: Baule Adrian , Sollich Peter 
Published: March 2023

AbstractNoise-induced escape from metastable states governs a plethora of transition phenomena in physics, chemistry, and biology. While the escape problem in the presence of thermal Gaussian noise has been well understood since the seminal works of Arrhenius and Kramers, many systems, in particular living ones, are effectively driven by non-Gaussian noise for which the conventional theory does not apply. Here we present a theoretical framework based on path integrals that allows the calculation of both escape rates and optimal escape paths for a generic class of non-Gaussian noises. We find that non-Gaussian noise always leads to more efficient escape and can enhance escape rates by many orders of magnitude compared with thermal noise, highlighting that away from equilibrium escape rates cannot be reliably modelled based on the traditional Arrhenius–Kramers result. Our analysis also identifies a new universality class of non-Gaussian noises, for which escape paths are dominated by large jumps.