bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of prognostic hub genes and therapeutic targets for selenium deficiency in chicks model through transcriptome profiling
Authors: Lingamgunta Lakshman Kumar , Aloor Bindu Prasuna , Dasari Sreenivasulu , Ramakrishnan Ranjani , Botlagunta Mahendran , Madikonda Ashok Kumar , Gopal Shankar , Sade Ankanna 
Published: May 2023

AbstractSelenium deficiency is a prevalent micronutrient deficiency that poses a major health concern worldwide. This study aimed to shed light on the molecular mechanisms underlying selenium deficiency using a chick model. Chickens were divided into control and selenium deficient groups. Plasma samples were collected to measure selenium concentration and transcriptome analyse were performed on oviduct samples. The results showed that selenium deficiency led to a significant reduction in plasma selenium levels and altered the expression of 10,266 differentially expressed genes (DEGs). These DEGs primarily regulated signal transduction and cell motility. The molecular function includes GTPase regulatory activity, and KEGG pathway analysis showed that they were mainly involved in the signal transduction. By using Cytoscape and CancerGeneNet tool, we identified 8 modules and 10 hub genes (FRK, JUN, PTPRC, ACTA2, MST1R, SDC4, SDC1, CXCL12, MX1 and EZR) associated with receptor tyrosine kinase pathway, Wnt and mTOR signaling pathways that may be closely related to cancer. These hub genes could be served as precise diagnostic and prognostic candidate biomarkers of selenium deficiency and potential targets for treatment strategies in both animals and humans. This study sheds light on the molecular basis of selenium deficiency and its potential impact on public health.
Dephasing by optical phonons in GaN defect single-photon emitters
Authors: Geng Yifei , Luo Jialun , van Deurzen Len , Xing Huili , Jena Debdeep , Fuchs Gregory David , Rana Farhan 
Published: May 2023

AbstractSingle-photon defect emitters (SPEs), especially those with magnetically and optically addressable spin states, in technologically mature wide bandgap semiconductors are attractive for realizing integrated platforms for quantum applications. Broadening of the zero phonon line (ZPL) caused by dephasing in solid state SPEs limits the indistinguishability of the emitted photons. Dephasing also limits the use of defect states in quantum information processing, sensing, and metrology. In most defect emitters, such as those in SiC and diamond, interaction with low-energy acoustic phonons determines the temperature dependence of the dephasing rate and the resulting broadening of the ZPL with the temperature obeys a power law. GaN hosts bright and stable single-photon emitters in the 600–700 nm wavelength range with strong ZPLs even at room temperature. In this work, we study the temperature dependence of the ZPL spectra of GaN SPEs integrated with solid immersion lenses with the goal of understanding the relevant dephasing mechanisms. At temperatures below ~ 50 K, the ZPL lineshape is found to be Gaussian and the ZPL linewidth is temperature independent and dominated by spectral diffusion. Above ~ 50 K, the linewidth increases monotonically with the temperature and the lineshape evolves into a Lorentzian. Quite remarkably, the temperature dependence of the linewidth does not follow a power law. We propose a model in which dephasing caused by absorption/emission of optical phonons in an elastic Raman process determines the temperature dependence of the lineshape and the linewidth. Our model explains the temperature dependence of the ZPL linewidth and lineshape in the entire 10–270 K temperature range explored in this work. The ~ 19 meV optical phonon energy extracted by fitting the model to the data matches remarkably well the ~ 18 meV zone center energy of the lowest optical phonon band ($$E_{2}(low)$$E2(low)) in GaN. Our work sheds light on the mechanisms responsible for linewidth broadening in GaN SPEs. Since a low energy optical phonon band ($$E_{2}(low)$$E2(low)) is a feature of most group III–V nitrides with a wurtzite crystal structure, including hBN and AlN, we expect our proposed mechanism to play an important role in defect emitters in these materials as well.
Kynurenine promotes Calcitonin secretion and reduces cortisol in the Japanese flounder Paralichthys olivaceus
Authors: Ikari Takahiro , Furusawa Yukihiro , Tabuchi Yoshiaki , Maruyama Yusuke , Hattori Atsuhiko , Kitani Yoichiro , Toyota Kenji , Nagami Arata , Hirayama Jun , Watanabe Kazuki , Shigematsu Atsushi , Rafiuddin Muhammad Ahya , Ogiso Shouzo , Fukushi Keisuke , Kuroda Kohei , Hatano Kaito , Sekiguchi Toshio , Kawashima Ryotaro , Srivastav Ajai K. , Nishiuchi Takumi , Sakatoku Akihiro , Yoshida Masa-aki , Matsubara Hajime , Suzuki Nobuo 
Published: May 2023

AbstractDeep ocean water (DOW) exerts positive effects on the growth of marine organisms, suggesting the presence of unknown component(s) that facilitate their aquaculture. We observed that DOW suppressed plasma cortisol (i.e., a stress marker) concentration in Japanese flounder (Paralichthys olivaceus) reared under high-density condition. RNA-sequencing analysis of flounder brains showed that when compared to surface seawater (SSW)-reared fish, DOW-reared fish had lower expression of hypothalamic (i.e., corticotropin-releasing hormone) and pituitary (i.e., proopiomelanocortin, including adrenocorticotropic hormone) hormone-encoding genes. Moreover, DOW-mediated regulation of gene expression was linked to decreased blood cortisol concentration in DOW-reared fish. Our results indicate that DOW activated osteoblasts in fish scales and facilitated the production of Calcitonin, a hypocalcemic hormone that acts as an analgesic. We then provide evidence that the Calcitonin produced is involved in the regulatory network of genes controlling cortisol secretion. In addition, the indole component kynurenine was identified as the component responsible for osteoblast activation in DOW. Furthermore, kynurenine increased plasma Calcitonin concentrations in flounders reared under high-density condition, while it decreased plasma cortisol concentration. Taken together, we propose that kynurenine in DOW exerts a cortisol-reducing effect in flounders by facilitating Calcitonin production by osteoblasts in the scales.
Survey of knowledge, and attitudes to storage practices preempting the occurrence of filamentous fungi and mycotoxins in some Ghanaian staple foods and processed products
Authors: Kortei Nii Korley , Badzi Sandra , Nanga Salifu , Wiafe-Kwagyan Michael , Amon Denick Nii Kotey , Odamtten George Tawia 
Published: May 2023

AbstractMycotoxigenic fungi can infect and produce potent mycotoxins in foodstuffs prior to harvest, during harvest (field fungi), and in storage after harvest (storage fungi), which when ingested, can result in adverse health effects. This study was aimed at assessing the knowledge, attitudes, and practices adopted by the Ghanaian populace to help mitigate the occurrence of molds and mycotoxins in foods. A cross-sectional survey involving a structured questionnaire was conducted with 642 respondents from twelve regions of Ghana. Descriptive statistics and analyses of variance were calculated. Correct Classification Rate (CCR) was measured to assess the utility of a logistic regression model. The results of the study showed that the majority of 299 (46.6%) of the respondents were between the ages of 18–25. Age and educational level were related to knowledge about the occurrence of fungi and mycotoxins in foods (p < 0.05). More than half the respondents, 50% indicated that they knew of aflatoxins as a major mycotoxin present in food. Higher education directly influenced on the knowledge of mycotoxicosis and the management of stored food to present intoxication by fungal metabolites. 502 (32.9%) knew that consuming foods with toxins could cause stomach aches. The most commonly consumed food commodity despite the presence of visible growth of fungi was bread (35.3%). The average KAP score for knowledge showed that, out of 100%, there was adequate knowledge (63.8%) among the members of the Ghanaian populace. Favorable environmental conditions of high humidity (> 85% ERH) and temperature (> 28–32 °C) enhance the proliferation of fungi in most foods and the attendant production of mycotoxins such as aflatoxins, ochratoxins, and fumonisins are associated with several severe human and animal health conditions; mycotoxicosis was associated with high fever, pain, vomiting, suppression of immunity, cancer, etc. when these foods are consumed on regular basis for a prolonged length of time. Future examination of the food items used for the School Feeding Programme in Ghana will offer opportunities to examine the risks of feeding youth with fungal-contaminated food preparations from providers.
BAIAP2L2 is a novel prognostic biomarker related to migration and invasion of HCC and associated with cuprotosis
Authors: Wei Hui , Yang Jing , Chen Xia , Liu Mengxiao , Zhang Huiyun , Sun Weiming , Wang Yuping , Zhou Yongning 
Published: May 2023

AbstractHepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, and its pathophysiological mechanisms remain unknown. IRSp53 family members, such as BAIAP2L1, participate in the progression of multiple tumors. However, the role of BAIAP2L2 in HCC remains unclear. This study comprehensively analyzed the potential role of BAIAP2L2 in HCC using bioinformatic techniques. The expression of BAIAP2L2 in HCC was analyzed using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), International Cancer Genome Consortium (ICGC), and Human Protein Atlas (HPA) databases and in vitro experiments. In addition, the prognostic value of BAIAP2L2 in HCC was analyzed using the TCGA database. TCGA and GEO database were used to analyze the role of BAIAP2L2 in immune features. We also explored the function of BAIAP2L2 in methylation and cuprotosis. The CellMiner database was used to analyze the relationship between BAIAP2L2 expression and drug sensitivity. Our study revealed that BAIAP2L2 is overexpressed in HCC and promotes the migration and invasion of HCC cells. BAIAP2L2 may affect the prognosis of HCC by regulating immunity, methylation, and cuprotosis. BAIAP2L2 is a novel HCC prognostic gene involved in immune infiltration associated with cuprotosis and may be a potential prognosis and therapeutic target for HCC.
Bending mechanics test and parameters calibration of ramie stalks
Authors: Si Shuning , Zhang Bin , Huang Jicheng , Shen Cheng , Tian Kunpeng , Liu Haolu , Zhang Yuanyuan 
Published: May 2023

AbstractResearch and development of ramie harvesting equipment is a key link to revitalize ramie industry, problems such as the tendency of stalks to tangle and clog the machine are very problematic, seriously affect the quality and fluency of the harvester. The structure of ramie stalk is complex, and the mechanical properties of each component vary greatly, collision between stalk and machine creates complex stress relationship. By building a finite element model, it is possible to analyze the stress state of the stalk during bending from a microscopic perspective, and to analyze the complex stress–strain situation within the stalk. The purpose of this paper is to establish a standard ramie stalk bending finite element model to provide a theoretical basis for the subsequent kinematics and dynamics. Firstly, material experiments were carried out on ramie straw. The structural and mechanical parameters of the straw components were obtained through measurement and calculation tests, and the force–deformation curves for straw bending were obtained. Bending finite element simulations were carried out on the basis of mechanical tests, and the parameters such as dynamic friction coefficient, wood Poisson's ratio and bast Poisson's ratio were determined by the central combination design. Then established an accurate bending finite element simulation model of ramie stalk, the accuracy of the model was verified at the end. In this paper, the key parameters of the ramie stalk model were calibrated through a combination of material tests and simulations. All parameters of the ramie stalk model were finally obtained, and the bending mechanical properties of the ramie stalk were analysed by applying finite element analysis. This bending mechanics simulation model can be used for kinematic and dynamics simulation analysis of conveying and baling to provide a theoretical basis for the structural design of the harvester. The methods explored here can be applied to other slender straw crops.
Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally
Authors: Lim Jinhwan , Shioda Toshihiro , Malott Kelli F. , Shioda Keiko , Odajima Junko , Leon Parada Kathleen N. , Nguyen Julie , Getze Samantha , Lee Melody , Nguyen Jonathon , Reshel Blakeley Samantha , Trinh Vienna , Truong Hong-An , Luderer Ulrike 
Published: May 2023

AbstractPeople are widely exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP). Prior studies showed that prenatal exposure to BaP depletes germ cells in ovaries, causing earlier onset of ovarian senescence post-natally; developing testes were affected at higher doses than ovaries. Our primary objective was to determine if prenatal BaP exposure results in transgenerational effects on ovaries and testes. We orally dosed pregnant germ cell-specific EGFP-expressing mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5–11.5 (F1 offspring) or E6.5–15.5 (F2 and F3). Ovarian germ cells at E13.5 and follicle numbers at postnatal day 21 were significantly decreased in F3 females at all doses of BaP; testicular germ cell numbers were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Next, we compared the ovarian effects of 2 mg/kg-day BaP dosing to wild type C57BL/6J F0 dams from E6.5–11.5 or E12.5–17.5. We observed no effects on F3 ovarian follicle numbers with either of the shorter dosing windows. Our results demonstrate that F0 BaP exposure from E6.5–15.5 decreased the number of and partially disrupted transcriptomic sexual identity of female germ cells transgenerationally.
An artificial neural network-based radiomics model for predicting the radiotherapy response of advanced esophageal squamous cell carcinoma patients: a multicenter study
Authors: Xie Yuchen , Liu Qiang , Ji Chao , Sun Yuchen , Zhang Shuliang , Hua Mingyu , Liu Xueting , Pan Shupei , Hu Weibin , Ma Yanfang , Wang Ying , Zhang Xiaozhi 
Published: May 2023

AbstractRadiotherapy benefits patients with advanced esophageal squamous cell carcinoma (ESCC) in terms of symptom relief and long-term survival. In contrast, a substantial proportion of ESCC patients have not benefited from radiotherapy. This study aimed to establish and validate an artificial neural network-based radiomics model for the pretreatment prediction of the radiotherapy response of advanced ESCC by using integrated data combined with feasible baseline characteristics of computed tomography. A total of 248 patients with advanced ESCC who underwent baseline CT and received radiotherapy were enrolled in this study and were analyzed by two types of radiomics models, machine learning and deep learning. As a result, the Att. Resnet50 pretrained network model indicated superior performance, with AUCs of 0.876, 0.802 and 0.732 in the training, internal validation, and external validation cohorts, respectively. Similarly, our Att. Resnet50 pretrained network model showed excellent calibration and significant clinical benefit according to the C index and decision curve analysis. Herein, a novel pretreatment radiomics model was established based on deep learning methods and could be used for radiotherapy response prediction in advanced ESCC patients, thus providing reliable evidence for therapeutic decision-making.
Fuel-cell parameter estimation based on improved gorilla troops technique
Authors: Shaheen Abdullah , El-Sehiemy Ragab , El-Fergany Attia , Ginidi Ahmed 
Published: May 2023

AbstractThe parameter extraction of the proton exchange membrane fuel cells (PEMFCs) is an active study area over the past few years to achieve accurate current/voltage (I/V) curves. This work proposes an advanced version of an improved gorilla troops technique (IGTT) to precisely estimate the PEMFC’s model parameters. The GTT's dual implementation of the migration approach enables boosting the exploitation phase and preventing becoming trapped in the local minima. Besides, a Tangent Flight Strategy (TFS) is incorporated with the exploitation stage for efficiently searching the search space. Using two common PEMFCs stacks of BCS 500W, and Modular SR-12, the developed IGTT is effectively applied. Furthermore, the two models are evaluated under varied partial temperature and pressure. In addition to this, different new recently inspired optimizers are employed for comparative validations namely supply demand optimization (SDO), flying foxes optimizer (FFO) and red fox optimizer (RFO). Also, a comparative assessment of the developed IGTT and the original GTT are tested to ten unconstrained benchmark functions following to the Congress on Evolutionary Computation (CEC) 2017. The proposed IGTT outperforms the standard GTT, grey wolf algorithm (GWA) and Particle swarm optimizer (PSO) in 92.5%, 87.5% and 92.5% of the statistical indices. Moreover, the viability of the IGTT is proved in comparison to various previously published frameworks-based parameter's identification of PEMFCs stacks. The obtained sum of squared errors (SSE) and the standard deviations (STD) are among the difficult approaches in this context and are quite competitive. For the PEMFCs stacks being studied, the developed IGTT achieves exceedingly small SSE values of 0.0117 and 0.000142 for BCS 500 and SR-12, respectively. Added to that, the IGTT gives superior performance compared to GTT, SDO, FFO and RFO obtaining the smallest SSE objective with the least STD ever.
Removing the association of random gene sets and survival time in cancers with positive random bias using fixed-point gene set
Authors: Maghsoudi Maryam , Aghdam Rosa , Eslahchi Changiz 
Published: May 2023

AbstractCancer research aims to identify genes that cause or control disease progression. Although a wide range of gene sets have been published, they are usually in poor agreement with one another. Furthermore, recent findings from a gene-expression cohort of different cancer types, known as positive random bias, showed that sets of genes chosen randomly are significantly associated with survival time much higher than expected. In this study, we propose a method based on Brouwer’s fixed-point theorem that employs significantly survival-associated random gene sets and reveals a small fixed-point gene set for cancers with a positive random bias property. These sets significantly correspond to cancer-related pathways with biological relevance for the progression and metastasis of the cancer types they represent. Our findings show that our proposed significant gene sets are biologically related to each cancer type available in the cancer genome atlas with the positive random bias property, and by using these sets, positive random bias is significantly more reduced in comparison with state-of-the-art methods in this field. The random bias property is removed in 8 of these 17 cancer types, and the number of random sets of genes associated with survival time is significantly reduced in the remaining 9 cancers.
Optically modified second harmonic generation in silicon oxynitride thin films via local layer heating
Authors: Lukeš Jakub , Kanclíř Vít , Václavík Jan , Melich Radek , Fuchs Ulrike , Žídek Karel 
Published: May 2023

AbstractStrong second harmonic generation (SHG) in silicon nitride has been extensively studied—among others, in terms of laser-induced SHG enhancement in Si3N4 waveguides. This enhancement has been ascribed to the all-optical poling induced by the coherent photogalvanic effect. Yet, an analogous process for Si3N4 thin films has not been reported. Our article reports on the observation of laser-induced threefold SHG enhancement in Si3N4 thin films. The observed enhancement has many features similar to all-optical poling, such as highly nonlinear power dependence, cumulative effect, or connection to the Si3N4–Si interface. However, identical experiments for low-oxygen silicon oxynitride thin films lead to complex behavior, including laser-induced SHG reduction. Following a thorough experimental study, including the effects of repetition rate or pulse length, the observed results were ascribed to heat-induced SHG variation. In addition to revealing a new mechanism of laser-induced SHG variation, our results also provide a means to identify this mechanism.
Structural insights into the bi-specific cross-over dual variable antibody architecture by cryo-EM
Authors: Fernandez-Martinez David , Tully Mark D. , Leonard Gordon , Mathieu Magali , Kandiah Eaazhisai 
Published: May 2023

AbstractMulti-specific antibodies (msAbs) are being developed as next generation antibody-based therapeutics. Knowledge of the three-dimensional structures, in the full antibody context, of their fragment antigen-binding (Fab) moieties with or without bound antigens is key to elucidating their therapeutic efficiency and stability. However, the flexibility of msAbs, a feature essential for their multi specificity, has hindered efforts in this direction. Cross-Over Dual Variable immunoglobulin (CODVIg) is a promising bispecific antibody format, designed to simultaneously target the interleukins IL4 and IL13. In this work we present the biophysical and structural characterisation of a CODVFab:IL13 complex in the full antibody context, using cryo-electron microscopy at an overall resolution of 4.2 Å. Unlike the 1:2 stoichiometry previously observed for CODVIg:IL4, CODVIg:IL13 shows a 1:1 stoichiometry. As well as providing details of the IL13-CODV binding interface, including the residues involved in the epitope-paratope region, the structure of CODVFab:IL13 also validates the use of labelling antibody as a new strategy for the single particle cryo-EM study of msAbs in complex with one, or more, antigens. This strategy reduced the inherent flexibility of the IL13 binding domain of CODV without inducing either structural changes at the epitope level or steric hindrance between the IL4 and IL13 binding regions of CODVIg. The work presented here thus also contributes to the development of methodology for the structural study of msAbs, a promising platform for cancer immunotherapy.