bluuebunny/crossref_metadata_2025_split huggingface dataset:
MDMA treatment paired with a trauma-cue promotes adaptive stress responses in a translational model of PTSD in rats
Authors: Arluk Shira , Matar Michael A. , Carmi Lior , Arbel Oded , Zohar Joseph , Todder Doron , Cohen Hagit 
Published: May 2022

AbstractMDMA (3,4-methylenedioxymethamphetamine), a synthetic ring-substituted amphetamine, combined with psychotherapy has demonstrated efficacy for the treatment of chronic posttraumatic stress disorder (PTSD) patients. This controlled prospective study aimed to assess the bio-behavioral underpinnings of MDMA in a translational model of PTSD. Rats exposed to predator-scent stress (PSS) were subjected to a trauma-cue at day 7 shortly after single-dose MDMA injection (5 mg/kg). The elevated plus maze and acoustic startle response tests were assessed on day 14 and served for classification into behavioral response groups. Freezing response to a further trauma-reminder was assessed on Day 15. The morphological characteristics of the dentate gyrus (DG) and basolateral amygdala (BLA) were subsequently examined. Hypothalamic–pituitary–adrenal axis and 5-hydroxytryptamine involvement were evaluated using: (1) corticosterone measurements at 2 h and 4 h after MDMA treatment, (2) Lewis strain rats with blunted HPA-response and (3) pharmacological receptor-blockade. MDMA treatment was effective in attenuating stress behavioral responses only when paired with memory reactivation by a trauma-cue. The effects of the treatment on behavior were associated with a commensurate normalization of the dendritic cytoarchitecture of DG and BLA neurons. Pretreatment with RU486, Ketanserin, or Pindolol prevented the above improvement in anxiety-like behavioral responses. MDMA treatment paired with memory reactivation reduced the prevalence rate of PTSD-phenotype 14 days later and normalized the cytoarchitecture changes induced by PSS (in dendritic complexities) compared to saline control. MDMA treatment paired with a trauma-cue may modify or update the original traumatic memory trace through reconsolidation processes. These anxiolytic-like effects seem to involve the HPA axis and 5-HT systems.
Anti-epileptic drugs and prostate cancer-specific mortality compared to non-users of anti-epileptic drugs in the Finnish Randomized Study of Screening for Prostate Cancer
Authors: Salminen Jukka K. , Mehtola Aino , Talala Kirsi , Taari Kimmo , Mäkinen Jussi , Peltola Jukka , Tammela Teuvo L. J. , Auvinen Anssi , Murtola Teemu J. 
Published: May 2022

Abstract
Background
Drugs with histone deacetylase inhibitory (HDACi) properties have shown to decrease prostate cancer (PCa) cell growth in vitro.

Methods
A cohort of 9261 PCa cases from the Finnish Randomized Study of Screening for Prostate Cancer (FinRSPC) was used to evaluate prostate cancer-specific mortality in men using anti-epileptic drugs (AEDs). A national subscription database was used to obtain information on medication use. Cox regression with AED use as a time-dependent variable was used to analyse prostate cancer mortality in men using AEDs compared to non-users, and in men using HDACi AEDs compared to users of other AEDs. The analysis was adjusted for age, screening trial arm, PCa risk group, primary treatment of PCa, Charlson co-morbidity score and concomitant use of other drugs.

Results
The use of AEDs, in general, was associated with an increased risk of PCa death. The use of HDACi AEDs was not significantly associated with decreased PCa mortality compared to use of other AEDs (HR 0.61, 95% CI 0.31–1.23).

Conclusions
AED usage is associated with elevated PCa mortality compared to non-users, likely reflecting the differences between men with epilepsy and those without. No benefit was observed from HDACi drugs compared to other AEDs.
Non-drug efflux function of ABCC5 promotes enzalutamide resistance in castration-resistant prostate cancer via upregulation of P65/AR-V7
Authors: Chen Haojie , Luo Jia , Chen Shaojun , Shi Bowen , Zheng Xiaocui , Ji Haiying , Zhang Xiaoqian , Yin Yujia , Du Kun , Ding Jie , Yu Yongjiang 
Published: May 2022

AbstractDrug resistance is responsible for castration-resistant prostate cancer (CRPC)-associated mortality. While ATP binding cassette subfamily C member 5 (ABCC5) has been reported to regulate multiple drug resistance, its drug-efflux function may not be the main reason underlying resistance to enzalutamide, an androgen receptor inhibitor. Here, we aimed to determine whether the non-drug efflux function of ABCC5 affects enzalutamide resistance. The ABCC5 expression data in patients with prostate cancer (PCa) were retrieved from The Cancer Genome Atlas and Gene Expression Omnibus, and their correlation with disease prognosis was analyzed. Immunohistochemical staining was performed on a cohort of 80 patient samples. Proliferation of enzalutamide-resistant 22RV1 and C4-2B cells was investigated using CCK-8, EdU, and colony formation assays. The effect of ABCC5 silencing on enzalutamide resensitization was evaluated in vitro and in vivo. Functional assays indicated that ABCC5 depletion resensitized enzalutamide-resistant cells to inhibit cell growth and impeded xenograft tumor proliferation. Mechanistically, luciferase and ChIP assays confirmed that P65 regulated AR expression and activity by binding to its promoter, while ABCC5-mediated resistance effected by AR-V7 (one of the widely studied AR splicing variants that meditate AR antagonist resistance) upregulation could be reversed by P65 knockdown. Furthermore, activation of the NF-κB pathway reversed the effects of ABCC5 knockdown by extra AR-V7 expression. Thus, ABCC5 might be a novel target for enzalutamide-resistant CRPC treatment.
Diagnostic accuracy of different keratoconus detection indices of pentacam in paediatric eyes
Authors: Hashem Ahmed Osama , Aziz Bassem Fayez , Wahba Sherine Shafik , Roshdy Maged Maher , Elawamry Amr Ismail 
Published: May 2022

AbstractObjectiveNo diagnostic gold standard for keratoconus in children and adolescents exists. Our objective was investigating the diagnostic accuracy of various indices for keratoconus (KC) detection in paediatric eyes.MethodsAll retrievable data of significance from 432 normal right paediatric eyes and 48 eyes of paediatric KC and forme fruste KC (FFKC), imaged by use of a rotating Scheimpflug camera (Oculyzer II, Pentacam HR) between December 2013 and October 2018 at Watany Eye Hospitals, Cairo, Egypt, including Scheimpflug images data, were collected. The area under the receiver operating characteristic curve (AUROC) was calculated for different indices in this retrospective descriptive study.ResultsAll 36 tested indices showed discriminative power differentiating KC and FFKC from normal corneas (AUROCP-value <0.05), except AC volume, AC angle, and horizontal decentrations of the steepest and thinnest points. The 32 indices showed variable degrees of diagnostic accuracy. The highest AUROC was that of the corneal assessment index from the relational thickness and other OCULUS values (CAIRO 8). Only 8 indices showed non-inferiority to it, namely, Ambrosio’s relational thickness maximum (ART max) and avg, the pachymetric progression index maximum (PPI max) and avg, the back elevation from the best-fit toric ellipsoid (BE BFTE), the KC index (KI), the topographic KC indices (TKC), and the index of height decentration (IHD) (P > 0.05).ConclusionsThe 8 most useful rotating Scheimpflug imaging indices for KC detection in paediatric eyes are CAIRO 8 followed by ART max and avg, PPI max and avg, BE BFTE, KI, TKC, and IHD.
Alterations in homologous recombination repair genes in prostate cancer brain metastases
Authors: Rodriguez-Calero Antonio , Gallon John , Akhoundova Dilara , Maletti Sina , Ferguson Alison , Cyrta Joanna , Amstutz Ursula , Garofoli Andrea , Paradiso Viola , Tomlins Scott A. , Hewer Ekkehard , Genitsch Vera , Fleischmann Achim , Vassella Erik , Rushing Elisabeth J. , Grobholz Rainer , Fischer Ingeborg , Jochum Wolfram , Cathomas Gieri , Osunkoya Adeboye O. , Bubendorf Lukas , Moch Holger , Thalmann George , Ng Charlotte K. Y. , Gillessen Silke , Piscuoglio Salvatore , Rubin Mark A. 
Published: May 2022

AbstractImproved survival rates for prostate cancer through more effective therapies have also led to an increase in the diagnosis of metastases to infrequent locations such as the brain. Here we investigate the repertoire of somatic genetic alterations present in brain metastases from 51 patients with prostate cancer brain metastases (PCBM). We highlight the clonal evolution occurring in PCBM and demonstrate an increased mutational burden, concomitant with an enrichment of the homologous recombination deficiency mutational signature in PCBM compared to non-brain metastases. Focusing on known pathogenic alterations within homologous recombination repair genes, we find 10 patients (19.6%) fulfilling the inclusion criteria used in the PROfound clinical trial, which assessed the efficacy of PARP inhibitors (PARPi) in homologous recombination deficient prostate cancer. Eight (15.7%) patients show biallelic loss of one of the 15 genes included in the trial, while 5 patients (9.8%) harbor pathogenic alterations in BRCA1/2 specifically. Uncovering these molecular features of PCBM may have therapeutic implications, suggesting the need of clinical trial enrollment of PCBM patients when evaluating potential benefit from PARPi.
Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry
Authors: D’Ascenzo Luigi , Popova Anna M. , Abernathy Scott , Sheng Kai , Limbach Patrick A. , Williamson James R. 
Published: May 2022

AbstractMass spectrometry is an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. The main features of Pytheas are flexible handling of isotope labeling and RNA modifications, with false discovery rate statistical validation based on sequence decoys. We demonstrate bottom-up mass spectrometry characterization of diverse RNA sequences, with broad applications in the biology of stable RNAs, and quality control of RNA therapeutics and mRNA vaccines.
Crystal structures of BMPRII extracellular domain in binary and ternary receptor complexes with BMP10
Authors: Guo Jingxu , Liu Bin , Thorikay Midory , Yu Minmin , Li Xiaoyan , Tong Zhen , Salmon Richard M. , Read Randy J. , ten Dijke Peter , Morrell Nicholas W. , Li Wei 
Published: May 2022

AbstractHeterozygous mutations in BMPR2 (bone morphogenetic protein (BMP) receptor type II) cause pulmonary arterial hypertension. BMPRII is a receptor for over 15 BMP ligands, but why BMPR2 mutations cause lung-specific pathology is unknown. To elucidate the molecular basis of BMP:BMPRII interactions, we report crystal structures of binary and ternary BMPRII receptor complexes with BMP10, which contain an ensemble of seven different BMP10:BMPRII 1:1 complexes. BMPRII binds BMP10 at the knuckle epitope, with the A-loop and β4 strand making BMPRII-specific interactions. The BMPRII binding surface on BMP10 is dynamic, and the affinity is weaker in the ternary complex than in the binary complex. Hydrophobic core and A-loop interactions are important in BMPRII-mediated signalling. Our data reveal how BMPRII is a low affinity receptor, implying that forming a signalling complex requires high concentrations of BMPRII, hence mutations will impact on tissues with highest BMPR2 expression such as the lung vasculature.
Auto-generated database of semiconductor band gaps using ChemDataExtractor
Authors: Dong Qingyang , Cole Jacqueline M. 
Published: May 2022

AbstractLarge-scale databases of band gap information about semiconductors that are curated from the scientific literature have significant usefulness for computational databases and general semiconductor materials research. This work presents an auto-generated database of 100,236 semiconductor band gap records, extracted from 128,776 journal articles with their associated temperature information. The database was produced using ChemDataExtractor version 2.0, a ‘chemistry-aware’ software toolkit that uses Natural Language Processing (NLP) and machine-learning methods to extract chemical data from scientific documents. The modified Snowball algorithm of ChemDataExtractor has been extended to incorporate nested models, optimized by hyperparameter analysis, and used together with the default NLP parsers to achieve optimal quality of the database. Evaluation of the database shows a weighted precision of 84% and a weighted recall of 65%. To the best of our knowledge, this is the largest open-source non-computational band gap database to date. Database records are available in CSV, JSON, and MongoDB formats, which are machine readable and can assist data mining and semiconductor materials discovery.
A database of refractive indices and dielectric constants auto-generated using ChemDataExtractor
Authors: Zhao Jiuyang , Cole Jacqueline M. 
Published: May 2022

AbstractThe ability to auto-generate databases of optical properties holds great potential for advancing optical research, especially with regards to the data-driven discovery of optical materials. An optical property database of refractive indices and dielectric constants is presented, which comprises a total of 49,076 refractive index and 60,804 dielectric constant data records on 11,054 unique chemicals. The database was auto-generated using the state-of-the-art natural language processing software, ChemDataExtractor, using a corpus of 388,461 scientific papers. The data repository offers a representative overview of the information on linear optical properties that resides in scientific papers from the past 30 years. Public availability of these data will enable a quick search for the optical property of certain materials. The large size of this repository will accelerate data-driven research on the design and prediction of optical materials and their properties. To the best of our knowledge, this is the first auto-generated database of optical properties from a large number of scientific papers. We provide a web interface to aid the use of our database.
A critical period for learning and plastic changes at hippocampal CA1 synapses
Authors: Sakimoto Yuya , Shintani Ako , Yoshiura Daiki , Goshima Makoto , Kida Hiroyuki , Mitsushima Dai 
Published: May 2022

AbstractPostnatal development of hippocampal function has been reported in many mammalian species, including humans. To obtain synaptic evidence, we analyzed developmental changes in plasticity after an inhibitory avoidance task in rats. Learning performance was low in infants (postnatal 2 weeks) but clearly improved from the juvenile period (3–4 weeks) to adulthood (8 weeks). One hour after the training, we prepared brain slices and sequentially recorded miniature excitatory postsynaptic currents (mEPSCs) and inhibitory postsynaptic currents (mIPSCs) from the same hippocampal CA1 neuron. Although the training failed to affect the amplitude of either mEPSCs or mIPSCs at 2 weeks, it increased mEPSC, but not mIPSC, amplitude at 3 weeks. At 4 weeks, the training had increased the amplitude of both mEPSCs and mIPSCs, whereas mIPSC, but not mEPSC, amplitude was increased at 8 weeks. Because early-life physiological functions can affect performance, we also evaluated sensory–motor functions together with emotional state and found adequate sensory/motor functions from infancy to adulthood. Moreover, by analyzing performance of rats in multiple hippocampal-dependent tasks, we found that the developmental changes in the performance are task dependent. Taken together, these findings delineate a critical period for learning and plastic changes at hippocampal CA1 synapses.
Functional identification of microRNA-centered complexes in C. elegans
Authors: Hebbar Shilpa , Panzade Ganesh , Vashisht Ajay A. , Wohlschlegel James A. , Veksler-Lublinsky Isana , Zinovyeva Anna Y. 
Published: May 2022

AbstractmicroRNAs (miRNAs) are crucial for normal development and physiology. To identify factors that might coordinate with miRNAs to regulate gene expression, we used 2′O-methylated oligonucleotides to precipitateCaenorhabditis eleganslet-7, miR-58, and miR-2 miRNAs and the associated proteins. A total of 211 proteins were identified through mass-spectrometry analysis of miRNA co-precipitates, which included previously identified interactors of key miRNA pathway components. Gene ontology analysis of the identified interactors revealed an enrichment for RNA binding proteins, suggesting that we captured proteins that may be involved in mRNA lifecycle. To determine which miRNA interactors are important for miRNA activity, we used RNAi to deplete putative miRNA co-factors in animals with compromised miRNA activity and looked for alterations of the miRNA mutant phenotypes. Depletion of 25 of 39 tested genes modified the miRNA mutant phenotypes in three sensitized backgrounds. Modulators of miRNA phenotypes ranged from RNA binding proteins RBD-1 and CEY-1 to metabolic factors such as DLST-1 and ECH-5, among others. The observed functional interactions suggest widespread coordination of these proteins with miRNAs to ultimately regulate gene expression. This study provides a foundation for future investigations aimed at deciphering the molecular mechanisms of miRNA-mediated gene regulation.
Association between circulating CD34-positive cell count and height loss among older men
Authors: Shimizu Yuji , Kawashiri Shin-Ya , Nobusue Kenichi , Nonaka Fumiaki , Tamai Mami , Honda Yukiko , Yamanashi Hirotomo , Nakamichi Seiko , Kiyama Masahiko , Hayashida Naomi , Nagata Yasuhiro , Maeda Takahiro 
Published: May 2022

AbstractHeight loss starting in middle age is reportedly significantly associated with death due to cardiovascular disease. Impaired blood flow is the main pathology in cardiovascular disease. Hematopoietic stem cells such as CD34-positive cells play an important role in maintaining the microcirculation and preventing impaired blood flow by activating endothelial repair and angiogenesis. Therefore, circulating CD34-positive cell count could be associated with height loss. To clarify the association between circulating CD34-positive cell count and height loss, we conducted a follow-up study of 363 Japanese men aged 60–69 years over 2 years. Height loss was defined as being in the highest quartile of height decrease per year. Independent of known cardiovascular risk factors, circulating CD34-positive cell count was significantly inversely associated with height loss. The fully adjusted odds ratio (OR) and 95% confidence interval (CI) of height loss for circulating CD34-positive cell count (logarithmic values) was 0.49 (0.32, 0.74). This study suggests that a lower capacity to maintain the microcirculation due to a fewer CD34-positive cells might affect height loss.
Influence of ionizing radiation and cell density on the kinetics of autocrine destruction and intercellular induction of apoptosis in precancerous cells
Authors: Abdelrazzak Abdelrazek B. , O’Neill Peter , Hill Mark A. 
Published: May 2022

AbstractIntercellular induction of apoptosis (IIA) represents a well-defined signaling model by which precancerous cells are selectively eradicated through reactive oxygen/nitrogen species and cytokine signaling from neighbour normal cells. Previously, we demonstrated that the IIA process could be enhanced by exposure of normal cells to very low doses of ionizing radiation as a result of perturbing the intercellular signaling. In this study, we investigate the kinetic behaviour of both autocrine destruction (AD) and IIA as a function of cell density of both precancerous and normal cells using an insert co-culture system and how exposure of normal cells to ionizing radiation influence the kinetics of apoptosis induction in precancerous cells. Increasing the seeding density of transformed cells shifts the kinetics of AD towards earlier times with the response plateauing only at high seeding densities. Likewise, when co-culturing precancerous cells with normal cells, increasing the seeding density of either normal or precancerous cells also shifts the kinetics of IIA response towards earlier times and plateau only at higher seeding densities. Irradiation of normal cells prior to co-culture further enhances the kinetics of IIA response, with the degree of enhancement dependent on the relative cell densities. These results demonstrate the pivotal role of the cell seeding density of normal and precancerous cells in modulating both AD and IIA. These results further support the proposition that ionizing radiation could result in an enhancement in the rate of removal of precancerous cells through the IIA process.
Intelligent modeling and optimization of titanium surface etching for dental implant application
Authors: Sadati Tilebon Seyyed Mohamad , Emamian Seyed Amirhossein , Ramezanpour Hosseinali , Yousefi Hashem , Özcan Mutlu , Naghib Seyed Morteza , Zare Yasser , Rhee Kyong Yop 
Published: May 2022

AbstractAcid-etching is one of the most popular processes for the surface treatment of dental implants. In this paper, acid-etching of commercially pure titanium (cpTi) in a 48% H2SO4 solution is investigated. The etching process time (0–8 h) and solution temperature (25–90 °C) are assumed to be the most effective operational conditions to affect the surface roughness parameters such as arithmetical mean deviation of the assessed profile on the surface (Ra) and average of maximum peak to valley height of the surface over considered length profile (Rz), as well as weight loss (WL) of the dental implants in etching process. For the first time, three multilayer perceptron artificial neural network (MLP-ANN) with two hidden layers was optimized to predict Ra, Rz, and WL. MLP is a feedforward class of ANN and ANN model that involves computations and mathematics which simulate the human–brain processes. The ANN models can properly predict Ra, Rz, and WL variations during etching as a function of process temperature and time. Moreover, WL can be increased to achieve a high Ra. At WL = 0, Ra of 0.5 μm is obtained, whereas Ra increases to 2 μm at WL = 0.78 μg/cm2. Also, ANN model was fed into a nonlinear sorting genetic algorithm (NSGA-II) to establish the optimization process and the ability of this method has been proven to predict the optimized etching conditions.