bluuebunny/crossref_metadata_2025_split huggingface dataset:
The critical roles of histone deacetylase 3 in the pathogenesis of solid organ injury
Authors: Ning Li , Rui Xiong , Bo Wang , Qing Geng 
Published: July 2021

AbstractHistone deacetylase 3 (HDAC3) plays a crucial role in chromatin remodeling, which, in turn, regulates gene transcription. Hence, HDAC3 has been implicated in various diseases, including ischemic injury, fibrosis, neurodegeneration, infections, and inflammatory conditions. In addition, HDAC3 plays vital roles under physiological conditions by regulating circadian rhythms, metabolism, and development. In this review, we summarize the current knowledge of the physiological functions of HDAC3 and its role in organ injury. We also discuss the therapeutic value of HDAC3 in various diseases.
Identification of a prognostic ferroptosis-related lncRNA signature in the tumor microenvironment of lung adenocarcinoma
Authors: Guo Yugang , Qu Zhongyu , Li Dandan , Bai Fanghui , Xing Juan , Ding Qian , Zhou Jiawei , Yao Lunguang , Xu Qian 
Published: July 2021

AbstractFerroptosis is closely linked to various cancers, including lung adenocarcinoma (LUAD); however, the factors involved in the regulation of ferroptosis-related genes are not well established. In this study, we identified and characterized ferroptosis-related long noncoding RNAs (lncRNAs) in LUAD. In particular, a coexpression network of ferroptosis-related mRNAs and lncRNAs from The Cancer Genome Atlas (TCGA) was constructed. Univariate and multivariate Cox proportional hazards analyses were performed to establish a prognostic ferroptosis-related lncRNA signature (FerRLSig). We obtained a prognostic risk model consisting of 10 ferroptosis-related lncRNAs: AL606489.1, AC106047.1, LINC02081, AC090559.1, AC026355.1, FAM83A-AS1, AL034397.3, AC092171.5, AC010980.2, and AC123595.1. High risk scores according to the FerRLSig were significantly associated with poor overall survival (hazard ratio (HR) = 1.412, 95% CI = 1.271–1.568; P < 0.001). Receiver operating characteristic (ROC) curves and a principal component analysis further supported the accuracy of the model. Next, a prognostic nomogram combining FerRLSig with clinical features was established and showed favorable predictive efficacy for survival risk stratification. In addition, gene set enrichment analysis (GSEA) revealed that FerRLSig is involved in many malignancy-associated immunoregulatory pathways. Based on the risk model, we found that the immune status and response to immunotherapy, chemotherapy, and targeted therapy differed significantly between the high-risk and low-risk groups. These results offer novel insights into the pathogenesis of LUAD, including the contribution of ferroptosis-related lncRNAs, and reveal a prognostic indicator with the potential to inform immunological research and treatment.
Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics
Authors: Pimmett Virginia L. , Dejean Matthieu , Fernandez Carola , Trullo Antonio , Bertrand Edouard , Radulescu Ovidiu , Lagha Mounia 
Published: July 2021

AbstractGenes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge in transcription is understanding how promoter composition dictates bursting, particularly in multicellular organisms. We investigate two key Drosophila developmental promoter motifs, the TATA box (TATA) and the Initiator (INR). Using live imaging in Drosophila embryos and new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds to minutes. TATA-containing promoters and INR-containing promoters exhibit distinct dynamics, with one or two separate rate-limiting steps respectively. A TATA box is associated with long active states, high rates of polymerase initiation, and short-lived, infrequent inactive states. In contrast, the INR motif leads to two inactive states, one of which relates to promoter-proximal polymerase pausing. Surprisingly, the model suggests pausing is not obligatory, but occurs stochastically for a subset of polymerases. Overall, our results provide a rationale for promoter switching during zygotic genome activation.
Reverse optogenetics of G protein signaling by zebrafish non-visual opsin Opn7b for synchronization of neuronal networks
Authors: Karapinar Raziye , Schwitalla Jan Claudius , Eickelbeck Dennis , Pakusch Johanna , Mücher Brix , Grömmke Michelle , Surdin Tatjana , Knöpfel Thomas , Mark Melanie D. , Siveke Ida , Herlitze Stefan 
Published: July 2021

AbstractOpn7b is a non-visual G protein-coupled receptor expressed in zebrafish. Here we find that Opn7b expressed in HEK cells constitutively activates the Gi/o pathway and illumination with blue/green light inactivates G protein-coupled inwardly rectifying potassium channels. This suggests that light acts as an inverse agonist for Opn7b and can be used as an optogenetic tool to inhibit neuronal networks in the dark and interrupt constitutive inhibition in the light. Consistent with this prediction, illumination of recombinant expressed Opn7b in cortical pyramidal cells results in increased neuronal activity. In awake mice, light stimulation of Opn7b expressed in pyramidal cells of somatosensory cortex reliably induces generalized epileptiform activity within a short (<10 s) delay after onset of stimulation. Our study demonstrates a reversed mechanism for G protein-coupled receptor control and Opn7b as a tool for controlling neural circuit properties.
Past and future trends of Egypt’s water consumption and its sources
Authors: Nikiel Catherine A. , Eltahir Elfatih A. B. 
Published: July 2021

AbstractFor millennia the Nile supplied Egypt with more water than needed. As the population grew and the economy expanded, demand on water increased accordingly. Here, we present a comprehensive analysis to reconstruct how total demand on water outstripped supply of the Nile water in the late 1970s, starting from a surplus of about 20 km3 per year in the 1960s leading to a deficit of about 40 km3 per year by the late 2010s. The gap is satisfied by import of virtual water. The role of economic growth in driving per capita demand on water is quantified based on detailed analysis of water use by agriculture and other sectors. We develop and test an empirical model of water demand in Egypt that relates demand on water to growth rates in the economy and population. Looking forward, we project that within this decade of the 2020 s, under nominal scenarios of population and economic growth, Egypt is likely to import more virtual water than the water supplied by the Nile, bringing into question the historical characterization of Egypt as “the gift of the Nile”.
Auditory input enhances somatosensory encoding and tactile goal-directed behavior
Authors: Godenzini L. , Alwis D. , Guzulaitis R. , Honnuraiah S. , Stuart G. J. , Palmer L. M. 
Published: July 2021

AbstractThe capacity of the brain to encode multiple types of sensory input is key to survival. Yet, how neurons integrate information from multiple sensory pathways and to what extent this influences behavior is largely unknown. Using two-photon Ca2+ imaging, optogenetics and electrophysiology in vivo and in vitro, we report the influence of auditory input on sensory encoding in the somatosensory cortex and show its impact on goal-directed behavior. Monosynaptic input from the auditory cortex enhanced dendritic and somatic encoding of tactile stimulation in layer 2/3 (L2/3), but not layer 5 (L5), pyramidal neurons in forepaw somatosensory cortex (S1). During a tactile-based goal-directed task, auditory input increased dendritic activity and reduced reaction time, which was abolished by photoinhibition of auditory cortex projections to forepaw S1. Taken together, these results indicate that dendrites of L2/3 pyramidal neurons encode multisensory information, leading to enhanced neuronal output and reduced response latency during goal-directed behavior.
Deacetylation as a receptor-regulated direct activation switch for pannexin channels
Authors: Chiu Yu-Hsin , Medina Christopher B. , Doyle Catherine A. , Zhou Ming , Narahari Adishesh K. , Sandilos Joanna K. , Gonye Elizabeth C. , Gao Hong-Yu , Guo Shih Yi , Parlak Mahmut , Lorenz Ulrike M. , Conrads Thomas P. , Desai Bimal N. , Ravichandran Kodi S. , Bayliss Douglas A. 
Published: July 2021

AbstractActivation of Pannexin 1 (PANX1) ion channels causes release of intercellular signaling molecules in a variety of (patho)physiological contexts. PANX1 can be activated by G protein-coupled receptors (GPCRs), including α1-adrenergic receptors (α1-ARs), but how receptor engagement leads to channel opening remains unclear. Here, we show that GPCR-mediated PANX1 activation can occur via channel deacetylation. We find that α1-AR-mediated activation of PANX1 channels requires Gαq but is independent of phospholipase C or intracellular calcium. Instead, α1-AR-mediated PANX1 activation involves RhoA, mammalian diaphanous (mDia)-related formin, and a cytosolic lysine deacetylase activated by mDia – histone deacetylase 6. HDAC6 associates with PANX1 and activates PANX1 channels, even in excised membrane patches, suggesting direct deacetylation of PANX1. Substitution of basally-acetylated intracellular lysine residues identified on PANX1 by mass spectrometry either prevents HDAC6-mediated activation (K140/409Q) or renders the channels constitutively active (K140R). These data define a non-canonical RhoA-mDia-HDAC6 signaling pathway for GαqPCR activation of PANX1 channels and uncover lysine acetylation-deacetylation as an ion channel silencing-activation mechanism.
Update on the effects of microgravity on the musculoskeletal system
Authors: Juhl Otto J. , Buettmann Evan G. , Friedman Michael A. , DeNapoli Rachel C. , Hoppock Gabriel A. , Donahue Henry J. 
Published: July 2021

AbstractWith the reignited push for manned spaceflight and the development of companies focused on commercializing spaceflight, increased human ventures into space are inevitable. However, this venture would not be without risk. The lower gravitational force, known as microgravity, that would be experienced during spaceflight significantly disrupts many physiological systems. One of the most notably affected systems is the musculoskeletal system, where exposure to microgravity causes both bone and skeletal muscle loss, both of which have significant clinical implications. In this review, we focus on recent advancements in our understanding of how exposure to microgravity affects the musculoskeletal system. We will focus on the catabolic effects microgravity exposure has on both bone and skeletal muscle cells, as well as their respective progenitor stem cells. Additionally, we report on the mechanisms that underlie bone and muscle tissue loss resulting from exposure to microgravity and then discuss current countermeasures being evaluated. We reveal the gaps in the current knowledge and expound upon how current research is filling these gaps while also identifying new avenues of study as we continue to pursue manned spaceflight.
Phenethylamine in chlorella alleviates high-fat diet-induced mouse liver damage by regulating generation of methylglyoxal
Authors: Zheng Yifeng , Martin-Morales Agustin , Wang Jing , Fujishima Masaki , Okumura Eri , Sato Kenji 
Published: July 2021

AbstractThis study examined the effects of oral administration of water extract of chlorella (WEC) (100 mg/kg bodyweight) and phenethylamine (10 μg/kg bodyweight) on high-fat diet (HFD)-induced liver damage in mice. Phenethylamine significantly mitigated HFD-induced lipid oxidation (generation of malondialdehyde) and liver damage without markedly decreasing hepatic lipid accumulation. WEC exerted similar effects although with decreased efficacy. In addition, WEC and phenethylamine decreased the methylglyoxal levels and increased the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein levels in the liver. Methylglyoxal is generated from substrates of GAPDH, dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. These facts indicate that methylglyoxal triggers oxidation of accumulated lipid, which generates malondialdehyde and consequently induces liver damage. Suppression of generation of toxic aldehydes by WEC and phenethylamine was also confirmed by maintaining hepatic cysteine, highly reactive to aldehydes. Thus, trace amounts of phenethylamine alleviate HFD-induced liver damage by regulating methylglyoxal via increase of GAPDH.
A large-scale multi-institutional study evaluating prognostic aspects of positive ascites cytology and effects of therapeutic interventions in epithelial ovarian cancer
Authors: Yoshihara Masato , Emoto Ryo , Kitami Kazuhisa , Iyoshi Shohei , Uno Kaname , Mogi Kazumasa , Tano Sho , Yoshikawa Nobuhisa , Matsui Shigeyuki , Kajiyama Hiroaki 
Published: July 2021

AbstractPositive ascites cytology is a strong prognostic factor in patients with early-stage ovarian cancer (OvCa). However, limited information is currently available on the impact of positive ascites cytology on patient prognoses under each clinical background. We herein investigated the comprehensive impact of positive ascites cytology on patients with epithelial OvCa and the effectiveness of additional therapeutic interventions, including complete staging surgery and chemotherapy. Among 4730 patients with malignant ovarian neoplasms, retrospectively identified in multiple institutions, 1906 with epithelial OvCa were included. In the investigation of its effects on clinical factors using a multivariate analysis, positive ascites cytology correlated with a poor prognosis. Positive ascites cytology had a significantly worse prognosis than those with negative cytology in all subgroups except for patients with stage IV tumors and a mucinous histology. Chemotherapy may be effective in reducing the negative impact of positive ascites cytology on the prognosis of patients in terms of progression-free and overall survivals, while complete staging surgery did not improve the prognosis of patients with positive ascites cytology. Collectively, our findings suggested that positive ascites cytology had a negative impact on the prognosis of patients with epithelial OvCa, but not those with stage IV tumors or a mucinous histology.
A new strategy to uncover fragile X proteomic biomarkers using the nascent proteome of peripheral blood mononuclear cells (PBMCs)
Authors: Dionne Olivier , Corbin François 
Published: July 2021

AbstractFragile X syndrome (FXS) is the most prevalent inherited cause of intellectual disabilities and autism spectrum disorders. FXS result from the loss of expression of the FMRP protein, an RNA-binding protein that regulates the expression of key synaptic effectors. FXS is also characterized by a wide array of behavioural, cognitive and metabolic impairments. The severity and penetrance of those comorbidities are extremely variable, meaning that a considerable phenotypic heterogeneity is found among fragile X individuals. Unfortunately, clinicians currently have no tools at their disposal to assay a patient prognosis upon diagnosis. Since the absence of FMRP was repeatedly associated with an aberrant protein synthesis, we decided to study the nascent proteome in order to screen for potential proteomic biomarkers of FXS. We used a BONCAT (Biorthogonal Non-canonical Amino Acids Tagging) method coupled to label-free mass spectrometry to purify and quantify nascent proteins of peripheral blood mononuclear cells (PBMCs) from 7 fragile X male patients and 7 age-matched controls. The proteomic analysis identified several proteins which were either up or downregulated in PBMCs from FXS individuals. Eleven of those proteins were considered as potential biomarkers, of which 5 were further validated by Western blot. The gene ontology enrichment analysis highlighted molecular pathways that may contribute to FXS physiopathology. Our results suggest that the nascent proteome of PBMCs is well suited for the discovery of FXS biomarkers.
Novel CuO/Mn3O4/ZnO nanocomposite with superior photocatalytic activity for removal of Rabeprazole from water
Authors: Raha Sauvik , Mohanta Dipyaman , Ahmaruzzaman Md. 
Published: July 2021

AbstractIn this work, a nanohybrid of CuO/Mn3O4/ZnO was generated through a simple hydrothermal based procedure. The CuO/Mn3O4/ZnO nanohybrid has been characterized using X-ray diffraction, transmission electron microscopy high resolution transmission electron microscopy, X-ray photoelectron spectroscopy, scanning electron microscopy and energy dispersive X-ray analysis. UV–visible spectrophotometry and photoluminescence techniques allowed evaluation of optical properties that additionally suggested the prevalence of strong interfacial interaction between the three moieties of the nanohybrid and suppressed electron–hole recombination. The hybrid photocatalyst brought on ~ 97.02 ± 1.15% disintegration of rabeprazole when illuminated with visible light. The progress of the photodegradation was in conformity with pseudo-first order kinetic model and had a velocity constant of 0.07773 min−1. Additionally, ~ 84.45% of total organic carbon removal was achieved while chemical oxygen demand was reduced by ~ 73.01%. Using high resolution liquid chromatograph mass spectrometry technique, identification of the degraded products was made and accordingly the mechanistic route of the aforesaid degradation was proposed.
Defect localization by an extended laser source on a hemisphere
Authors: Veira Canle Daniel , Mäkinen Joni , Blomqvist Richard , Gritsevich Maria , Salmi Ari , Hæggström Edward 
Published: July 2021

AbstractThe primary goal of this study is to localize a defect (cavity) in a curved geometry. Curved topologies exhibit multiple resonances and the presence of hotspots for acoustic waves. Launching acoustic waves along a specific direction e.g. by means of an extended laser source reduces the complexity of the scattering problem. We performed experiments to demonstrate the use of a laser line source and verified the experimental results in FEM simulations. In both cases, we could locate and determine the size of a pit in a steel hemisphere which allowed us to visualize the defect on a 3D model of the sample. Such an approach could benefit patients by enabling contactless inspection of acetabular cups.
Correlation between gastroesophageal flap valve abnormality and novel parameters in patients with gastroesophageal reflux disease symptoms by the lyon consensus
Authors: Guo Zihao , Wu Yanhong , Zhan Yutao , Zhang Chuan 
Published: July 2021

AbstractGastroesophageal flap valve (GEFV) grading is a simple and reproducible parameter. There is limited information about the association between GEFV abnormality and novel parameters in patients with gastroesophageal reflux disease(GERD) symptoms by the Lyon Consensus. To investigate the value of GEFV grading in GERD, the clinical data of 320 patients with GERD symptoms who underwent endoscopy, 24-h multichannel intraluminal impedance-pH (MII-pH) monitoring, and high-resolution manometry (HRM) were retrospectively analyzed. The percentage of acid exposure time (AET%)(4.2 [1.5–7.4] vs. 1.3 [0.3–4.2], P < 0.001) and the proportion of abnormal esophagogastric junction (EGJ) morphology (71 [87.7%] vs. 172 [72.0%], P = 0.011) were significantly higher, while the mean nocturnal baseline impedance (MNBI) (2068.3 [1658.4–2432.4] vs. 2228.5 [1794.8–2705.3]Ω, P = 0.012) and post-reflux swallow-induced peristaltic wave index (PSPWI) (19.7 [13.9–29.0] vs. 33.3 [25.0–44.0]%, P < 0.001) were significantly lower in the abnormal GEFV group compared with the normal GEFV group. AET% and EGJ morphology showed positive correlations with GEFV grade, while PSPWI and MNBI showed negative correlations. Patients with an abnormal GEFV had a significantly greater risk of conclusive evidence of GERD compared to those with a normal GEFV (OR 3.035, 95% CI 1.758–5.240, P < 0.001). Further, when identifying patients with conclusive evidence of GERD, abnormal GEFV had a specificity of 80.4% (95% CI 75.3–85.5%). GEFV grading might be regarded as supportive evidence for GERD diagnosis.
Niche partitioning among dead wood-dependent beetles
Authors: Horák Jakub 
Published: July 2021

AbstractNiche partitioning among species with virtually the same requirements is a fundamental concept in ecology. Nevertheless, some authors suggest that niches have little involvement in structuring communities. This study was done in the Pardubice Region (Czech Republic) on saproxylic beetles with morphologically similar larvae and very specific requirements, which are related to their obligatory dependence on dead wood material: Cucujus cinnaberinus, Pyrochroa coccinea, and Schizotus pectinicornis. This work was performed on 232 dead wood pieces at the landscape scale over six years. Based on the factors studied, the relationships among these species indicated that their co-occurrence based on species presence and absence was low, which indicated niche partitioning. However, based on analyses of habitat requirements and species composition using observed species abundances, there was no strong evidence for niche partitioning at either studied habitat levels, the tree and the microhabitat. The most likely reasons for the lack of strong niche partitioning were that dead wood is a rich resource and co-occurrence of saproxylic community was not driven by resource competition. This might be consistent with the theory that biodiversity could be controlled by the neutral drift of species abundance. Nevertheless, niche partitioning could be ongoing, meaning that the expanding C. cinnaberinus may have an advantage over the pyrochroids and could dominate in the long term.
Multi-pass probing for high-sensitivity tomographic interferometry
Authors: Karatodorov Stefan , Lera Roberto , Raclavsky Marek , Lorenz Sebastian , Chaulagain Uddhab , Nejdl Jaroslav 
Published: July 2021

AbstractOptical probing is an indispensable tool in research and development. In fact, it has always been the most natural way for humankind to explore nature. However, objects consisting of transparent materials with a refractive index close to unity, such as low-density gas jets, are a typical example of samples that often reach the sensitivity limits of optical probing techniques. We introduce an advanced optical probing method employing multiple passes of the probe through the object to increase phase sensitivity, and relay-imaging of the object between individual passes to preserve spatial resolution. An interferometer with four-passes was set up and the concept was validated by tomographic characterization of low-density supersonic gas jets. The results show an evident increase of sensitivity, which allows for the accurate quantitation of fine features such as a shock formed by an obstacle or a barrel shock on the jet boundary in low ambient gas pressures. Despite its limitations in temporal resolution, this novel method has demonstrated an increase in phase sensitivity in transmission, however, it can also be employed to boost the absorption or polarization contrast of weakly interacting objects in both transmission and reflection setups, thus, upgrading the sensitivity of various optical characterization methods.