bluuebunny/crossref_metadata_2025_split huggingface dataset:
H3K23/H3K36 hypoacetylation and HDAC1 up-regulation are associated with adverse consequences in obstructive sleep apnea patients
Authors: Chen Yung-Che , Hsu Po-Yuan , Chin Chien-Hung , Hsiao Chang-Chun , Liou Chia-Wei , Wang Ting-Ya , Lin Yong-Yong , Lee Chiu-Ping , Lin Hsin-Ching , Lin Meng-Chih , Su Mao-Chang 
Published: October 2021

AbstractThe aim of this study is to determine the roles of global histone acetylation (Ac)/methylation (me), their modifying enzymes, and gene-specific histone enrichment in obstructive sleep apnea (OSA). Global histone modifications, and their modifying enzyme expressions were assessed in peripheral blood mononuclear cells from 56 patients with OSA and 16 matched subjects with primary snoring (PS). HIF-1α gene promoter-specific H3K36Ac enrichment was assessed in another cohort (28 OSA, 8 PS). Both global histone H3K23Ac and H3K36Ac expressions were decreased in OSA patients versus PS subjects. H3K23Ac expressions were further decreased in OSA patients with prevalent hypertension. HDAC1 expressions were higher in OSA patients, especially in those with excessive daytime sleepiness, and reduced after more than 6 months of continuous positive airway pressure treatment. H3K79me3 expression was increased in those with high C-reactive protein levels. Decreased KDM6B protein expressions were noted in those with a high hypoxic load, and associated with a higher risk for incident cardiovascular events or hypertension. HIF-1α gene promoter-specific H3K36Ac enrichment was decreased in OSA patients versus PS subjects. In vitro intermittent hypoxia with re-oxygenation stimuli resulted in HDAC1 over-expression and HIF-1α gene promoter-specific H3K36Ac under-expression, while HDAC1 inhibitor, SAHA, reversed oxidative stress through inhibiting NOX1. In conclusions, H3K23/H3K36 hypoacetylation is associated with the development of hypertension and disease severity in sleep-disordered breathing patients, probably through up-regulation of HDAC1, while H3K79 hypermethylation is associated with higher risk of cardiovascular diseases, probably through down-regulation of KDM6B.
Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds
Authors: D’Arpa Peter , Karna S. L. Rajasekhar , Chen Tsute , Leung Kai P. 
Published: October 2021

AbstractIn burn patients Pseudomonas aeruginosa infection is a major cause of morbidity. Analysis of the pathogen’s gene expression as it transitions from colonization to acute and then biofilm wound infection may provide strategies for infection control. Toward this goal, we seeded log-phase P. aeruginosa (PAO1) into 3-day-old, full-thickness excision wounds (rabbit ear) and harvested the bacteria during colonization (Hrs 2 and 6), acute infection (Hr 24), and biofilm infection (Days 5 and 9) for transcriptome analysis (RNA-Seq). After 2–6 h in the wound, genes for metabolism and cell replication were down-regulated while wound-adaptation genes were up-regulated (vs. expression in log-phase culture). As the infection progressed from acute to biofilm infection, more genes became up-regulated than down-regulated, but the down-regulated genes enriched in more pathways, likely because the genes and pathways that bacteria already colonizing wounds up-regulate to establish biofilm infection are less known. Across the stages of infection, carbon-utilization pathways shifted. During acute infection, itaconate produced by myeloid cells appears to have been a carbon source because myeloid cell infiltration and the expression of the host gene, ACOD1, for itaconate production peaked coincidently with the expression of the PAO1 genes for itaconate transport and catabolism. Additionally, branched-chain amino acids are suggested to be a carbon source in acute infection and in biofilm infection. In biofilm infection, fatty acid degradation was also up-regulated. These carbon sources feed into the glyoxylate cycle that was coincidently up-regulated, suggesting it provided the precursors for P. aeruginosa to synthesize macromolecules in establishing wound infection.
Domestic risk factors for increased rodent abundance in a Lassa fever endemic region of rural Upper Guinea
Authors: Clark Julia , Yakob Laith , Douno Moussa , Lamine Joseph , Magassouba N.’Faly , Fichet-Calvet Elisabeth , Mari-Saez Almudena 
Published: October 2021

AbstractLassa fever (LF) is a viral haemorrhagic fever endemic in West Africa and spread primarily by the multimammate rat,Mastomys natalensis. As there is no vaccine, reduction of rodent-human transmission is essential for disease control. As the household is thought to be a key site of transmission, understanding domestic risk factors forM. natalensisabundance is crucial. Rodent captures in conjunction with domestic surveys were carried out in 6 villages in an area of rural Upper Guinea with high LF endemicity. 120 rodent traps were set in rooms along a transect in each village for three nights, and the survey was administered in each household on the transects. This study was able to detect several domestic risk factors for increased rodent abundance in rural Upper Guinea. Regression analysis demonstrated that having > 8 holes (RR = 1.8 [1.0004–3.2, p = 0.048), the presence of rodent burrows (RR = 2.3 [1.6–3.23, p = 0.000003), and being in a multi-room square building (RR = 2.0 [1.3–2.9], p = 0.001) were associated with increased rodent abundance. The most addressable of these may be rodent burrows, as burrow patching is a relatively simple process that may reduce rodent entry. Further study is warranted to explicitly link domestic rodent abundance to LF risk, to better characterize domestic risk factors, and to evaluate how household rodent-proofing interventions could contribute to LF control.
Deep Bayesian Gaussian processes for uncertainty estimation in electronic health records
Authors: Li Yikuan , Rao Shishir , Hassaine Abdelaali , Ramakrishnan Rema , Canoy Dexter , Salimi-Khorshidi Gholamreza , Mamouei Mohammad , Lukasiewicz Thomas , Rahimi Kazem 
Published: October 2021

AbstractOne major impediment to the wider use of deep learning for clinical decision making is the difficulty of assigning a level of confidence to model predictions. Currently, deep Bayesian neural networks and sparse Gaussian processes are the main two scalable uncertainty estimation methods. However, deep Bayesian neural networks suffer from lack of expressiveness, and more expressive models such as deep kernel learning, which is an extension of sparse Gaussian process, captures only the uncertainty from the higher-level latent space. Therefore, the deep learning model under it lacks interpretability and ignores uncertainty from the raw data. In this paper, we merge features of the deep Bayesian learning framework with deep kernel learning to leverage the strengths of both methods for a more comprehensive uncertainty estimation. Through a series of experiments on predicting the first incidence of heart failure, diabetes and depression applied to large-scale electronic medical records, we demonstrate that our method is better at capturing uncertainty than both Gaussian processes and deep Bayesian neural networks in terms of indicating data insufficiency and identifying misclassifications, with a comparable generalization performance. Furthermore, by assessing the accuracy and area under the receiver operating characteristic curve over the predictive probability, we show that our method is less susceptible to making overconfident predictions, especially for the minority class in imbalanced datasets. Finally, we demonstrate how uncertainty information derived by the model can inform risk factor analysis towards model interpretability.
Effects of global warming on Mediterranean coral forests
Authors: Chimienti Giovanni , De Padova Diana , Adamo Maria , Mossa Michele , Bottalico Antonella , Lisco Anna , Ungaro Nicola , Mastrototaro Francesco 
Published: October 2021

AbstractThe effects of global warming have been addressed on coral reefs in tropical areas, while it is still unclear how coral forests are reacting, particularly at temperate latitudes. Here we show how mesophotic coral forests are affected by global warming in the Mediterranean Sea. We highlight how the current warming trend is causing the lowering of the thermocline and it is enhancing mucilaginous blooms. These stressors are facilitating a massive macroalgal epibiosis on living corals, here reported for the first time from different areas in the Western and Central Mediterranean Sea. We provide a focus of this phenomenon at Tremiti Islands Marine Protected Area (Adriatic Sea), were the density of the endemic red gorgonian Paramuricea clavata decreased of up to 47% in 5 years, while up to the 96% of the living corals showed signs of stress and macroalgal epibiosis. Only populations deeper than 60 m depth were not touched by this emerging phenomenon. Spot observations performed at Tuscan Archipelago and Tavolara Marine Protected Area (Tyrrhenian Sea) suggest that this this combination of stressors is likely widespread at basin scale.
The accuracy of several pose estimation methods for 3D joint centre localisation
Authors: Needham Laurie , Evans Murray , Cosker Darren P. , Wade Logan , McGuigan Polly M. , Bilzon James L. , Colyer Steffi L. 
Published: October 2021

AbstractHuman movement researchers are often restricted to laboratory environments and data capture techniques that are time and/or resource intensive. Markerless pose estimation algorithms show great potential to facilitate large scale movement studies ‘in the wild’, i.e., outside of the constraints imposed by marker-based motion capture. However, the accuracy of such algorithms has not yet been fully evaluated. We computed 3D joint centre locations using several pre-trained deep-learning based pose estimation methods (OpenPose, AlphaPose, DeepLabCut) and compared to marker-based motion capture. Participants performed walking, running and jumping activities while marker-based motion capture data and multi-camera high speed images (200 Hz) were captured. The pose estimation algorithms were applied to 2D image data and 3D joint centre locations were reconstructed. Pose estimation derived joint centres demonstrated systematic differences at the hip and knee (~ 30–50 mm), most likely due to mislabeling of ground truth data in the training datasets. Where systematic differences were lower, e.g., the ankle, differences of 1–15 mm were observed depending on the activity. Markerless motion capture represents a highly promising emerging technology that could free movement scientists from laboratory environments but 3D joint centre locations are not yet consistently comparable to marker-based motion capture.
Mouse Dspp frameshift model of human dentinogenesis imperfecta
Authors: Liang Tian , Hu Yuanyuan , Zhang Hong , Xu Qian , Smith Charles E. , Zhang Chuhua , Kim Jung-Wook , Wang Shih-Kai , Saunders Thomas L. , Lu Yongbo , Hu Jan C.-C. , Simmer James P. 
Published: October 2021

AbstractNon-syndromic inherited defects of tooth dentin are caused by two classes of dominant negative/gain-of-function mutations in dentin sialophosphoprotein (DSPP): 5′ mutations affecting an N-terminal targeting sequence and 3′ mutations that shift translation into the − 1 reading frame. DSPP defects cause an overlapping spectrum of phenotypes classified as dentin dysplasia type II and dentinogenesis imperfecta types II and III. Using CRISPR/Cas9, we generated a Dspp−1fs mouse model by introducing a FLAG-tag followed by a single nucleotide deletion that translated 493 extraneous amino acids before termination. Developing incisors and/or molars from this mouse and a DsppP19L mouse were characterized by morphological assessment, bSEM, nanohardness testing, histological analysis, in situ hybridization and immunohistochemistry. DsppP19L dentin contained dentinal tubules but grew slowly and was softer and less mineralized than the wild-type. DsppP19L incisor enamel was softer than normal, while molar enamel showed reduced rod/interrod definition. Dspp−1fs dentin formation was analogous to reparative dentin: it lacked dentinal tubules, contained cellular debris, and was significantly softer and thinner than Dspp+/+ and DsppP19L dentin. The Dspp−1fs incisor enamel appeared normal and was comparable to the wild-type in hardness. We conclude that 5′ and 3′ Dspp mutations cause dental malformations through different pathological mechanisms and can be regarded as distinct disorders.
Integrated computational analyses reveal novel insights into the stromal microenvironment of SHH-subtype medulloblastoma
Authors: Landry Alexander P. , Samuel Nardin , Spears Julian , Zador Zsolt 
Published: October 2021

AbstractMedulloblastoma is the most common malignant brain tumour of childhood. While our understanding of this disease has progressed substantially in recent years, the role of tumour microenvironment remains unclear. Given the increasing role of microenvironment-targeted therapeutics in other cancers, this study was aimed at further exploring its role in medulloblastoma. Multiple computational techniques were used to analyze open-source bulk and single cell RNA seq data from primary samples derived from all subgroups of medulloblastoma. Gene expression is used to infer stromal subpopulations, and network-based approaches are used to identify potential therapeutic targets. Bulk data was obtained from 763 medulloblastoma samples and single cell data from an additional 7241 cells from 23 tumours. Independent bulk (285 tumours) and single cell (32,868 cells from 29 tumours) validation cohorts were used to verify results. The SHH subgroup was found to be enriched in stromal activity, including the epithelial-to-mesenchymal transition, while group 3 is comparatively stroma-suppressed. Several receptor and ligand candidates underlying this difference are identified which we find to correlate with metastatic potential of SHH medulloblastoma. Additionally, a biologically active gradient is detected within SHH medulloblastoma, from “stroma-active” to “stroma-suppressed” cells which may have relevance to targeted therapy. This study serves to further elucidate the role of the stromal microenvironment in SHH-subgroup medulloblastoma and identify novel treatment possibilities for this challenging disease.
Non-destructive mid-IR spectroscopy with quantum cascade laser can detect ethylene gas dynamics of apple cultivar ‘Fuji’ in real time
Authors: Yumoto Masaki , Kawata Yasushi , Abe Tetsuya , Matsuyama Tomoki , Wada Satoshi 
Published: October 2021

AbstractMany plants, including fruits and vegetables, release biogenic gases containing various volatile organic compounds such as ethylene (C2H4), which is a gaseous phytohormone. Non-destructive and in-situ gas sampling technology to detect trace C2H4 released from plants in real time would be attractive for visualising the ageing, ripening, and defence reactions of plants. In this study, we developed a C2H4 detection system with a detection limit of 0.8 ppb (3σ) using laser absorption spectroscopy. The C2H4 detection system consists of a mid-infrared quantum cascade laser oscillated at 10.5 µm, a multi-pass gas cell, a mid-IR photodetector, and a gas sampling system. Using non-destructive and in-situ gas sampling, while maintaining the internal pressure of the multi-pass gas cell at low pressure, the change in trace C2H4 concentration released from apples (Malus domestica Borkh.) can be observed in real time. We succeeded in observing C2H4 concentration changes with a time resolution of 1 s, while changing the atmospheric gas and surface temperature of apples from the ‘Fuji’ cultivar. This technique allows the visualisation of detailed C2H4 dynamics in plant environmental response, which may be promising for further progress in plant physiology, agriculture, and food science.
Identification of serum prognostic biomarkers of severe COVID-19 using a quantitative proteomic approach
Authors: Kimura Yayoi , Nakai Yusuke , Shin Jihye , Hara Miyui , Takeda Yuriko , Kubo Sousuke , Jeremiah Sundararaj Stanleyraj , Ino Yoko , Akiyama Tomoko , Moriyama Kayano , Sakai Kazuya , Saji Ryo , Nishii Mototsugu , Kitamura Hideya , Murohashi Kota , Yamamoto Kouji , Kaneko Takeshi , Takeuchi Ichiro , Hagiwara Eri , Ogura Takashi , Hasegawa Hideki , Tamura Tomohiko , Yamanaka Takeharu , Ryo Akihide 
Published: October 2021

AbstractThe COVID-19 pandemic is an unprecedented threat to humanity that has provoked global health concerns. Since the etiopathogenesis of this illness is not fully characterized, the prognostic factors enabling treatment decisions have not been well documented. Accurately predicting the progression of the disease would aid in appropriate patient categorization and thus help determine the best treatment option. Here, we have introduced a proteomic approach utilizing data-independent acquisition mass spectrometry (DIA-MS) to identify the serum proteins that are closely associated with COVID-19 prognosis. Twenty-seven proteins were differentially expressed between severely ill COVID-19 patients with an adverse or favorable prognosis. Ingenuity Pathway Analysis revealed that 15 of the 27 proteins might be regulated by cytokine signaling relevant to interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF), and their differential expression was implicated in the systemic inflammatory response and in cardiovascular disorders. We further evaluated practical predictors of the clinical prognosis of severe COVID-19 patients. Subsequent ELISA assays revealed that CHI3L1 and IGFALS may serve as highly sensitive prognostic markers. Our findings can help formulate a diagnostic approach for accurately identifying COVID-19 patients with severe disease and for providing appropriate treatment based on their predicted prognosis.
Optimization of fish gelatin drying processes and characterization of its properties
Authors: da Silva Araújo Cleidiane , Pino-Hernández Enrique , Souza Batista Jáira Thayse , Sarkis Peixoto Joele Maria Regina , de Arimateia Rodrigues do Rego José , Henriques Lourenço Lúcia de Fátima 
Published: October 2021

AbstractFish skin is a raw material used for gelatin production. It can satisfy consumers with specific socio-cultural and religious needs. Different technologies have been studied for drying gelatin. Therefore, it is relevant to understand the influence of drying conditions on the final product. This study aims to optimize drying methods such as convection hot air alone and combined with infrared radiation to obtain gelatin from acoupa weakfish skin by using composite central rotational designs 22 and 23 and response surface methodology. The gelatin obtained from the optimized conditions were characterized based on their physical, chemical, technological, and functional properties. The desirability function results show the convection hot air as the most effective method when conducted at 59.14 °C for 12.35 h. Infrared radiation at 70 °C for 2.0 h and convective drying at 70 °C for 3.5 h were the best condition of the combined process. The gelatins obtained had gel strength of 298.00 and 507.33 g and emulsion activity index of 82.46 and 62.77 m2/g in the combined and convective methods, respectively, and protein content above 90%. These results indicate that the processes studied can be used to produce gelatin with suitable technological and functional properties for several applications.
A compact platform for the investigation of material dynamics in quasi-isentropic compression to ~ 19 GPa
Authors: Lu Yu , Chen Kaiguo , Cheng Cheng , Zhou Zhongyu , Luo Binqiang , Chen Xuemiao , Zhang Xuping , Wang Guiji , Tan Fuli , Zhao Jianheng , Gu Zhuowei , Sun Chengwei 
Published: October 2021

AbstractThis paper reports on the development of a magnetically driven high-velocity implosion experiment conducted on the CQ-3 facility, a compact pulsed power generator with a load current of 2.1 MA. The current generates a high Lorentz force between inner and outer liners made from 2024 aluminum. Equally positioned photonic Doppler velocimetry probes record the liner velocities. In experiment CQ3-Shot137, the inner liner imploded with a radial converging velocity of 6.57 km/s while the outer liner expanded at a much lower velocity. One-dimensional magneto-hydrodynamics simulation with proper material models provided curves of velocity versus time that agree well with the experimental measurements. Simulation then shows that the inner liner underwent a shock-less compression to approximately 19 GPa and reached an off-Hugoniot high-pressure state. According to the scaling law that the maximum loading pressure is proportional to the square of the load current amplitude, the results demonstrate that such a compact capacitor bank as CQ-3 has the potential to generate pressure as high as 100 GPa within the inner liner in such an implosion experiment. It is emphasized that the technique described in this paper can be easily replicated at low cost.
Uncovering of intraspecies macular heterogeneity in cynomolgus monkeys using hybrid machine learning optical coherence tomography image segmentation
Authors: Maloca Peter M. , Seeger Christine , Booler Helen , Valmaggia Philippe , Kawamoto Ken , Kaba Qayim , Inglin Nadja , Balaskas Konstantinos , Egan Catherine , Tufail Adnan , Scholl Hendrik P. N. , Hasler Pascal W. , Denk Nora 
Published: October 2021

AbstractThe fovea is a depression in the center of the macula and is the site of the highest visual acuity. Optical coherence tomography (OCT) has contributed considerably in elucidating the pathologic changes in the fovea and is now being considered as an accompanying imaging method in drug development, such as antivascular endothelial growth factor and its safety profiling. Because animal numbers are limited in preclinical studies and automatized image evaluation tools have not yet been routinely employed, essential reference data describing the morphologic variations in macular thickness in laboratory cynomolgus monkeys are sparse to nonexistent. A hybrid machine learning algorithm was applied for automated OCT image processing and measurements of central retina thickness and surface area values. Morphological variations and the effects of sex and geographical origin were determined. Based on our findings, the fovea parameters are specific to the geographic origin. Despite morphological similarities among cynomolgus monkeys, considerable variations in the foveolar contour, even within the same species but from different geographic origins, were found. The results of the reference database show that not only the entire retinal thickness, but also the macular subfields, should be considered when designing preclinical studies and in the interpretation of foveal data.