Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of LSH in the establishment of epigenetic gene silencing

7 Chapter 1 Introduction . 9 1.1 DNA packaging into chromatin . 9 1.2 Epigenetic modifications and gene regulation . 11 1.3 DNA methylation . 13 1.3. 1 Distribution of DNA methylation and function in gene regulation . 14 1.3. 2 DNA methyltransferases . 17 1.3. 3 DNA methylation reprogramming during embryonic mammalian development . 21 1.4 Chromatin modifications: chemical modification of histone tails . 23 1.4. 1 Distribution and function of histone modifications . 25 1.4. 2 Histone methylation crosstalk with DNA methylation . 26 1.5 ATP-dependent chromatin remodelers . 28 1.5. 1 Classification of ATP-dependent chromatin remodelers . 29 1.5. 2 Domain architecture and mechanism of action of ATP-dependent chromatin remodelers . 31 1.5. 3 Functional diversity of ATP-dependent chromatin remodelers . 33 1.6 LSH, an ATP dependent chromatin remodeler . 34 1.6. 1 Domain architecture of LSH . 34 1.6. 2 Role of LSH in DNA methylation . 36 1.6. 3 Involvement of LSH in other biological processes and disease . 38 1.7 Aims . 41 Chapter 2 Materials and Methods . 42 2.1 Materials . 42 2.1.1 Antibodies . 42 2.1.2 Cell lines . 43
Deep representation learning for domain adaptatable classification of infrared spectral imaging data

Motivation Applying infrared microscopy in the context of tissue diagnostics heavily relies on computationally preprocessing the infrared pixel spectra that constitute an infrared microscopic image. Existing approaches involve physical models, which are non-linear in nature and lead to classifiers that do not generalize well, e.g. across different types of tissue preparation. Furthermore, existing preprocessing approaches involve iterative procedures that are computationally demanding, so that computation time required for preprocessing does not keep pace with recent progress in infrared microscopes which can capture whole-slide images within minutes. Results We investigate the application of stacked contractive autoencoders as an unsupervised approach to preprocess infrared microscopic pixel spectra, followed by supervised fine-tuning to obtain neural networks that can reliably resolve tissue structure. To validate the robustness of the resulting classifier, we demonstrate that a network trained on embedded tissue can be transferred to classify fresh frozen tissue. The features obtained from unsupervised pretraining thus generalize across the large spectral differences between embedded and fresh frozen tissue, where under previous approaches seperate classifiers had to be trained from scratch. Availability Our implementation can be downloaded from https://github.com/arnrau/SCAE_IR_Spectral_Imaging Contact axel.mosig@bph.rub. de
Wrinkle-like slip pulse on a fault between different

Pulses of slip velocity can propagate on a planar interface governed by a constant coefficient of friction, where the interface separates different elastic materials. Such pulses have been found in two-dimensional plane strain finite difference calculations of slip on a fault between elastic media with wave speeds differing by 20%. The self-sustaining propagation of the slip pulse arises from interaction between normal and tangential deformation that exists only with a material contrast. These calculations confirm the prediction of Weertman [1980] that a dislocation propagating steadily along a material interface has a tensile change of normal traction with the same pulse shape as slip velocity. The self-sustaining pulse is associated with a rapid transition from a head wave traveling along the interface with the S wave speed of the faster material, to an opposite polarity body wave traveling with the slower S speed. Slip occurs during the reversal of normal particle velocity. The pulse can propagate in a region with constant coefficient of friction and an initial stress state below the frictional criterion. Propagation occurs in only one direction, the direction of slip in the more compliant medium, with rupture velocity near the slower S wave speed. Displacement is larger in the softer medium, which is displaced away from the fault during the passage of the slip pulse. Motion is analogous to a propagating wrinkle in a carpet. The amplitude of slip remains approximately constant during propagation, but the pulse width decreases and the amplitudes of slip velocity and stress change increase. The tensile change of normal traction increases until absolute normal traction reaches zero. The pulse can be generated as a secondary effect of a drop of shear stress in an asperity. The pulse shape is unstable, and the initial slip pulse can change during propagation into a collection of sharper pulses. Such a pulse enables slip to occur with little loss of energy to friction, while at the same time increasing irregularity of stress and slip at the source.
Slope and distance from buildings are easy-to-retrieve proxies for estimating livestock site-use intensity in alpine summer pastures

Regardless of the issue, most of the research carried out on summer pastures of European Alps had to consider the effects of grazing management, as it is an intrinsic component of alpine environment. The management intensity of grazing livestock is measured in terms of livestock stocking rate, but not always a direct measure of it is easily retrievable. Therefore, the aim of the research was to test the reliability of proxies easily retrievable from open data sources (i.e. slope and distance from buildings) in approximating the pastoral site-use intensity. To test the proxies’ effectiveness two different approaches were used. With the first one, the proxies’ reliability was assessed in a case-study conducted at farm scale by using the number of positions gathered with GPS collars, which are a reliable measure of livestock site-use intensity. With the second, the proxies’ reliability was assessed by means of five Vegetation Ecological Groups (VEGs), used as a tool for indirect quantification of livestock site-use intensity at regional scale (thirty-two alpine valleys of the Western Italian Alps, Piedmont Region—Italy). At farm scale, distance from buildings and slope were both reliable predictors of the number of GPS locations as assessed with a Generalized Additive Model. Results of Generalized Linear Models at the regional scale showed that the values of both the slope and the distance from buildings were able to separate VEGs along the same site-use intensity gradient assessed by modelling the number of GPS locations at farm scale. By testing proxies’ reliability both with a direct (i.e. GPS collar positions) and indirect (i.e. VEGs) measurement of livestock site-use intensity, results indicated that slope and distance from buildings can be considered effective surrogates of site-use intensity gradient in alpine grasslands managed under livestock grazing. Therefore, when the level of site-use intensity in research carried out in alpine summer pastures is not directly available, a reliable solution consists in the use of the terrain slope and the distance from buildings, which are also easily retrievable from open data sources or computable.
A Comparison Between Transcutaneous Bilirubin and Total Serum Bilirubin Levels for the Management of Jaundice in Preterm Neonates by Bland-Altman Plot

Objective To compare the bilirubin levels measured by transcutaneous bilirubinometer and serum samples for the management of jaundice in preterm neonates. Methods The study was a prospective comparative observational study conducted in a tertiary care neonatal unit of Odisha from January 2019 to June 2020. All inborn and outborn neonates with a gestational age of 280/7 weeks to 366/7 weeks with the clinical diagnosis of neonatal jaundice were included in the study. Transcutaneous bilirubin (TcB) was estimated by Dragger jaundice meter JM-105 and simultaneously venous blood and total serum bilirubin levels (TSB) were measured by diazonium method. The comparison between TcB and TSB values was analyzed by direct linear correlation in scatter plot and Bland-Altman plot. Results A total of 167 preterm neonates (66, 28-336/7 and 111, 34-366/7), with a mean gestational age 33.55 ±2.36 weeks and a mean birth weight of 1960 ± 613 grams, were analyzed. The mean TSB and TcB levels were 12.99 ± 3.47 mg/dl (min-max 4.9-18.3 mg/dl) and 14.156 ± 4.71 mg/dl (min-max 4-20.1 mg/dL), respectively. The TcB is excellently correlated with TSB with a correlation coefficient of r =0.948, p ≤0.001. The bias difference between TcB and TSB is -1.16 (95% CI: 2.35, -4.6) mg/dl. The correlation coefficients between 28-336/7 weeks gestational age groups (r = 0.944) and 34-366/7gestational age (r = 0.950) were similar. Conclusion TcB is well correlated with TSB level in preterm neonates. Hence, TcB can be used for the guidance of management in these neonates.
Seroprevalence of viral infections in captive rhesus and cynomolgus macaques

Abstract Macaques serve as important animal models for biomedical research. Viral infection of macaques can compromise animal health as well as the results of biomedical research, and infected animals constitute an occupational health risk. Therefore, monitoring macaque colonies for viral infection is an important task. We used a commercial chip-based assay to analyze sera of 231 macaques for the presence of antibody responses against nine animal and human viruses. We report high seroprevalence of cytomegalovirus (CMV), lymphocryptovirus (LCV), rhesus rhadinovirus (RRV) and simian foamy virus (SFV) antibodies in all age groups. In contrast, antibodies against simian retrovirus type D (SRV/D) and simian T cell leukemia virus (STLV) were detected only in 5 % and 10 % of animals, respectively, and were only found in adult or aged animals. Moreover, none of the animals had antibodies against herpes B virus (BV), in keeping with the results of in-house tests previously used for screening. Finally, an increased seroprevalence of measles virus antibodies in animals with extensive exposure to multiple humans for extended periods of time was observed. However, most of these animals were obtained from external sources, and a lack of information on the measles antibody status of the animals at the time of arrival precluded drawing reliable conclusions from the data. In sum, we show, that in the colony studied, CMV, LCV, RRV and SFV infection was ubiquitous and likely acquired early in life while SRV/D and STLV infection was rare and likely acquired during adulthood.
Clinical Outcome between Ticagrelor versus Clopidogrel in Patients with Acute Coronary Syndrome and Diabetes

Background The increased thrombotic risk in patients with acute coronary syndrome (ACS) and diabetes highlights the need for adequate antithrombotic protection. We aimed to compare the 6-month clinical outcomes between ticagrelor and clopidogrel in patients with ACS and diabetes. Methods and Results The study was a single-center, prospective, randomized, open-label, blinded endpoint, and controlled registry trial. A total of 270 ACS patients with diabetes were randomly assigned in a 1 : 1 ratio to either the ticagrelor group or the clopidogrel group. Follow-up was performed for 6 months, and the data on efficacy outcomes and bleeding events were collected. At 6 months, complete follow-up data were available for 266 (98.5%) of 270 patients, and 4 were lost to follow-up. There was no significant difference in the survival rate of the effective endpoints between the ticagrelor group (n = 133) and the clopidogrel group (n = 133) (HR 0.83, 95% CI 0.44–1.56, p = 0.561), but the incidence of bleeding events in the ticagrelor group was higher than that in the clopidogrel group (HR 1.76, 95% CI 1.00–3.10, p = 0.049). Conclusion Ticagrelor did not improve the composite of nonfatal MI, target vessel revascularization, rehospitalization, stroke, and death from any cause; however, it significantly increased the incidence of bleeding events defined by the Bleeding Academic Research Consortium (BARC) criteria in Chinese patients with ACS and diabetes during the 6-month follow-up compared with clopidogrel.
Molecular Signatures of Human Chronic Atrial Fibrillation in Primary Mitral Regurgitation

Objectives Transcriptomics of atrial fibrillation (AFib) in the setting of chronic primary mitral regurgitation (MR) remains to be characterized. We aimed to compare the gene expression profiles of patients with degenerative MR in AFib and sinus rhythm (SR) for a clearer picture of AFib pathophysiology. Methods After transcriptomic analysis and bioinformatics (n = 59), differentially expressed genes were defined using 1.5-fold change as the threshold. Additionally, independent datasets from GEO were included as meta-analyses. Results QRT-PCR analysis confirmed that AFib persistence was associated with increased expression molecular changes underlying a transition to heart failure (NPPB, P = 0.002; ANGPTL2, P = 0.002; IGFBP2, P = 0.010), structural remodeling including changes in the extracellular matrix and cellular stress response (COLQ, P = 0.003; COMP, P = 0.028; DHRS9, P = 0.038; CHGB, P = 0.038), and cellular stress response (DNAJA4, P = 0.038). Furthermore, AFib persistence was associated with decreased expression of the targets of structural remodeling (BMP7, P = 0.021) and electrical remodeling (CACNB2, P = 0.035; MCOLN3, P = 0.035) in both left and right atrial samples. The transmission electron microscopic analysis confirmed ultrastructural atrial remodeling and autophagy in human AFib atrial samples. Conclusions Atrial cardiomyocyte remodeling in persistent AFib is closely linked to alterations in gene expression profiles compared to SR in patients with primary MR. Study findings may lead to novel therapeutic targets. This trial is registered with ClinicalTrials.gov identifier: NCT00970034.
Analysis of Hydrological Processes Applying the HSPF Model in Selected Watersheds in Alabama, Mississippi, and Puerto Rico

The goal of this study was to evaluate the Hydrological Simulation Program – FORTRAN (HSPF) to gain more insight in the underlying causes and mechanisms of hydrological processes in an upland basin in Alabama and Mississippi (1,856-km2 Luxapallila Creek), a humid subtropical watershed in coastal Alabama (140-km2 Fish River), and a steep-slope tropical catchment in Puerto Rico (99-km2 Rio Caonillas). For each watershed model, rainfall, potential evapotranspiration, and streamflow time series from January 1999 to December 2000 were used to calibrate model parameters and 2001 time series were applied to verify model results. In each study area, actual evapotranspiration was the main mechanism of water loss followed by river discharge. Annual baseflow values ranged from 58% of total discharge in Luxapallila Creek basin to 84% of total discharge in Fish River watershed. In Luxapallila Creek and Fish River, interflow was the primary mechanism of direct runoff; however, surface runoff was the main process of direct runoff in Rio Caonillas. The HSPF model was successfully adapted to model daily streamflow processes in Luxapallila Creek basin and Rio Caonillas catchment with coefficient of determination and Nash and Sutcliffe coefficient values between 0.61 and 0.71 for the entire period; however, the Fish River watershed model performance was poor. The poor performance is likely due to the lack of rainfall time series available within the watershed boundaries. In general, this study showed the robustness of the HSPF model in extreme environments (small catchments vs. large basins, flat vs. hilly areas, low vs. moderate/high runoff potential, tropical marine vs. humid subtropical climates).
Blue City

Feel lonely? What about reading books? Book is one of the greatest friends to accompany while in your lonely time. When you have no friends and activities somewhere and sometimes, reading book can be a great choice. This is not only for spending the time, it will increase the knowledge. Of course the b=benefits to take will relate to what kind of book that you are reading. And now, we will concern you to try reading the blue city as one of the reading material to finish quickly.
Innovation by in-wheel-motor drive unit

The in-wheel-motor (IWM) will be the most important key technology in the near future to be used by electric vehicles (including fuel cell vehicles). In the past 100 years of the internal combustion engine, several kinds of vehicle packages have been developed, for example, front-engine front-wheel drive, front-engine rear-wheel drive, mid-engine rear-wheel drive, and rear-engine rear-wheel drive. However, a conclusive solution for the best package has not been found. Combining electric drive and IWM enables both good vehicle dynamics and a roomy interior. In addition, the responsiveness of IWM raises the performance of the dynamic control to an even higher level.
Flood risk management for the RUA of Hanoi: Importance of community perception of catastrophic flood risk in disaster risk planning

Purpose – This paper aims to investigate reasons for unusual overdevelopment of floodplain areas outside river dyke, provide an insight into the importance of community perception of catastrophic flood risk in the riverside urban areas (RUA) of Hanoi and establishes the need for participatory disaster management planning and disaster management education in the study location.Design/methodology/approach – Structured survey was conducted in five wards in the RUA to understand how residents perceived flood risk.Findings – The low perception of catastrophic flood risk among communities was found to be an important factor in the continued development of the RUA and led to the trust in their houses as a prominent protective solution. Moreover, the flood vulnerability of the areas has been increasing due to the missing link between local authorities and community.Research limitations/implications – This paper examines community perception of flood risk as one of main factors. Other factors such as availability .
Development of nanostructured lipid carriers containing the antimicrobial ciprofloxacin for topical application

Ciprofloxacin (CIP), a broad spectrum antibacterial agent from the fluoroquinolone family, blocks the activity of the bacterial DNA gyrase. CIP has a limited aqueous solubility and fast clearance rate. Nanostructured lipid carriers (NLC) are drug delivery carriers very appropriate to upload hydrophobic drugs, improving their bioavailability, stability and potency. This work describes the development of NLC containing CIP, their physicochemical characterization and antimicrobial activity, in vitro. NLC particles (215-355 nm) of low size polidispersion (PDI 0.08-0.31) and negative zeta potentials (|20.7-38.7| mV) were prepared; scanning electron microscopy revealed their spherical shapes and regular contour. The particles remained stable during 365 days of storage at 25°C. The encapsulation efficiency of CIP ranged from 72.5 - 95.2%, with a sustained release profile (48 h). Preliminary antimicrobial susceptibility tests revealed a 30% increase in CIP action, when encapsulated in NLC. These proof-of-concept results show the great pharmaceutical and technological potential of the developed nanoformulations. After further tests we believe that NLC-CIP can come to be a novel pharmaceutical form to potentiate the antibiotic effect, reducing its dosage and undesirable side effects.
DEEPCON: Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout

Background Exciting new opportunities have arisen to solve the protein contact prediction problem from the progress in neural networks and the availability of a large number of homologous sequences through high-throughput sequencing. In this work, we study how deep convolutional neural network methods (ConvNets) may be best designed and developed to solve this long-standing problem. Method With publicly available datasets, we designed and trained various ConvNet architectures. We tested several recent deep learning techniques including wide residual networks, dropouts, and dilated convolutions. We studied the improvements in the precision of medium-range and long-range contacts, and compared the performance of our best architectures with the ones used in existing state-of-the-art methods. Results The proposed ConvNet architectures predict contacts with significantly more precision than the architectures used in several state-of-the-art methods. When trained using the DeepCov dataset consisting of 3,456 proteins and tested on PSICOV dataset of 150 proteins, our architectures achieve up to 15% higher precision when L/2 long-range contacts are evaluated. Similarly, when trained using the DNCON2 dataset consisting of 1,426 proteins and tested on 84 protein domains in the CASP12 dataset, our single network achieves 4.8% higher precision than the ensembled DNCON2 method when top L long-range contacts are evaluated. DEEPCON will be made publicly available at https://github.com/badriadhikari/DEEPCON/.
Cathepsin C Is Involved in Macrophage M1 Polarization via p38/MAPK Pathway in Sudden Cardiac Death

This study was aimed at identifying molecular markers associated with the pathogenesis of sudden cardiac death (SCD). It provides a proteomic analysis of human left anterior descending coronary artery from subjects diagnosed with SCD through histological examination and cases of nondisease accidental deaths through autopsy. A total of 2784 proteins were obtained from label-free quantitative proteomic analysis. This included a total of 265 differential proteins which were involved in SCD-related processes, such as inflammation, muscle system process regulation, metal ion transport, and lysosomal pathway. Western blotting was carried out to measure the expressions of cathepsin C (CTSC), focal adhesion kinase (FAK), p-FAK, and proteins related to the p38/MAPK signaling pathway, whereas immunohistochemistry was performed to determine the localization and expression of CTSC, TNF-α, and CD206 in arterial tissues. It was found that CTSC were the most expressed proteins with a significant upward trend in SCD cases. Besides, CTSC regulated macrophage polarization to M1 through the FAK-induced p38/MAPK signaling pathway. This promoted the release of inflammatory factors and eventually increased the inflammatory response. In conclusion, this study implies that CTSC may be one of the key molecular targets for promoting macrophage M1 polarization in SCD, which may provide new therapeutic insights into the treatment of inflammatory diseases.