gebhart/patrepeval huggingface dataset:
Bone metabolism and adipokines: are there perspectives for bone diseases drug discovery? (2014)

Introduction: Over the past 20 years, the idea that white adipose tissue (WAT) is simply an energy depot organ has been radically changed. Indeed, present understanding suggests WAT to be an endocrine organ capable of producing and secreting a wide variety of proteins termed adipokines. These adipokines appear to be relevant factors involved in a number of different functions, including metabolism, immune response, inflammation and bone metabolism.Areas covered: In this review, the authors focus on the effects of several adipose tissue-derived factors in bone pathophysiology. They also consider how the modification of the adipokine network could potentially lead to promising treatment options for bone diseases.Expert opinion: There are currently substantial developments being made in the understanding of the interplay between bone metabolism and the metabolic system. These insights could potentially lead to the development of new treatment strategies and interventions with the aim of successful outcomes in many people affected by bone disorders. Specifically, future research should look into the intimate mechanisms regulating peripheral and central activity of adipokines as it has potential for novel drug discovery.
Simultaneous Rapid Thermal Growth of Gate and Interpoly Oxides for Analog MOS Applications (1992)

Rapid thermal oxidation is applied to simultaneously grow the gate and capacitor oxides in a mixed analog/digital metal oxide semiconductor (MOS) process with polysilicon‐polysilicon capacitors. This technique allows the use of a high temperature for polysilicon oxidation, which provides increased dielectric strength while avoiding diffusion of the active device boron threshold adjust implant and associated short‐channel effects in p‐channel transistors. A process has been developed which gives gate oxide breakdown fields in excess of 13 MV/cm for 17 nm gate oxides and over 8 MV/cm for 27 nm capacitor (interpoly) oxides while providing submicron n‐ and p‐channel MOSFETs with electrically long‐channel behavior.
A brief look at railroad communication vulnerabilities (2005)

Recent terrorist bombings of commuter trains in Madrid have shown that railroads still face attacks by terrorists. There are also increasing hacking attempts against all kinds of electronic systems. Since railroads are increasing their dependence on electronic systems, this presents a new way for railroads to be disrupted. This paper is a review of wireless communications used by railroads in the United States. We look at the protocols used and aspects of security in relation to these communications.
ChemInform Abstract: RACEMIZATION‐FREE ESTERIFICATION OF 2‐NITROPHENYLSULFENYL‐PROTECTED AMINO ACIDS BY DICYCLOHEXYLCARBODIIMIDE‐4‐DIMETHYLAMINOPYRIDINE (1983)

Abstract Das geschützte Phenylalaninderivat (I) reagiert mit Alkoholen (II) in Gegenwart von Dicyclohexylcarbodiimid (DCC) und 4‐Dimethylaminopyridin (DMAP) zu den Estern (III), die über (IV) in die Verbindungen (V) umgewandelt werden.
Supplementary Table 3 from The Splicing Factor PTBP1 Represses <i>TP63 γ</i> Isoform Production in Squamous Cell Carcinoma (2023)

&lt;p&gt;Differential gene expression&lt;/p&gt;
Pituitary adenylate cyclase‐activating polypeptide promotes the survival of basal forebrain cholinergic neurons in vitro and in vivo: comparison with effects of nerve growth factor (2000)

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a member of the vasointestinal polypeptide gene family for which neurotrophic activity has been postulated. PACAP mRNA is expressed in the developing and adult hippocampus, which is the principal target region of septal cholinergic neurons. We therefore studied the effects of PACAP on septal cholinergic neurons. In primary cultures from septum of embryonic and postnatal rats, PACAP increased the number of neurons immunohistochemically stained for the low-affinity nerve growth factor (NGF) receptor p75 and for the enzyme choline acetyltransferase (ChAT). PACAP also caused a corresponding increase in ChAT activity. In comparison, NGF had a greater effect than PACAP on the number of p75- and ChAT-positive neurons in these cultures. In vivo, following fimbria fornix transection, the number of immunohistochemically stained septal cholinergic neurons fell significantly to 18% in rats given continuous intracerebroventricular infusion of vehicle, whereas in rats given NGF the number of these neurons did not differ significantly from unoperated controls. In PACAP-treated rats the number was 48% of unoperated values, which represented a significant increase compared with vehicle-treated rats and a significant decrease compared with NGF-treated rats or unoperated controls. Double-staining experiments revealed that most ChAT-positive neurons in rat medial septum also express PACAP receptor 1. Together the results show that PACAP promotes the survival of septal cholinergic neurons in vitro, and after injury in vivo, suggesting that PACAP acts as a neurotrophic factor influencing the development and maintenance of these neurons.
Isomerization of diastereoisomeric alkene complexes of the formula [(η5-C5H5)Re(NO)(PPh3)(H2CCHR)]+; the alkene enantioface bound to the metal can ‘flip’ without alkene dissociation (1990)

Deuterium labelling experiments show that the title reaction is intramolecular, and does not proceed by rotation of the [[double bond, length half m-dash]] CHR terminus; a mechanism involving a C-H ‘σ bond complex’ is proposed.
DNA DAMAGE: DETECTION STRATEGIES (2008)

Even under the best of circumstances, DNA is constantly subjected to chemical modifications. Several types of DNA damage such as SSB (single strand break), DSB (double strand break), CPDs (cyclobutane pyrimidine dimers), 6-4PPs (6-4 photoproducts) and their Dewar valence isomers have been identified that result from alkylating agents, hydrolytic deamination, free radicals and reactive oxygen species formed by various photochemical processes including UV radiation. There are a number of strategies such as PCR (polymerase chain reaction), comet, halo, TUNEL (Terminal deoxyribonucleotidyltransferase-mediated deoxyuridine triphosphate nick end labeling) assay, HPLC-Electrospray tandem mass spectrometry, FISH (Fluorescence in situ hybridization), FCM (Flow cytometry), annexin V labeling, immunological assays including immunofluorescent and chemiluminescence thymine dimer detection, immunohistochemical assay, Enzyme-linked immunosorbent assay (ELISA), Radio immunoassay (RIA), Gas chromatography-mass spectrometry and electrochemical methods, that are commonly used to detect DNA damage in various organisms. The main aim of this review is to present a brief account of the above mentioned DNA damage detection strategies for the convenience of interested readers.
Detection of Cocaine Use with Wireless Electrocardiogram Sensors (2020)

In recent years, the ability to continuously monitor activities, health, and lifestyles of individuals using sensor technologies has reached unprecedented levels. Such ubiquitous physiological sensing has the potential to profoundly improve our understanding of human behavior, leading to more targeted treatments for a variety of disorders. The long terms goal of this work is development of novel computational tools to support the study of addiction in the context of cocaine use. The current paper takes the first step in this important direction by posing a simple, but crucial question: Can cocaine use be reliably detected using wearable on-body sensors and current machine learning algorithms? We select wireless ECG as the most promising sensing modality for cocaine use detection. The main contributions in this paper include the presentation of a novel clinical study of cocaine use in which a unique set of wireless ECG data were collected, the description of a computational pipeline for inferring morphological features from noisy wireless ECG waveforms, and the evaluation of cocaine use detection algorithms based on data-driven and knowledge-based feature representations. Our results show that cocaine use can be detected with AUC levels above 0.9 in both the within-subjects and between-subjects cases at the 32mg/70kg dosage level.
Composition and yield of non-cellulosic and cellulosic sugars in soluble and particulate fractions during consolidated bioprocessing of poplar biomass by Clostridium thermocellum (2021)

Abstract Background Terrestrial plant biomass is the primary renewable carbon feedstock for enabling transition to a sustainable bioeconomy. Consolidated bioprocessing (CBP) by the cellulolytic thermophile Clostridium thermocellum offers a single step microbial platform for production of biofuels and biochemicals via simultaneous solubilization of carbohydrates from lignocellulosic biomass and conversion to products. Here, solubilization of cell wall cellulosic, hemicellulosic, and pectic polysaccharides in the liquor and solid residues generated during CBP of poplar biomass by C. thermocellum was analyzed. Results The total amount of biomass solubilized in the C. thermocellum fermentation platform was 5.8, 10.3, and 13.7% of milled non-pretreated poplar after 24, 48, and 120 h, respectively. When combined, these results demonstrate solubilization of 24% cellulose and 17% non-cellulosic sugars after 120 h, consistent with prior reports. The solubilization of non-cellulosic sugars by C. thermocellum compared to uninoculated control fermentations was 13 to 36% of arabinose (Ara), xylose (Xyl), galactose (Gal), mannose (Man), and glucose (Glc); and 15% and 3% of fucose and glucuronic acid, respectively. No rhamnose was solubilized and 71% of the galacturonic acid (GalA) was solubilized. These results indicate that C. thermocellum may be selective for the types and/or rate of solubilization of the non-cellulosic wall polymers. Xyl, Man, and Glc were found to accumulate in the fermentation liquor at levels greater than in uninoculated control fermentations, whereas Ara and Gal did not accumulate, suggesting that C. thermocellum solubilizes both hemicelluloses and pectins but utilizes them differently. After five days of fermentation, the amount of Rha in the solid residues increased 27%, indicating that the Rha-containing polymers ( i.e ., rhamnogalacturonan I, RG-I) were not effectively solubilized by C. thermocellum CBP. Comparison of the sugars in the liquor versus solid residue showed that C. thermocellum solubilized hemicellulosic xylan and mannan but did not fully utilize them, solubilized and appeared to utilize pectic homogalacturonan, and did not solubilize pectic RG-I. Conclusions The significant increase in Rha in poplar solid residues following CBP indicates that C. thermocellum did not solubilize RG-I. These results support the hypothesis that this pectic glycan may be a barrier for efficient solubilization of poplar by C. thermocellum .
Parallel Computation of Fuel Jet Diffusion Flame with Dynamic Subdomain Boundary Moving Method. (1998)

Fuel jet diffusion flame flow was simulated by parallel computing on two workstasions of NEC 4800 series with CPU chip of R 4400. MPI, Massage Passing Interface was employed for communication between them. The domain decomposition technique plays an important role in increasing the effciency of parallel processing. In this paper, the dynamic subdomain boundary moving method, where the subdomain boundary is moved to optimize the load balance of each workstation, was applied to calculate a combustion flow. As a result, it was found that the present method was effective when the load balance was disturbed by other users' processes.
Preliminary study on the freeze-drying of human bone marrow-derived mesenchymal stem cells (2010)

Long-term preservation and easy transportation of human bone marrow-derived mesenchymal stem cells (hBM-MSCs) will facilitate their application in medical treatment and bioengineering. A pilot study on the freeze-drying of hBM-MSCs was carried out. hBM-MSCs were loaded with trehalose. The glass transition temperature of the freeze-drying suspension was measured to provide information for the cooling and primary drying experiment. After freeze-drying, various rehydration processes were tested. The highest recovery rate of hBM-MSCs was (69.33±13.08)%. Possible methods to improve freeze-drying outcomes are discussed. In conclusion, the present study has laid a foundation for the freeze-drying hBM-MSCs.
Transitioning DNA-Engineered Nanoparticle Superlattices from Solution to the Solid State* (2020)

In the assembly and crystallization of nanoparticles into ordered lattices, DNA is a powerful structure-directing ligand because its programmability allows for a priori control over the lattice symmetries and lattice constants of the nanoparticle superstructures. Silica encapsulation is a technique commonly used to stabilize inorganic nanoparticles of varying chemical compositions and morphologies against aggregation or oxidation. To verify that the particles remained ordered after the encapsulation process, structural characterization was carried out using small-angle X-ray scattering. Because the unmodified nanoparticle superlattices are held together by DNA, there is an inherent “melting temperature” of the crystal at and above which the lattice dissociates and the nanoparticles become redispersed in solution. During the assembly stage of nanoparticle crystallization, DNA is a useful tool for controlling the structural characteristics of the superlattice due to its ability to form programmable “bonds” between nanoparticles. Nanoparticle functionalization, purification, and crystallization were carried out using literature procedures described extensively elsewhere.
MODELING WEB NAVIGATION USING GRAMMATICAL INFERENCE (2008)

In this article, a method that models user navigation on the web, as opposed to a single website, is presented, aiming to assist the user by recommending pages. User modeling is done through data mining of web usage logs, resulting in aggregate, rather than personal models. The proposed approach extends grammatical inference methods by introducing an extra merging criterion, which examines the semantic similarity of automaton states. The experimental results showed that the method does indeed facilitate the modeling of web navigation, which was not possible with the existing web usage mining methods. However, a content-based recommendation model is shown to still outperform the proposed method, which suggests that the knowledge of the navigation sequence does not contribute to the recommendation process. This is due to the thematic cohesion of navigation sessions, in comparison to the large thematic diversity of web usage data. Among three variants of the proposed method, the one based on Blue Fringe, that examines a larger space of possible merges, performs better.
Halogen activation and radical cycling initiated by imidazole-2-carboxaldehyde photochemistry (2019)

Abstract. Atmospheric aerosol particles can contain light absorbing organic compounds, also referred to as brown carbon (BrC). In the context of the ocean surface and of sea spray aerosol deriving from the latter, light absorbing organic species are also referred to as chromophoric dissolved organic matter (CDOM). Many BrC or CDOM species (especially carbonyls, dicarbonyls or aromatic carbonyls such as imidazole-2-carboxaldehyde (IC)), referred to as photosensitizers, form triplet excited states upon UV-VIS light absorption. These triplet excited states are strong oxidants and may initiate catalytic radical reaction cycles within atmospheric aerosol particles and at their surface, therefore increasing the reactive oxygen species (ROS) production within atmospheric aerosol particles. Triplet states (or ROS resulting from them) can also react with halides generating halogen radicals and additionally molecular halogens compounds, which can be released into the gas phase and may thus contribute to halogen activation. In this work we study the influence of bromide and iodide on the photosensitized HO2 production and release upon UV irradiation of films in a coated wall flow tube (CWFT) containing IC in a matrix of citric acid (CA). Additionally we measured the iodine release upon irradiation of IC/CA films in the CWFT. We use a kinetic model to interpret our results and to assess radical production and iodine release in sea-spray particles. As indicated by the experimental results and confirmed by the model, significant recycling of halogen species occurs via scavenging reactions with HO2, to prevent the full and immediate release of the molecular halogen (bromine and iodine) produced, while partially shutting down the HOx chemistry. The recycling efficiency is higher and affected by diffusion limitations at high viscosity. Our findings also show that halides can increase substantially the BrC or CDOM photosensitized HO2 production (which in turn promotes radical and ROS production) by reacting with triplet statesin sea-spray particles. The iodine production within sea salt aerosol particles due to iodide oxidation by ozone is estimated at 5.9 × 10−5 M s−1 assuming ozone equilibration in the particle. Under diffusion limitation this activation can drop several orders of magnitude in an aged, organic-rich sea-spray derived aerosol (1.1 × 10−7 M s−1 for an ozone diffusion coefficient of 10−12 cm2 s−1). The estimated iodine production from BrC photochemistry amounts to 2.5 × 10−7 M s−1. This indicates that BrC photochemistry can exceed O3 reactive uptake in controlling the rates of iodine activation from sea spray particles under dry or cold conditions where diffusion is slow within particles.
Novel CFD Techniques For In-Cylinder Flows On Tetrahedral Grids (1998)

&lt;div class="htmlview paragraph"&gt;An innovative approach for computing in-cylinder flowfields on tetrahedral grids is developed and demonstrated. The primary focus of the preliminary work presented in this paper is the development of an efficient mesh motion scheme for realistic engine geometries. An automated cell layering technique has been devised which embeds/deletes layers of tetrahedral cells as the cylinder flow domain expands/shrinks. The ability to compute in-cylinder flows using this new “multi-zone” concept is demonstrated for a twin-valve gasoline engine.&lt;/div&gt;
Increase in barrier height of Al/n-GaAs contacts induced by high current (1986)

High forward-gate current (HFGC) density induces an increase of the Al/n-GaAs barrier height from 0.8 to 0.96 eV, thus suggesting the formation of an Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> As layer at the interface. Results show that this interaction is more enhanced by the electron current from the semiconductor to the metal than by thermal treatments. The intense electron flow is believed to contribute to the breaking of the interfacial oxide layer present at the metal-semiconductor interface, thus promoting Al/GaAs interdiffusion. Data were obtained on power MESFET's with Al metallized gate.
Genetic analysis of host–parasite coevolution in human malaria (1997)

Recent twin studies of clinical malaria and immune responses to malaria antigens have underscored the importance of both major histocompatability complex (MHC) and non-MHC genes in determining variable susceptibility and immune responsiveness. By using a combination of whole genome genetic linkage studies of families and candidate genes analysis, non-MHC genes are being mapped and identified. Human leucocyte antigen (HLA) genotype was found to affect susceptibility to severe malaria in a large study of West African children. T lymphocytes that may mediate such resistance have been identified and their target antigens and epitopes characterized. Some of these epitopes show substantial polymorphism, which appears to result from immune selection pressure. Natural variant epitopes have been found to escape T-cell recognition in cytolytic and other T-cell assays. More recently a novel immune escape mechanism has been described in viral infections, altered peptide ligand antagonism, whereby variants of a T-cell epitope can downregulate or ablate a T cell response to the index peptide. The likely implications of such immune escape mechanisms for the population structure of malaria parasites, for HLA associations with malaria infection and disease, and for the design of new malaria vaccines, are discussed. The evolutionary consequences of such molecular interactions can be assessed by using mathematical models that capture the dynamic of variable host and parasite molecules. Combined genetic, immunological and mathematical analysis of host and parasite variants in natural populations can identify some mechanisms driving host-parasite coevolution.
Ectopeptidases in tumour biology: a review. (2006)

Cell membrane-bound proteolytic enzymes (ectopeptidases) are integral membrane proteins, orientated asymmetrically with the catalytic site exposed to the extracellular surface, which enables a versatile range of physiological and pathological functions. Ectopeptidases may regulate the release of many growth factors and their receptors into the circulation, as well as activating or inactivating circulating signalling molecules, thereby regulating the availability of ligands for the corresponding receptors. Additionally, many of these ectopeptidases have functions not limited to proteolysis, but are able in themselves to function as receptors, transducing intracellular signals. A versatile range of functions, such as the modulation of cell-signalling, matrix degradation, cell adhesion and migration, which are particularly important for tumour cell growth and dissemination, are attributed largely to the ectopeptidases. Even a minor disruption in the normal proteolytic equilibrium can influence tumor progression, and a range of ectopeptidases, including neutral endopeptidase 24.11, aminopeptidase N, dipeptidyl peptidase IV, angiotensin-converting enzyme, and the disintegrin-metalloproteinases, have been shown to be involved in tumour development and metastasis. The ability to degrade and inactivate peptide hormones and growth factors, with the resultant modulation of the tumour-host interface, may play an important role in the pathogenesis, development or progression of a range of cancers, and the extracellular orientation of the ectopeptidases makes them particularly accessible, and therefore interesting, with regard to therapeutical applications.
Geographic distribution and molecular analysis of porcine reproductive and respiratory syndrome viruses circulating in swine farms in the Republic of Korea between 2013 and 2016 (2018)

This up-to-date information regarding recent field PRRSVs should be taken into consideration when creating strategies for the application of PRRS control measures, including vaccination in the field.