gebhart/patrepeval huggingface dataset:
The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures (2022)

All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, <i>Enterobacteriaceae</i>, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying <i>Legionella</i> and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.
Tailoring Wing Structures for Reduced Drag Penalty in Off-Design Flight Conditions (2004)

The induced drag penalty associated with off-design flight conditions is investigated. The investigation is limited to off-design flight conditions at a lower lift coefficient than the design lift coefficient. Two types of total angle of incidence distribution obtained at the design condition are studied. One is the distribution for elliptic spanloads and the other is the spanload distribution for straight-line wrapped surfaces. It is shown that the penalty
may be significant as the structural deformation changes the total angle of incidence distribution and the spanload. The penalty is higher for the wing with the near optimal elliptic spanload at the design flight condition. The wing with straight-line wrapped surfaces does not have the minimum induced drag at the design condition. However, it is found to be insensitive to the structural deformation.
Empirical model of the photon path length for a single fiber reflectance spectroscopy device (2009)

A reflectance spectroscopic device that utilizes a single fiber for both light delivery and collection has advantages over classical multi-fiber probes. This study presents a novel empirical relationship between the single fiber path length and the combined effect of both the absorption coefficient, mua (range: 0.1-6 mm-1), and the reduced scattering coefficient, micro's (range: 0.3 - 10 mm-1), for different anisotropy values (0.75 and 0.92), and is applicable to probes containing a wide range of fiber diameters (range: 200-2000 microm). The results indicate that the model is capable of accurately predicting the single fiber path length over a wide range (r = 0.995; range: 180-3940 microm) and predictions do not show bias as a function of either microa or micro's .
Oculomotor and Perceptual Adaptation to Natural Scenes Statistics (2018)

As we explore the 3D environment with our eyes, binocular coordination is required to allow both eyes to land on the object of interest quickly and accurately. From an analysis of natural-scene statistics, we know that points in the upper visual field are likely to be farther than the current fixation point, that points in the lower field are likely to be nearer, and that points to the left and right of fixation are likely to be farther. We investigated whether binocular eye movements are biased toward landing on the most likely depths in different parts of the visual field. We measured where the eyes land in depth when making upward, downward, leftward, and rightward saccades without visual feedback (aka open loop). The results show that open-loop movements are divergent with upward, leftward, and rightward saccades, and convergent with downward saccades. In other words, the initial landing points for binocular, open-loop saccades are consistent with the statistics of natural scenes. We also investigated whether this oculomotor behavior is compatible with the positions of corresponding retinal points in the two eyes. The externalization of those points is the horopter, which is the locus of points in space where stereo depth is most accurate. We asked whether the landing points for binocular, open-loop saccades tend to be on the horopter. We found that they are, which means that when the eyes move to a new position, the observed convergence or divergence is biased toward placing the landing point near the horopter such that that point stimulates corresponding points. Our results show that the oculomotor system is adapted to the statistics of natural scenes. Meeting abstract presented at VSS 2018
A simple synthesis of kaurenoic esters and other derivatives and evaluation of their antifungal activity (2005)

Representative esters derived from kaurenoic acid were prepared in order to evaluate their antifungal properties. Alkyl and substituted benzyl esters were obtained in good yield under mild conditions by esterification of kaurenoic acid with the corresponding alkyl halide in KOH-acetone. All synthesized compounds were tested for antifungal properties against pathogenic yeasts, hialohyphomycetes and dermatophytes. Kaurenoic acid and derivatives containing a free carboxyl group were moderately active against dermatophytes.
Intracellular Ca2+ signals evoked by stimulation of nicotinic acetylcholine receptors in SH‐SY5Y cells: contribution of voltage‐operated Ca2+ channels and Ca2+ stores (2002)

Neuronal nicotinic acetylcholine receptors (nAChR) can regulate several neuronal processes through Ca2+-dependent mechanisms. The versatility of nAChR-mediated responses presumably reflects the spatial and temporal characteristics of local changes in intracellular Ca2+ arising from a variety of sources. The aim of this study was to analyse the components of nicotine-evoked Ca2+ signals in SH-SY5Y cells, by monitoring fluorescence changes in cells loaded with fluo-3 AM. Nicotine (30 microm) generated a rapid elevation in cytoplasmic Ca2+ that was partially and additively inhibited (40%) by alpha7 and alpha3beta2* nAChR subtype selective antagonists; alpha3beta4* nAChR probably account for the remaining response (60%). A substantial blockade (80%) by CdCl2 (100 microm) indicates that voltage-operated Ca2+ channels (VOCC) mediate most of the nicotine-evoked response, although the alpha7 selective antagonist alpha-bungarotoxin (40 nm) further decreased the CdCl2- resistant component. The elevation of intracellular Ca2+ levels provoked by nicotine was sustained for at least 10 min and required the persistent activation of nAChR throughout the response. Intracellular Ca2+ stores were implicated in both the initial and sustained nicotine-evoked Ca2+ responses, by the blockade observed after ryanodine (30 microm) and the inositoltriphosphate (IP3)-receptor antagonist, xestospongin-c (10 microm). Thus, nAChR subtypes are differentially coupled to specific sources of Ca2+: activation of nAChR induces a sustained elevation of intracellular Ca2+ levels which is highly dependent on the activation of VOCC, and also involves Ca2+ release from ryanodine and IP3-dependent intracellular stores. Moreover, the alpha7, but not alpha3beta2* nAChR, are responsible for a fraction of the VOCC-independent nicotine-evoked Ca2+ increase that appears to be functionally coupled to ryanodine sensitive Ca2+ stores.
Use of yeast cell walls; β-1, 3/1, 6-glucans; and mannoproteins in broiler chicken diets (2009)

Two experiments were carried out to evaluate the effect of dietary addition of yeast cell wall (YCW); beta-1, 3/1, 6-glucan (BG); and mannoprotein complex (MP) purified fractions in broilers. In experiment 1, there was a control diet and 5 experimental diets containing, respectively: 10 mg of avilamycin (AVI)/kg of feed, 500 mg of YCW/kg of feed, 95 mg of MP/kg of feed, 145 mg of BG/kg of feed, and 95 mg of MP plus 145 mg of BG/kg of feed. All birds were vaccinated via drinking water against Newcastle disease virus at 9 d of age. At 42 d, chickens fed AVI, YCW, MP + BG, and BG diets had similar BW not significantly different from chickens fed the control diet. The antibody response of Newcastle disease virus vaccine was not affected by any experimental treatment. Broilers fed MP + BG diet had greater thymus weights (P </= 0.05), as a percentage of BW than those from the control and AVI treatments, but similar with respect to YCW and BG treatments. In experiment 2, there was a group-fed basal diet and 3 additional experimental groups receiving the basal diet supplemented with, respectively: 500 mg of YCW/kg of feed, 190 mg of MP/kg of feed, and 227 mg of BG/kg of feed. At 42 d of age, no difference in broiler growth rates was observed. Samples of the jejunum were collected at 21 d of age to determine villus height. Significantly higher villus height was observed in YCW, MP, and BG groups compared with that of the control group. The relative percentage of liver weight (P </= 0.01) was lower in broilers fed YCW than in broilers fed the control diet, but no differences were observed in respect to chickens fed BG. Data of these studies suggested that the changes in thymus and liver relative weights and villus morphology of broilers were induced with the same intensity by the use of complete YCW, MP + BG, and BG supplements.
LBODP050 Examination Of The Effectiveness Of Diabetic Nephropathy Treatment Targeting Chrebp Activity (2022)

Abstract Diabetic nephropathy (DN) is the main cause of chronic kidney disease (CKD) and is characterized by elevated urinary albumin to creatinine ratio (UACR) and serum creatinine, and decreased glomerular filtration rate. Anti hypertensive agents are used for DN treatment, however, the effects of these drugs are insufficient, and the establishment of more effective treatment methods is desired. Carbohydrate responsive element binding protein (ChREBP) is one of the factors reported to be involved in the onset and progression of DN (1). Furthermore, whole body ablation of ChREBP suggested that the progression of DN was suppressed in the rodent model (2). On the other hand, the effectiveness of pharmaceutical ChREBP suppression is unclear, thus, we performed administration experiment to DN model mice using ChREBP activity inhibitor and examined the effects of pharmaceutical ChREBP activity suppression on renal function of diabetic mice. First, we established high-throughput screening system capable of detecting ChREBP activity and performed screening of Tohoku university compound library. The result compound, D-532, was ChREBP activity specific inhibitor without cell toxicity. D-532 directly binds to DNA-binding domain of ChREBP, and inhibits the transcriptional activity. We next performed administration experiment using type I DN model mice. D-532 treatment group showed an improvement tendency of the low body weight compared with that of vehicle treatment group, while it had no effect on blood glucose level. About renal functions, both of UACR and serum creatinine were significantly lower in D-532 treatment group. Importantly, renal tissues such as glomeruli and renal tubules were preserved in D-532 treatment group compared with in vehicle treatment group. In vivo as well, D-532 suppressed ChREBP target genes mRNA expression, and RNA-seq analysis with mice renal cortex RNA at the end of D-532 administration experiment indicated that D-532 suppressed excessive oxidative stress through the ChREBP activation under diabetes. These results indicate that ChREBP suppression is effective on DN rodent model, and ChREBP activity inhibitor D-532 may have potential as a new treatment for DN in the future. Reference: (1) Suzuki et al., Endocr J. 2019 Mar 28;67(3): 335-345. (2) Zhang et al., Eur Rev Med Pharmacol Sci. 2017 Jan;21(1): 42-47. Presentation: No date and time listed
From agriculture residue to upgraded product: The thermochemical conversion of sugarcane bagasse for fuel and chemical products (2019)

A holistic investigation considering the sugarcane bagasse characterization, fast pyrolysis and upgrading of bio-oil applying two nickel-based catalysts is presented. The bio-oil composition is correlated to the bagasse building blocks, and the hydrotreatment reaction pathways are identified. Despite the high ash content of 6.75 wt%, 60.1 wt% of bio-oil was obtained by fast pyrolysis, attributed to low concentration of potassium (0.08 wt%) and low humidity (2.80 wt%) observed in the bagasse. Upgraded bio-oil with 60.3% less water and 43.3% less oxygen were obtained with Ni/SiO2, resulting in an HHV 63% higher compared to bagasse. Ni-Cr/SiO2 showed the highest hydrogenation activity and the highest conversion of acids, converting 25.7% of acetic acid and 14.95% of propionic acid while Ni/SiO2 was more active for conversion of compounds containing aromatic groups. The higher viscosity of upgraded oils in comparison to the fast pyrolysis bio-oil indicates that the stabilization during the heating ramp can be improved to suppress polymerization. Hence, sugarcane bagasse is an attractive feedstock with an overall final yield of 30.5 wt% of the upgraded product.
Joint maximum likelihood decoding with limited number of receive antennas in overloaded MIMO-OFDM system (2013)

This paper presents a joint decoding scheme for block coded signals in an overloaded multiple-input multiple-output (MIMO)-OFDM system. In a normal MIMO-OFDM system, the number of the transmit antenna is the same as that of the received antenna. In the conventional MIMO system, symbol detection is carried out over the signals received by multiple antenna elements and is separated from decoding. However, in order to increase the throughput of the system, a more number of antenna elements is required, which leads to larger power consumption owing to additional radio frequency (RF) units. Instead of splitting detection and decoding, in this paper, a joint maximum likelihood (ML) decoding scheme in an overloaded MIMO-OFDM system is presented. Based on ideal interleaving, independence among coded symbols spread over subcarriers is assumed. As an example of the proposed system, bit error rate performance of Hamming coded and spatially multiplexed signals with the joint ML decoding on a Rayleigh fading channel is investigated. Furthermore, a complexity reduction scheme of the joint ML decoding is also evaluated through computer simulation and bit error performance with the proposed complexity reduction scheme is presented.
The Role of Nebulizer Gas Flow in Electrosonic Spray Ionization (ESSI) (2011)

In this work, we investigated the role of the nebulizer gas flow in electrosonic spray ionization (ESSI), by systematically studying the relation between the flow and the ion signals of proteins, such as cytochrome c and holomyoglobin using ESSI-mass spectrometry (MS). When a neutral solution was delivered with a small sample flow rate (≤5 μL/min), no obvious transition from electrospray ionization (ESI) to ESSI was found as the gas velocity varies from subsonic to supersonic speed. Droplets mostly experienced acceleration instead of breakup by the high-speed nebulizer gas. On the contrary, using particular experimental conditions, such as an acidic solution or high sample flow rate (≥200 μL/min), more folded protein ions appear to be kept in droplets of diminishing size due to breakup by the high-speed nebulizer gas in ESSI compared with ESI. Theoretical analyses and numerical simulations were also performed to explain the observed phenomena. These systematic studies clarify the ionization mechanism of ESSI and provide valuable insight for optimizing ESSI and other popular pneumatically assisted electrospray ionization methods for future applications.
Abstract 17507: Simulation of Transcatheter Aortic Valve Replacement and Assessment of Regurgitation in in-vitro Pulsatile Model With Patient-specific Anatomy (2016)

Introduction: Aortic regurgitation (AR) following transcatheter aortic valve replacement (TAVR) has been shown to be associated with increased mortality. However, regurgitant volume cannot be direc...
Improved Low-Reynolds-Number k-e Model Based on Direct Numerical Simulation Data (1998)

An improved low-Reynolds-number κ-e turbulence model is proposed. The model is designed not only to conform with the near-wall characteristics obtained with direct numerical simulation data but also to possess the correct asymptotic behavior in the vicinity of the wall. The key features of this model are the adoption of the Taylor microscale in the damping function and the inclusion of the pressure diffusion terms in the κ and e equations. Further applications of the present model to a two-dimensional backward-facing step flow indicate that the present model reproduces correctly the skin-friction and near-wall heat transfer coefficients
Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy (2016)

Dilated cardiomyopathy (DCM) is one of the main causes of heart failure (called cardiomyopathies) in adults. Alterations in epigenetic regulation (i.e., DNA methylation) have been implicated in the development of DCM. Here, we identified a total of 1828 differentially methylated probes (DMPs) using the Infinium 450K HumanMethylation Bead chip by comparing the methylomes between 18 left ventricles and 9 right ventricles. Alterations in DNA methylation levels were observed mainly in lowly methylated regions corresponding to promoter-proximal regions, which become hypermethylated in severely affected left ventricles. Subsequent mRNA microarray analysis showed that the effect of DNA methylation on gene expression regulation is not unidirectional but is controlled by the functional sub-network context. DMPs were significantly enriched in the transcription factor binding sites (TFBSs) we tested. Alterations in DNA methylation were specifically enriched in the cis-regulatory regions of cardiac development genes, the majority of which are involved in ventricular development (e.g., TBX5 and HAND1).
Papulopustular Eruptions on Inner Thighs (2023)

ABSTRACT Teledermatology is a term to describe the provision of dermatologic medical services through telecommunication technology. This is a teledermatology case of papulopustular eruptions on the inner thighs.
A Study on Transimpedance Amplifier in 0. 35 µm CMOS Technology (2012)

This paper presents a design of the transimpedance amplifier using 0.35m CMOS technology. In the proposed transimpedance amplifier, feedback resistor R F of conventional transimpedance amplifier has been replaced by NMOS transistor as an active feedback resistor. This circuit operates at 3.3V power supply voltage and for a photocurrent of 0.5A.The proposed transimpedance amplifier having low noise, high gain and large dynamic range. The simulated results of transimpedance gain in single stage and three stage transimpedance amplifiers is 4.43 M and 4.39 M at gate voltage of 0.4V. Power dissipation of single stage and three stage transimpedance amplifier is 602.04 W and 1.781mW at gate voltage of 2.0V.
X‐linked mental retardation with alacrima and achalasia—Triple A syndrome or a new syndrome? (2011)

We describe a consanguineous Israeli Arab kindred with five males in two interrelated families with intellectual disabilities, alacrima, achalasia, and mild autonomic dysfunction. Adrenal function is normal. Their phenotype is similar to the phenotype observed in autosomal recessive Triple A syndrome except for the presence of mental retardation in all affected individuals. The pedigree is compatible with either X-linked or autosomal recessive inheritance. Sequencing of the AAAS gene causing autosomal recessive Triple A syndrome did not reveal mutations. Genotyping of affected family members identified a 16.4 Mb continuous segment of identical alleles shared by the patients between markers rs2748314 and rs5906782 on Xp11.23-p21, establishing linkage to chromosome X. This study further confirms genetic heterogeneity in Triple A syndrome and points to a clinically different subtype including significant cognitive impairment.
Ambroxol Increases the Choline but Not Fatty Acid Incorporation into Lung Phospholipids in Experimental Lung Disorders (1987)

Ambroxol, a drug capable of elevating the phospholipid content in healthy rabbit lungs, was tested on two models of experimental lung injury, lung changes in sepsis induced by a peritonitis and in bromcarbamide intoxication. The phospholipid content of the lungs and the synthesis of the individual phospholipids phosphatidylcholine (PC) and sphingomyeline were measured in vitro by incubation of lung slices with labeled phospholipid precursors. Influenced by the drug, the phospholipid content increases to 132% in the peritonitis experiments and to 111% in the bromcarbamide experiments. The peritonitis experiments show the increase in phospholipid synthesis to result from an enhanced choline incorporation into PC up to 192% and into sphingomyeline up to 630%. The values for the bromcarbamide experiments are 411% for PC and 485% for sphingomyeline, respectively. There was no statistically significant difference in the incorporation of fatty acids in the treated and untreated animals. We conclude that ambroxol possibly stimulates the phospholipid synthesis in injured lungs by stimulating the choline phosphatcytidyltransferase, but not the incorporation of fatty acids into PC in those lungs. These findings may be important to the surfactant system of the lung consisting mainly of PC.
Gap junctions support the sustained phase of hypoxic pulmonary vasoconstriction by facilitating calcium sensitization (2013)

These results imply that GJs are critically involved in the signalling pathways leading to Rho kinase-dependent Ca²⁺ sensitization during sustained HPV, but not elevation of intracellular Ca²⁺, and may explain the dependence of the former on an intact endothelium.
Dynamic Tracking Algorithm for Time-Varying Neuronal Network Connectivity using Wide-Field Optical Image Video Sequences (2020)

Propagation of signals between neurons and brain regions provides information about the functional properties of neural networks, and thus information transfer. Advances in optical imaging and statistical analyses of acquired optical signals have yielded various metrics for inferring neural connectivity, and hence for mapping signal intercorrelation. However, a single coefficient is traditionally derived to classify the connection strength between two cells, ignoring the fact that neural systems are inherently time-variant systems. To overcome these limitations, we utilized a time-varying Pearson's correlation coefficient, spike-sorting, wavelet transform, and wavelet coherence of calcium transients from DIV 12-15 hippocampal neurons from GCaMP6s mice after applying various concentrations of glutamate. Results provide a comprehensive overview of resulting firing patterns, network connectivity, signal directionality, and network properties. Together, these metrics provide a more comprehensive and robust method of analyzing transient neural signals, and enable future investigations for tracking the effects of different stimuli on network properties.