gebhart/patrepeval huggingface dataset:
Recent advances in blood‐related proteomics (2005)

Blood is divided in two compartments, namely, plasma and cells. The latter contain red blood cells, leukocytes, and platelets. From a descriptive medical discipline, hematology has evolved towards a pioneering discipline where molecular biology has permitted the development of prognostic and diagnostic indicators for disease. The recent advance in MS and protein separation now allows similar progress in the analysis of proteins. Proteomics offers great promise for the study of proteins in plasma/serum, indeed a number of proteomics databases for plasma/serum have been established. This is a very complex body fluid containing lipids, carbohydrates, amino acids, vitamins, nucleic acids, hormones, and proteins. About 1500 different proteins have recently been identified, and a number of potential new markers of diseases have been characterized. Here, examples of the enormous promise of plasma/serum proteomic analysis for diagnostic/prognostic markers and information on disease mechanism are given. Within the blood are also a large number of different blood cell types that potentially hold similar information. Proteomics of red blood cells, until now, has not improved our knowledge of these cells, in contrast to the major progresses achieved while studying platelets and leukocytes. In the future, proteomics will change several aspects of hematology.
Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain (2017)

High gut microbiome diversity, high-fibre intake and OTUs implicated in animal models of improved energy metabolism are all correlated with lower term weight gain in humans independently of calorie intake and other confounders.
AN INTRODUCTION TO LOW-DENSITY PARITY-CHECK CODES (2003)

International Telemetering Conference Proceedings / October 20-23, 2003 / Riviera Hotel and Convention Center, Las Vegas, Nevada
Vitamin K deficiency: the linking pin between COPD and cardiovascular diseases? (2017)

Cardiovascular diseases are prevalent in patients with chronic obstructive pulmonary disease (COPD). Their coexistence implies that many COPD patients require anticoagulation therapy. Although more and more replaced by direct oral anticoagulants, vitamin K antagonists (VKAs) are still widely used. VKAs induce profound deficiency of vitamin K, a key activator in the coagulation pathway. It is recognized however that vitamin K is also an essential cofactor in the activation of other extrahepatic proteins, such as matrix Gla protein (MGP), a potent inhibitor of arterial calcification. No or insufficient MGP activation by the use of VKAs is associated with a rapid progression of vascular calcification, which may enhance the risk for overt cardiovascular disease. Vitamin K consumption, on the other hand, seems to have a protective effect on the mineralization of arteries. Furthermore, vascular calcification mutually relates to elastin degradation, which is accelerated in patients with COPD associating with impaired survival. In this commentary, we hypothesize that vitamin K is a critical determinant to the rate of elastin degradation. We speculate on the potential link between poor vitamin K status and crucial mechanisms of COPD pathogenesis and raise concerns about the use of VKAs in patients with this disease. Future intervention studies are needed to explore if vitamin K supplementation is able to reduce elastin degradation and vascular calcification in COPD patients.
Cesium Lead Bromide Perovskite-Based Lithium–Oxygen Batteries (2021)

The main challenge for lithium-oxygen (Li-O<sub>2</sub>) batteries is their sluggish oxygen evolution reaction (OER) kinetics and high charge overpotentials caused by the poorly conductive discharge products of lithium peroxide (Li<sub>2</sub>O<sub>2</sub>). In this contribution, the cesium lead bromide perovskite (CsPbBr<sub>3</sub>) nanocrystals were first employed as a high-performance cathode for Li-O<sub>2</sub> batteries. The battery with a CsPbBr<sub>3</sub> cathode can exhibit the lowest charge overpotential of 0.5 V and the best cycling performance of 400 cycles among all the reported perovskite-based Li-O<sub>2</sub> cells, which represents a new benchmark. Most importantly, the density functional theory (DFT) calculations further prove that the rate limitation step during OER processes is the decomposition of LiO<sub>2</sub> to form O<sub>2</sub> and Li<sup>+</sup>, and the weak adsorption strength between CsPbBr<sub>3</sub> surfaces and LiO<sub>2</sub> results in a low charge overpotential for the CsPbBr<sub>3</sub>-based Li-O<sub>2</sub> battery. This work first demonstrates the good potential of CsPbBr<sub>3</sub> for application in metal-air batteries.
Treatment of Human Embryonic Stem Cells with Different Combinations of Priming and Inducing Factors Toward Definitive Endoderm (2012)

Despite the enormous progress in studying definitive endoderm (DE) differentiation from human embryonic stem cells (hESCs), none of the reported protocols have produced a universal, cost-effective, and competent DE with the capability to further differentiate into endodermal derivatives. In this study, by using a 2-step differentiation strategy, we have treated hESCs for 1 day with "priming" small molecules (SM), [stauprimide, NSC-308848, rapamycin (Rapa), and/or CHIR] and for the next 3 days with "inducing" SM (LY294002, cymarin, IDE1, and/or IDE2) in conjunction with activin A. In the positive control group, we treated hESCs with Wnt3a (25 ng/mL) for 1 day and activin A (100 ng/mL; W/A100-A100) for the next 3 days. Gene expression analysis showed that treatment of hESCs with 100 nM Rapa and 50 ng/mL activin A (Rapa-A50) out of 25 combinations of factors gave rise to higher expressions of 2 DE-specific genes, SOX17 and FOXA2. Similar results were obtained after treating 2 other hESC lines with this regimen. To investigate the competency of Rapa-A50-induced DE for further differentiation into endodermal derivatives, these cells and W/A100-A100-induced DE cells (positive control) were further differentiated into pancreatic progenitors (PP), then into pancreatic endocrine (PE) cells using 5 previously described differentiation protocols. Gene analysis of differentiated cells showed that the established protocols were insufficient to enable universal differentiation into PE, whereas Rapa-A50-induced DE cells were more competent for PP differentiation in a protocol-dependent manner. Additionally, Rapa-A50-induced DE had the capability to differentiate into hepatocyte-like cells (HLCs) as efficiently as W/A100-A100-induced DE. These data have indicated that hESCs primed with Rapa, and induced by a lower concentration of activin A, could lead to DE that had the capability to further differentiate into HLCs and PP cells, but not PE cells. Thus, current protocols for the differentiation of DE into PE still need additional study.
Adaptive multichannel digital filter with lattice-escalator hybrid structure (2002)

An adaptive multichannel digital filter structure that can be used in multichannel noise-cancelling applications is described. The proposed structure is a hybrid of the lattice and the escalator (Gram-Schmidt) structures, and the coefficients are updated using the least-mean-square algorithm. In the lattice-escalator hybrid structure, complete decorrelation of multiple reference signals is achieved by successively generating forward prediction error vectors via the lattice structure and decorrelating the elements of the error vectors using escalator linear combiners at each lattice stage. Simulation results indicate that the convergence speed of the hybrid structure is as fast as the escalator realization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Short-Term Effect of Estrogen on Human Bone Marrow Fat (2015)

Bone marrow fat, an unique component of the bone marrow cavity increases with aging and menopause and is inversely related to bone mass. Sex steroids may be involved in the regulation of bone marrow fat, because men have higher bone marrow fat than women and clinical observations have suggested that the variation in bone marrow fat fraction is greater in premenopausal compared to postmenopausal women and men. We hypothesized that the menstrual cycle and/or estrogen affects the bone marrow fat fraction. First, we measured vertebral bone marrow fat fraction with Dixon Quantitative Chemical Shift MRI (QCSI) twice a week during 1 month in 10 regularly ovulating women. The vertebral bone marrow fat fraction increased 0.02 (95% CI, 0.00 to 0.03) during the follicular phase (p = 0.033), and showed a nonsignificant decrease of 0.02 (95% CI, -0.01 to 0.04) during the luteal phase (p = 0.091). To determine the effect of estrogen on bone marrow fat, we measured vertebral bone marrow fat fraction every week for 6 consecutive weeks in 6 postmenopausal women before, during, and after 2 weeks of oral 17-β estradiol treatment (2 mg/day). Bone marrow fat fraction decreased by 0.05 (95% CI, 0.01 to 0.09) from 0.48 (95% CI, 0.42 to 0.53) to 0.43 (95% CI, 0.34 to 0.51) during 17-β estradiol administration (p < 0.001) and increased again after cessation. During 17-β estradiol administration the bone formation marker procollagen type I N propeptide (P1NP) increased (p = 0.034) and the bone resorption marker C-terminal crosslinking telopeptides of collagen type I (CTx) decreased (p < 0.001). In conclusion, we described the variation in vertebral bone marrow fat fraction among ovulating premenopausal women. And among postmenopausal women, we demonstrated that 17-β estradiol rapidly reduces the marrow fat fraction, suggesting that 17-β estradiol regulates bone marrow fat independent of bone mass.
Joint de-noising and fusion of 2D video and depth map sequences sensed by low-powered tof range sensor (2013)

We propose a joint de-noising and data fusion approach where the fused modalities come from conventional high-resolution photo or video camera and low-resolution range sensor of Time-of-flight (ToF) type, operating in restricted conditions of low-emitting power and low number of sensor elements. Our approach includes identifying the various noise sources and suggesting suitable remedies at particular stages of data sensing and fusion. More specifically, fixed pattern noise and system noise are treated at a preliminary denoising stage working on range data only. In contrast to other 2D video/depth fusion approaches, which suggest working in planar coordinates, our approach includes additional denoising refinement in the space of 3D world coordinate system (i.e. point cloud space). Furthermore, the high-resolution grid resampling is performed as an iterative non-uniform to uniform resampling based on the Richardson method. This improves the performance compared to approaches based on low-to-high grid upsampling and subsequent refinement. We report experimental results where the achieved quality of fused data is the same as if the ToF sensor was operating in normal (low-noise) sensing mode.
Effect of the acute and chronic administration of the selective 5‐HT<sub>6</sub> receptor antagonist SB‐271046 on the activity of midbrain dopamine neurons in rats: An in vivo electrophysiological study (2004)

This study examined the effect of the acute and repeated per os (p.o.) administration of the selective 5-HT(6) receptor antagonist SB-271046, on the number, as well as the firing pattern of spontaneously active dopamine (DA) neurons in the rat substantia nigra pars compacta (SNC) and ventral tegmental area (VTA) in anesthetized male Sprague-Dawley rats. This was accomplished using the technique of extracellular in vivo electrophysiology. A single p.o. administration of either 1, 3, or 10 mg/kg of SB-271046 did not significantly alter the number of spontaneously active SNC DA neurons per stereotaxic electrode tract compared to vehicle-treated animals. The acute administration of either 1 or 3 mg/kg of SB-271046 did not significantly alter the number of spontaneously active VTA DA neurons. In contrast, a significant decrease in the number of spontaneously active VTA DA neurons was observed after a single administration of 10 mg/kg of SB-271046 compared to vehicle-treated animals. The acute p.o. administration of SB-271046 significantly altered the firing pattern parameters of all (bursting + nonbursting DA neurons) DA neurons, particularly those in the VTA, compared to vehicle-treated animals. The repeated p.o. administration (once per day for 21 days) of 1, 3, or 10 mg/kg of SB-271046 did not significantly alter the number of spontaneously active VTA DA neurons compared to vehicle-treated animals. The repeated administration of 3 or 10 mg/kg of SB-271046 significantly increased the number of spontaneously active SNC DA neurons compared to vehicle controls. Overall, the repeated administration of SB-271046 had relatively little effect on the firing pattern of midbrain DA neurons. The results obtained following the chronic administration of SB-271046 show that this compound has a profile different from that of typical or atypical antipsychotic drugs in this model. Clinical studies are required to understand what role 5-HT(6) receptor blockade might eventually play in the treatment of schizophrenia.
Neural network acoustic model with decision tree clustered triphones (2008)

This article tries to compare the performance of neural network and Gaussian mixture acoustic models (GMMs). We argue that using a multi layer perceptron as an emission probability estimator in hidden Markov model based automatic speech recognition can lead to better results than when the more traditional Gaussian mixtures are applied. We present a solution on how to model triphone phonetic units with neural networks and we show that this also leads to better performance in comparison with GMMs. The superior performance of the neural networks comes at a cost of extremely long training times.
Design and implementation of IMU-based human arm motion capture system (2012)

This paper presents the design of a generic inertial measurement unit (IMU) module for motion capture system. The module consists of 32-bit microcontroller with gyroscope, accelerometer, and magnetometer to provide orientation estimation of human limbs. An orientation estimation algorithm that compensates magnetic distortion is implemented. Our main contribution is on the sensor network which is low cost but high speed. We developed a serial-chain network for sensors interconnection in which UART communication is used. We also consider frame alignment issue in developing human arm motion capture to improve tracking accuracy. A simple frame calibration method is implemented and tested.
Influence of process parameters on chemical-mechanical polishing of copper (1998)

Chemical-mechanical polishing (CMP) appears to be the most promising technology for global planarization of device topography and metal patterning in the damascene technique. Cu has been recently studied as a candidate material for future integrated circuit metallization because of its low resistivity and better electromigration resistance than current Al alloy interconnects. In order to achieve a highly reliable CMP process for Cu delineation it is necessary to examine the limitations of the process. Integrating Cu CMP into an interconnect processing sequence requires a detailed understanding of how process parameters affect different aspects of the CMP process and therefore the quality of the patterned lines.
CREB is a critical regulator of normal hematopoiesis and leukemogenesis (2007)

The cAMP-responsive element binding protein (CREB) is a 43-kDa nuclear transcription factor that regulates cell growth, memory, and glucose homeostasis. We showed previously that CREB is amplified in myeloid leukemia blasts and expressed at higher levels in leukemia stem cells from patients with myeloid leukemia. CREB transgenic mice develop myeloproliferative disease after 1 year, but not leukemia, suggesting that CREB contributes to but is not sufficient for leukemogenesis. Here, we show that CREB is most highly expressed in lineage negative hematopoietic stem cells (HSCs). To understand the role of CREB in hematopoietic progenitors and leukemia cells, we examined the effects of RNA interference (RNAi) to knock down CREB expression in vitro and in vivo. Transduction of primary HSCs or myeloid leukemia cells with lentiviral CREB shRNAs resulted in decreased proliferation of stem cells, cell- cycle abnormalities, and inhibition of CREB transcription. Mice that received transplants of bone marrow transduced with CREB shRNA had decreased committed progenitors compared with control mice. Mice injected with Ba/F3 cells expressing either Bcr-Abl wild-type or T315I mutation with CREB shRNA had delayed leukemic infiltration by bioluminescence imaging and prolonged median survival. Our results suggest that CREB is critical for normal myelopoiesis and leukemia cell proliferation.
Gold is acting more like a risk asset than a safe haven : commodities (2012)

The gold price peaked above $1 570 / oz ahead of the latest Euro-debt talks, and analysts reckon we might get some renewed investor interest - mainly sovereign wealth funds and central banks looking to buy as prices edge lower.
Sonifying ECoG seizure data with overtone mapping: a strategy for creating auditory gestalt from correlated multichannel data (2012)

Presented at the 18th International Conference on Auditory Display (ICAD2012) on June 18-21, 2012 in Atlanta, Georgia.
Variability in Hepatitis B Virus DNA: Phylogenetic, Epidemiological and Clinical Implications (1996)

Hepatitis B virus has the smallest of all known human DNA virus genomes (3.2 kb) and a unique replication strategy with an intermediate reverse transcription step. The naturally occurring genetic variability between different HBV strains provides the basis for phylogenetic analysis. Four main genotypes of HBV have been found, with the possible existence of 1 or 2 more. The different genotypes largely follow a distinctive geographical distribution. Point mutations and nucleotide deletions in the genes (pre-S and S) encoding different forms of the surface protein have been shown to arise both spontaneously and after interferon treatment or vaccination. An immune escape mechanism is believed to be the reason for these mutations. The clinical implications of variations in the HBV X gene have not been widely studied, but these variations may be of importance in the development of hepatocellular carcinoma. Seroconversion from HBeAg to anti-HBe can be correlated with specific changes in the core promoter, and/or with a translational stop in precore codon 28. In both cases the production of HBeAg protein would be shut off. Mutations in the precore region may have a larger impact at another level, by inhibiting or enhancing viral replication through changes in folding of the transcript.
An anthropometric comparison between young female spanish and brazilian dancers (2000)

Not much is known about the influence of dance on the morphological and anthropometric development of young and teenager dancers. Bibliography on the subject is almost nonexistent, given the difficulty to find studies about this type of population. It is very important to control the morphological development of girls that study dance in order to quantify, qualify and achieve better results. Therefore, the purpose of this study was to compare the anthropometric characteristics of two populations: one group of classical ballet dancers, average age 11.12 ± 1.00, from Porto Alegre, Brazil, and the other group including dancers of Spanish dance and classical ballet, with an average age of 11.50 ± 0.94, from Cordoba, Spain. A parallel was established between the populations, comparing and relating the data obtained. Fifty anthropometrical variables were measured, including body weight, stature, height, skinfolds, girths, breadths and lengths, based on the ISAK (International Society of the Advancement of kinanthropometry) protocol, proposed by Ross and Marfell-Jones (1991). Descriptive statistical methodology was used in order to obtain a database for the two samples studied and the t test was used to compare their data. The conclusion was that the two groups are very similar despite the fact that a few statistically different variables were found. These differences were mainly related to breadths.
Data without (operational) variables (2001)

Application of this framework to text, including editorials and free answers to questionnaires as well as application to (social) survey data, supports their its for these purposes and the cartographic methods suggest that micro theories embedded in these methods reduce the load of a priori assumptions “normally” required for both text analysis and survey analysis. The applications suggest a research path applicable to “ordinary” sociological variables, including education, income, occupation, and gender, that shifts the burden of argument away from variance explained criteria and toward an integration of theory and method, guided by principles of parsimony and consistency. Quantitative sociology has grown by borrowing methods from the experimental sciences even though, for the most part, our data are observational. Where the procedures of experimental science can be applied, data analysis can exploit simplifying assumptions because good experimental design removes correlations among independent variables that exist nature, outside the experiment, as well as effects of unmeasured variables. Where the science is, of necessity, observational, these simplifications can not be guaranteed and, as a result, the analyses reached through by use of some of the standard “workhorse” techniques of the statistical repertoire may not be valid and conclusions reached by the application of these techniques are in doubt. This paper explores an alternative framework for data analysis in quanitative sociology, bypassing the statistics associated with experimental methods. Specifically, it explores generalizations of the method and quantitative theory used by physical surveyors, generalizing them to the needs of observational data.
Image Inpainting by Band Matching, Seamless Cloning and Area Sub-Division (2008)

We propose a novel image inpainting method composed of two parts: band matching and seamless cloning. In band matching, a band enclosing the boundary of a missing region is compared to those from the other parts of the image. The inner area of the minimum difference band is then copied to the missing region. Even though this band matching results in successful inpainting in many practical applications, brightness discontinuity (a seam) may appear between the filled missing region and its neighborhood. We apply seamless cloning to remove such discontinuity between the two regions. However, since this basic method using one patch may not deal with cases where there are abrupt changes of color or brightness along the boundary, we furthermore devise one more step: target sub-division. The target area is subdivided into small sub-areas, and the band matching and seamless cloning are applied to each of them. The multiple results from the sub-division are then ordered according to inpainting quality, which is measured based on the edge map or discontinuity map along the boundary band.
Risk management of digital certificates in ad hoc and P2P networks (2008)

In nonhierarchical public key infrastructure (PKI), any user can be a certificate authority (CA) to issue digital certificates to other users. As there is no single root CA, it is difficult to check the validity of certificates issued by unknown CAs. It is very risky to trust them without in-depth analysis. How users issue certificates in the real world has not been studied. Solomon Aschpsilas conformity experiment reveals that peoplespsila decisions are influenced by others. To reduce the risk of trusting malicious certificate issuers, we propose two novel methods, micro method and macro method, for users to make trust decisions based on the relationships among the CAs. They will improve the security in ad hoc networks and peer-to-peer (P2P) communications.