gebhart/patrepeval huggingface dataset:
Reciprocating flow-based centrifugal microfluidics mixer (2009)

Proper mixing of reagents is of paramount importance for an efficient chemical reaction. While on a large scale there are many good solutions for quantitative mixing of reagents, as of today, efficient and inexpensive fluid mixing in the nanoliter and microliter volume range is still a challenge. Complete, i.e., quantitative mixing is of special importance in any small-scale analytical application because the scarcity of analytes and the low volume of the reagents demand efficient utilization of all available reaction components. In this paper we demonstrate the design and fabrication of a novel centrifugal force-based unit for fast mixing of fluids in the nanoliter to microliter volume range. The device consists of a number of chambers (including two loading chambers, one pressure chamber, and one mixing chamber) that are connected through a network of microchannels, and is made by bonding a slab of polydimethylsiloxane (PDMS) to a glass slide. The PDMS slab was cast using a SU-8 master mold fabricated by a two-level photolithography process. This microfluidic mixer exploits centrifugal force and pneumatic pressure to reciprocate the flow of fluid samples in order to minimize the amount of sample and the time of mixing. The process of mixing was monitored by utilizing the planar laser induced fluorescence (PLIF) technique. A time series of high resolution images of the mixing chamber were analyzed for the spatial distribution of light intensities as the two fluids (suspension of red fluorescent particles and water) mixed. Histograms of the fluorescent emissions within the mixing chamber during different stages of the mixing process were created to quantify the level of mixing of the mixing fluids. The results suggest that quantitative mixing was achieved in less than 3 min. This device can be employed as a stand alone mixing unit or may be integrated into a disk-based microfluidic system where, in addition to mixing, several other sample preparation steps may be included.
Activation of the nuclear receptor FXR improves hyperglycemia and hyperlipidemia in diabetic mice (2006)

Farnesoid X receptor (FXR) plays an important role in maintaining bile acid and cholesterol homeostasis. Here we demonstrate that FXR also regulates glucose metabolism. Activation of FXR by the synthetic agonist GW4064 or hepatic overexpression of constitutively active FXR by adenovirus-mediated gene transfer significantly lowered blood glucose levels in both diabetic db/db and wild-type mice. Consistent with these data, FXR null mice exhibited glucose intolerance and insulin insensitivity. We further demonstrate that activation of FXR in db/db mice repressed hepatic gluconeogenic genes and increased hepatic glycogen synthesis and glycogen content by a mechanism that involves enhanced insulin sensitivity. In view of its central roles in coordinating regulation of both glucose and lipid metabolism, we propose that FXR agonists are promising therapeutic agents for treatment of diabetes mellitus.
High-rate space-time layered OFDM (2002)

We derive a layered space-time scheme for multi-antenna orthogonal frequency-division multiplexed transmissions over frequency-selective channels. Compared with existing alternatives, the proposed scheme can attain very high spectral efficiency as well as improved performance. Enhanced diversity gains document its superior performance that is also tested by simulation.
Large-Scale Identification and Quantification of Covalent Modifications in Therapeutic Proteins (2009)

Covalent modifications on therapeutic proteins are traditionally monitored by chromatographic techniques, which quantify limited number of protein modifications at a time. In this report, computer algorithms for automated analyses of liquid chromatography/tandem mass spectrometry (LC/MS/MS) data for large-scale identification and quantification of known and unknown modifications are described. Peptide identification is achieved by comparing the experimental fragmentation spectrum to the predicted spectrum of each native or modified peptide. Peak areas of related peptide ions under their selected-ion chromatograms (SIC) are used for relative quantification of modified peptides. A matched window function is used to generate SIC for more reliable quantification. In an LC/MS/MS analysis of a tryptic digestion of an IgG2 monoclonal antibody, 1712 peptide ions were identified with a false-discovery rate of approximately 0.4%, and 227 modifications were identified and quantified. The accuracy of the mass spectrometry-based quantification is evaluated by comparing the abundance of different glycoforms determined by mass spectrometry to that determined by a fluorescence-based chromatography method. This large-scale method may potentially replace many chromatographic methods for assessing the quality attributes of therapeutic proteins.
Pathophysiology, treatment, and animal and cellular models of human ischemic stroke (2011)

Stroke is the world's second leading cause of mortality, with a high incidence of severe morbidity in surviving victims. There are currently relatively few treatment options available to minimize tissue death following a stroke. As such, there is a pressing need to explore, at a molecular, cellular, tissue, and whole body level, the mechanisms leading to damage and death of CNS tissue following an ischemic brain event. This review explores the etiology and pathogenesis of ischemic stroke, and provides a general model of such. The pathophysiology of cerebral ischemic injury is explained, and experimental animal models of global and focal ischemic stroke, and in vitro cellular stroke models, are described in detail along with experimental strategies to analyze the injuries. In particular, the technical aspects of these stroke models are assessed and critically evaluated, along with detailed descriptions of the current best-practice murine models of ischemic stroke. Finally, we review preclinical studies using different strategies in experimental models, followed by an evaluation of results of recent, and failed attempts of neuroprotection in human clinical trials. We also explore new and emerging approaches for the prevention and treatment of stroke. In this regard, we note that single-target drug therapies for stroke therapy, have thus far universally failed in clinical trials. The need to investigate new targets for stroke treatments, which have pleiotropic therapeutic effects in the brain, is explored as an alternate strategy, and some such possible targets are elaborated. Developing therapeutic treatments for ischemic stroke is an intrinsically difficult endeavour. The heterogeneity of the causes, the anatomical complexity of the brain, and the practicalities of the victim receiving both timely and effective treatment, conspire against developing effective drug therapies. This should in no way be a disincentive to research, but instead, a clarion call to intensify efforts to ameliorate suffering and death from this common health catastrophe. This review aims to summarize both the present experimental and clinical state-of-the art, and to guide future research directions.
Identification of Web Query Intent Based on Query Text and Web Knowledge (2010)

In this paper, we propose a novel approach to identifying user intents of search engine queries. Specifically, we recast it as a classification problem, in which four types of features are adopted. The classification features are based on deep linguistic analysis of queries as well as search engine feedbacks. We evaluate the method with the real web query data. The results show that about 88% of the test queries can be correctly identified with the classification framework via combining all the 4 types of features.
A panel of genes methylated with high frequency in colorectal cancer (2014)

This study has characterised a panel of 23 genes that show elevated DNA methylation in >50% of CRC tissue relative to non-neoplastic tissue. Six of these genes (SOX21, SLC6A15, NPY, GRASP, ST8SIA1 and ZSCAN18) show very low methylation in non-neoplastic colorectal tissue and are candidate biomarkers for stool-based assays, while 11 genes (BCAT1, COL4A2, DLX5, FGF5, FOXF1, FOXI2, GRASP, IKZF1, IRF4, SDC2 and SOX21) have very low methylation in peripheral blood DNA and are suitable for further evaluation as blood-based diagnostic markers.
PHOSPHONOACETATE DERIVATIVES OF OLIGODEOXYRIBONUCLEOTIDES (1996)

Abstract A deoxyribodinucleotide phosphonoacetate derivative has been prepared, separated into individual diastereomers, and incorporated into oligodeoxyribonucleotides possessing alternating phosphodiester and phosphonoacetate backbone linkages. The hybridization properties and enzymatic stabilities of these oligonucleotides have been studied.
Rules of the Road: Predicting Driving Behavior with a Convolutional Model of Semantic Interactions (2019)

We focus on the problem of predicting future states of entities in complex, real-world driving scenarios. Previous research has used low-level signals to predict short time horizons, and has not addressed how to leverage key assets relied upon heavily by industry self-driving systems: (1) large 3D perception efforts which provide highly accurate 3D states of agents with rich attributes, and (2) detailed and accurate semantic maps of the environment (lanes, traffic lights, crosswalks, etc). We present a unified representation which encodes such high-level semantic information in a spatial grid, allowing the use of deep convolutional models to fuse complex scene context. This enables learning entity-entity and entity-environment interactions with simple, feed-forward computations in each timestep within an overall temporal model of an agent's behavior. We propose different ways of modelling the future as a distribution over future states using standard supervised learning. We introduce a novel dataset providing industry-grade rich perception and semantic inputs, and empirically show we can effectively learn fundamentals of driving behavior.
Two Different Subunits Associate to Create Isoform-Specific Platelet-derived Growth Factor Receptors (1989)

Recent evidence has demonstrated that there is more than one form of platelet-derived growth factor (PDGF) receptor and that these receptors differ in their specificity for the multiple isoforms of PDGF. We present evidence that high affinity binding of PDGF requires association of two different receptor subunits: an alpha-subunit that can bind either a B- or an A-chain of PDGF, and a beta-subunit that can bind only a B-chain. The alpha- and beta-subunits appear to be similar in size but can be distinguished by binding specificity and by an antireceptor monoclonal antibody, PR7212, which recognizes only the beta-subunit. In the absence of PDGF, these subunits either exist separately or form rapidly reversible complexes. In the presence of PDGF, receptor subunits of appropriate specificity interact with a PDGF molecule to form a high affinity complex. Both the absolute and relative numbers of these two PDGF receptor subunits vary on different cell types and correspond to differences in the mitogenic sensitivity of cells to the different PDGF isoforms.
Gamma-rays induced morphological changes in gladiolus (2010)

A three year mutagenesis programme was Carried out using physical mutagens (gamma rays) on four Cultivars of gladiolus viz. Peter Pear (V1), Advance Red (V2), White Prosperity (V3) and Nova Lux (V4). Three sets of each variety, consisting of 20 uniform corms and each corm 30 g (5cm diameter) in weight, were irradiated With 5, 10 & 15 KRD of gamma rays at N.B.R.I., Lucknow in Feb., 2007. A set of 10 untreated corms of each variety was used as control. Reduction in survival rate.root length, no. of spike/plant, no. of floret/spike, days to flower, self life, vase life, floret size, no. of corm/plant and weight of corm/plant were observed after irradiation and with Increase in exposure of gamma rays. In M1 generation, significant increase in plant height and spike length at 5 KRD & stunted growth of plant/spike length at 10KRD gamma irradiation were observed in all cultivars of gladiolus. Morphological abnormalities in leaf and plants with abnormal leaves increased with increase in exposure of gamma rays. Positive correlation exists between doses of gamma rays and number of spike/plant in M1 generation. Floret/spike was positively correlated to 5 KRD gamma irradiation and it was become negative at higher doses of irradiation. In all the cultivars the intensity of inhibition increased with increasing exposures though lower exposure in some cases was stimulatory. Cent per cent mortality was recorded in plants treated with 15 KRD gamma rays and eliminated from population at the end of first year. On the basis of present observation it may be concluded that 5 to 10 KRD doses of gamma rays are suitable for induction of somatic mutation in various cultivars of gladiolus.
Detection of O antigens inEscherichia coli (2011)

Lipopolysaccharide on the surface of Escherichia coli constitutes the O antigens which are important virulence factors that are targets of both the innate and adaptive immune systems and play a major role in host-pathogen interactions. O antigens are responsible for antigenic specificity of the strain and determine the O serogroup. The designation of O serogroups is important for classifying E. coli strains, for epidemiological studies, in tracing the source of outbreaks of gastrointestinal or other illness, and for linking the source to the infection. For conventional serogroup identification, serotyping by agglutination reactions against antisera developed for each of the O serogroups has been used. In the last decade, many O-antigen gene clusters that encode for the enzymes responsible for the synthesis of the variable oligosaccharide region on the surface of the bacteria have been sequenced and characterized. Unique gene sequences within the O-antigen gene clusters have been targeted for identification and detection of many O groups using the polymerase chain reaction and microarrays. This review summarizes current knowledge on the DNA sequences of the O-antigen gene clusters, genetic-based methods for O-group determination and detection of pathogenic E. coli based on O-antigen and virulence gene detection, and provides perspectives on future developments in the field.
Chemical Patterning and Physical Refinement of Reactive Superhydrophobic Surfaces (2012)

An approach to the modification and post-fabrication chemical patterning of amine-reactive superhydrophobic surfaces is reported. The approach is based on the layer-by-layer fabrication of azlactone-containing polymer multilayers, and permits the direct covalent attachment and subsequent patterning of chemical and biological "inks" using a variety of practical and low-cost pattern-transfer methods.
Intravenous Delivery of siRNA Targeting CD47 Effectively Inhibits Melanoma Tumor Growth and Lung Metastasis (2013)

CD47 is a "self marker" that is usually overexpressed on the surface of cancer cells to enable them to escape immunosurveillance. Recognition of CD47 by its receptor, signal regulatory protein α (SIRPα), which is expressed in the macrophages, inhibits phagocytic destruction of cancer cells by the macrophages. In this study, we have first shown that clinical isolates of human melanoma significantly upregulate CD47, possibly as a mechanism to defend themselves against the macrophages. We then exploited RNA interference (RNAi) technology to test the hypothesis that knocking down CD47 in the tumor cells will render them targets for macrophage destruction; hence, creating a novel anti-cancer therapy. Anti-CD47 siRNA was encapsulated in a liposome-protamine-hyaluronic acid (LPH) nanoparticle (NP) formulation to address the challenge of targeted delivery of siRNA-based therapeutics in vivo. Efficient silencing of CD47 in tumor tissues with systemic administration of LPH(CD47) also significantly inhibited the growth of melanoma tumors. In a lung metastasis model, LPH(CD47) efficiently inhibited lung metastasis to about 27% of the untreated control. Moreover, no hematopoietic toxicity was observed in the animals that received multiple doses of LPH(CD47). Our findings indicate CD47 as a potential prognostic marker for melanoma development as well as a target for therapeutic intervention with RNAi-based nanomedicines.
Mouse Fibroblasts Are Reprogrammed to Oct-4 and Rex-1 Gene Expression and Alkaline Phosphatase Activity by Embryonic Stem Cell Extracts (2007)

A recent remarkable study has shown that when mouse NIH-3T3 fibroblasts are exposed to an embryonic stem cell (ESC) extract, the majority of them expresses the Oct-4 gene, form ESC-like colonies, and embryoid-like bodies that differentiate into cells of the three germ layers. The use of cell extracts for inducing cell dedifferentiation could be a powerful system to obtain large quantities of pluripotent cells. It is thus of crucial importance that the robustness of this method of cell transdifferentiation is tested by other laboratories before it is advanced to a more ambitious use in cell therapy programs. We report here our experimental observations using the same reprogramming protocol on STO and NIH-3T3 mouse fibroblasts. Three are the main results: first, we confirmed an enduring reprogramming activity of the ESC extract, although on a much smaller number of cells that varies from approximately 0.003 to 0.04% of the total population of fibroblasts and with an effect limited to the induction of Oct-4 and Rex-1 gene expression and alkaline phosphatase activity. Second, the expression of OCT-4, SSEA-1, and Forssman antigen proteins was never detected. Third, our work has clearly demonstrated that ESCs may survive the procedure of extract preparation, may be source of contamination that is expanded in culture and give false positive results.
Monoclonal Antibody Clearance (2006)

The neonatal Fc receptor (FcRn) plays a critical role in regulating IgG homeostasis in vivo. There are mixed reports on whether modification of the interaction with FcRn can be used as an engineering strategy to improve the pharmacokinetic and pharmacodynamic properties of monoclonal antibodies. We tested whether the T250Q/M428L mutations, which improved the pharmacokinetics of humanized IgGs in the rhesus monkey, would translate to a pharmacokinetic benefit in both cynomolgus monkeys and mice when constructed on a different humanized IgG framework (anti-tumor necrosis factor-alpha (TNFalpha)). The T250Q/M428L anti-TNFalpha variant displayed an approximately 40-fold increase in binding affinity to cynomolgus monkey FcRn (C-FcRn) at pH 6.0, with maintenance of the pH binding dependence. We also constructed another anti-TNFalpha variant (P257I/Q311I) whose binding kinetics with the C-FcRn was similar to that of the T250Q/M428L variant. The binding affinity of the T250Q/M428L variant for murine FcRn was increased approximately 500-fold, with maintenance of pH dependence. In contrast to the interaction with C-FcRn, this interaction was driven mainly by a decrease in the rate of dissociation. Despite the improved in vitro binding properties of the anti-TNFalpha T250Q/M428L and P257I/Q311I variants to C-FcRn, the pharmacokinetic profiles of these molecules were not differentiated from the wild-type antibody in cynomolgus monkeys after intravenous administration. When administered intravenously to mice, the T250Q/M428L anti-TNFalpha variant displayed improved pharmacokinetics, characterized by an approximately 2-fold slower clearance than the wild-type antibody. The discrepancy between these data and previously reported benefits in rhesus monkeys and the inability of these mutations to translate to improved kinetics across species may be related to a number of factors. We propose extending consideration to differences in the absolute IgG-FcRn affinity, the kinetics of the IgG/FcRn interaction, and differences in the relative involvement of this pathway in the context of other factors influencing the disposition or elimination of monoclonal antibodies.
GestureAnalyzer (2014)

Understanding the intent behind human gestures is a critical problem in the design of gestural interactions. A common method to observe and understand how users express gestures is to use elicitation studies. However, these studies require time-consuming analysis of user data to identify gesture patterns. Also, the analysis by humans cannot describe gestures in as detail as in data-based representations of motion features. In this paper, we present GestureAnalyzer, a system that supports exploratory analysis of gesture patterns by applying interactive clustering and visualization techniques to motion tracking data. GestureAnalyzer enables rapid categorization of similar gestures, and visual investigation of various geometric and kinematic properties of user gestures. We describe the system components, and then demonstrate its utility through a case study on mid-air hand gestures obtained from elicitation studies.
Oxidation of wool: effect of hydrogen peroxide on wool (1936)

The purpose of this investigation was to provide quantitative data showing the effect of oxidizing agents on wool as a basis for studying all processes in which wool is exposed to oxidation reactions. The work reported in this paper deals only with the effect of hydrogen peroxide.
The Effect of Fabric Structural Parameters and Fiber Type on the Comfort-Related Properties of Commercial Apparel Fabrics (2015)

The effect of fabric structural parameters and fiber type on the comfort-related properties, namely water vapor resistance and thermal resistance, of commercial apparel (suiting) fabrics, containing both natural and man-made fibers have been studied using a Permetest. The effects of the various fabric parameters on the comfort-related properties were determined and quantified using multiple regression analyses and best fit regression equations. It was found that the fabric parameters, mass and thickness in particular, had a much greater effect on the comfort-related properties, than did the fiber type or blend, or fabric structure.
Identification and Characterization of Microvesicles Secreted by 3T3-L1 Adipocytes: Redox- and Hormone-Dependent Induction of Milk Fat Globule-Epidermal Growth Factor 8-Associated Microvesicles (2007)

Adipocytes are now recognized as endocrine cells secreting adipocytokines, regulating multiple metabolic pathways. In this study, we addressed secretion of microvesicles by 3T3-L1 adipocytes. We found that MFG-E8, one of the exosomal proteins, was present in the microvesicles and was distributed in the sucrose density fractions with 1.13-1.20 g/ml, which has been reported for exosomes. Several integral, cytosolic, and nuclear proteins such as caveolin-1, c-Src kinase, and heat shock protein 70 were also found to be microvesicle components. Unexpectedly, adiponectin was also substantially distributed in the microvesicle fractions. Furthermore, proteomic analysis of the microvesicles revealed that many other proteins such as extracellular matrix-related proteins were also present. Microvesicles secreted by 3T3-L1 adipocytes exhibited heterogeneity in size and comprised both smaller exosome-like and larger membrane vesicles as revealed by electron microscopy. Milk fat globule-epidermal growth factor 8 (MFG-E8)-associated adiposomes exhibited binding activity toward phosphatidylserine and apoptotic cells. MFG-E8 in the microvesicles was reduced when cultured in the low-glucose medium or cultured in the high-glucose medium with antioxidant N-acetyl cysteine. Insulin and TNF-alpha also up-regulated MFG-E8 in the microvesicles. Moreover, MFG-E8 was strongly up-regulated in the hypertrophic adipose tissue, predominantly in adipocyte fractions, of diet-induced obese C57BL/6 mice, where increased oxidative stress is induced. Thus, it is suggested that microvesicles, especially MFG-E8-associated ones, modulate adipose functions under redox- and hormone-dependent regulation. Based on the above findings, the adipocyte-derived microvesicles were named adiposomes.