gebhart/patrepeval huggingface dataset:
Quantitation of the Area of Overlap between Second-Derivative Amide I Infrared Spectra To Determine the Structural Similarity of a Protein in Different States (1996)

Maintaining a native-like structure of protein pharmaceuticals during lyophilization is an important aspect of formulation. Infrared spectroscopy can be used to evaluate the effectiveness of formulations in protecting the secondary structural integrity of proteins in the dried solid. This necessitates making quantitative comparisons of the overall similarity of infrared spectra in the conformationally sensitive amide I region. We initially used the correlation coefficient r, as defined by Prestrelski et al. (Biophys. J. 1993, 65, 661-671), for this quantitation. Occasionally, we noticed that the r value did not agree with a visual assessment of the spectral similarity. In some cases this was due to an offset in baselines, which led artifactually to an unreasonably low r value. Conversely, if the spectra were baseline corrected and there existed a large similarity between peak positions, but differences in relative peak heights, the r value would be unreasonably high. Our approach to avoiding these problems is to use area-normalized second-derivative spectra. We have found that quantitating the area of overlap between area-normalized spectra provides a reliable, objective method to compare overall spectral similarity. In the current report, we demonstrate this method with selected protein spectra, which were taken from experiments where unfolding was induced by lyophilization or guanidine hydrochloride, and artificial data sets. With this analysis, we document how problems associated with calculation of the correlation coefficient, r, are avoided.
Videofluoroscopic evaluation of prosthetic fit and residual limbs following transtibial amputation. (1998)

The clinical examination of residual limb complications is usually subjective and may lead to inappropriate, expensive adjustments or replacement of the prosthesis. Plain films and xeroradiography only provide static images of the residual limb and socket. The purpose of this pilot study was to develop a videofluoroscopic technique to evaluate dynamic residual limb-socket relationships during gait. Sixteen videofluoroscopic studies were performed in subjects with transtibial amputation. Anteroposterior (A-P) and lateral views were obtained. The wide view field was better than the coned view. The optimal settings were found to be in the 80 to 110 kV range during manual setting (mean values: 86.3 kV in A-P view, and 88.9 kV in lateral view). The following information was obtained: A-P residual limb motion, piston action, rolling of soft tissues, and dynamic relationships of various pressure-sensitive and pressure-tolerant parts of the residual limb with the inner socket. We consider videofluoroscopy to be a potentially valuable diagnostic procedure for evaluating difficult prosthetic fitting problems and residual limb complications, and providing a better understanding of the residual limb-socket interface during different phases of the gait cycle.
FUNCTION AND SPECIFICITY OF HUMAN NATURAL KILLER CELL RECEPTORS (1997)

In humans, natural killer lymphocytes express HLA class I-specific inhibitory receptors belonging to at least two different molecular families. The first is represented by members of the Ig superfamily that are involved in the recognition of different groups of HLA class I alleles, and the second is represented by a molecular complex formed by CD94 and NKG2A that displays a broad specificity for various class I molecules including the 'non-classical' HLA-G molecules. In addition to the inhibitory receptors, a series of activating receptors has been identified. Some display the same specificities as the corresponding inhibiting receptors and can be viewed as HLA class I-specific activating receptors. Another group of activating receptors appear to be involved in the cytolytic activity against HLA-'negative' target cells. These receptors are clearly non-MHC specific and, under physiological conditions, their function is suppressed by the HLA class I-specific inhibitory receptors.
High-Output Saturation Power Variable Confinement Slab-Coupled Optical Waveguide Amplifier (2011)

A variable optical confinement concept was incorporated into a slab-coupled optical waveguide amplifier to increase output saturation power. This amplifier demonstrates an unsaturated gain of 21.1 dB and an output saturation power of +27.6 dBm.
The case for cothymia: mixed anxiety and depression as a single diagnosis (2001)

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Liquid crystal–carbon nanotube dispersions (2005)

Parallel alignment of nanotubes can be obtained by dispersion in a self-organizing anisotropic fluid such as a nematic liquid crystal. Exploiting the cooperative reorientation of liquid crystals, the overall direction of the nanotube alignment can be controlled both statically and dynamically by the application of external fields. These can be electric, magnetic, mechanic, or even optic in nature. Employing multiwall as well as single-wall carbon nanotubes, we show their parallel alignment along a uniform liquid crystal director field and electrically verify their reorientation behavior for two complementary geometries. These demonstrate electrically controlled carbon nanotube OFF–ON and ON–OFF switches. Further applicational potential will be outlined.
Scalable routing protocols for mobile ad hoc networks (2002)

The growing interest in mobile ad hoc network techniques has resulted in many routing protocol proposals. Scalability issues in ad hoc networks are attracting increasing attention these days. We survey the routing protocols that address scalability. The routing protocols included in the survey fall into three categories: flat routing protocols; hierarchical routing approaches; GPS augmented geographical routing schemes. The article compares the scalability properties and operational features of the protocols and discusses challenges in future routing protocol designs.
Collections of Copper Nanocrystals Characterized by Different Sizes and Shapes:  Optical Response of These Nanoobjects (2004)

The use of reverse micelles makes it possible to produce copper nanocrystals characterized by various sizes and shapes. By increasing the water content, the average size of the metallic nanocrystals increases from 3 to 13 nm. Structural investigations clearly indicate the formation of pure copper with various crystallographic structures. The absorption spectra of the corresponding colloidal solutions exhibit two plasmon modes in the UV−visible range, around 560 and 640 nm. The progressive emergence of the first mode (Mie's resonance of a perfect sphere) with the increase in the mean particle size is attributed to a mere finite-size effect. The second resonance is explained in terms of nanocrystal shape.
Biochemical and NMR studies on structure and release conditions of RNA‐containing vesicles shed by human colon adenocarcinoma cells (1989)

Large amounts of particulate material, mostly lipid vesicles, are released by human colon adenocarcinoma HCT-8R cells when they are packed at high density in saline solution. RNA is also present in the released structures. Vesicle sheding is displayed only by healthy and viable cells. The process, in our experimental conditions, lasts up to 40 min, and can be restored by supplementing cells with nutrients and oxygen. RNA and lipids give rise to IH and 3IP NMR signals. The process is somehow related to a thermotropic transition observed by means of IH NMR spectroscopy for peculiar lipid domains in the plasma membrane. Analysis of 3IP NMR spectra of the phosphodiester groups, upon pH variation, indicates strong interaction between RNA and proteins in an assembled structure. A constant amount of polyA+ RNA can be recovered from the vesicles. The electrophoretic pattern and in vitro protein synthesis indicate that mRNA can be isolated as a functionally active molecule with a major 5 Kb fraction.
Role of selective peroxisome proliferator‐activated receptor modulators in managing cardiometabolic disease: tale of a roller‐coaster (2014)

Abstract Atherogenic dyslipidaemia is a hypertriglyceridaemic phenotype, associated with increased plasma concentrations of small, dense low‐density lipoprotein ( sdLDL ) particles, triglyceride‐rich lipoproteins ( TRLs ) and non‐high‐density lipoprotein cholesterol (non‐ HDL ‐C), and low HDL particles. Atherogenic dyslipidaemia commonly accompanies several metabolic disorders including type 2 diabetes, metabolic syndrome, non‐alcoholic fatty liver disease ( NAFLD ) and obesity, and increases the risk of cardiovascular disease ( CVD ). Statins significantly lower plasma LDL ‐cholesterol and CVD risk, but their efficacy in correcting hypertriglyceridaemia is limited. Untreated hypertriglyceridaemia may partly account for residual risk of CVD in patients on statin treatment. Activators of peroxisome proliferator‐activated receptor ( PPAR ) α are more effective in correcting TRL and HDL metabolism than statins. A dual PPARα /δ agonist ( GFT ‐505) may have additional benefits on hepatic insulin sensitivity, steatosis and fibrosis. Selective PPAR modulators ( SPPARMs ) have the potential of increasing therapeutic specificity, while reducing unwanted off‐target effects. This review provides a summary of findings from randomized controlled trials of the efficacy of fenofibrate (as the most widely used PPARα agonist) and novel selective PPARα ( ABT ‐335 and k‐877), PPARα /δ ( GFT ‐505), PPARδ ( MBX ‐8025 and GW501516 ) and PPARγ ( INT131 ) agonists in the treatment of atherogenic dyslipidaemia and NAFLD .
Design and analysis of a switched-capacitor-based step-up DC/DC converter with continuous input current (1999)

This paper presents the use of the current control scheme in switched-capacitor (SC)-based step-up dc/dc converter. It not only includes all positive characteristics of previous SC converters, including small size, light weight, high power density, and the amenability to IC hybridization, but also has the prominent features of continuous input current waveform and better regulation capability than the traditional SC converters. The problem of conducted electromagnetic interference with the supply network, which generally exists in previous SC converters, is highly suppressed. The concept of energy transfer is achieved by using dual SC step-up converter cells operating in antiphase. Each cell is switching between two topologies for the same duration. The dc voltage conversion ratio is controlled by the current control scheme in order to adjust the charging profile of the capacitors. A generalized n-stage converter is presented and is analyzed by a simplified third-order state-space equation set. The static and dynamic behaviors and the design constraints of the converter are derived. A prototype of the 30 W 5 V/12 V two-stage converter has been built, giving an overall efficiency of 78% with power density of 15 W/in/sup 3/. Its stability of operation is also presented.
A novel TRPV4-specific agonist inhibits monocyte adhesion and atherosclerosis (2016)

TRPV4 ion channel mediates vascular mechanosensitivity and vasodilation. Here, we sought to explore whether non-mechanical activation of TRPV4 could limit vascular inflammation and atherosclerosis. We found that GSK1016790A, a potent and specific small-molecule agonist of TRPV4, induces the phosphorylation and activation of eNOS partially through the AMPK pathway. Moreover, GSK1016790A inhibited TNF-α-induced monocyte adhesion to human endothelial cells. Mice given GSK1016790A showed increased phosphorylation of eNOS and AMPK in the aorta and decreased leukocyte adhesion to TNF-α-inflamed endothelium. Importantly, oral administration of GSK1016790A reduced atherosclerotic plaque formation in ApoE deficient mice fed a Western-type diet. Together, the present study suggests that pharmacological activation of TRPV4 may serve as a potential therapeutic approach to treat atherosclerosis.
Improving Calibration of 3-D Video Oculography Systems (2004)

Eye movement recordings with video-based techniques have become very popular, as long as they are restricted to the horizontal and vertical movements of the eye. Reliable measurement of the torsional component of eye movements, which is especially important in the diagnosis and investigation of pathologies, has remained a coveted goal. One of the main reasons is unresolved technical difficulties in the analysis of video-based images of the eye. Based on simulations, we present solutions to two of the primary problems: a robust and reliable calibration of horizontal and vertical eye movement recordings, and the extraction of suitable iris patterns for the determination of the torsional eye position component.
Regulation of Phosphate Homeostasis by PTH, Vitamin D, and FGF23 (2010)

In contrast to the regulation of calcium homeostasis, which has been extensively studied over the past several decades, relatively little is known about the regulation of phosphate homeostasis. Fibroblast growth factor 23 (FGF23) is part of a previously unrecognized hormonal bone-parathyroid-kidney axis, which is modulated by PTH, 1,25(OH)(2)-vitamin D (1,25(OH)(2)D), dietary and serum phosphorus levels. Synthesis and secretion of FGF23 by osteocytes are positively regulated by 1,25(OH)(2)D and serum phosphorus and negatively regulated, through yet unknown mechanisms, by the phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX) and by dentin matrix protein 1 (DMP1). In turn, FGF23 inhibits the synthesis of 1,25(OH)(2)D, and it may negatively regulate the secretion of parathyroid hormone (PTH) from the parathyroid glands. However, FGF23 synergizes with PTH to increase renal phosphate excretion by reducing expression of the renal sodium-phosphate cotransporters NaPi-IIa and NaPi-IIc in the proximal tubules. Most insights gained into the regulation of phosphate homeostasis by these factors are derived from human genetic disorders and genetically engineered mice, which are reviewed in this paper.
Regulatory T cells in virus infections (2006)

This review discusses situations when the magnitude and function of immune responses to virus infection are influenced by regulatory T cells (Tregs). The focus is on CD4+ CD25+ forkhead box protein 3+ natural Tregs (nTregs). The immune response may be limited in magnitude and efficacy when animals with normal nTreg function are infected with virus. This limitation can be observed both in vitro and in vivo. In the case of herpes simplex virus (HSV), animals depleted of nTregs prior to infection more effectively control the virus. With some virus infections, Treg responses (either nTregs or interleukin-10-dependent adaptive Tregs) appear to contribute to immune dysfunction, accounting for viral persistence and chronic tissue damage. This may occur with hepatitis C virus and some retrovirus infections that include human immunodeficiency virus (HIV). Under other circumstances, the nTreg response is judged to be beneficial, as it may help limit the severity of tissue damage associated with an immunoinflammatory reaction to virus infection. Such a situation occurs in HSV-induced immunopathological lesions in the eye. With HIV, nTregs may help limit chronic immune activation that may precede collapse of the immune system. This review also discusses how virus infections become recognized by nTreg responses and how such responses might be manipulated to increase immunity or to limit virus-induced immunopathology.
In situ hybridization (1987)

These proceedings collect papers on genetic aspects of neurobiology. Topics include: gene expression in mammalian cells, in situ hybridization with RNA probes, mRNA in brain cells, neuropeptide gene expression, genetic mapping, and localization of peptide hormone gene expression.
Enhancement of Complement Activation and Opsonophagocytosis by Complexes of Mannose-Binding Lectin with Mannose-Binding Lectin-Associated Serine Protease After Binding to Staphylococcus aureus (2002)

Human mannose-binding lectin (MBL) is a serum protein of the innate immune system that circulates as a complex with a group of so-called MBL-associated serine proteases (MASP-1, MASP-2, and MASP-3). Complexes of MBL-MASP2 are able to activate the complement system in an Ab and C1-independent fashion after binding of the lectin to appropriate microbial sugar arrays. We have evaluated the additive effect of the lectin pathway relative to other complement activation pathways and the subsequent effect on neutrophil phagocytosis. Complement activation in the sera of MBL-deficient individuals was studied with and without the addition of exogenous MBL-MASP. Flow cytometry was used to measure the deposition of C4, factor B, C3b, and iC3b on Staphylococcus aureus. Deposition of the first cleavage product of the lectin pathway, C4b, was increased using the sera of three different MBL-deficient individuals when exogenous MBL-MASP was added. Factor B was deposited in association with C4, but there was no evidence of independent alternative pathway activation. Similar enhancement of C3b deposition was also observed, with evidence of elevated amounts of C3b processed to iC3b. The increase in opsonic C3 fragments mediated by MBL was associated with a significant increase in the uptake of organisms by neutrophils. We also observed significant increases in phagocytosis with MBL-MASPs that were independent of complement activation. We conclude that MBL-MASP makes a major contribution to complement-mediated host defense mechanisms.
Removal of psoralen monoadducts and crosslinks by human cell free extracts (1991)

Human cell free extracts are capable of carrying out damage-induced DNA synthesis in response to DNA damage by UV, psoralen, and cisplatin. We show that this damage-induced DNA synthesis is associated with removal of psoralen adducts and therefore is 'repair synthesis' and not an aberrant DNA synthesis reaction potentiated by DNA deformed by adducts. By comparing the denaturable fraction of psoralen adducted DNA which becomes labeled in the repair reaction to that of terminally labeled DNA (without repair) we have found that all DNA synthesis induced by psoralen monoadducts is the consequence of removal of these adducts. By the same approach we have obtained preliminary evidence that this in vitro system is capable of removing psoralen crosslinks as well.
Recent Advances of Biologically Inspired 3D Microfluidic Hydrogel Cell Culture Systems (2015)

The application of hydrogels as a matrix for 3-dimensional cell cultures has become an indispensable tool in tissue engineering, biotechnology and biomedical research due to the improved functionality and viability of the in vitro biological system. The combination of 3-dimensional hydrogel cell cultures with microchip technology further allows (i) spatial and temporal control of cell growth, (ii) application of defined mechanical (e.g., shear, strain, stretch) and chemical (e.g., gradients) stimuli, as well as (iii) monitoring of dynamic cellular responses using integrated sensing strategies. The main advantage of hydrogels for microfluidic cell cultures, however, is their mimicry of extracellular matrix structures including adequate porosity for cellular organization, biocompatibility, and representative stiffness, all key parameters that promote native-like tissue function. This review focuses primarily on recent advances in biologically inspired microfluidic systems that are based on 3-dimensional hydrogel cell cultures and discusses advantages and current challenges, various applications of microfluidic hydrogel cell cultures and future perspectives.
Sequential Nitrification and Denitrification in a Divided Cell Attached Growth Bioelectrochemical Reactor (2005)

A divided cell bioelectrochemical reactor comprised of two upflow submerged columns packed with Celite biocarrier was operated to generate oxic and anoxic compartments where the nitrified effluent from the first column was denitrified in the second for sequential nitrification-denitrification of a simulated wastewater. The experiments were carried out at current intensities of 0.5 mA/cm2 and 1.0 mA/cm2 over six phases. The wastewater pH decreased after contacting the oxic (nitrifying) compartment due to the acid equivalents produced electrolytically and during biological nitrification. The wastewater pH subsequently increased after contacting the anoxic (denitrifying) compartment due to the base equivalents produced electrolytically and the acid equivalents consumed during denitrification. At a current intensity of 0.5 mA/cm2, up to 56% of the influent nitrogen was removed on average during Phases I to III prior to operating at a higher current density. The nitrogen removal efficiency dropped to 15% at a current density of 1.0 mA/cm2 because of the pH inhibition and excess gases produced in the nitrification column. The reactor system did not recover from the inhibition.
Multiple Ser/Thr-rich degrons mediate the degradation of Ci/Gli by the Cul3-HIB/SPOP E3 ubiquitin ligase (2009)

The Cul3-based E3 ubiquitin ligases regulate many cellular processes using a large family of BTB domain-containing proteins as their target recognition components, but how they recognize targets remains unknown. Here we identify and characterize degrons that mediate the degradation of the Hedgehog pathway transcription factor cubitus interruptus (Ci)/Gli by Cul3-Hedghog-induced MATH and BTB domain-containing protein (HIB)/SPOP. Ci uses multiple Ser/Thr (S/T)-rich motifs that bind HIB cooperatively to mediate its degradation. We provide evidence that both HIB and Ci form dimers/oligomers and engage in multivalent interactions, which underlies the in vivo cooperativity among individual HIB-binding sites. We find that similar S/T-rich motifs are present in Gli proteins as well as in numerous HIB-interacting proteins and mediate Gli degradation by SPOP. Our results provide a mechanistic insight into how HIB/SPOP recognizes its substrates and have important implications for the genome-wide prediction of substrates for Cul3-based E3 ligases.
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome (2011)

Recent exponential growth in the throughput of next-generation DNA sequencing platforms has dramatically spurred the use of accessible and scalable targeted resequencing approaches. This includes candidate region diagnostic resequencing and novel variant validation from whole genome or exome sequencing analysis. We have previously demonstrated that selective genomic circularization is a robust in-solution approach for capturing and resequencing thousands of target human genome loci such as exons and regulatory sequences. To facilitate the design and production of customized capture assays for any given region in the human genome, we developed the Human OligoGenome Resource (http://oligogenome.stanford.edu/). This online database contains over 21 million capture oligonucleotide sequences. It enables one to create customized and highly multiplexed resequencing assays of target regions across the human genome and is not restricted to coding regions. In total, this resource provides 92.1% in silico coverage of the human genome. The online server allows researchers to download a complete repository of oligonucleotide probes and design customized capture assays to target multiple regions throughout the human genome. The website has query tools for selecting and evaluating capture oligonucleotides from specified genomic regions.
Overexpression of tumour necrosis factor-alpha-converting enzyme in psoriasis (2005)

The findings of the present study suggest that elevation of TACE mRNA in psoriatic lesions is due to many cells, particularly mast cells, that function in lesional psoriatic skin as an important source of TNF-alpha and other cytokines.