gebhart/patrepeval huggingface dataset:
Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module (2016)

We report the development and initial evaluation of a 13 m path length Structures for Lossless Manipulations (SLIM) module for achieving high resolution separations using traveling waves (TW) with ion mobility (IM) spectrometry. The TW SLIM module was fabricated using two mirror-image printed circuit boards with appropriately configured RF, DC, and TW electrodes and positioned with a 2.75 mm intersurface gap. Ions were effectively confined in field-generated conduits between the surfaces by RF-generated pseudopotential fields and moved losslessly through a serpentine path including 44 "U" turns using TWs. The ion mobility resolution was characterized at different pressures, gaps between the SLIM surfaces, and TW and RF parameters. After initial optimization, the SLIM IM-MS module provided about 5-fold higher resolution separations than present commercially available drift tube or traveling wave IM-MS platforms. Peak capacity and peak generation rates achieved were 246 and 370 s(-1), respectively, at a TW speed of 148 m/s. The high resolution achieved in the TW SLIM IM-MS enabled, e.g., isomeric sugars (lacto-N-fucopentaose I and lacto-N-fucopentaose II) to be baseline resolved, and peptides from an albumin tryptic digest were much better resolved than with existing commercial IM-MS platforms. The present work also provides a foundation for the development of much higher resolution SLIM devices based upon both considerably longer path lengths and multipass designs.
New developments in our understanding of acne pathogenesis and treatment (2009)

Interest in sebaceous gland physiology and its diseases is rapidly increasing. We provide a summarized update of the current knowledge of the pathobiology of acne vulgaris and new treatment concepts that have emerged in the last 3 years (2005-2008). We have tried to answer questions arising from the exploration of sebaceous gland biology, hormonal factors, hyperkeratinization, role of bacteria, sebum, nutrition, cytokines and toll-like receptors (TLRs). Sebaceous glands play an important role as active participants in the innate immunity of the skin. They produce neuropeptides, excrete antimicrobial peptides and exhibit characteristics of stem cells. Androgens affect sebocytes and infundibular keratinocytes in a complex manner influencing cellular differentiation, proliferation, lipogenesis and comedogenesis. Retention hyperkeratosis in closed comedones and inflammatory papules is attributable to a disorder of terminal keratinocyte differentiation. Propionibacterium acnes, by acting on TLR-2, may stimulate the secretion of cytokines, such as interleukin (IL)-6 and IL-8 by follicular keratinocytes and IL-8 and -12 in macrophages, giving rise to inflammation. Certain P. acnes species may induce an immunological reaction by stimulating the production of sebocyte and keratinocyte antimicrobial peptides, which play an important role in the innate immunity of the follicle. Qualitative changes of sebum lipids induce alteration of keratinocyte differentiation and induce IL-1 secretion, contributing to the development of follicular hyperkeratosis. High glycemic load food and milk may induce increased tissue levels of 5alpha-dihydrotestosterone. These new aspects of acne pathogenesis lead to the considerations of possible customized therapeutic regimens. Current research is expected to lead to innovative treatments in the near future.
Alkaloid Determination in Crude Extracts from Cortex Quebracho and Opium Applying Capillary Electrophoresis and Capillary Electrophoresis- Mass Spectrometry Coupling. (1997)

The applicability of capillary electrophoresis with UV and electrospray ionisation (ESI)-mass spectrometric detection to the determination of alkaloids in crude extracts of Cortex Quebracho and opium has been investigated. The use of a buffer electrolyte consisting of aqueous ammonium acetate (pH 3.1) and acetonitrile resulted in a high performance of peak resolution. Most of the alkaloids have been identified according to the signal of the protonated molecular ion in the ESI mass spectrum
Microsphere-Based Rolling Circle Amplification Microarray for the Detection of DNA and Proteins in a Single Assay (2009)

We describe a high-density microarray for simultaneous detection of proteins and DNA in a single test. In this system, Rolling Circle Amplification (RCA) was used as a signal amplification method for both protein and nucleic acid detection. The microsphere sensors were tested with synthetic DNA and purified recombinant protein analytes. The target DNA sequence was designed from a highly conserved gene that encodes the outer membrane protein P6 (OMP-P6) of both typeable and nontypeable strains of Haemophilus influenzae. The proinflammatory mediators IL-6 and IL-8 were selected as target proteins. Capture antibodies were first immobilized on fluorescently encoded microspheres. The microspheres were then loaded into the etched microwells of an imaging optical fiber bundle. A sandwich assay was performed for target proteins IL-6 and IL-8 using biotin-labeled secondary antibodies. Biotinylated capture DNA probes were then attached to the detection antibodies via an avidin bridge. A padlock probe, complementary to the target sequence, was subsequently hybridized to the capture probe. In the presence of the target sequence, the padlock probe was ligated, and this circular sequence was used for RCA. Following RCA, multiple fluorescently labeled signal probes were hybridized to each amplified sequence, and the microarray was imaged using an epi-fluorescence microscope. With this assay, detection limits down to 10 fM and 1 pM were achieved for proteins and target DNA, respectively. In addition to this new approach for detecting both protein and DNA in a single test using RCA, the limit of detection for IL-8 and IL-6 was improved by 3 orders of magnitude compared to similar microsphere-based assays.
An HMM-based threshold model approach for gesture recognition (1999)

A new method is developed using the hidden Markov model (HMM) based technique. To handle nongesture patterns, we introduce the concept of a threshold model that calculates the likelihood threshold of an input pattern and provides a confirmation mechanism for the provisionally matched gesture patterns. The threshold model is a weak model for all trained gestures in the sense that its likelihood is smaller than that of the dedicated gesture model for a given gesture. Consequently, the likelihood can be used as an adaptive threshold for selecting proper gesture model. It has, however, a large number of states and needs to be reduced because the threshold model is constructed by collecting the states of all gesture models in the system. To overcome this problem, the states with similar probability distributions are merged, utilizing the relative entropy measure. Experimental results show that the proposed method can successfully extract trained gestures from continuous hand motion with 93.14% reliability.
Abnormal Viscosity Increment Observed for an Ionic Liquid by Dissolving Lithium Chloride (2008)

The effect of adding an inorganic salt, lithium chloride, and water on the viscosity of an ionic liquid, 1-n-butyl-3-methylimidazolium chloride (BmimCl), was investigated by shear stress measurements with a rheometer. The shear rate dependence of the viscosity showed shear thinning behavior, which implies that some structure should exist in the liquid and the structure should change at high shear rates. Addition of LiCl enhances the viscosity of BmimCl. The logarithmic value of zero-shear viscosity, eta(0), of BmimCl increases linearly and largely with increasing added salt content. The increasing rate of the viscosity by addition of LiCl was about 10 times larger than that for an aqueous solution of LiCl. When water is added into BmimCl, viscosity decreased. The increasing rate of the viscosity by addition of LiCl for BmimCl with about 5 wt % of water was almost the same as that for BmimCl without addition of water.
Oxazoles : synthesis, reactions, and spectroscopy (2003)

Abbreviations.1. Synthesis and Reactions of Oxazoles (D.C. Palmer and S. Venkatraman).2. Spectroscopic Properties of Oxazoles (D. Lowe).3. Oxazole Diels-Alder Reactions (J.I. Levin and L.M. Laakso).4. Mesoionic Oxazoles (G.W. Gribble).Author Index.Subject Index.
Acoustic cloak for airborne sound by inverse design (2011)

This Letter presents practical realization of a two-dimensional low loss acoustic cloak for airborne sound obtained by inverse design. The cloak consists of 120 aluminum cylinders of 15 mm diameter surrounding the cloaked object—a cylinder of diameter 22.5 cm. The position of each cylinder in the cloak is optimized using the data from two different techniques: genetic algorithm and simulated annealing. The operation frequency of this cloak is 3061 Hz with the bandwidth of about 100 Hz. Being a multi-step approach to the desired cloaking, the inverse design is also valid, in principle, for non-symmetric cylinders and even for three-dimensional objects.
MicroRNA profiling in hepatocellular tumors is associated with clinical features and oncogene/tumor suppressor gene mutations (2008)

Hepatocellular tumors may have a distinct miRNA expression fingerprint according to malignancy, risk factors, and oncogene/tumor suppressor gene alterations. Dissecting these relationships provides a new hypothesis to understand the functional impact of miRNA deregulation in liver tumorigenesis and the promising use of miRNAs as diagnostic markers.
Compressive sensing over networks (2010)

In this paper, we demonstrate some applications of compressive sensing over networks. We make a connection between compressive sensing and traditional information theoretic techniques in source coding and channel coding. Our results provide an explicit trade-off between the rate and the decoding complexity. The key difference of compressive sensing and traditional information theoretic approaches is at their decoding side. Although optimal decoders to recover the original signal, compressed by source coding have high complexity, the compressive sensing decoder is a linear or convex optimization. First, we investigate applications of compressive sensing on distributed compression of correlated sources. Here, by using compressive sensing, we propose a compression scheme for a family of correlated sources with a modularized decoder, providing a trade-off between the compression rate and the decoding complexity. We call this scheme Sparse Distributed Compression. We use this compression scheme for a general multicast network with correlated sources. Here, we first decode some of the sources by a network decoding technique and then, we use a compressive sensing decoder to obtain the whole sources. Then, we investigate applications of compressive sensing on channel coding. We propose a coding scheme that combines compressive sensing and random channel coding for a high-SNR point-to-point Gaussian channel. We call this scheme Sparse Channel Coding. We propose a modularized decoder providing a trade-off between the capacity loss and the decoding complexity. At the receiver side, first, we use a compressive sensing decoder on a noisy signal to obtain a noisy estimate of the original signal and then, we apply a traditional channel coding decoder to find the original signal.
miR-132 inhibits lung cancer cell migration and invasion by targeting SOX4. (2015)

Our finding provides new insight into the mechanism of NSCLC progression. Therapeutically, miR-132 may serve as a potential target in the treatment of human lung cancer.
Studies of Jak/STAT3 expression and signalling in psoriasis identifies STAT3‐Ser727 phosphorylation as a modulator of transcriptional activity (2013)

Jak/Tyk proteins have recently aroused as possible therapeutic targets for the treatment of psoriasis. In psoriasis, these proteins signal through STAT molecules including STAT3, and STAT3 expression and activation has been shown augmented in psoriatic lesions. Here, we characterized the expression of Jak/Tyk proteins in lesional compared with non-lesional psoriatic skin. Jak1, Jak2 mRNA and protein and Tyk2 mRNA appeared to be downregulated, whereas Jak3 mRNA expression was increased. Moreover, STAT3 expression and activation was examined in psoriasis. STAT3 is activated at two phosphorylation sites: Tyr705 and Ser727. Both phosphorylation sites were phosphorylated in lesional psoriatic skin. The activation of STAT3 by Jak/Tyk proteins was studied in cultured normal human keratinocytes. Tyr705 phosphorylation was induced by IL-6 and IL-20 in a Jak2-dependent manner, and moreover, phosphorylation of Tyr705 produced a strong increase in STAT3 transcriptional activity. TNFα, 12-O-Tetradecanoylphorbol 13-acetate (TPA) and UVB irradiation induced Ser727 phosphorylation of STAT3 in an ERK1/2- and p38 MAPK-dependent manner, which resulted in a modulatory effect on STAT3 transcriptional activity. Our results demonstrate how different signalling pathways can integrate and lead to regulation of STAT3 transcriptional activity.
Nonisotopic DNA detection system employing elastase and a fluorogenic rhodamine substrate (1993)

An alternative fluorescence-based method has been developed for the direct detection of small quantities of DNA in solution. In this system, a serine protease (elastase) is coupled to a DNA oligonucleotide through a disulfide linkage. A bis-(tetraalanine)-derivatized rhodamine molecule BZTAlaR) has been synthesized for use as a substrate. BZTAlaR is nonfluorescent in its derivatized form and shows negligible hydrolysis in solution. Cleavage of the tetraalanyl groups from the rhodamine portion of the molecule restores its fluorescence. Hybridization of the elastase-oligonucleotide conjugate to its target, capture of the conjugate-target complex with streptavidin-coated magnetic beads, addition of substrate, and subsequent detection of the target by fluorescence are accomplished in solution. Hybridization is rapid and specific, with over 90% of a target sequence successfully hybridized and captured. This method exhibits low background and an amplified fluorescent signal over time, resulting in a current detection limit of 0.49 fmol of elastase alone, or 2.64 fmol of conjugate, within 2 h.
Trichloroacetic acid-induced unfolding of bovine pancreatic ribonuclease. Existence of molten globule-like state. (1994)

The exposure of ribonuclease A to trichloroacetic acid was earlier shown to alter the conformation of the protein resulting in reduced enzymatic activity (Sagar, A. J., Subbiah, V., and Pandit, M. W. (1989) Biochim. Biophys. Acta 995, 144-150). We have studied the structure and enzymatic activity of ribonuclease A treated with trichloroacetic acid over a wide range of acid concentrations (0-40%). The far ultraviolet circular dichroism spectra of ribonuclease A, on exposure to acid concentrations less than 10%, indicated an exceptionally high degree of chiral structure. Exposure of ribonuclease A to acid concentrations between 10 and 30% resulted in the formation of a molecule with significant chiral structure (conventionally assigned to residual secondary structure) but reduced tertiary structure (characteristics very similar to those of molten globule). Increased binding of the hydrophobic probe 1-anilinonaphthalene-8-sulfonate to the enzyme treated with 15-30% acid, as compared with the untreated or completely unfolded protein, supported the existence of a state having characteristics of molten globule. Reversed phase high performance liquid chromatography corroborated the data obtained by circular dichroism as well as 1-anilino-naphthalene-8-sulfonate-binding studies. Beyond acid concentrations of 30%, the ribonuclease is completely denatured. The trichloroacetic acid-induced unfolding is shown to be completely reversible.
Incidence of the V600K mutation among melanoma patients with BRAF mutations, and potential therapeutic response to the specific BRAF inhibitor PLX4032 (2010)

Activating mutations in BRAF kinase are common in melanomas. Clinical trials with PLX4032, the mutant-BRAF inhibitor, show promising preliminary results in patients selected for the presence of V600E mutation. However, activating V600K mutation is the other most common mutation, yet patients with this variant are currently excluded from the PLX4032 trials. Here we present evidence that a patient bearing the BRAF V600K mutation responded remarkably to PLX4032, suggesting that clinical trials should include all patients with activating BRAF V600E/K mutations.
Electron conduction in molecular wires. I. A scattering formalism (1994)

We extend a model originally intended for the description of the scanning tunneling microscope (STM) current in molecular imaging of one-dimensional systems, to encompass the more general process of electron transfer between two reservoirs of states. In the STM problem, the reservoirs are naturally associated with the metal density of states of the electrodes. In the molecular electron transfer problem, the identification of the reservoirs with the Franck–Condon weighted density of vibrational states allows a number of fruitful connections with the theory of nonadiabatic electron transfer (ET) in molecules to be established. In this article, we present an exact procedure, based on Löwdin’s partitioning technique, to determine the Green’s function and the T matrix, relevant to the transport process. We obtain compact expressions for the conductance and the density of states in the limit of small applied voltage and low temperature, and discuss the important case where the molecular wire is described by a tight-binding Hamiltonian. Finally, we discuss some physical implications of the model.
Structure−Function Studies of Human Apolipoprotein A-V:  A Regulator of Plasma Lipid Homeostasis (2003)

To investigate structure and function relations of a new member of the exchangeable apolipoprotein family that modulates plasma lipid levels, recombinant human apolipoprotein (apo) A-V was produced in Escherichia coli and isolated by a combination of nickel chelation affinity chromatography and reversed-phase HPLC. Antibodies directed against apoA-V were generated and employed in immunoblotting experiments. Anti-apoA-V IgG gave a strong response against recombinant apoA-V from E. coli and human apoA-V expressed in transgenic mice, but did not recognize human apoA-I or apoA-IV. In neutral-pH buffers, at concentrations of >0.1 mg/mL, isolated lipid-free apoA-V is poorly soluble. By contrast, apoA-V is soluble in 50 mM sodium citrate (pH 3.0). Far-UV circular dichroism analysis and spectral deconvolution reveal that apoA-V possesses 32% alpha-helix, 33% beta-sheet, 16% beta-turn, and 18% random coil secondary structure conformers. Temperature-induced denaturation studies gave rise to a transition midpoint of 47.1 degrees C. Upon being cooled to ambient temperature from 85 degrees C, apoA-V failed to recover all of the negative ellipticity present in unheated apoA-V. ApoA-V interacts with bilayer vesicles of dimyristoylphosphatidylcholine to form discoidal complexes with diameters in the range of 15-20 nm. However, apoA-V was a poor activator of lecithin:cholesterol acyltransferase where the activity was 8.5 +/- 1.8% of that of apoA-I. Furthermore, apoA-V failed to support enhanced efflux of cholesterol from cAMP-treated J774 macrophages, although low levels of efflux were obtained from unstimulated cells. Taken together, the results demonstrate recombinant apoA-V possesses unique structural and functional characteristics, in keeping with its proposed role in the modulation of plasma lipid levels.
Genetic basis of virulence in Shigella species (1991)

Shigella species and enteroinvasive strains of Escherichia coli cause disease by invasion of the colonic epithelium, and this invasive phenotype is mediated by genes carried on 180- to 240-kb plasmids. In addition, at least eight loci on the Shigella chromosome are necessary for full expression of virulence. The products of these genes can be classified as (i) virulence determinants that directly affect the ability of shigellae to survive in the intestinal tissues, e.g., the aerobactin siderophore (iucABCD and iutA), superoxide dismutase (sodB), and somatic antigen expression (rfa and rfb); (ii) cytotoxins that contribute to the severity of disease, e.g., the Shiga toxin (stx) and a putative analog of this toxin (flu); and (iii) regulatory loci that affect the expression of plasmid genes, e.g., ompR-envZ, which mediates response to changes in osmolarity, virR (osmZ), which mediates response to changes in temperature, and kcpA, which affects the translation of the plasmid virG (icsA) gene which is associated with intracellular bacterial mobility and intracellular bacterial spread. A single plasmid regulatory gene (virF) controls a virulence-associated plasmid regulon including virG (icsA) and two invasion-related loci, i.e., (i) ipaABCD, encoding invasion plasmid antigens that may be structural components of the Shigella invasion determinant; and (ii) invAKJH (mxi), which is necessary for insertion of invasion plasmid antigens into the outer membrane.
A low-noise, 900-MHz VCO in 0.6-μm CMOS (1999)

This paper describes a low-noise, 900-MHz, voltage-controlled oscillator (VCO) fabricated in a 0.6-/spl mu/m CMOS technology. The VCO consists of four-stage fully differential delay cells performing full switching. It utilizes dual-delay path techniques to achieve high oscillation frequency and obtain a wide tuning range. The VCO operates at 750 MHz to 1.2 GHz, and the tuning range is as large as 50%. The measured results of the phase noise are -101 dBc/Hz at 100-kHz offset and -117 dBc/Hz at 600-kHz offset from the carrier frequency. This value is comparable to that of LC-based integrated oscillators. The oscillator consumes 10 mA from a 3.0-V power supply. A prototype frequency synthesizer with the VCO is also implemented in the same technology, and the measured phase noise of the synthesizer is -113 dSc/Hz at 100-kHz offset.
Acetaminophen‐related acute liver failure in the United States (2008)

Acetaminophen overdoses are the number one cause of acute liver failure (ALF) in the United States; they account for 50% of all cases of ALF and carry a 30% mortality. Nevertheless, acetaminophen is a highly successful product with sales easily exceeding a billion dollars annually. A narcotic-containing acetaminophen preparation is the number one generic drug sold in the United States. Historically, a strong association was claimed with alcohol as a co-factor and the accidental nature of ingestions was emphasized but the association with alcohol remains a matter of debate. Recently, a very reliable assay has been developed which detects a byproduct of the toxic reaction, acetaminophen-CYS adducts, protein-acetaminophen compounds that are released from damaged hepatocytes in similar fashion to aminotransferases. The US Acute Liver Failure Study Group is a multi-center network established to gather data prospectively on all forms of acute liver failure, a rare but often fatal condition. The group has data on more than 500 acetaminophen cases and described 275 of them in detail in a recent paper. The clinical pattern of presentation is somewhat different in the US compared with the UK, since nearly half are considered to be unintentional, the result of overuse of acetaminophen-containing compounds for pain relief, without suicidal intent. Despite the relatively good prognosis for acetaminophen overdoses, 30% die once acute liver failure occurs and this is the largest cause of death in the entire ALF registry.