gebhart/patrepeval huggingface dataset:
Selective and Blanket Electroless Copper Deposition for Ultralarge Scale Integration (1997)

Electroless Cu thermodynamics, electrochemistry, mechanism, kinetics, and mass transport are reviewed. Electroless Cu deposition is a thermodynamically favorable and kinetically inhibited process, with two electrochemical reactions including anodic oxidation of a reducing agent and cathodic reduction of metal ions occurring simultaneously, with a multistep catalytic redox mechanism, an Arrhenius type of rate equation, and mass‐transport limited reaction in narrow and deep features such as subhalf micron trenches and vias of high aspect ratios (>3). Selective and blanket electroless Cu deposition from formaldehyde‐based solutions with ethylenediaminetetraacetic acid as a complexing agent was investigated for trench/via filling applications. A single‐wafer electroless Cu deposition system with up to 8 in. wafer capability has been designed and manufactured. An electroless Cu deposition solution and operation conditions have been optimized to obtain electroless Cu films at high deposition rate (∼75 to 120 nm/min), with low resistivity (ρ 2 μΩ cm), low surface roughness (Ra ∼ 10 to 15 nm for ∼1.5 μm thick deposits) and good electrical uniformity (std dev <3% for 6 in. wafers and 5 to 7% for 8 in. wafers). A novel dry seeding method on sputtered Cu/Al bilayers has been developed to provide protection of Cu catalytic properties from passivation by using an Al sacrificial layer and to obtain uniform initiation and blanket growth of electroless Cu by in situ Al dissolution in the plating bath. Electroless Cu films blanket deposited on sputtered Cu/Al seed layer were conformal with 100% step coverage. A novel wet seeding method has been developed with Cu contact displacement deposition on a TiN diffusion barrier to provide selective and blanket electroless copper plating. Subhalf micron (down to 0.3 μm) trenches and vias of high aspect ratios (up to 5:1) were completely filled for both blanket and selective electroless deposition modes.
cDNA Cloning and Expression of Bovine UDP-N-Acetylglucosamine:α1,3-d-Mannoside β1,4-N-Acetylglucosaminyltransferase IV (1998)

UDP-N-acetylglucosamine:alpha1,3-D-mannoside beta1, 4-N-acetylglucosaminyltransferase (GnT-IV) is one of the essential enzymes in the production of tri- and tetra-antennary Asn-linked sugar chains. Recently, we have successfully purified GnT-IV from bovine small intestine. Based on the partial amino acid sequence of the purified bovine GnT-IV enzyme, its cDNA has been cloned from bovine small intestine. The open reading frame is 1,605 base pairs long, and this sequence produced GnT-IV activity on transient expression in COS-7 cells. Although the deduced amino acid sequence does not have any significant homology with other known N-acetylglucosaminyltransferases (GnTs), the hydrophobicity profile showed a typical type II transmembrane protein structure, which is common to many glycosyltransferases. N-terminal amino acid sequencing of the purified GnT-IV revealed that 92 amino acids, including a transmembrane region, were truncated during purification. Of the three potential N-glycosylation sites Asn-458 was actually glycosylated in the purified enzyme, although this N-glycosylation site could be abolished without any reduction in GnT-IV activity. Serial deletions at both the N and C termini proved that the catalytic domain of GnT-IV is located in the central region of the enzyme. The GnT-IV mRNA level correlated with enzymatic activity in the various bovine tissues tested.
The role of mucosal immunity and host genetics in defining intestinal commensal bacteria (2010)

Genetic and mucosal immunity strongly influence the composition and function of enteric commensal bacteria. This understanding should help develop strategies to correct dysfunctional altered microbiota in genetically susceptible individuals, better diagnose and correct potential dysbiosis in high-risk individuals at a preclinical stage, and therapeutically target pathogenic bacterial species that help drive chronic inflammatory conditions.
Triptolide-Induced Transcriptional Arrest Is Associated with Changes in Nuclear Substructure (2008)

Triptolide, an active component of the medicinal herb lei gong teng, is a potent anticancer and anti-inflammatory therapeutic. It potently inhibits nuclear factor-kappaB transcriptional activation after DNA binding, although a precise mechanism is as yet unknown. Here, we report that triptolide also induces distinct nuclear substructural changes in HeLa cells. These changes in the nucleolus and nuclear speckles are reversible and dependent on both time and concentration. Furthermore, nuclear changes occurred within hours of triptolide treatment and were calcium and caspase independent. Rounding of nuclear speckles, an indication of transcriptional arrest, was evident and was associated with a decrease in RNA polymerase II (RNA Pol II) COOH-terminal domain Ser(2) phosphorylation. Additionally, the nucleolus disassembled and RNA Pol I activity declined after RNA Pol II inhibition. We therefore conclude that triptolide causes global transcriptional arrest as evidenced by inactivity of RNA Pol I and II and the subsequent alteration in nuclear substructure.
Functional Antibody CDR3 Fusion Proteins with Enhanced Pharmacological Properties (2013)

Real staying power: A subset of bovine antibodies (blue, see scheme) feature an ultralong CDR3 loop that forms an antiparallel β-sheet stalk, terminating in a folded, disulfide cross-linked knob domain. Fusion of a polypeptide (red) into this unique CDR3 motif provides a novel strategy for generating polypeptide therapeutics with enhanced pharmacokinetics and pharmacodynamics. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Lymphocyte activation gene-3, a MHC class II ligand expressed on activated T cells, stimulates TNF-alpha and IL-12 production by monocytes and dendritic cells. (1999)

Lymphocyte activation gene-3 (LAG-3) is an MHC class II ligand structurally and genetically related to CD4. Although its expression is restricted to activated T cells and NK cells, the functions of LAG-3 remain to be elucidated. Here, we report on the expression and function of LAG-3 on proinflammatory bystander T cells that are activated in the absence of TCR engagement. LAG-3 is expressed at high levels on human T cells cocultured with autologous monocytes and IL-2 and synergizes with the low levels of CD40 ligand (CD40L) expressed on these cells to trigger TNF-alpha and IL-12 production by monocytes. Indeed, anti-LAG-3 mAb inhibits both IL-12 and IFN-gamma production in IL-2-stimulated cocultures of T cells and autologous monocytes. Soluble LAG-3Ig fusion protein markedly enhances IL-12 production by monocytes stimulated with infra-optimal concentrations of sCD40L, whereas it directly stimulates monocyte-derived dendritic cells (DC) for the production of TNF-alpha and IL-12, unravelling an enhanced responsiveness to MHC class II engagemenent in DC as compared with activated monocytes. Thus similar to CD40L, LAG-3 may be involved in the proinflammatory activity of cytokine-activated bystander T cells and most importantly it may directly activate DC.
Contribution of AMPA, NMDA, and GABAAReceptors to Temporal Pattern of Postsynaptic Responses in the Inferior Colliculus of the Rat (2004)

The central nucleus of the inferior colliculus (ICC) is a major site of synaptic interaction in the central auditory system. To understand how ICC neurons integrate excitatory and inhibitory inputs for processing temporal information, we examined postsynaptic responses of ICC neurons to repetitive stimulation of the lateral lemniscus at 10-100 Hz in rat brain slices. The excitatory synaptic currents mediated by AMPA and NMDA receptors and the inhibitory current mediated by GABA(A) receptors were pharmacologically isolated and recorded by whole-cell patch-clamp techniques. The response kinetics of AMPA receptor-mediated EPSCs and GABA(A) receptor-mediated IPSCs were similar and much faster than those of NMDA receptor-mediated EPSCs. AMPA EPSCs could follow each pulse of stimulation at a rate of 10-100 Hz but showed response depression during the course of repetitive stimulation. GABA(A) IPSCs could also follow stimulus pulses over this frequency range but showed depression at low rates and facilitation at higher rates. NMDA EPSCs showed facilitation and temporal summation in response to repetitive stimulation, which was most pronounced at higher rates of stimulation. GABA(A) inhibition suppressed activation of NMDA receptors and reduced both the degree of AMPA EPSC depression and the extent of temporal summation of NMDA EPSCs. The results indicate that GABA(A) receptor-mediated inhibition plays a crucial role in maintaining the balance of excitation and inhibition and in allowing ICC neurons to process temporal information more precisely.
Multi-view Video Coding via Dense Depth Estimation (2007)

A geometry-based multi-view video coding (MVC) method is proposed. In order to utilize the spatial redundancies between multiple views, the scene geometry is estimated as dense depth maps. The dense depth estimation problem is modeled by using a Markov random field (MRF) and solved via the belief propagation algorithm. Relying on these depth maps of the scene, novel view estimates of the intermediate views of the multi-view set is obtained with a 3D warping algorithm, which also performs hole-filling in the occlusion regions. The proposed MVC method, based on H.264 standard, encodes a number of reference views in a standard manner, whereas the residuals of the novel view predictions are encoded separately. The proposed MVC method is compared against simulcast coding of each view, yielding better rate-distortion performance, especially at lower bitrates.
Nanoparticle-Based Delivery System for Application of siRNA In Vivo (2010)

Small interfering RNAs (siRNAs) silence the expression of specific target genes by mediating RNA interference (RNAi) in mammalian cells. siRNAs have not only been widely used as a valuable tool for functional genomics research, but they also have demonstrated great potential in biomedical therapeutic applications for diseases caused by abnormal gene overexpression or mutation. One of the most important issues to overcome before full clinical application is the development of effective administration methods for siRNAs to the target tissue or cells in vivo, which is highly dependent on the delivery system. Currently, there are two major kinds of in vivo delivery systems: viral or nonviral. As one of the nonviral carrier systems, nanoparticles, combinations of liposomes and cationic polymer complexes, have exhibited improved in vivo stability, target specificity, and cell/tissue uptake and internalization of the encapsulated RNAi oligos, which result in more effective silencing with less cellular toxicity and immune stimulation. This review will discuss the latest advancements in nanoparticle-mediated RNAi delivery systems, including nano-materials, preparation, and characteristics. In conjunction, the clinical trial cases related to the nanoparticle-siRNA complexes will be highlighted. The safety issues of nanoparticles used in vivo will also be mentioned. Finally, this review will summarize the perspectives for future applications of nanoparticle-mediated RNAi delivery systems.
<title>Short pulse amplification in tunable solid state materials</title> (1990)

We describe our work on the amplification of short pulses in tunable solid state materials; specifically alexandrite and Ti:sapphire. Our goal is to amplify femtosecond range pulses to the joule level in a table top size laser. We will describe our results which show that such a laser is now feasible.
Global Analyses of Transcriptomes and Proteomes of a Parent Strain and an l -Threonine-Overproducing Mutant Strain (2003)

We compared the transcriptome, proteome, and nucleotide sequences between the parent strain Escherichia coli W3110 and the L-threonine-overproducing mutant E. coli TF5015. DNA macroarrays were used to measure mRNA levels for all of the genes of E. coli, and two-dimensional gel electrophoresis was used to compare protein levels. It was observed that only 54 of 4,290 genes (1.3%) exhibited differential expression profiles. Typically, genes such as aceA, aceB, icdA, gltA, glnA, leu operon, proA, thrA, thrC, and yigJ, which are involved in the glyoxylate shunt, the tricarboxylic acid cycle, and amino acid biosynthesis (L-glutamine, L-leucine, proline, and L-threonine), were significantly upregulated, whereas the genes dadAX, hdeA, hdeB, ompF, oppA, oppB, oppF, yfiD, and many ribosomal protein genes were downregulated in TF5015 compared to W3110. The differential expression such as upregulation of thr operon and expression of yigJ would result in an accumulation of L-threonine in TF5015. Furthermore, two significant mutations, thrA345 and ilvA97, which are essential for overproduction of L-threonine, were identified in TF5015 by the sequence analysis. In particular, expression of the mutated thrABC (pATF92) in W3110 resulted in a significant incremental effect on L-threonine production. Upregulation of aceBA and downregulation of b1795, hdeAB, oppA, and yfiD seem to be linked to a low accumulation of acetate in TF5015. Such comprehensive analyses provide information regarding the regulatory mechanism of L-threonine production and the physiological consequences in the mutant stain.
Clinical and metabolic correction of pompe disease by enzyme therapy in acid maltase-deficient quail. (1998)

Pompe disease is a fatal genetic muscle disorder caused by a deficiency of acid alpha-glucosidase (GAA), a glycogen degrading lysosomal enzyme. GAA-deficient (AMD) Japanese quails exhibit progressive myopathy and cannot lift their wings, fly, or right themselves from the supine position (flip test). Six 4-wk-old acid maltase-deficient quails, with the clinical symptoms listed, were intravenously injected with 14 or 4.2 mg/kg of precursor form of recombinant human GAA or buffer alone every 2-3 d for 18 d (seven injections). On day 18, both high dose-treated birds (14 mg/kg) scored positive flip tests and flapped their wings, and one bird flew up more than 100 cm. GAA activity increased in most of the tissues examined. In heart and liver, glycogen levels dropped to normal and histopathology was normal. In pectoralis muscle, morphology was essentially normal, except for increased glycogen granules. In sharp contrast, sham-treated quail muscle had markedly increased glycogen granules, multi-vesicular autophagosomes, and inter- and intrafascicular fatty infiltrations. Low dose-treated birds (4.2 mg/kg) improved less biochemically and histopathologically than high dose birds, indicating a dose-dependent response. Additional experiment with intermediate doses and extended treatment (four birds, 5.7-9 mg/kg for 45 d) halted the progression of the disease. Our data is the first to show that an exogenous protein can target to muscle and produce muscle improvement. These data also suggest enzyme replacement with recombinant human GAA is a promising therapy for human Pompe disease.
A synthetic peptide elicits antibodies reactive with the external glycoprotein of human T cell lymphotropic virus type I (1991)

A synthetic peptide derived from the external glycoprotein of human T cell lymphotropic virus type I (HTLV-I) (Env-5; amino acids 242 to 256) reacted with IgG antibodies in serum specimens from HTLV-I-infected individuals. C-terminal residues of Env-5 were crucial for the antibody reactivity. Polyclonal rabbit antibodies to Env-5 did not inhibit syncytium formation but such antibodies reacted specifically with gp68env and gp46env glycoproteins of HTLV-I in an immunoblot analysis. Immunoprecipitation of the surface-labelled MT-2 (HTLV-I-infected) cell line with anti-Env-5 precipitated the gp68env precursor protein. It was concluded that peptide Env-5 mimics a surface-exposed epitope on the HTLV-I external glycoprotein.
Thirty-Year Trends (1975 to 2005) in the Magnitude of, Management of, and Hospital Death Rates Associated With Cardiogenic Shock in Patients With Acute Myocardial Infarction (2009)

Our findings indicate improving trends in the hospital prognosis associated with cardiogenic shock. Given the high death rates associated with this clinical complication, monitoring future trends in the incidence and death rates and the factors associated with an increased risk for developing cardiogenic shock remains warranted.
Rapid screening of antibiotic toxicity in an automated microdroplet system (2012)

We report an automated microfluidic platform for 'digitally' screening the composition space of droplets containing cocktails of small molecules and demonstrate the features of this system by studying epistatic interactions between antibiotics and Escherichia coli ATCC 25922. This system has several key characteristics: (i) it uses small (<100 μL) samples of liquids and suspensions of bacteria that are introduced directly into the chip; (ii) it generates a sequence of droplets with compositions, including reagents and bacterial cell suspensions that are programmed by the user; (iii) it exports the sequence of droplets to an external segment of tubing that is subsequently disconnected for incubation and storage; and (iv) after incubation of bacteria in droplets, the droplets are injected into a second device equipped with an in-line fiber optic spectrophotometer that measures cell growth. The system generates and fuses droplets with precise (<1% in standard deviation) control of liquid volumes and of the concentrations of input substrates. We demonstrate the application of this technology in determining the minimum inhibitory concentration and pair-wise interactions of ampicillin, tetracycline, and chloramphenicol against E. coli. The experiments consumed small volumes of reagents and required minutes to create the droplets and several hours for their incubation and analysis.
Early type I interferon‐mediated signals on B cells specifically enhance antiviral humoral responses (2006)

Type I interferons (IFN-I) limit viral spread by inducing antiviral genes in infected target cells and by shaping the adaptive response through induction of additional cytokines. Vesicular stomatitis virus (VSV) efficiently triggers the production of IFN-I in mice, and it is suggested that IFN-alpha is induced after binding of VSV to TLR7 in infected cells. Our study with virus-specific B cell receptor-transgenic mice demonstrates here that IFN-I directly fuel early humoral immune responses in vivo. VSV-specific B cells that lacked IFN-alpha/beta receptors were considerably impaired in plasma cell formation and in generating antiviral IgM. At low viral titers, production of IFN-alpha following VSV infection was independent of TLR7-mediated signals. Interestingly, however, TLR7 ligation in B cells increased the formation of early antiviral IgM. These findings indicate that IFN-alpha-mediated augmentation of specific B cell responses is a partially TLR7- and virus dose-dependent mechanism.
Is urokinase gene 3'-UTR polymorphism associated with prostate cancer? (2005)

Urokinase gene is believed to play a key role in tissue degradation and cell migration under various normal and pathological conditions, including cancer invasion and metastasis. It may be responsible in the development of prostate cancer (CaP), although there is lack of genetic evidence. Our aim was to study single nucleotide polymorphism (C/T) in 3'-untranslated region to investigate the possibility. DNA was extracted from blood samples of 103 CaP patients and 107 normal controls. Polymerase chain reaction (PCR) based restriction analysis was used to identify the C/T polymorphism of the urokinase gene. Significant difference in the frequency distribution of CT and TT genotypes in CaP patients as compared to normal was observed (p=0.04). Two folds risk for prostate cancer with T alleles in north Indian population was apparent. We also observed significant association for TT genotypes with higher Gleason score of tumors in CaP patients (p<0.05). A positive association was also evident in tobacco users having T alleles with risk of CaP. Our findings demonstrated a positive association of T allele of 3'UTR of urokinase gene with the risk of prostate cancer. We therefore hypothesize that C/T polymorphism may influence the etiology of CaP and is likely to become another new marker.
Cooperative positioning with multiple robots (2002)

A number of positioning identification techniques have been used for mobile robots. Dead reckoning is a popular method, but is not reliable when a robot travels long distances or over an uneven surface because of variations in wheel diameter and wheel slippage. The landmark method, which estimates the current position relative to landmarks, cannot be used in an uncharted environment. The authors propose a new method called "cooperative positioning with multiple robots". For cooperative positioning, the authors divide the robots into two groups, A and B. One group, say A, remains stationary and acts as a landmark while group B moves. The moving group B then stops and acts as a landmark for group A. This "dance" is repeated until the target robot position are reached. Cooperative positioning has a far lower accumulated positioning error than dead reckoning, and can work in three-dimensions which is not possible with dead reckoning. Also, this method has inherent landmarks and therefore works in uncharted environments. This paper discusses the positioning accuracy of the authors' method with error variances for an example with three mobile robots.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of cyclic AMP-regulated chloride conductance in the pigmented rabbit conjunctival epithelial cells (2002)

We have previously reported that the pigmented rabbit conjunctiva is a Cl- secreting tissue, subject to cAMP, Ca2+, and PKC modulation. The present study was conducted to characterize, at the cellular and molecular levels, cAMP-regulated Cl- channels in rabbit conjunctival epithelial cells. cAMP-inducible Cl- channel properties were evaluated by monitoring the whole-cell currents using patch clamp techniques. Results showed that 10 microM forskolin significantly stimulated a glibenclamide-inhibitable whole-cell conductance by approximately five-fold. Furthermore, reduction of the Cl- concentration in the bathing solution through partial substitution of NaCl with Na-isethionate resulted in a rightward shift of the reversal potential for both baseline and forskolin-stimulated whole-cell currents from 0 to values close to the theoretical Cl- reversal potential predicted by the Nernst equation. Western blot analysis with a monoclonal antibody recognizing the epitope in the C-terminus of the cystic fibrosis transmembrane conductance regulator (CFTR) showed a positive band at its molecular weight, approximately 170 kD. Immunostaining under confocal microscopy revealed a CFTR specific signal in the apical sections of primary conjunctival epithelial cells. In addition, RT-PCR detection amplified a cDNA fragment 100% identical to the predicted portion of the cloned rabbit CFTR message. The stage is thus set for determining the extent of CFTR contribution to cAMP-regulated Cl- conductance in pigmented rabbit conjunctival epithelial cells.