gebhart/patrepeval huggingface dataset:
Investigation of Early Plasma Evolution Induced by Ultrashort Laser Pulses (2012)

Early plasma is generated owing to high intensity laser irradiation of target and the subsequent target material ionization. Its dynamics plays a significant role in laser-material interaction, especially in the air environment(1-11). Early plasma evolution has been captured through pump-probe shadowgraphy(1-3) and interferometry(1,4-7). However, the studied time frames and applied laser parameter ranges are limited. For example, direct examinations of plasma front locations and electron number densities within a delay time of 100 picosecond (ps) with respect to the laser pulse peak are still very few, especially for the ultrashort pulse of a duration around 100 femtosecond (fs) and a low power density around 10(14) W/cm(2). Early plasma generated under these conditions has only been captured recently with high temporal and spatial resolutions(12). The detailed setup strategy and procedures of this high precision measurement will be illustrated in this paper. The rationale of the measurement is optical pump-probe shadowgraphy: one ultrashort laser pulse is split to a pump pulse and a probe pulse, while the delay time between them can be adjusted by changing their beam path lengths. The pump pulse ablates the target and generates the early plasma, and the probe pulse propagates through the plasma region and detects the non-uniformity of electron number density. In addition, animations are generated using the calculated results from the simulation model of Ref. (12) to illustrate the plasma formation and evolution with a very high resolution (0.04 ~ 1 ps). Both the experimental method and the simulation method can be applied to a broad range of time frames and laser parameters. These methods can be used to examine the early plasma generated not only from metals, but also from semiconductors and insulators.
A visual feature based video identifying system for the TV commercial's monitoring (2006)

For companies, TV commercials are very important way to introduce and advertise their products. It is expensive to put an advertisement on TV. So these companies generally charge other companies to verify that their TV commercials are actually broadcasted as contracted. Currently, these monitoring are done manually. All the TV programs and their air-times are recorded at the same time. Then an agent checks the start time and the end time of a TV-commercial. Video retrieval and matching techniques can be used to monitor TV commercials automatically. By extracting visual identified features, we can measure the similarities and identify a target video from thousands of videos. In this paper, we designed the visual feature DB and implemented video matching system. To construct the DB, we extracted scene change information and dominant colors of commercial clips. By combining the features, we can identify TV commercials
Low temperature plasma activated direct wafer bonding (2012)

The bonding behavior of a low temperature direct wafer bonding process was studied for Si wafers with native oxide and Si wafers with thermal oxide. It was found that high bond strength could be achieved without annealing already at RT. Silicon bulk strength could be reached with annealing at 200°C.
Selective activation of PPARγ in skeletal muscle induces endogenous production of adiponectin and protects mice from diet-induced insulin resistance (2009)

The nuclear receptor peroxisome proliferator-activated receptor (PPAR)gamma plays a key role in regulating whole body glucose homeostasis and insulin sensitivity. Although it is expressed most highly in adipose, it is also present at lower levels in many tissues, including skeletal muscle. The role muscle PPARgamma plays in metabolic regulation and in mediating the antidiabetic effects of the thiazolidinediones is not understood. The goal of this work was to examine the molecular and physiological effects of PPARgamma activation in muscle cells. We found that pharmacological activation of PPARgamma in primary cultured myocytes, and genetic activation of muscle PPARgamma in muscle tissue of transgenic mice, induced the production of adiponectin directly from muscle cells. This muscle-produced adiponectin was functional and capable of stimulating adiponectin signaling in myocytes. In addition, elevated skeletal muscle PPARgamma activity in transgenic mice provided a significant protection from high-fat diet-induced insulin resistance and associated changes in muscle phenotype, including reduced myocyte lipid content and an increase in the proportion of oxidative muscle fiber types. Our findings demonstrate that PPARgamma activation in skeletal muscle can have a significant protective effect on whole body glucose homeostasis and insulin resistance and that myocytes can produce and secrete functional adiponectin in a PPARgamma-dependent manner. We propose that activation of PPARgamma in myocytes induces a local production of adiponectin that acts on muscle tissue to improve insulin sensitivity.
Role of Nitric Oxide and Cyclic Guanosine 3′,5′-Monophosphate in the Estrogen Regulation of Cervical Epithelial Permeability* (2000)

Treatment of cultured human cervical epithelia on filters with 17beta-estradiol increases paracellular permeability in a time- and dose-related manner (EC50, 1.1 nM). The objective of the present study was to understand the molecular mechanisms of estrogen action. In cultured human cervical epithelial cells the nitric oxide (NO) donors sodium nitroprusside (SNP) and N-[ethoxycarbonyl]-3-[4-morpholinyl]sydnoneimine (SIN-I) and the cell-permeable cGMP analog 8-bromo-cGMP (8-Br-cGMP) increased paracellular permeability. In estrogen-treated cells SNP and 8-Br-cGMP increased permeability to a lesser degree than in estrogen-deprived cells, suggesting that NO and cGMP mediate the effect of estrogen on permeability. Tamoxifen blocked the estrogen-induced increase in permeability, but it had no effect on increases in permeability that were induced by SNP or by 8-Br-cGMP. LY-83583 (blocker of guanylate cyclase) attenuated the effect of SNP, whereas KT-5823 (blocker of cGMP-dependent protein kinase) abrogated the effects of both SNP and 8-Br-cGMP. Treatment with 17beta-estradiol increased NO release and cellular cGMP in a dose-related manner (EC50, approximately 1 nM), and the effects were inhibited by tamoxifen. Treatment with SNP increased cGMP maximally, even in estrogen-deficient cells. LY-83583 blocked the estrogen-induced increase in cGMP, but neither LY-83583 nor KT-5823 had a significant effect on the estrogen-induced increases in NO release and cellular cGMP. The NO synthase (NOS) inhibitor N(G)-nitro-L-arginine methyl ester decreased NO release, and pretreatment of cells with L-arginine reversed the effect. Cultured human cervical epithelial cells express messenger RNA for the NOS isoforms endothelial NOS (ecNOS), brain NOS, and inducible NOS. 17beta-Estradiol up-regulated ecNOS messenger RNA, and tamoxifen blocked the effect. Based on these results we suggest that the effect of estradiol on permeability involves four signaling steps: 1) activation of estrogen receptors, 2) increase in ecNOS transcription and up-regulation of NO activity, 3) NO activation of guanylate cyclase and increase in cGMP, and 4) cGMP activation of cGMP-dependent protein kinase.
Abstract C238: Polyacetal polymer-based anti-HER2 antibody-drug conjugate employing cysteine bioconjugation through thioether linkage allows a high drug loading of dolastatin-derived payload with excellent pharmacokinetics and potent anti-tumor activity. (2013)

Abstract The application of biodegradable, polyacetal polymers to antibody-drug conjugate (ADC) design can provide numerous advantages, including significantly higher capacity for drug payload (∼20 drugs per antibody), the use of payloads with low potency that are not suitable for direct conjugation, the improvement of physicochemical properties for ADC, especially with highly hydrophobic payloads and the use of protein recognition scaffolds beyond the commonly used IgGs. The basis of this novel polyacetal polymer-based conjugation system is a hydrophilic, fully biodegradable polyacetal carrier (PHF or poly(1-hydroxymethylethylene hydroxymethylformal, or Fleximer®) modified with chemically orthogonal linkers. One linker is used to covalently attach a targeting moiety (mAb or alternative), while a second, chemically distinct linker is used to attach a drug payload and to control the mechanism and rate of drug release. Previously, we have reported potent anti-tumor activity with trastuzumab-s-Dolaflexin™, an anti-HER2 ADC composed of trastuzumab and a proprietary dolastatin derivative coupled to a Fleximer scaffold (Dolaflexin™). In that example, Dolaflexin was conjugated to the antibody through interchain cysteine residues via a hindered disulfide linkage (AACR Annual Meeting 2013 Abstract #4331). Unlike direct drug-cysteine linked ADCs that can result in destabilization of antibody by disruption of interchain disulfide bridges, we have shown that Dolaflexin conjugation via cysteines in the antibody hinge region stabilizes the resulting ADCs through the formation of inter-chain bridge structures. Trastuzumab-s-Dolaflexin ADC exhibited a prolonged plasma half-life, tumor-specific accumulation, and potent anti-tumor activity in vivo. Here, we report a novel trastuzumab-m-Dolaflexin ADC using a maleimide linker that further enhances the pharmacokinetics of the ADC and demonstrates complete regressions of established HER2+ BT-474 xenograft tumors in SCID mice even at a single dose of 2.5 mg/kg. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C238. Citation Format: Joshua Thomas, Alex Yurkovetskiy, Natalya Bodyak, Mao Yin, Patrick Conlon, Cheri Stevenson, Alex Uttard, Liu Qin, Dmitry Gumerov, Elena Ter-Ovaneysan, Michael DeVit, Laura L. Poling, Peter U. Park, Timothy B. Lowinger. Polyacetal polymer-based anti-HER2 antibody-drug conjugate employing cysteine bioconjugation through thioether linkage allows a high drug loading of dolastatin-derived payload with excellent pharmacokinetics and potent anti-tumor activity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C238.
A Virtual Environment for the Treatment of Chronic Combat-Related Post-Traumatic Stress Disorder (1999)

Post-traumatic stress disorder (PTSD) is one of the most disabling psychopathological conditions affecting the veteran population. An estimated 830,000 U.S. veterans currently have symptoms of chronic combat-related PTSD. No therapeutic approach has proven to be consistently effective in the management of combat-related PTSD. Behavior therapies with an exposure element have proven more effective than most other types of treatment, but a significant number of patients do not seem to benefit from them, possibly because of difficulties imagining, visualizing, or describing their traumatic experiences. In this article, we describe Virtual Vietnam, a set of two virtual environments we have developed for the treatment of combat-related PTSD, and its use as one component of a comprehensive treatment program.
Keynote address I: Programming the cloud (2011)

Client + cloud computing is a disruptive, new computing platform, combining diverse client devices - PCs, smartphones, sensors, and single-function and embedded devices - with the unlimited, on-demand computation and data storage offered by cloud computing services such as Amazon's AWS or Microsoft's Windows Azure. As with every advance in computing, programming is a fundamental challenge as client + cloud computing combines many difficult aspects of software development. Systems built for this world are inherently parallel and distributed, run on unreliable hardware, and must be continually available - a challenging programming model for even the most skilled programmers. How then do ordinary programmers develop software for the Cloud? This talk presents one answer, Orleansis a software framework for building client + cloud applications. Orleans encourages use of simple concurrency patterns that are easy to understand and implement correctly, building on an actor-like model with declarative specification of persistence, replication, and consistency and using lightweight transactions to support the development of reliable and scalable client + cloud software.
Neural Network Incorporating Meal Information Improves Accuracy of Short-Time Prediction of Glucose Concentration (2012)

Diabetes mellitus is one of the most common chronic diseases, and a clinically important task in its management is the prevention of hypo/hyperglycemic events. This can be achieved by exploiting continuous glucose monitoring (CGM) devices and suitable short-term prediction algorithms able to infer future glycemia in real time. In the literature, several methods for short-time glucose prediction have been proposed, most of which do not exploit information on meals, and use past CGM readings only. In this paper, we propose an algorithm for short-time glucose prediction using past CGM sensor readings and information on carbohydrate intake. The predictor combines a neural network (NN) model and a first-order polynomial extrapolation algorithm, used in parallel to describe, respectively, the nonlinear and the linear components of glucose dynamics. Information on the glucose rate of appearance after a meal is described by a previously published physiological model. The method is assessed on 20 simulated datasets and on 9 real Abbott FreeStyle Navigator datasets, and its performance is successfully compared with that of a recently proposed NN glucose predictor. Results suggest that exploiting meal information improves the accuracy of short-time glucose prediction.
Immunoselection of cDNAs to avian intestinal calcium binding protein 28K and a novel calmodulin-like protein: assessment of mRNA regulation by the vitamin D hormone (1987)

Calcium's role in a variety of cellular processes has been well documented. The storage, distribution, and delivery of calcium are regulated by a family of binding proteins including troponin C, calmodulin, parvalbumin, and vitamin D dependent calcium binding protein (CaBP-28), all of which have evolved from a common ancestral gene. To evaluate vitamin D regulation of gene transcription, a CaBP-28 cDNA (767 base pairs) was isolated from a chicken intestine lambda gt11 library utilizing a polyvalent CaBP-28 antibody as a probe. Coincident with the identification of the CaBP-28 cDNA, a group of cDNAs also was isolated (with the anti-CaBP-28 antibody) that demonstrated 84% nucleotide homology and 99% deduced amino acid homology with chicken brain calmodulin (CaM). This new CaM-like cDNA was named neoCaM. There is little nucleotide homology between the CaBP-28 cDNA and neoCaM. The CaBP-28 cDNA hybridizes with three transcripts of 2000, 2900, and 3300 bases which are dramatically induced by 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], while the neoCaM cDNA recognizes three distinct (from CaBP-28) transcripts. Two of these mRNAs are 1400 and 1800 bases as described for brain CaM, but another larger 4000-base transcript is detected with neoCaM. Neither the CaM nor the neoCaM transcript reveals any modulation by 1,25(OH)2D3. Herein, we discuss the possible significance of not only the isolation of both cDNAs with a single antibody but also the relation of neoCaM to other well-characterized CaM cDNAs.
Factors affecting Potassium Balance During Frusemide Administration (1984)

We investigated the effects of Na+ intake, the renin-angiotensin-aldosterone system and anti-diuretic hormone (ADH) on K+ balance during 3 days of frusemide administration to six normal subjects. Subjects received 40 mg of frusemide for 3 days during three different protocols: Na+ intake 270 mmol/day (high salt); Na+ intake 20 mmol/day to stimulate the renin-angiotensin-aldosterone system (low salt); Na+ intake 270 mmol/day plus captopril (25 mg/6 h) to prevent activation of the renin-angiotensin-aldosterone system. In a fourth protocol, a water load was given during high salt intake to prevent ADH release and then frusemide was given. During high salt intake, frusemide increased K+ excretion (UKV) over 3 h, but the loss was counterbalanced by subsequent renal K+ retention so that daily K+ balance was neutral. During low salt intake, the magnitude of the acute kaliuresis following the first dose of frusemide and the slope of the linear relationship between UKV and the log of frusemide excretion were increased compared with that found during the high salt intake. In addition, low salt intake abolished the compensatory renal retention of K+ after frusemide and cumulative K+ balance over 3 days of diuretic administration was uniformly negative (-86 +/- 7 mmol/3 days; P less than 0.001). Captopril abolished the rise in plasma aldosterone concentration induced by frusemide. The acute kaliuresis after frusemide was unchanged compared with that observed during high salt intake. The compensatory reduction in UKV occurring after the diuretic was slightly potentiated. In fact, captopril given without the diuretic induced a small positive K+ balance.(ABSTRACT TRUNCATED AT 250 WORDS)
A method for computing hadron-nucleus cross sections in fully active sampling calorimetric targets (2022)

Interaction cross section measurements in fixed-target scattering experiments are typically performed by measuring the attenuation of a beam of particles that is incident upon a target slab of material. A fully active sampling calorimeter, such as the time projection chamber, is a more voluminous target that can be treated as a series of smaller target slabs. We present a method of computing hadron-nucleus interaction cross sections for data taken with fully active sampling calorimeters that is robust even if the target is comprised of numerous slabs of various thicknesses.
A shortcut to identifying small molecule signals that regulate behavior and development in Caenorhabditis elegans (2009)

Small molecule metabolites play important roles in Caenorhabditis elegans biology, but effective approaches for identifying their chemical structures are lacking. Recent studies revealed that a family of glycosides, the ascarosides, differentially regulate C. elegans development and behavior. Low concentrations of ascarosides attract males and thus appear to be part of the C. elegans sex pheromone, whereas higher concentrations induce developmental arrest at the dauer stage, an alternative, nonaging larval stage. The ascarosides act synergistically, which presented challenges for their identification via traditional activity-guided fractionation. As a result the chemical characterization of the dauer and male attracting pheromones remained incomplete. Here, we describe the identification of several additional pheromone components by using a recently developed NMR-spectroscopic approach, differential analysis by 2D NMR spectroscopy (DANS), which simplifies linking small molecule metabolites with their biological function. DANS-based comparison of wild-type C. elegans and a signaling-deficient mutant, daf-22, enabled identification of 3 known and 4 previously undescribed ascarosides, including a compound that features a p-aminobenzoic acid subunit. Biological testing of synthetic samples of these compounds revealed additional evidence for synergy and provided insights into structure-activity relationships. Using a combination of the three most active ascarosides allowed full reconstitution of the male-attracting activity of wild-type pheromone extract. Our results highlight the efficacy of DANS as a method for identifying small-molecule metabolites and placing them within a specific genetic context. This study further supports the hypothesis that ascarosides represent a structurally diverse set of nematode signaling molecules regulating major life history traits.
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles (2021)

Abstract Migraine affects over a billion individuals worldwide but its genetic underpinning remains largely unknown. This genome-wide association study (GWAS) of 102,084 migraine cases and 771,257 controls identified 123 loci of which 86 are novel. The loci provide an opportunity to evaluate shared and distinct genetic components in the two main migraine subtypes: migraine with aura and migraine without aura. A stratification of the risk loci using 29,679 cases with subtype information, of which approximately half have never been used in a GWAS before, indicated three risk variants that appear specific for migraine with aura (in HMOX2, CACNA1A and MPPED2 ), two that appear specific for migraine without aura (near SPINK2 and near FECH ), and nine that increase susceptibility for migraine regardless of subtype. The new risk loci include genes encoding recent migraine-specific drug targets, namely calcitonin gene-related peptide ( CALCA/CALCB ) and serotonin 1F receptor ( HTR1F ). Overall, genomic annotations among migraine-associated variants were enriched in both vascular and central nervous system tissue/cell types supporting unequivocally that neurovascular mechanisms underlie migraine pathophysiology.
Insight into Ca‐Substitution Effects on O3‐Type NaNi1/3Fe1/3Mn1/3O2 Cathode Materials for Sodium‐Ion Batteries Application (2018)

O3-type NaNi<sub>1/3</sub> Fe<sub>1/3</sub> Mn<sub>1/3</sub> O<sub>2</sub> (NaNFM) is well investigated as a promising cathode material for sodium-ion batteries (SIBs), but the cycling stability of NaNFM still needs to be improved by using novel electrolytes or optimizing their structure with the substitution of different elements sites. To enlarge the alkali-layer distance inside the layer structure of NaNFM may benefit Na<sup>+</sup> diffusion. Herein, the effect of Ca-substitution is reported in Na sites on the structural and electrochemical properties of Na<sub>1-</sub><sub>x</sub> Ca<sub>x</sub><sub>/2</sub> NFM (x = 0, 0.05, 0.1). X-ray diffraction (XRD) patterns of the prepared Na<sub>1-</sub><sub>x</sub> Ca<sub>x</sub><sub>/2</sub> NFM samples show single α-NaFeO<sub>2</sub> type phase with slightly increased alkali-layer distance as Ca content increases. The cycling stabilities of Ca-substituted samples are remarkably improved. The Na<sub>0.9</sub> Ca<sub>0.05</sub> Ni<sub>1/3</sub> Fe<sub>1/3</sub> Mn<sub>1/3</sub> O<sub>2</sub> (Na<sub>0.9</sub> Ca<sub>0.05</sub> NFM) cathode delivers a capacity of 116.3 mAh g<sup>-1</sup> with capacity retention of 92% after 200 cycles at 1C rate. In operando XRD indicates a reversible structural evolution through an O3-P3-P3-O3 sequence of Na<sub>0.9</sub> Ca<sub>0.05</sub> NFM cathode during cycling. Compared to NaNMF, the Na<sub>0.9</sub> Ca<sub>0.05</sub> NFM cathode shows a wider voltage range in pure P3 phase state during the charge/discharge process and exhibits better structure recoverability after cycling. The superior cycling stability of Na<sub>0.9</sub> Ca<sub>0.05</sub> NFM makes it a promising material for practical applications in sodium-ion batteries.