gebhart/patrepeval huggingface dataset:
Major depressive disorder: remission of associated symptoms. (2006)

Major depressive disorder (MDD) is a highly prevalent disease often associated with significant medical comorbidity. However, limited data are available examining the associated symptoms of MDD, especially the painful physical symptoms that frequently occur in patients. The presence of these physical symptoms greatly reduces a clinician's ability to recognize and diagnose MDD, ultimately leading to poor treatment outcome. While the treatment goal of MDD is complete remission of all symptoms and the patient's return to full-functioning capacity, if physical symptoms persist, the patient does not achieve functional recovery. Severe consequences have been associated with incomplete remission and residual symptoms, including greater disability and health care costs, plus the increased risk of relapse, morbidity, and mortality. In the treatment of MDD, the noradrenergic, serotonergic, and dopaminergic neural pathways have been found to be affected by depression. More specifically, these neural pathways may correlate with certain psychological and physical symptoms of depression. By studying the effects of antidepressant medications on specific neurotransmitters, antidepressant therapies could be matched to treat specific symptoms of depression. To achieve the goal of remission, clinicians must first determine the best rating method to identify and accurately evaluate the physical symptoms of depression in addition to the core mood symptoms. Therefore, further studies are needed to aid our assessment of physical symptoms and to meet the challenge of effectively matching treatments to a patient's specific symptoms.
Parallel implementation of 3-D iterative reconstruction with intra-node image update for the jPET-D4 (2007)

the use of small crystals in new PET scanners results in large number of line-of-response (LOR). Thus, fully 3D image reconstruction becomes time consuming especially for iterative algorithms. One of the methods to speed-up image reconstruction is by parallel computing with computer cluster. However, as number of computing node increases, the parallel efficiency decreases mainly due to network transfer delay. Network delay is significant particularly for iterative reconstruction algorithms with large subset size, such as RAMLA. In this paper, we propose a way to reduce data transfer between nodes by allowing intra-node image update. In details, few intra-node updates for L-1 number of sub-iterations are performed in each slave thread before a global update is done at the master thread. We implemented a normal parallel version and the proposed intra-node update version of RAMLA for the jPET-D4 scanner by using MPICH2 library. We evaluated it with four workstations, each with two dual-core opteron 2.8GHz processors. There are total of 16 slave threads. Each slave thread calculates different set of LORs which are divided according to ring difference numbers. We accessed image quality of the proposed method with a hotspot phantom generated by GATE simulator. With subset size of 48, log likelihood is compared between normal RAMLA and intra-node update version of L = 4, 8, and 16. The difference in log likelihood is negligible even for L=16. Other than simulation, we also reconstruct a Hoffman phantom data from FDG experiment. No image artifact is observed for simulation as well as experiment images. In our implementation, computation time is reduced by 15% with L=16. More significant saving in calculating time is expected with larger subset size by optimizing the relaxation parameter. With intra-node update, we showed the possibility to speed up computation without much deterioration in the image quality.
Control of Glycolytic Flux by AMP-Activated Protein Kinase in Tumor Cells Adapted to Low pH (2012)

Tumor cells grow in nutrient- and oxygen-deprived microenvironments and adapt to the suboptimal growth conditions by altering their metabolic pathways. This adaptation process commonly results in a tumor phenotype that displays a high rate of aerobic glycolysis and aggressive tumor characteristics. The glucose regulatory molecule, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), is a bifunctional enzyme that is central to glycolytic flux and is downstream of the metabolic stress sensor AMP-activated protein kinase (AMPK), which has been suggested to modulate glycolysis and possibly activate isoforms of PFKFB, specifically PFKFB3 expressed in tumor cells. Our results demonstrated that long-term low pH exposure induced AMPK activation, which resulted in the up-regulation of PFKFB3 and an increase in its serine residue phosphorylation. Pharmacologic activation of AMPK resulted in an increase in PFKFB3 as well as an increase in glucose consumption, whereas in contrast, inhibition of AMPK resulted in the down-regulation of PFKFB3 and decreased glycolysis. PFKFB3 overexpression in DB-1 tumor cells induced a high rate of glycolysis and inhibited oxygen consumption, confirming its role in controlling glycolytic flux. These results show that low pH is a physiological stress that can promote a glycolytic phenotype commonly associated with tumorigenesis. The implications are that the tumor microenviroment contributes to tumor growth and treatment resistance.
HIV-1 Protease Inhibitor, Ritonavir (2004)

We previously showed that HIV-1 protease inhibitors (PIs) slowed the proliferation of human myeloid leukemia cells and enhanced their differentiation in the presence of all-trans-retinoic acid. In this study, we found that PIs, including ritonavir, saquinavir, and indinavir, inhibited the growth of DU145 and PC-3 androgen-independent prostate cancer cells as measured by a clonal proliferation assay. Recent studies showed that ritonavir inhibited cytochrome P450 3A4 enzyme (CYP3A4) in liver microsomes. The CYP3A4 is involved in drug metabolism and acquisition of drug resistance. To clarify the drug interaction between ritonavir and other anticancer drugs, we cultured DU145 cells with docetaxel either alone or in combination with ritonavir. Ritonavir enhanced the antiproliferative and proapoptotic effects of docetaxel in the hormonally independent DU145 prostate cancer cells in vitro as measured by the clonogenic soft agar assay and detection of the activated form of caspase-3 and cleavage of poly(ADP-ribose) polymerase using Western blot analysis. Real-time PCR showed that docetaxel induced the expression of CYP3A4 at the transcriptional level, and ritonavir (10(-5) mol/L) completely blocked this induction. An ELISA-based assay also showed that ritonavir inhibited DNA binding activity of nuclear factor kappaB (NFkappaB) in DU145 cells, which is a contributor to drug resistance in cancer cells. Furthermore, combination treatment of docetaxel and ritonavir dramatically inhibited the growth of DU145 cells present as tumor xenografts in BNX nude mice compared with either drug alone. Importantly, docetaxel induced expression of CYP3A4 in DU145 xenografts, and ritonavir completely blocked this induction. Ritonavir also inhibited NFkappaB DNA binding activity in DU145 xenografts. Extensive histologic analyses of the liver, spleen, kidneys, bone marrow, skin, and subcutaneous fat pads from these mice showed no abnormalities. In summary, combination therapy of ritonavir and anticancer drugs holds promise for the treatment of individuals with advanced, drug resistant cancers.
Kinetic and Mechanistic Studies of Carboxylic Acid–Bisoxazoline Chain‐Coupling Reactions (2003)

Abstract Kinetic studies of the reactions between a model carboxylic acid and bisoxazoline coupling agents, namely 2,2′‐(1,3‐phenylene)bis(2‐oxazoline) ( mbox ), 2,2′‐(1,4‐phenylene)bis(2‐oxazoline) ( pbox ), and 2,2′‐(2,6‐pyridylene)bis(2‐oxazoline) ( pybox ), were carried out in bulk at 140–220 °C. A second‐order two‐step reaction mechanism was proposed and was verified by the experimental results. The results also indicate that the reactivity of the oxazoline groups is unchanged after the reaction of the other oxazoline group of the same coupling agent moiety, that is, oxazoline groups are equireactive. Rate constants and activation enthalpies and entropies were determined, allowing the comparison of bisoxazoline reactivity. The following reactivity order was found: pybox &gt; mbox &gt; pbox . The formation of a stabilized protonated complex is postulated to explain the much higher reaction rate observed with the new coupling agent pybox . Variation of the experimental concentrations of reactants and reaction products versus time. magnified image Variation of the experimental concentrations of reactants and reaction products versus time.
Loose social organisation of AB strain zebrafish groups in a two-patch environment (2019)

We study the collective behaviour of zebrafish shoals of different numbers of individuals (1, 2, 3, 5, 7, 10 and 20 AB zebrafish Danio rerio) in a constraint environment composed of two identical square rooms connected by a corridor. This simple set-up is similar to a natural patchy environment. We track the positions and the identities of the fish and compute the metrics at the group and at the individual levels. First, we show that the number of fish affects the behaviour of each individual in a group, the cohesion of the groups, the preferential interactions and the transition dynamics between the two rooms. Second, during collective departures, we show that the rankings of exit correspond to the topological organisations of the fish prior to their collective departure. This spatial organisation appears in the group a few seconds before a collective departure. These results provide new evidences on the spatial organisation of the groups and the effect of the number of fish on individual and collective behaviours in a patchy environment.
Modelling a continuous process with discrete simulation techniques and its application to LNG supply chains (2004)

We discuss the problem of modelling an LNG supply chain efficiently. The production, processing, transportation and consumption of LNG (liquid natural gas) and the associated products are a topic of major interest in the energy industry. While the problem is apparently continuous, analysis suggests that this problem can be modelled using discrete, deterministic techniques. A method involving a modification of the three phase discrete technique was used. Analysis of the way in which the effects of an event spread leads to a method by which excessive recalculation can be avoided, yielding a model that is computationally very efficient.
Effects of Nitrogen and Sulfur Nutrition on Grain Composition and Properties of Wheat and Related Cereals (2011)

This chapter contains sections titled: Abstract Introduction Effect of nitrogen on grain protein content Effect of nitrogen on grain protein nutrition and quality Effect of grain nitrogen on protein composition and functional properties of wheat Effect of sulfur on grain protein composition and functional properties of wheat Effects of nitrogen and sulfur on protein composition and malting quality of barley Effects of nitrogen on β-glucan in oats Effect of nitrogen and sulfur nutrition on other cereal grain components Nutritional control of storage protein gene expression Conclusions Acknowledgments References
Nonenzymatic Glycosylation of Laminin and the Laminin Peptide CIKVAVS Inhibits Neurite Outgrowth (1993)

Nerve regeneration in diabetic animals is delayed and qualitatively impaired, but the mechanisms responsible for these defects have not been elucidated. The extracellular matrix protein laminin promotes the extension of neuronal processes, and recent studies have localized neurite-promoting activity to a lysine-containing sequence (IKVAV) within the laminin molecule. Because long-lived molecules such as laminin are likely to accumulate excessive amounts of nonenzymatic glycosylation products in diabetic subjects, we have investigated whether such adduct formation on laminin or the IKVAV peptide affects their neurite-promoting properties. These studies used the murine neuroblastoma cell line NB2a, which extends neurites on laminin when differentiated by cAMP. Neurite outgrowth in NB2a cells plated on glycosylated laminin was significantly decreased from that occurring on unmodified laminin. Similarly, neurite outgrowth in NB2a cells plated on glycosylated IKVAV peptide was inhibited compared with that observed on native IKVAV. These data suggest that nonenzymatic glycosylation of a biologically active domain within laminin may contribute to impaired nerve regeneration in diabetes.
Association of CD247 Polymorphisms with Rheumatoid Arthritis: A Replication Study and a Meta-Analysis (2013)

Given the role of CD247 in the response of the T cells, its entailment in autoimmune diseases and in order to better clarify the role of this gene in RA susceptibility, we aimed to analyze CD247 gene variants previously associated with other autoimmune diseases (rs1052237, rs2056626 and rs864537) in a large independent European Caucasian population. However, no evidence of association was found for the analyzed CD247 single-nucleotide polymorphisms (SNPs) with RA and with the presence/absence of anti-cyclic citrullinated polypeptide. We performed a meta-analysis including previously published GWAS data from the rs864537 variant, revealing an overall genome-wide significant association between this CD247 SNP and RA with anti-CCP (OR = 0.90, CI 95% = 0.87-0.93, Poverall = 2.1×10(-10)). Our results show for first time a GWAS-level association between this CD247 polymorphism and RA risk.
Reduced number of discrete velocities for a flow description by lattice Boltzmann theory (2012)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Jae Wan Shim; Reduced number of discrete velocities for a flow description by lattice Boltzmann theory. AIP Conference Proceedings 27 November 2012; 1501 (1): 405–408. https://doi.org/10.1063/1.4769553 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
The Programming Language Aspects of ThingLab, a Constraint-Oriented Simulation Laboratory (1981)

The programming language aspects of a graphic simulation laboratory named ThingLab are presented.
Low-complexity distributed algorithms for uplink CoMP in heterogeneous LTE networks (2016)

Coordinated multi-point transmission (CoMP) techniques are being touted as enabling technologies for interference mitigation in next generation heterogeneous wireless networks (HetNets). In this paper, we present a comparative performance study of uplink (UL) CoMP algorithms for the 3GPP LTE HetNets. Focusing on a distributed and functionally-split architecture, we consider six distinct UL-CoMP algorithms: 1. Joint reception in the frequency-domain (JRFD) 2. Two-stage equalization (TSEQ) 3. Log-likelihood ratio exchange (LLR-E) 4. Symmetric TSEQ (S-TSEQ) 5. Transport block selection diversity (TBSD) 6. Coordinated scheduling with adaptive interference mitigation (CS-AIM) where JRFD, TSEQ, S-TSEQ, TBSD and CS-AIM are our main contributions in this paper, and quantify their relative performances via the post-processing signal-to-interference-plus-noise ratio distributions. We also compare the CoMP-specific front-haul rate requirements for all the schemes considered in this paper. Our results indicate that, with a linear minimum mean-square error receiver, the JRFD and TSEQ have identical performances, whereas S-TSEQ relaxes the front-haul latency requirements while approaching the performance of TSEQ. Furthermore, in a HetNet environment, we find that CS-AIM provides an attractive alternative to TBSD and LLR-E with a significantly reduced CoMP-specific front-haul rate requirement.
Simulations of Neutron Multiplicity Measurements of a Weapons-Grade Plutonium Sphere with MCNP-PoliMi (2010)

Abstract not provided.
The essential genomic landscape of the commensal Bifidobacterium breve UCC2003 (2017)

Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.
Spumaviruses isolated from sources containing agents of non‐A, non‐B (NANB) hepatitis do not cause NANB hepatitis (1988)

Serum and liver tissue containing infective non-A, non-B hepatitis virus were shown to contain a retrovirus-like agent that replicated when inoculated into chimpanzee liver cell cultures in vitro. The virus appeared to assemble its core particles in association with tubular structures reminiscent of those characteristically seen in non-A, non-B hepatitis virus-infected chimpanzee liver in vivo, and produced syncytial cytopathic effects in a number of continuous and a primary mammalian liver cells. The agents were neutralized by acute and convalescent sera from human and chimpanzee cases of non-A, non-B hepatitis, as well as by antisera against simian spumavirus type 7, but not type 6. Aluminum chloride failed to abolish viral infectivity. There was no evidence of virus replication or hepatitis in chimpanzees inoculated with a seventh passage of one of the isolates. Thus the data suggest that the isolates are not causally related to non-A, non-B hepatitis, as was previously postulated.
Modification of the PROTO-II accelerator power flow for multi-purpose use (1985)

Abstract : PROTO-II is a nominal 10 TW, 320 kJ accelerator which has been used to study imploding plasma physics for the last few years. The machine has been modified to make it useful as a bremsstrahlung radiation source and to lower the inductance for better energy coupling to gas puff loads. The triplate water transmission line has been converted to a 4-line horizontal 8-plate transformer section feeding a 4-layer insulator stack, using a multiple rod crossover network. Hinged plates allow a constant impedance transmission line for gas puff applications and make a 2:1 impedance transformer for bremsstrahlung applications. For Gas Puff operation, vertical MITLs connect the 4-layer stack to the load. For bremsstrahlung operation, conical MITL plates connect each of the four lines to feed one side of a 2-cathode ring electron beam diode. Circuit simulations of the power flow predict up to 270 kJ of energy at 1.0 MV into the Gas Puff diode and up to 230 kJ at 1 .5 MV into the electron beam diode. Accelerator performance under the new configuration is discussed.
MPCVD Manufacturing Si/C of Li(ion) battery Anodes-Compatibility With New Type Imidazole-Based Electrolytes (2011)

Abstract not Available.
Short-Range Millimetric-Wave Radar System for Occupancy Sensing Application (2018)

Ever-increasing demands of energy consumption have propelled the need for a robust occupancy sensor. Occupancy sensors can be used to control lighting, heating, ventilation, and air conditioning (HVAC) in smart homes, as well as other presence-related loads in commercial, office, and public spaces. The evolution of ubiquitous sensing technologies, such as frequency modulated continuous wave radar, has led to the development of reliable occupancy sensors that can facilitate energy savings by being responsive to human presence and regulate energy load by intelligently adapting to their environment. We, in this article, present a short-range 60 GHz compact radar sensor that can enable detection and counting of people in a space by monitoring people's vital signs, minute motions, and major bodily motions. We present the radar-based occupancy sensing solution and experimentally validate the performance of the proposed system.
Atomic layer control in Sr-Cu-O artificial lattice growth (1994)

Atomic layer growth control of the infinite-layer compound, SrCuO2, based artificial lattices is demonstrated on SrTiO3 (100). Two different patterns have been observed by reflection high-energy electron diffraction during the alternating supply of strontium and copper metal under the flow of NO2. The intensity of the incommensurate streak increases with an increasing supply of Cu and decreases to zero with an increasing supply of Sr. Precise control of atomic layer growth is successfully carried out by in situ intensity monitoring of the incommensurate streak.
A robust design against comb electrode spacing variations for in-plane switching mode thin-film transistor liquid-crystal displays (2005)

A method to reduce the transmittance nonuniformity caused by comb electrode spacing variations of in-plane switching mode thin-film transistor liquid-crystal displays is proposed. The method is based on the compensation of the effect of the comb electrode spacing variations with effective driving voltage variation via feed-through voltage in the thin-film transistor addressing. The conditions for this compensation were analyzed theoretically taking into account gate delay (recharging) effects. It was observed that the common dc driving was superior to the common inversion driving in terms of compensation efficiency. An alternative driving method was proposed to enhance the compensation in common inversion driving.
Yeast killer plasmid mutations affecting toxin secretion and activity and toxin immunity function. (1982)

M double-stranded RNA (MdsRNA) plasmid mutants were obtained by mutagenesis and screening of a diploid killer culture partially heat cured of the plasmid, so that a high proportion of the cells could be expected to have only on M plasmid. Mutants with neutral (nonkiller [K-], immune [R+]) or suicide (killer [K+], sensitive [R-] phenotypes were examined. All mutants became K- R- sensitives on heat curing of the MdsRNA plasmid, and showed cytoplasmic inheritance by random spore analysis. In some cases, M plasmid mutations were indicated by altered mobility of the MdsRNA by agarose gel electrophoresis or by altered size of in vitro translation products from denatured dsRNA. Neutral mutants were of two types: nonsecretors of the toxin protein or secretors of an inactive toxin. Of three neutral nonsecretors examined, one (NLP-1), probably a nonsense mutation, made a smaller protoxin precursor in vitro and in vivo, and two made full-size protoxin molecules. The in vivo protoxin of 43,000 molecular weight was unstable in the wild type and kinetically showed a precursor-product relationship to the processed, secreted 11,000-molecular-weight toxin. In one nonsecretor (N1), the protoxin appeared more stable in a pulse-chase experiment, and could be altered in a recognition site required for protein processing.