gebhart/patrepeval huggingface dataset:
Virtual reality testing of multi-modal integration in schizophrenic patients. (2005)

Our goal is to develop a new family of automatic tools for the diagnosis of schizophrenia, using Virtual Reality Technology (VRT). VRT is specifically suitable for this purpose, because it allows for multi-modal stimulation in a complex setup, and the simultaneous measurement of multiple parameters. In this work we studied sensory integration within working memory, in a navigation task through a VR maze. Along the way subjects pass through multiple rooms that include three doors each, only one of which can be used to legally exit the room. Specifically, each door is characterized by three features (color, shape and sound), and only one combination of features -- as determined by a transient opening rule -- is legal. The opening rule changes over time. Subjects must learn the rule and use it for successful navigation throughout the maze. 39 schizophrenic patients and 21 healthy controls participated in this study. Upon completion, each subject was assigned a performance profile, including various error scores, response time, navigation ability and strategy. We developed a classification procedure based on the subjects' performance profile, which correctly predicted 85% of the schizophrenic patients (and all the controls). We observed that a number of parameters showed significant correlation with standard diagnosis scores (PANSS), suggesting the potential use of our measurements for future diagnosis of schizophrenia. On the other hand, our patients did not show unusual repetition of response despite stimulus cessation (called perseveration in classical studies of schizophrenia), which is usually considered a robust marker of the disease. Interestingly, this deficit only appeared in our study when subjects did not receive proper explanation of the task.
Compiler orchestrated prefetching via speculation and predication (2004)

This paper introduces a compiler orchestrated prefetching system as a unified framework geared toward ameliorating the gap between processing speeds and memory access latencies. We focus the scope of the optimization on specific subsets of the program dependence graph that succinctly characterize the memory access pattern of both regular array-based applications and irregular pointer-intensive programs. We illustrate how program embedded precomputation via speculative execution can accurately predict and effectively prefetch future memory references with negligible overhead. The proposed techniques reduce the total running time of seven SPEC benchmarks and two OLDEN benchmarks by 27% on an Itanium 2 processor. The improvements are in addition to several state-of-the-art optimizations including software pipelining and data prefetching. In addition, we use cycle-accurate simulations to identify important and lightweight architectural innovations that further mitigate the memory system bottleneck. In particular, we focus on the notoriously challenging class of pointer-chasing applications, and demonstrate how they may benefit from a novel scheme of it sentineled prefetching . Our results for twelve SPEC benchmarks demonstrate that 45% of the processor stalls that are caused by the memory system are avoidable. The techniques in this paper can effectively mask long memory latencies with little instruction overhead, and can readily contribute to the performance of processors today.
A Dual Slotted Ring Organization for Reducing Memory Access Latency in Distributed Shared Memory System (2001)

Advances in circuit and integration technology are continuously boosting the speed of processors. One of the main challenges presented by such developments is the effective use of powerful processors in shared memory multiprocessor system. We believe that the interconnection problem is not solved even for small scale shared memory multiprocessor, since the speed of shared buses is unlikely to keep up with the bandwidth requirements of new powerful processors. In the past few years, point-to-point unidirectional connection have emerged as a very promising interconnection technology. The single slotted ring is the simplest form point-to-point interconnection. The main limitation of the single slotted ring architecture is that latency of access increase linearly with the number of the processors in the ring. Because of this, we proposed the dual slotted ring as an alternative to single slotted ring for cache-based multiprocessor system. In this paper, we analyze the proposed dual slotted ring architecture using new snooping protocol and enforce simulation to compare it with single slotted ring.
A holistic high-throughput screening framework for biofuel feedstock assessment that characterises variations in soluble sugars and cell wall composition in Sorghum bicolor (2013)

This methodology has been demonstrated as an efficient and effective way to screen large biofuel feedstock populations for biomass, soluble sugar concentrations, and cell wall digestibility simultaneously allowing a total fermentable yield calculation. It unifies and simplifies previous screening methodologies to produce a holistic assessment of biofuel feedstock potential.
Estudio del impacto ambiental de geopolímeros de arcilla (2019)

En los últimos años, la problemática ambiental ha impulsado la investigación de materiales alternativos que ayuden a aminorar el impacto derivado de la construcción. En este contexto, los materiales alcalinamente activados se han presentado como una alternativa interesante a materiales convencionales que incorporan gran cantidad de energía. A diferencia de trabajos previos, el objetivo de esta investigación fue evaluar el impacto ambiental incorporado de bloques experimentales de arcilla “geopolimerizada”, tomando en cuenta su resistencia a la compresión y comparándolos con ladrillos de arcilla cocida y bloques de tierra comprimida (BTC). Para la fabricación de los bloques experimentales de arcilla “geopolimerizada” se usó arcilla natural, no expuesta a procesos previos de deshidroxilación, con un contenido de 49% en peso de caolinita y un activador alcalino basado en NaOH. En el proceso de fabricación, las mezclas fueron expuestas a temperaturas que oscilaron entre 80 y 120ºC durante 2 a 24 horas. Los ladrillos experimentales de arcilla “geopolimerizada”, con la formulación adecuada, alcanzaron resistencias a la compresión superiores a 20MPa con una reducción del 80-90% del impacto ambiental en comparación con los ladrillos comunes de arcilla cocida.
Nemo‐like kinase is involved in NGF‐induced neurite outgrowth via phosphorylating MAP1B and paxillin (2009)

Nerve growth factor (NGF) promotes neurite outgrowth through regulating cytoskeletal organization and cell adhesion. These activities are modulated by protein phosphorylation. Nemo-like kinase (NLK) is an evolutionarily conserved MAP kinase-like kinase that phosphorylates several transcription factors. Although NLK is known to be expressed at relatively high levels in the nervous system, its function is not well understood. We found that NGF promotes the translocation of NLK to PC12 cells' leading edges, and triggers NLK kinase activity in them. Activated NLK directly phosphorylates microtubule-associated protein-1B (MAP1B) and the focal adhesion adaptor protein, paxillin. Knockdown of NLK attenuates the phosphorylation of both paxillin and MAP1B and inhibits both the NGF-induced re-distribution of F-actin and neurite outgrowth. We also discovered that NLK is a LiCl-sensitive kinase. LiCl is known to block NGF-induced neurite outgrowth and the phosphorylation of MAP1B and paxillin in PC12 cells. Therefore, the effects of LiCl are mediated in part by blocking NLK activity. These results suggest that NLK controls the dynamics of the cytoskeleton downstream of NGF signaling.
K-1926 Effect of Injection Rate and Fuel Property on the Combustion Characteristics in a Direct-Injection Gasoline Engine (2001)

This paper presents a study on the effect of injection rate on the performance and emissions in a direct injection gasoline engine. Five kinds of swirl injectors were utilized; their static injection rates were 600, 700, 800, 900 and 1000cc/min at the injection pressure of 7MPa. The BSFC is shown to have its optimum at lower rate of dynamic injection rate 10.7×10^<-2>cm^3/ms which is attributable to the combustion efficiency variation due to the behavior of droplet concentration. Two other factors of mechanical efficiency and cycle efficiency determining the thermal efficiency are discussed in comparison with the results of port injection operation.
A fast Predictive-Corrective Mass Spring method in cloth simulation (2010)

Physically-based cloth animation has been a hot topic to the graphics community for more than a decade. Among the physically-based models used in cloth animation, elastically deformable models have been used successfully in order to give a representation of the behavior. We present a novel PCMS (Predictive-Corrective Mass-Spring) algorithm in cloth simulation which combines the advantages of both BMS and an advanced numerical integration method, namely low computational costs and large time steps. The numerical and rendering results show that a speed-up of more than an order of magnitude over the commonly used mass-spring method while the simulation results are in agreement with real cloth behavior. In addition, the super-elastic effect will be effectively controlled without dynamic inverse constraints on deformation rates.
Colorectal cancer: update on recent advances and their impact on screening protocols. (2000)

As the third leading cause of cancer cases and deaths in the United States, colorectal cancer has been an area of intense interest. The objectives of this article are, through a review of the literature published between 1995 to 1998, to examine current trends in the epidemiology of colorectal cancer, new information on genetic, dietary, and other risk factors; to evaluate the effectiveness of current screening guidelines for various populations; to review information on chemoprevention; and finally to examine new concepts on the horizon in the area of colorectal cancer research. Much of the recent research in the field has focused on etiology, dietary, and other risk factors. Many genetic factors have been discovered, which serve to elucidate the mechanism of pathogenesis of colorectal cancer as well as offer possible targets for treatment strategies. Dietary and risk factors for colorectal cancer may pave the way for chemoprevention. In light of the most recent information on colorectal cancer, one is able to more accurately assess current screening guidelines for their effectiveness in all populations based on epidemiologic data, as well as evaluate more novel screening strategies for their possible utility in the future. In addition to a review of the most up-to-date literature, the authors also provide their recommendations for screening based on the evidence in which the review of the literature provides. Finally, current and future treatment options are discussed. It is our hope that the physicians will find this review useful in the evaluation and care of patients at risk of developing colorectal cancer.
Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis (2022)

Charting the emergence of eukaryotic traits is important for understanding the characteristics of organisms that contributed to eukaryogenesis. Asgard archaea and eukaryotes are the only organisms known to possess regulated actin cytoskeletons. Here, we determined that gelsolins (2DGels) from Lokiarchaeota (Loki) and Heimdallarchaeota (Heim) are capable of regulating eukaryotic actin dynamics in vitro and when expressed in eukaryotic cells. The actin filament severing and capping, and actin monomer sequestering, functionalities of 2DGels are strictly calcium controlled. We determined the X-ray structures of Heim and Loki 2DGels bound actin monomers. Each structure possesses common and distinct calcium-binding sites. Loki2DGel has an unusual WH2-like motif (LVDV) between its two gelsolin domains, in which the aspartic acid coordinates a calcium ion at the interface with actin. We conclude that the calcium-regulated actin cytoskeleton predates eukaryogenesis and emerged in the predecessors of the last common ancestor of Loki, Heim and Thorarchaeota.
Effective Design of Layout-Friendly EDT Decompressor (2020)

This paper proposes an innovative design methodology for layout-friendly decompressor used in EDT compression architecture. A segmented decompressor architecture is proposed, in which each segment drives a subset of scan chains. The EDT input channel injectors are carefully selected to maximize the encoding capacity for all scan chains. Experimental results with several large industrial designs demonstrate that using the proposed technology, the routing congestion introduced by EDT decompressor is reduced significantly with negligible impact on test coverage and improved pattern count.
Histamine dose-response curves in asthma: reproducibility and sensitivity of different indices to assess response. (1983)

In 18 clinically stable asthmatic patients histamine inhalation challenges were performed with a Wright's nebuliser and tidal volume breathing for two minutes on two to four occasions for each subject at a maximum interval of two weeks. The response was measured in terms of specific lung conductance (sGL) by the subtraction technique, maximum partial and maximum complete expiratory flow at 40% and 50% of vital capacity respectively (Vmax40p and Vmax50c), and FEV1 from the maximum flow-volume curve. Dose-response curves were analysed for (1) provocative concentration (PC) of histamine causing a 20% fall in FEV1 and a 40% change in the other measurements; (2) threshold concentration (TC)--the concentration at which changes in the measurement exceed 2 SD from control values; (3) reactivity (R)--the slope of the dose-response curve beyond TC. We found that PC20-FEV1 was the most reproducible index, the 95% confidence intervals based on a single determination being +/- 1.6 single two-fold concentration difference. PC20-FEV1 was more reproducible than PC values for other measurements and more reproducible than any of the TC values. The 95% confidence intervals based on a single determination of R varied from +/- 52% to +/- 74% change/log histamine concentration. Both sGL and Vmax40p detected the bronchoconstrictor response assessed by PC and TC at a significantly lower histamine concentration than FEV1 (p less than 0.01 and p less than 0.05 respectively). PC and TC results showed a significant correlation, but neither were correlated with R.
ChemInform Abstract: A SIMS Investigation of Hydrogen Penetration of Titanium Electrodes (1989)

Abstract carried out using a spectrometer which is able to detect and image hydrogen confirms that during prolonged corrosion of Ti in acidic solutions a stable titanium hydride phase is built up which extends to a considerable depth (several microns) in the metal.
ChemInform Abstract: Photochemical and Photophysical Studies of Bicyclo(4.3.0)non‐1(6)‐en‐2‐ one. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 5 from Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer (2023)

&lt;p&gt;PDF file - 28K, Percent of assembled contigs significantly enriched for mutation patterns consistent with evidence of SHM in breast (A, B) and ovarian (C, D) tumors.&lt;/p&gt;
Study of Development of a Dust-proof Oil Cooler (2008)

A typical louvered-fin oil cooler can be easily contaminated under dusty environment hence resulting in poor performance of a heat exchanger. Thus, in this study, a dust-proof oil cooler has been studied with a unique shape of a 3-dimensional wavy fin since non-louvered fins could have better performance under dusty environment compared to louvered fins. Recently, they have been introduced to commercial and constructional vehicles in Japan. At first numerical analysis has been done to optimize the angle of the wavy fin so that the oil cooler developed can satisfy the target performance. The wavy fin has been then made with roll-forming and roll-pitch stands, and a prototype of an oil cooler with the wavy fin has been finally built with brazing. The performance test showed that the heat release rate of the oil cooler was well beyond the target, 4.94kW and the air-side pressure drop was below the criterion, 0.19kPa. In addition, the results showed that the numerical prediction was effective enough to design the dust-proof oil cooler that satisfies the performance criteria.
Naturally Occurring Dominant Negative Variants of Stat5 (1996)

Stat5 was initially identified as a prolactin-induced member of the signal transducer and activator of transcription (Stat) family in sheep. However, Stat5 is also activated in the response to a variety of cytokines. In mice, and possibly in other species, there exist two Stat5 genes (Stat5a and Stat5b) that encode proteins of 92 and 94 kDa that are 95% identical. In the studies described here, we demonstrate that naturally occurring carboxyl-truncated, variant Stat5 proteins of 77 and 80 kDa exist and that these proteins are inducibly tyrosine phosphorylated in the response to several cytokines and form heterodimers with the full-length, wild-type proteins. Using expression constructs encoding truncated forms, we demonstrate that the truncated forms can be tyrosine phosphorylated and bind DNA. Surprisingly, the tyrosine phosphorylation of the carboxyl-truncated forms is considerably more stable than that of the wild-type proteins. Overexpression of a carboxyl-truncated Stat5a in cells resulted in the specific inhibition of the transcriptional activation by interleukin-3 of the genes for oncostatin M (Osm) and the cytokine-inducible, SH2 domain-containing gene (Cis), both of which have been shown to be normally regulated by Stat5. Although Stat5 dominantly suppressed the induction of these genes, no effects on cell proliferation were observed. Together, the results demonstrate the natural existence of potentially dominantly suppressive variants of Stat5 and implicate the carboxyl domain of Stats in transcriptional regulation and functions related to dephosphorylation.
Key Physicochemical Determinants in the Antimicrobial Peptide RiLK1 Promote Amphipathic Structures (2021)

Antimicrobial peptides (AMPs) represent a skilled class of new antibiotics, due to their broad range of activity, rapid killing, and low bacterial resistance. Many efforts have been made to discover AMPs with improved performances, i.e., high antimicrobial activity, low cytotoxicity against human cells, stability against proteolytic degradation, and low costs of production. In the design of new AMPs, several physicochemical features, such as hydrophobicity, net positive charge, propensity to assume amphipathic conformation, and self-assembling properties, must be considered. Starting from the sequence of the dodecapeptide 1018-K6, we designed a new 10-aminoacid peptide, namely RiLK1, which is highly effective against both fungi and Gram-positive and -negative bacteria at low micromolar concentrations without causing human cell cytotoxicity. In order to find the structural reasons explaining the improved performance of RiLK1 versus 1018-K6, a comparative analysis of the two peptides was carried out with a combination of CD, NMR, and fluorescence spectroscopies, while their self-assembling properties were analyzed by optical and atomic force microscopies. Interestingly, the different spectroscopic and microscopic profiles exhibited by the two peptides, including the propensity of RiLK1 to adopt helix arrangements in contrast to 1018-K6, could explain the improved bactericidal, antifungal, and anti-biofilm activities shown by the new peptide against a panel of food pathogens.
Analysis of cholesterol levels in lipoprotein(a) with anion-exchange chromatography (2009)

We previously established an analysis method for determining the cholesterol levels of five major lipoprotein classes [HDL, LDL, intermediate density lipoprotein (IDL), VLDL, and chylomicrons] in serum by an anion-exchange (AEX)-HPLC method, but lipoprotein(a) [Lp(a)], a well-known risk factor for atherosclerotic diseases, was not determinable. Therefore, we established new AEX-HPLC separation conditions for analyzing the cholesterol levels of six lipoprotein classes, including Lp(a). Serum lipoproteins were separated by HPLC with a diethylaminoethyl-ligand nonporous polymer-based column by elution with a stepwise gradient of the sodium perchlorate concentration. In this improved method, HDL, LDL, IDL, VLDL, chylomicrons, and Lp(a) were each eluted from the column. The cholesterol levels of the eluted lipoproteins were measured enzymatically by a postcolumn reaction. The within-day assay and between-day assay coefficients of variation for the lipoprotein cholesterol levels were in the ranges of 0.29-11.86% and 0.57-11.99%, respectively. The Lp(a) cholesterol levels determined by AEX-HPLC were significantly correlated with the amounts of Lp(a) protein measured by an immunoturbidimetry method available commercially (r = 0.9503, P < 0.0001). Taken together, this AEX-HPLC method may be effectively applied to the analysis of serum lipoproteins with high levels of Lp(a).
Selective inhibition of ADAR2-catalyzed editing of the serotonin 2c receptor pre-mRNA by a helix-threading peptide (2010)

RNA editing by adenosine deamination is a form of epigenetic control of gene expression wherein the ADAR enzymes convert adenosine to inosine in RNA often changing the meaning of codons. The pre-mRNA for the 2c subtype of serotonin receptor (5-HT2cR) is shown here to support small molecule binding near known editing sites. Furthermore, a helix-threading peptide binds this site and inhibits the in vitro reaction of ADAR2 in an RNA-substrate selective manner. This is the first example of substrate-selective inhibition of editing by an RNA-binding small molecule and sets the stage for the development of new reagents capable of controlling gene function through manipulation of mRNA editing.
Synthesis of L‐Propargylglycine and Derivatives (1976)

Abstract The chemical synthesis of L ‐propargylglycine ( L ‐Pra) and of various derivatives is described. The new amino acid is a starting material for carboranylalanine (Car) and for tritiated norleucine.