gebhart/patrepeval huggingface dataset:
<i>Candida albicans</i> Tup1 Is Involved in Farnesol-Mediated Inhibition of Filamentous-Growth Induction (2008)

Candida albicans is a dimorphic fungus that can interconvert between yeast and filamentous forms. Its ability to regulate morphogenesis is strongly correlated with virulence. Tup1, a transcriptional repressor, and the signaling molecule farnesol are both capable of negatively regulating the yeast to filamentous conversion. Based on this overlap in function, we tested the hypothesis that the cellular response to farnesol involves, in part, the activation of Tup1. Tup1 functions with the DNA binding proteins Nrg1 and Rfg1 as a transcription regulator to repress the expression of hypha-specific genes. The tup1/tup1 and nrg1/nrg1 mutants, but not the rfg1/rfg1 mutant, failed to respond to farnesol. Treatment of C. albicans cells with farnesol caused a small but consistent increase in both TUP1 mRNA and protein levels. Importantly, this increase corresponds with the commitment point, beyond which added farnesol no longer blocks germ tube formation, and it correlates with a strong decrease in the expression of two Tup1-regulated hypha-specific genes, HWP1 and RBT1. Tup1 probably plays a direct role in the response to farnesol because farnesol suppresses the haploinsufficient phenotype of a TUP1/tup1 heterozygote. Farnesol did not affect EFG1 (a transcription regulator of filament development), NRG1, or RFG1 mRNA levels, demonstrating specific gene regulation in response to farnesol. Furthermore, the tup1/tup1 and nrg1/nrg1 mutants produced 17- and 19-fold more farnesol, respectively, than the parental strain. These levels of excess farnesol are sufficient to block filamentation in a wild-type strain. Our data are consistent with the role of Tup1 as a crucial component of the response to farnesol in C. albicans.
Machine-Learning Foundations: The Probabilistic Framework (2001)

This chapter contains sections titled: Introduction: Bayesian Modeling, The Cox Jaynes Axioms, Bayesian Inference and Induction, Model Structures: Graphical Models and Other Tricks, Summary
Reducing communication cost in scalable shared memory systems. (1998)

Distributed shared-memory systems provide scalable performance and a convenient model for parallel programming. However, their non-uniform memory latency often makes it difficult to develop efficient parallel applications. Future systems should reduce communication cost to achieve better programmability and performance. We have developed a methodology, and implemented a suite of tools, to guide the search for improved codes and systems. As the result of one such search, we recommend a remote data caching technique that significantly reduces communication cost. We analyze applications by instrumenting their assembly-code sources. During execution, an instrumented application pipes a detailed trace to configuration independent (CIAT) and configuration dependent (CDAT) analysis tools. CIAT characterizes inherent application characteristics that do not change from one configuration to another, including working sets, concurrency, sharing behavior, and communication patterns, variation over time, slack, and locality. CDAT simulates the trace on a particular hardware model, and is easily retargeted to new systems. CIAT is faster than detailed simulation; however, CDAT directly provides more information about a specific configuration. The combination of the two tools constitutes a comprehensive and efficient methodology. We calibrate existing systems using carefully designed microbenchmarks that characterize local
Decision-making support system for human resource allocation in product development projects (2006)

Recent dismal economic conditions and a ruthlessly competitive environment have forced many companies to restructure, or reorganize their priorities. For such companies, the concentration of various resources upon their particular corporate strong points has become a central strategy. Consequently, there has been a rapid increase in the importance of (1) selecting profitable projects from a wealth of possible alternatives and (2) optimizing the allocation of current resources among the selected projects. This paper proposes an optimization system for project selection that not only yields the most beneficial project set, but also the optimum allocation of human resources for the selected projects. The optimization system consists of two algorithms, namely (1) a project selection algorithm for choosing the set of projects that maximizes the total estimated profit, and (2) a human resource allocation algorithm for optimally placing human resources among the selected projects, having considered the satisfaction level provided by each employee's skills, personal motivation and career goals.
CovS/CovR of group B streptococcus: a two‐component global regulatory system involved in virulence (2004)

In this study, we carried out a detailed structural and functional analysis of a Streptococcus agalactiae (GBS) two-component system which is orthologous to the CovS/CovR (CsrS/CsrR) regulatory system of Streptococcus pyogenes. In GBS, covR and covS are part of a seven gene operon transcribed from two promoters that are not regulated by CovR. A DeltacovSR mutant was found to display dramatic phenotypic changes such as increased haemolytic activity and reduced CAMP activity on blood agar. Adherence of the DeltacovSR mutant to epithelial cells was greatly increased and analysis by transmission electron microscopy revealed the presence at its surface of a fibrous extracellular matrix that might be involved in these intercellular interactions. However, the DeltacovSR mutant was unable to initiate growth in RPMI and its viability in human normal serum was greatly impaired. A major finding of this phenotypic analysis was that the CovS/CovR system is important for GBS virulence, as a 3 log increase of the LD(50) of the mutant strain was observed in the neonate rat sepsis model. The pleiotropic phenotype of the DeltacovSR mutant is in full agreement with the large number of genes controlled by CovS/CovR as seen by expression profiling analysis, many of which encode potentially secreted or cell surface-associated proteins: 76 genes are repressed whereas 63 were positively regulated. CovR was shown to bind directly to the regulatory regions of several of these genes and a consensus CovR recognition sequence was proposed using both DNase I footprinting and computational analyses.
Conformational Diversity Versus Nucleic Acid Triplex Stability, a Combinatorial Study (2001)

The stability of a triple helix formed between a DNA duplex and an incoming oligonucleotide strand strongly depends on the solvent conditions and on intrinsic chemical and conformational factors. Attempts to increase triple helix stability in the past included chemical modification of the backbone, sugar ring, and bases in the third strand. However, the predictive power of such modifications is still rather poor. We therefore developed a method that allows for rapid screening of conformationally diverse third strand oligonucleotides for triplex stability in the parallel pairing motif to a given DNA double helix sequence. Combinatorial libraries of oligonucleotides of the requisite (fixed) base composition and length that vary in their sugar unit (ribose or deoxyribose) at each position were generated. After affinity chromatography against their corresponding immobilized DNA target duplex, utilizing a temperature gradient as the selection criterion, the oligonucleotides forming the most stable triple helices were selected and characterized by physicochemical methods. Thus, a series of oligonucleotides were identified that allowed us to define basic rules for triple helix stability in this conformationally diverse system. It was found that ribocytidines in the third strand increase triplex stability relative to deoxyribocytidines independently of the neighboring bases and position along the strand. However, remarkable sequence-dependent differences in stability were found for (deoxy)thymidines and uridines.
Deterministic process groups in dOS (2010)

Current multiprocessor systems execute parallel and concurrent software nondeterministically: even when given precisely the same input, two executions of the same program may produce different output. This severely complicates debugging, testing, and automatic replication for fault-tolerance. Previous efforts to address this issue have focused primarily on record and replay, but making execution actually deterministic would address the problem at the root.Our goals in this work are twofold: (1) to provide fully deterministic execution of arbitrary, unmodified, multithreaded programs as an OS service; and (2) to make all sources of intentional nondeterminism, such as network I/O, be explicit and controllable. To this end we propose a new OS abstraction, the Deterministic Process Group (DPG). All communication between threads and processes internal to a DPG happens deterministically, including implicit communication via shared-memory accesses, as well as communication via OS channels such as pipes, signals, and the filesystem. To deal with fundamentally nondeterministic external events, our abstraction includes the shim layer, a programmable interface that interposes on all interaction between a DPG and the external world, making determinism useful even for reactive applications.We implemented the DPG abstraction as an extension to Linux and demonstrate its benefits with three use cases: plain deterministic execution; replicated execution; and record and replay by logging just external input. We evaluated our implementation on both parallel and reactive workloads, including Apache, Chromium, and PARSEC.
Random isolation of gene activator elements from the human genome. (1986)

Long-range-acting gene activator elements were randomly isolated from the human genome by functional selection. HeLa cells were transfected with an enhancer trap, a plasmid containing an enhancerless xanthine-guanosine phosphoribosyltransferase (gpt) gene transcribed from the simian virus 40 early promoter, and stably transformed GPT+ cells were selected. From several transformants, human DNA sequences flanking the enhancer trap were cloned. Two gene activators (GA1 and GA2) were found in the cloned human DNAs. GA1 and GA2 showed strong enhancer activity both in a stable transformation assay and in a transient expression assay. They had functional properties similar to those of other known enhancers: GA1 and GA2 activated the expression of a linked gene over distances of at least 5 kilobases both upstream and downstream in an orientation-independent fashion. GA1 may be required for the initial establishment of gene activation but was not essential for the maintenance of active expression. GA1 and GA2 were active not only in HeLa cells but also in other types of human cells, such as neuroblastoma cells. This indicates a limited but relatively broad cell type specificity. The HeLa genome contains multiple copies of GA1, while GA2 exists once in the genome.
Finite Memory Output Feedback Control for Unmanned Aerial Vehicle (2018)

In this paper, we propose a novel control strategy, a finite memory output feedback control (FMOFC), for an unmanned aerial vehicle (UAV). The proposed control strategy is designed with the estimated states obtained by stacking a finite N number of measurements, and the finite N number is defined as the horizon size, which represents the finite memory structure of the system. Through extending the concept of the horizon size by introducing a vector form to the augmented horizon size, the UAV is considered as a parallel system in terms of four independent states. Furthermore, the controller gain of the FMOFC is derived from the reconstructed parallel system under not only the finite memory structure, but also unbiasedness. Because of those constraints, the FMOFC exhibits a robust performance even in the presence of disturbance or unexpected noises from uncertainties, computational errors, and sudden changes in environments. The fast convergence and robust performance under disturbance or unexpected noises of the proposed control strategy are demonstrated through experimental results.
A Novel Sol–Gel Method for Large‐Scale Production of Nanopowders: Preparation of Li <sub>1.5</sub> Al <sub>0.5</sub> Ti <sub>1.5</sub> ( <scp>PO</scp> <sub>4</sub> ) <sub>3</sub> as an Example (2015)

Sol–gel synthesis is an extensively used method for the preparation of nanopowders. However, complicated or expensive precursors, and the necessity of using organic solvent and/or heat assistance limit the method to laboratory‐scaled level. An aqueous‐based sol–gel method with spontaneous sol and gel formation is developed in this study. It can be applied on a large scale to synthesize compounds with Ti 4+ and PO 4 3− as major components with low cost. Al‐substituted LiTi 2 ( PO 4 ) 3 ( LATP ) has been widely investigated as a promising candidate for solid electrolyte in Li‐ion or Li‐air batteries. Major challenges such as unsatisfactory phase purity, low sintering activity, and high production costs are faced during the fabrication of LATP . In this study, as a sample application, Li 1.5 Al 0.5 Ti 1.5 ( PO 4 ) 3 ( LATP 05) is conveniently prepared on a large scale by the novel sol–gel method with high phase purity, active densification behavior and high conductivity.
The Use of Small-Scale Specimens for Testing Irradiated Material (1986)

Description Twenty-two papers appear in this volume. The papers are divided into two areas: • strength and ductility • fatigue and fracture
Scale-Up of Agitation Fluidized Bed Granulation. III. Effects of Powder Feed Weight and Blade Angle on Granule Size, Density and Shape. (1995)

This paper presents the experimental results of a study on the scale-up characteristics of granule comopaction and sphericity in an agitation fluidized bed granulation. A pharmaceutical standard formulation was granulated using agitation fluidized bed of three sizes (vessel diameter : 125, 230, 500 mm). The effects of powder feed weight and agitator blade angle on the granule properties of size, density and shape were studied. It was found that granules were compressed and made spherical with an increase in agitator blade angle and vessel scale, while they were not influenced by the powder feed ratio.
Deep Packet Inspection on Commodity Hardware using FastFlow (2014)

The analysis of packet payload is mandatory for network security and traffic monitoring applications. The computational cost of this activity pushed the industry towards hardware-assisted deep packet inspection (DPI) that have the disadvantage of being more expensive and less flexible.
EOS from soldering irons connected to faulty 120VAC receptacles (2005)

Certain types of 120 VAC receptacles used in circuit card assembly production areas were discovered to have intermittently faulty grounding contacts. These receptacles have been in use in a number of facilities and are likely to be found throughout the industry. Soldering irons connected to a faulty ground can impart EOS to devices being assembled, and failures have been clearly identified to have been caused by exposure to open-grounded irons. This paper reports on work we have done to 1) determine the receptacle problem, 2) measure and model the EOS, and 3) assess device susceptibility and damage risk.
Suppression of phonon transport in multiple Si/PtSi heterostructures (2015)

Using a Green function method based on an atomic vibration model, herein we report the results from our investigation of phonon transport through multiple Si/PtSi layered structures. In contrast with values predicted using elastic wave theory and an impedance mismatch method, we find that a detailed atomic-vibration approach exhibits significantly suppressed phonon transport and leads to a 30-times reduction of the thermal conductance, compared to that of Si bulk. We attribute the origin of the suppression to the lack of PtSi phonon modes in the energy range of 20–30 meV, and to the effects of interface scattering between Si and PtSi layers.
Naratriptan is Effective and Well Tolerated in the Acute Treatment of Migraine. Results of a Double‐Blind, Placebo‐Controlled, Parallel‐Group Study (1997)

Naratriptan is effective and well tolerated for the acute treatment of migraine. The 2.5-mg dose appears to offer the optimum ratio of efficacy to tolerability.
Amphibian Limb Regeneration: Rebuilding a Complex Structure (1997)

The ability to regenerate complex structures is widespread in metazoan phylogeny, but among vertebrates the urodele amphibians are exceptional. Adult urodeles can regenerate their limbs by local formation of a mesenchymal growth zone or blastema. The generation of blastemal cells depends not only on the local extracellular environment after amputation or wounding but also on the ability to reenter the cell cycle from the differentiated state. The blastema replaces structures appropriate to its proximodistal position. Axial identity is probably encoded as a graded property that controls cellular growth and movement through local cell interactions. The molecular basis is not understood, but proximodistal identity in newt blastemal cells may be respecified by signaling through a retinoic acid receptor isoform. The possibility of inducing a blastema on a mammalian limb cannot be discounted, although the molecular constraints are becoming clearer as we understand more about the mechanisms of urodele regeneration.
Plasma Magnesium and Calcium in Depression (1969)

Recent investigations suggest that there may be an abnormality of calcium and magnesium in depressive illness. Flach (1964) followed the urinary excretion of calcium in depressed patients maintained on a constant intake of calcium before and during recovery. Those patients that recovered showed a significant decrease in the excretion of calcium. Coirault et al. (1959) reported an increase in ionized calcium and a decrease in total plasma calcium on recovery from depression. Cade (1964) reported considerably raised total plasma magnesium levels in depressed patients both before and after recovery. A connection between affective disorders and calcium metabolism is suggested by the common occurrence of such states in both hypo- and hypercalcaemia (Denco and Kaelbling, 1962; Rookus and Speelman, 1961). The present paper reports an investigation into total and ionized plasma calcium and magnesium in a group of depressed patients both before and after recovery. The effects of lithium carbonate, a compound used in the treatment and prophylaxis of affective disorders (Baastrup and Schou, 1967; Schou, 1963) on plasma concentrations of magnesium and calcium was also investigated.
<i>Campylobacter jejuni</i> FlpA Binds Fibronectin and Is Required for Maximal Host Cell Adherence (2009)

Campylobacter jejuni is one of the most frequent bacterial causes of food-borne gastrointestinal disease in developed countries. Previous work indicates that the binding of C. jejuni to human intestinal cells is crucial for host colonization and disease. Fibronectin (Fn), a major constituent of the extracellular matrix, is a approximately 250-kDa glycoprotein present at regions of cell-to-cell contact in the intestinal epithelium. Fn is composed of three types of repeating units: type I (approximately 45 amino acids), type II (approximately 60 amino acids), and type III (approximately 90 amino acids). The deduced amino acid sequence of C. jejuni flpA (Cj1279c) contains at least three Fn type III domains. Based on the presence of the Fn type III domains, we hypothesized that FlpA contributes to the binding of C. jejuni to human INT 407 epithelial cells and Fn. We assessed the contribution of FlpA in C. jejuni binding to host cells by in vitro adherence assays with a C. jejuni wild-type strain and a C. jejuni flpA mutant and binding of purified FlpA protein to Fn by enzyme-linked immunosorbent assay (ELISA). Adherence assays revealed the binding of the C. jejuni flpA mutant to INT 407 epithelial cells was significantly reduced compared with that for a wild-type strain. In addition, rabbit polyclonal serum generated against FlpA blocked C. jejuni adherence to INT 407 cells in a concentration-dependent manner. Binding of FlpA to Fn was found to be dose dependent and saturable by ELISA, demonstrating the specificity of the interaction. Based on these data, we conclude that FlpA mediates C. jejuni attachment to host epithelial cells via Fn binding.
A model for system reliability with common-cause failures (1989)

A model for the analysis of systems subject to common-cause failures is proposed. The system consists of a finite number of components that are subject to: (1) statistically independent failures, and (2) external failure causes (they need not be mutually statistically independent) for groups of components. Applications to fault-tree analysis and network reliability problems are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Comparison of extraction methods for the isolation of volatile compounds from distilled alcoholic beverages (1994)

Abstract Batch and continuous solvent extraction methods were evaluated, using an alcoholic model system, to select the best alternative for the isolation of volatile aroma compounds from distilled alcoholic beverages. Recoveries using pentane, pentane‐diethyl ether (2:1) and dichloromethane were compared. Pentane extraction produced the best results, particularly by a continuous procedure for 6 h.
Studies on the Liver to Kidney Switch of Erythropoietin Production (1981)

Although the liver is the major site of erythropoietin (Ep) production in the fetus, this function is assumed by kidneys in the adult. The mechanisms underlying the liver to kidney switch of Ep formation are not understood. We studied the natural progression of this transition in sheep by measuring Ep production in response to anemia in normal and bilaterally nephrectomized fetal and newborn sheep beginning at about 80 d gestation (normal gestation: 140 d). Removal of both kidneys before induction of anemia did not affect Ep formation up to about 120 d of gestation. A significant reduction (29%, P < 0.02) in Ep synthesis was first noted at about 130 d of gestation (initiation of switch). This level of nephrectomy-induced reduction of Ep formation persisted until about 15 d after birth. Thereafter, bilateral nephrectomy caused further significant decreases (P < 0.05) in Ep production, gradually resulting in near total absence of Ep production at about day 40 postpartum (completion of switch). Chronic administration of testosterone (12 mg/wk) or estradiole benzoate (1.5 mg/d, 5 d/wk) to the fetus/newborn beginning at 85-90 d of gestation enhanced or suppressed erythropoiesis, respectively, but failed to affect the time at which the liver to kidney switch was initiated and/or completed. By contrast, a significant delay (P < 0.001) in the onset, but not completion of the switch occurred in animals that were either thyroidectomized or rendered chronically anemic beginning in the second third of the gestation period. Administration of thyroxin (1.2 mg/d, 5 d/wk) to thyroidectomized fetus/newborns not only prevented the delay in the initiation of the switch, but also accelerated the rate at which the switch was completed. These results demonstrate that in sheep (a) the liver to kidney switch of Ep production is initiated in utero during the last third of the gestation period, but is completed after birth, (b) this transition occurs gradually; the assumption of Ep producing capacity by the kidney is not preceded by an abrupt loss of hepatic Ep formation; and (c) the switch is not affected by changes in sex hormone levels during the prenatal-postnatal growth periods, but is profoundly influenced by alterations in thyroid hormone and oxygen supply-demand levels.