gebhart/patrepeval huggingface dataset:
Role for the Ubiquitin-Proteasome System in the Vacuolar Degradation of Ste6p, the <b>a</b>-Factor Transporter in <i>Saccharomyces cerevisiae</i> (1998)

Ste6p, the a-factor transporter in Saccharomyces cerevisiae, is a multispanning membrane protein with 12 transmembrane spans and two cytosolic ATP binding domains. Ste6p belongs to the ATP binding cassette (ABC) superfamily and provides an excellent model for examining the intracellular trafficking of a complex polytopic membrane protein in yeast. Previous studies have shown that Ste6p undergoes constitutive endocytosis from the plasma membrane, followed by delivery to the vacuole, where it is degraded in a Pep4p-dependent manner, even though only a small portion of Ste6p is exposed to the vacuolar lumen where the Pep4p-dependent proteases reside. Ste6p is known to be ubiquitinated, a modification that may facilitate its endocytosis. In the present study, we further investigated the intracellular trafficking of Ste6p, focusing on the role of the ubiquitin-proteasome machinery in the metabolic degradation of Ste6p. We demonstrate by pulse-chase analysis that the degradation of Ste6p is impaired in mutants that exhibit defects in the activity of the proteasome (doa4 and pre1,2). Likewise, by immunofluorescence, we observe that Ste6p accumulates in the vacuole in the doa4 mutant, as it does in the vacuolar protease-deficient pep4 mutant. One model consistent with our results is that the degradation of Ste6p, the bulk of which is exposed to the cytosol, requires the activity of both the cytosolic proteasomal degradative machinery and the vacuolar lumenal proteases, acting in a synergistic fashion. Alternatively, we discuss a second model whereby the ubiquitin-proteasome system may indirectly influence the Pep4p-dependent vacuolar degradation of Ste6p. This study establishes that Ste6p is distinctive in that two independent degradative systems (the vacuolar Pep4p-dependent proteases and the cytosolic proteasome) are both involved, either directly or indirectly, in the metabolic degradation of a single substrate.
Novel regulatory properties of the IE1 and IE0 transactivators encoded by the baculovirus Autographa californica multicapsid nuclear polyhedrosis virus (1991)

The baculovirus Autographa californica multicapsid nuclear polyhedrosis virus expresses two immediate-early genes from the HindIII-G region (map units 90.4 to 96.8) of the genome. During the early phase of infection, nonspliced 1.9-kb and spliced 2.1-kb transcripts are expressed which encode the IE1 and IE0 (spliced IE1) gene products, respectively. These two gene products differ only in that IE0 contains an additional 54 amino acids at the amino terminus. RNA analysis of these two genes during infection revealed that they were differentially expressed. IE1 was expressed early and late, whereas IE0 was expressed only early in infection. The regulation of these two immediate-early genes was analyzed by transient expression assays. The IE1 gene product stimulated expression of IE1 promoter-directed expression but down-regulated expression from the IE0 promoter. The IE0 gene product also transactivated the IE1 promoter but did not affect expression from its own promoter. Unlike IE1, which transactivates the delayed early 39K gene in the presence and absence of the homologous region (hr) enhancers, IE0 transactivated the 39K promoter only in the presence of cis-linked hr5 enhancer. The results of this study in conjunction with previous results suggest that the IE1 gene encodes a multifunctional gene product that may be involved in (i) repression of immediate-early gene expression, (ii) continued expression of its own gene product during infection, and (iii) transactivation of the delayed early and late classes of genes.
MLGA a rapid and cost-efficient assay for gene copy-number analysis (2007)

Structural variation is an important cause of genetic variation. Whole genome analysis techniques can efficiently identify copy-number variable regions but there is a need for targeted methods, to verify and accurately size variable regions, and to diagnose large sample cohorts. We have developed a technique based on multiplex amplification of size-coded selectively circularized genomic fragments, which is robust, cheaper and more rapid than current multiplex targeted copy-number assays.
The use of combination therapy in pulmonary arterial hypertension: new developments (2009)

There is a strong clinical rationale for combination therapy in pulmonary arterial hypertension (PAH), as several pathological pathways have been implicated in its pathogenesis and no single agent has yet been shown to deliver completely satisfactory results. Registry data indicate that use of combination therapy is in fact common in existing clinical practice, even though support has been largely empirical or derived from small-scale observational studies. Data from large, adequately powered, randomised controlled trials of combination therapy in PAH are now emerging and suggest that combination therapy may be clinically beneficial. Studies of bosentan in combination with prostanoids and phosphodiesterase (PDE)-5 inhibitors show consistent evidence of improvements in exercise capacity compared with placebo. Similar improvements have been observed with PDE-5 inhibitors in combination with prostanoids. The appropriate timing of combination therapy requires further evaluation but goal-oriented therapy using combinations of oral and inhaled drugs has been shown to provide acceptable long-term results in patients with advanced PAH. Monitoring should be performed regularly and be based on repeatable, noninvasive, measurable parameters that have prognostic value.
LETHALS, STERILES AND DEFICIENCIES IN A REGION OF THE <i>X</i> CHROMOSOME OF <i>CAENORHABDITIS ELEGANS</i> (1979)

Twenty-one X-linked recessive lethal and sterile mutations balanced by an unlinked X-chromosome duplication have been identified following EMS treatment of the small nematode, Caenorhabditis elegans. The mutations have been assigned by complementation analysis to 14 genes, four of which have more than one mutant allele. Four mutants, all alleles, are temperature-sensitive embryonic lethals. Twelve mutants, in ten genes, are early larval lethals. Two mutants are late larval lethals, and the expression of one of these is influenced by the number of X chromosomes in the genotype. Two mutants are maternal-effect lethals; for both, oocytes made by mutant hermaphrodites are rescuable by wild-type sperm. One of the maternal-effect lethals and two larval lethals are allelic. One mutant makes defective sperm. The lethals and steriles have been mapped by recombination and by complementation testing against 19 deficiencies identified after X-ray treatment. The deficiencies divide the region, about 15% of the X-chromosome linkage map, into at least nine segments. The deficiencies have also been used to check the phenotypes of hemizygous lethal and sterile hermaphrodites.
Planning method used in visual programming for sequence-control program design with sequential function chart (1997)

The planning method adopted in the visual programming system for sequence-control program specification design (VIPS/S-SFCD) is described. VIPS/S-SFCD is based on two unique features: (1) an example-based programming technique in which designers specify the initial states and goal conditions of equipment blocks using visual representations; and (2) a planning method that infers machine actions and generates control program specifications. The planning method is based on a state-space model and uses scope to make the searches more efficient. To investigate the effectiveness of the method, VIPS/S-SFCD was used to experimentally generate control program specifications for an existing steel plant. The results showed that the quality of the control program specifications generated by the planner was equal to that achieved by a design specialist, and the time required for designing control programs was much shorter. Using VIPS/S-SFCD, errors in writing specifications are reduced because designers can easily understand the initial and goal state of an equipment block and the sequence of state transitions. The reliability of the specifications is improved because VIPS/S-SFCD generates valid segments of the specifications. The design time is also reduced because designers can use high-level instructions that closely reflect their thought processes.
Non-Fumigant Nematicides Registered for Vegetable Crop (2020)

Non-fumigant nematicides are formulated as liquids or granules that are moved through the soil by water. This 4-page fact sheet written by T. T. Watson and J. A. Desaeger and published by the UF/IFAS Entomology and Nematology Department is a major revision. It was first published in 1999 and most recently revised in April 2019. The fact sheet lists and describes chemical and biological non-fumigant nematicides and provides some information about how these products work against nematode pests.https://edis.ifas.ufl.edu/ng033
A Probabilistic Model for Using Social Networks in Personalized Item Recommendation (2015)

Preference-based recommendation systems have transformed how we consume media. By analyzing usage data, these methods uncover our latent preferences for items (such as articles or movies) and form recommendations based on the behavior of others with similar tastes. But traditional preference-based recommendations do not account for the social aspect of consumption, where a trusted friend might point us to an interesting item that does not match our typical preferences. In this work, we aim to bridge the gap between preference- and social-based recommendations. We develop social Poisson factorization (SPF), a probabilistic model that incorporates social network information into a traditional factorization method; SPF introduces the social aspect to algorithmic recommendation. We develop a scalable algorithm for analyzing data with SPF, and demonstrate that it outperforms competing methods on six real-world datasets; data sources include a social reader and Etsy.
High-Density Board Fabrication Techniques (1982)

A variety of construction methods can be used to form high-density printed-circuit boards. The electrical and mechanical requirements of a design strongly influence the choice of processes used to produce the finished product. The introduction of physically large high-density boards required the development of many new processes, several of which are critical to the electrical performance of the composite. In this paper the process sequence employed in the fabrication of the 3081 high-density board is described, with particular emphasis on the selection of the critical processes used in its manufacture. The 3081 registration system is also discussed, and a new method for merging through-hole location data with the data representing the location of the conducting layers is presented.
The Active Site of a Zinc-Dependent Metalloproteinase Influences the Computed p<i>K</i><sub>a</sub> of Ligands Coordinated to the Catalytic Zinc Ion (2002)

TNF-alpha converting enzyme (TACE) is a multidomain, membrane-anchored protein that includes a Zn-dependent protease domain. It releases the soluble form of cytokine tumor necrosis factor-alpha (TNF-alpha) from its membrane-bound precursor. TACE is a metalloprotease containing a catalytic glutamic acid, Glu-406, and a Zn(2+) ion ligated to three imidazoles. The protonation states of the active site glutamic acid and inhibitors are important factors in understanding the potency of inhibitors with acidic zinc-ligating groups such as hydroxamic and carboxylic acids. Density functional methods were utilized to compute pK(a) values using a model of the catalytic site of TACE and to predict a concomitant mechanism of binding, consistent with lowering the pK(a) of the bound ligand and raising the pK(a) of the active site Glu-406. Weak acids, such as hydroxamic acids, bind in their neutral form and then transfer an acidic proton to Glu-406. Stronger acids, such as carboxylic acids, bind in their anionic form and require preprotonation of Glu-406. Similar binding events would be expected for other zinc-dependent proteases.
The identification of a domain in Escherichia coli elongation factor Tu that interacts with elongation factor Ts. (1992)

A method has been developed to search for the elongation factor Tu (EF-Tu) domain(s) that interact with elongation factor Ts (EF-Ts). This method is based on the suppression of Escherichia coli EF-Tu-dominant negative mutation K136E, a mutation that exerts its effect by sequestering EF-Ts. We have identified nine single-amino acid- substituted suppression mutations in the region 146-199 of EF-Tu. These mutations are R154C, P168L, A174V, K176E, D181G, E190K, D196G, S197F, and I199V. All suppression mutations but one (R154C) significantly affect EF-Tu's ability to interact with EF-Ts under equilibrium conditions. Moreover, with the exception of mutation A174V, the GDP affinity of EF-Tu appears to be relatively unaffected by these mutations. These results suggest that the domain of residues 154 to 199 on EF-Tu is involved in interacting with EF-Ts. These suppression mutations are also capable of suppressing dominant negative mutants N135D and N135I to various degrees. This suggests that dominant negative mutants N135D and N135I are likely to have the same molecular basis as the K136E mutation. The method we have developed in this study is versatile and can be readily adapted to map other regions of EF-Tu. A model of EF-Ts-catalyzed guanine-nucleotide exchange is discussed.
Image Dataset for Visual Objects Classification in 3D Printing (2018)

The rapid development in additive manufacturing (AM), also known as 3D printing, has brought about potential risk and security issues along with significant benefits. In order to enhance the security level of the 3D printing process, the present research aims to detect and recognize illegal components using deep learning. In this work, we collected a dataset of 61,340 2D images (28x28 for each image) of 10 classes including guns and other non-gun objects, corresponding to the projection results of the original 3D models. To validate the dataset, we train a convolutional neural network (CNN) model for gun classification which can achieve 98.16% classification accuracy.
Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games (2015)

We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study.
Software patterns (1996)

article Free Access Share on Software patterns Authors: Douglas C. Schmidt Computer Science at Washington University, St. Louis, Mo. Computer Science at Washington University, St. Louis, Mo.View Profile , Mohamed Fayad University of Nevada, Reno University of Nevada, RenoView Profile , Ralph E. Johnson Computer Science department, University of Illinois at Urbana-Champaign Computer Science department, University of Illinois at Urbana-ChampaignView Profile Authors Info & Claims Communications of the ACMVolume 39Issue 10Oct. 1996 pp 37–39https://doi.org/10.1145/236156.236164Published:01 October 1996Publication History 94citation2,542DownloadsMetricsTotal Citations94Total Downloads2,542Last 12 Months183Last 6 weeks14 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Interactions between Neutrophils and Pseudomonas aeruginosa in Cystic Fibrosis (2017)

Cystic fibrosis (CF) affects 70,000 patients worldwide. Morbidity and mortality in CF is largely caused by lung complications due to the triad of impaired mucociliary clearance, microbial infections and chronic inflammation. Cystic fibrosis airway inflammation is mediated by robust infiltration of polymorphonuclear neutrophil granulocytes (PMNs, neutrophils). Neutrophils are not capable of clearing lung infections and contribute to tissue damage by releasing their dangerous cargo. Pseudomonas aeruginosa is an opportunistic pathogen causing infections in immunocompromised individuals. P. aeruginosa is a main respiratory pathogen in CF infecting most patients. Although PMNs are key to attack and clear P. aeruginosa in immunocompetent individuals, PMNs fail to do so in CF. Understanding why neutrophils cannot clear P. aeruginosa in CF is essential to design novel therapies. This review provides an overview of the antimicrobial mechanisms by which PMNs attack and eliminate P. aeruginosa. It also summarizes current advances in our understanding of why PMNs are incapable of clearing P. aeruginosa and how this bacterium adapts to and resists PMN-mediated killing in the airways of CF patients chronically infected with P. aeruginosa.
Sequential gradient pneumatic compression enhances venous ulcer healing: a randomized trial. (1990)

The treatment of venous ulcers has remained largely unchanged for centuries. The application of properly applied graduated compression bandages, the use of graduated compression stockings, and surgery have been shown to achieve healing. However, some ulcers persist despite appropriate management. A randomized study was undertaken to compare two regimens of treatment for such patients. Both regimens included ulcer debridement, cleaning, nonadherent dressing, and graduated compression stockings. In one regimen, sequential gradient intermittent pneumatic compression was applied for 4 hours each day. Only one of 24 patients in the control group had complete healing of all ulcers compared with 10 of 21 patients healed in the intermittent pneumatic compression group. The median rate of ulcer healing in the control group was 2.1% area per week compared to 19.8% area per week in the intermittent pneumatic compression group. The results indicate that sequential gradient intermittent pneumatic compression is beneficial in the treatment of venous ulcers.
Obesity: How Big a Problem? (1998)

Numerous studies have linked being overweight to increased risk for heart disease, diabetes, and cancer; moreover, according to the Institute of Medicine, fat people in the United States are costing citizens more than $70 billion annually both in direct health care costs and in indirect costs such as lost productivity. But recently many obesity experts have come to believe that these alarms have been overstated, partly because many studies don9t account for confounding factors associated with obesity, such as a sedentary lifestyle, that may be even more dangerous. They also note that there is scant proof that losing weight actually improves longevity, especially in people who are otherwise healthy. As a result, they say that not everyone needs to shed his or her extra pounds, but that the decision should be made individually, based on each person9s risks, which depend not only on weight but also on age, distribution of body fat, family history of disease, and current health problems such as high blood pressure. Needless to say, this revisionism has stirred plenty of controversy, as other experts maintain that obesity is the driver for health risks including high lipid levels, high blood pressure, and high blood sugar.
Protection afforded by preconditioning to the diabetic heart against ischaemic injury (1998)

These results suggest that IPC affords protection to endothelial function in resistance coronary arteries of diabetic hearts. To achieve this protection, a more extensive IPC is needed, which may be related to a longer exposure to adenosine.
ChemInform Abstract: DIPHENYLPHOSPHINO DERIVATIVES OF MALEIC AND FUMARIC ACID DIALKYL ESTERS: FORMATION, PROPERTIES, CRYSTAL AND MOLECULAR STRUCTURES (1979)

Abstract Die 1:1‐molare Umsetzung der Dichlormaleinsäurediester (II) mit dem Silylphosphin (III) führt zu den Monophosphin‐ Derivaten (I).
A 0.5 V/100 MHz over-V/sub CC/ grounded data storage (OVGS) SRAM cell architecture with boosted bit-line and offset source over-driving schemes (1996)

This paper proposes a 0.5 V/100 MHz/sub-5 mW-operated 1-Mbit SRAM cell architecture which uses an over-V/sub CC/ grounded data storage (OVGS) scheme. The key target of OVGS is to minimize the charge amount supplied from the embedded charge pump circuits, which are required to boost the effective gate to source voltage (V/sub 0/=V/sub GS/-V/sub T/) up to 0.8 V necessary to achieve 100 MHz-operation even at 0.5 V single power-supply. Thus, the key low-power strategy of OVGS is putting the right (higher efficiency) boosted power-supply from the charge pump circuit into the right position in the SRAM cell. This paper focuses on why OVGS can realize a greater saving of the charge amount supplied from the boosted power-line and can reduce the power dissipation to /spl les/1/30.4 and /spl les/1/3.9 compared to the previously reported negative source drive (NSD) scheme (Mizuno et al., 1995) and negative word-line drive (NWD) scheme (Itoh et al., 1996), respectively, while achieving a 0.5 V/100 MHz-operation.
Full-Wave Analysis of Dielectric Frequency-Selective Surfaces Using a Vectorial Modal Method (2004)

A novel vectorial modal method is presented for studying guidance and scattering of frequency-selective structures based on lossy all-dielectric multilayered waveguide gratings for both TE and TM polarizations. The wave equation for the transverse magnetic field is written in terms of a linear differential operator satisfying an eigenvalue equation. The definition of an auxiliary problem whose eigenvectors satisfy an orthogonality relationship allows for a matrix representation of the eigenvalue equation. Our proposed technique has been applied to the study of lossy all-dielectric periodic guiding media with periodicity in one dimension. This method yields the propagation constants and field distributions in such media. The reflection and transmission coefficients of a single layer under a plane-wave excitation can be obtained by imposing the boundary conditions. Study of the scattering parameters of the whole multilayered structure is accomplished by the cascade connection of components as characterized by their scattering parameters. Results obtained with this method for the propagation characteristics of a one-dimensional periodic dielectric medium are compared with those presented by other authors, and results for the scattering of several dielectric frequency-selective surfaces (DFSS) are compared with both theoretical and experimental results presented in the literature, finding a very good agreement. A symmetrical band-stop filter with a single waveguide grating is also demonstrated theoretically.