gebhart/patrepeval huggingface dataset:
The Gap1 general amino acid permease acts as an amino acid sensor for activation of protein kinase A targets in the yeast Saccharomyces cerevisiae (2003)

Addition of a nitrogen source to yeast (Saccharomyces cerevisiae) cells starved for nitrogen on a glucose-containing medium triggers activation of protein kinase A (PKA) targets through a pathway that requires for sustained activation both a fermentable carbon source and a complete growth medium (fermentable growth medium induced or FGM pathway). Trehalase is activated, trehalose and glycogen content as well as heat resistance drop rapidly, STRE-controlled genes are repressed, and ribosomal protein genes are induced. We show that the rapid effect of amino acids on these targets specifically requires the general amino acid permease Gap1. In the gap1Delta strain, transport of high concentrations of l-citrulline occurs at a high rate but without activation of trehalase. Metabolism of the amino acids is not required. Point mutants in Gap1 with reduced or deficient transport also showed reduced or deficient signalling. However, two mutations, S391A and S397A, were identified with a differential effect on transport and signalling for l-glutamate and l-citrulline. Specific truncations of the C-terminus of Gap1 (e.g. last 14 or 26 amino acids) did not reduce transport activity but caused the same phenotype as in strains with constitutively high PKA activity also during growth with ammonium as sole nitrogen source. The overactive PKA phenotype was abolished by mutations in the Tpk1 or Tpk2 catalytic subunits. We conclude that Gap1 acts as an amino acid sensor for rapid activation of the FGM signalling pathway which controls the PKA targets, that transport through Gap1 is connected to signalling and that specific truncations of the C-terminus result in permanently activating Gap1 alleles.
Diagnostic approaches to the renal mass. (1989)

In order to put these various diagnostic techniques in perspective, we present the following as our algorithm for evaluating a renal mass diagnosed by IVP or US. IVP=intravenous urography US=ultrasound
Isolation and Immunosuppressive Effects of 6″-O-Acetylginsenoside Rb1 Extracted from North American Ginseng (2014)

Extraction of medicinally active components from natural health products has become an emerging source for drug discovery. Of particular interest for this work was the finding and testing of a new ginsenoside from North American ginseng (Panax quinquefolius). In the present study, a large amount of 6″-O-acetylginsenoside Rb1, compound 7, was found using ultrasonic extraction of North American ginseng with DMSO aqueous solution. This new ginsenoside was well identified with MS, FTIR, and 1D (1H and 13C) and 2D (gCOSY, gHSQC, and gHMBC) NMR. Subsequent bioassay experiments confirmed that compound 7 demonstrated an additional immunosuppressive activity towards inhibiting the production of nitric oxide and tumor necrosis factor alpha in lipopolysaccharide-induced macrophage cells in a dose-dependent manner using murine macrophages. This new ginsenoside is encouraging for the further exploration and development of novel drugs.
zfishbook: connecting you to a world of zebrafish revertible mutants (2011)

zfishbook is an internet-based openly accessible database of revertible protein trap gene-breaking transposon (GBT) insertional mutants in the zebrafish, Danio rerio. In these lines, a monomeric red fluorescent protein (mRFP) is encoded by an artificial 3' exon, resulting in a translational fusion to endogenous loci. The natural transparency of the zebrafish embryo and larvae greatly facilitates the expression annotation of tagged loci using new capillary-based SCORE imaging methods. Molecular annotation of each line is facilitated by cloning methods such as 5'-Rapid Amplification of cDNA Ends (RACE) and inverse polymerase chain reaction (PCR). zfishbook (http://zfishbook.org) represents a central hub for molecular, expression and mutational information about GBT lines from the International Zebrafish Protein Trap Consortium (IZPTC) that includes researchers from around the globe. zfishbook is open to community-wide contributions including expression and functional annotation. zfishbook also represents a central location for information on how to obtain these lines from diverse members of the IZPTC and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information.
Arbuscular mycorrhizal induced changes to plant growth and root system morphology in Prunus cerasifera (1995)

We compared root system morphogenesis of micropropogated transplants of Prunus cerasifera L. inoculated with either of the arbuscular mycorrhizal (AM) fungi Glomus mosseae or Glomus intraradices or with the ericoid mycorrhizal species Hymenoscyphus ericae. All plants were grown in sand culture, irrigated with a nutrient solution that included a soluble source of phosphorus, for 75 days after transplanting. Arbuscular mycorrhizal colonization increased both the survival and growth (by over 100%) of transplants compared with either uninoculated controls or transplants inoculated with H. ericae. Arbuscular mycorrhizal colonization increased root, stem and leaf weights, leaf area, root length and specific leaf area, and it decreased root length/leaf area ratio, root/shoot weight ratio and specific root length. Both uptake of phosphorus and its concentration in leaves were increased by AM infection, although the time course of the relationships between intensity of AM infection and P nutrition were complex and suggested a role for factors other than nutrition. The time course for the development of infection varied. It was most rapid with G. mosseae, but it was ultimately higher with G. intraradices. None of the treatments significantly affected the lengths of adventitious roots or the first-, second- or third-order laterals that developed from them. Arbuscular mycorrhizal colonization increased the intensity of branching in all root orders with the effect being most obvious on first-order lateral roots where the number of branches increased from under 100 to over 300 brances m(-1). As a result, although first-order laterals made up 55% of the root systems of control plants, the comparable value was 36% in AM-infected plants. In contrast, second-order laterals represented 25% of control root systems, but 50% of AM-colonized root systems. Glomus intraradices but not G. mosseae increased root diameter. Anatomical studies revealed no changes in the overall form of the root tip, although there were changes in the diameter of the root cap, cell numbers and cell size. Hymenoscyphus ericae increased the duration of the metaphase index. Both AM fungal treatments increased the concentrations of soluble proteins in root extracts and modified the protein profiles by the elimination and addition of protein bands detected by PAGE analysis. We conclude that AM fungal inoculation influenced processes in the root system at different levels, but not all effects were due to improved P nutrition or increased physiological age.
The RF H− ion source project at RAL (2018)

A project to design and construct an RF-driven long-lifetime volume production ion source producing 30 mA of H− with 50 Hz repetition rate and 1.5% duty factor at 35 keV energy for the ISIS Neutron and Muon Source has been started at Rutherford Appleton Laboratory. The development of the new ion source aims at replacing the caesiated Penning-type surface plasma ion source that has served the ISIS facility since 1980s. The design of the ion source is based on recent developments at CERN demonstrating 30 mA H− in volume mode with less than 50 kW of RF-power but at lower repetition rate of 0.8 Hz. This paper describes the physics design of the ion source and the status of the project. The magnetic field, extraction optics, RF system and preferred plasma ignition scheme are discussed in detail.
Honoraries Stress Scholarship, Professions (1959)

The next time you see a girl wearing ribbons of white and gold or maroon and pink, take a second look because she's a pretty special person.
Building data mining solutions with OLE DB for DM and XML for analysis (2005)

A data mining component is included in Microsoft SQL Server 2000 and SQL Server 2005, one of the most popular DBMSs. This gives a push for data mining technologies to move from a niche towards the mainstream. Apart from a few algorithms, the main contribution of SQL Server Data Mining is the implementation of OLE DB for Data Mining. OLE DB for Data mining is an industrial standard led by Microsoft and supported by a number of ISVs. It leverages two existing relational technologies: SQL and OLE DB. It defines a SQL language for data mining based on a relational concept. More recently, Microsoft, Hyperion, SAS and a few other BI vendors formed the XML for Analysis Council. XML for Analysis covers both OLAP and Data Mining. The goal is to allow consumer applications to query various BI packages from different platforms. This paper gives an overview of OLE DB for Data Mining and XML for Analysis. It also shows how to build data mining application using these APIs.
Enhanced Oral Bioavailability of Piroxicam in Rats by Hyaluronate Microspheres (2007)

To enhance the dissolution and oral bioavailability of poorly water soluble piroxicam, the piroxicam-loaded hyaluronic microspheres were prepared with various ratios of piroxicam, sodium hyaluronate and polyethylene glycol 4000 (PEG) using a spray dryer, and their physicochemical properties such as shape, size, drug-loading efficiency and dissolution were investigated. The pharmacokinetic study of piroxicam-loaded hyaluronic micropheres in rats was then performed compared to piroxicam powder. The piroxicam-loaded hyaluronic microspheres, spherical in shape, had the geometric mean diameters of about 1.5 microm and drug loading efficiency of about 90%, irrespective of ratio of piroxicam/sodium hyaluronate/PEG. The hyaluronic microspheres containing PEG gave significantly higher dissolution rates of drug than did piroxicam powder, PEG-based solid dispersion system and hyaluronic microspheres without PEG, suggesting that the hyaluronic microsphere with sodium hyaluronate and PEG was more useful for improving the dissolution rate of poorly water soluble piroxicam. The piroxicam-loaded hyaluronic microcapsule composed of (piroxicam/sodium hyaluronate/PEG; 2: 20: 1) gave about threefold improved dissolution of drug in water for 4 h compared to piroxicam powder. It showed higher plasma concentrations of drug compared to piroxicam powder. It gave significantly higher AUC and faster Tmax of piroxicam than did piroxicam powder. In particular, the AUC of piroxicam from hyaluronic microsphere was about twofold higher than that from piroxicam powder, suggesting that it could enhance the oral bioavailability of piroxicam. Thus, the hyaluronic microsphere developed using spray-drying technique with sodium hyaluronate and PEG was a more effective oral dosage form for poorly water soluble piroxicam.
Solute removal dynamics in CAPD (1983)

CAPD療法において, 個々の患者に対する治療条件 (透析液量, 透析液組成, 治療時間, スケジュールなど) を定めることは, 維持透析確立の上で重要な課題といえる. そこで本研究ではfirst stepとしてCAPDの溶質除去特性をcompartment modelの手法を用いて検討した.CAPDの溶質除去特性を他の血液浄化法のそれと比較する場合, 各治療で定義されたクリアランスCLを [l/wk] の単位に換算して評価する場合が多い. しかしこのCLでは治療時間, 血漿濃度レベルが異なるため厳密に除去特性を比較検討したことにならない. そこで本研究では経時的にサンプリングした血漿濃度をcompartment modelに入力して得られる1週間平均溶質濃度CS, さらに溶質生成速度Gを除去した1週間平均クリアランスCL (=G/CS) を除去特性比較のための指標として用いた.まずすでに報告されたG, 細胞膜透過係数KC, 腹膜での物質移動容量係数KAおよび反撥係数σなどのパラメーターの値を用いて体液量39lの仮想患者のCSを推算した. その結果CAPD施行時のBUN, creatinine, UAの値はそれぞれ87.0, 25.3, 8.43mg/dlと臨床値に比べて高値を示し, これらの物質のGが減少していることが推測された. そこで実際のCAPD患者の血漿濃度の平均値をCSとして逆にGを推算したところ, BUN, creatinine, UAのGの値はそれぞれ7.29, 0.96, 0.347となり, 導入前HD施行時の10.4, 1.38, 0.429に比べて20-30%減少していることが明らかとなった.これに伴い, HD, HF, CAPDのCS, CLを推算したところ, 溶質除去特性を表わす溶質の分子量MWとCLの関係についてはCAPDとHFはきわめて類似した傾向を示した. 一方, MWとCSとの関係は前述のGの低下の影響が加味されて, HD, HFの長所を合せたHDF施行時に近い濃度レベルを示した.
High power diode laser beam scanning in multi-kilowatt range (2004)

During the last years a new laser beam scanning system for heat treatment of metals with high power diode lasers was developed. The new external scanning optics is an optional tool, that can be used with common standard high power diode lasers (focal distance ≥ 300 mm). It works with high power diode lasers in the multi-kilowatt range up to 5 kilowatt laser power. The new system opens the door to a wide field of applications, that were not possible before. Heat treatment of metal surfaces with a track width of more than 50 mm at once is one of the capabilities. Furthermore different approaches were gone to make the handling of the system more easier for the user. Real-time temperature control with cycle times in the range of microseconds ensures a reproducible hardening result even for complex 3D-shaped parts with difficult heat flow conditions. The latest status of the developments and examples are presented.
Specimen Collection and Handling (2008)

Preanalytical variables can alter the analysis of blood-derived samples. Prior to the analysis of a blood sample, multiple steps are necessary to generate the desired specimen. The choice of blood specimens, its collection, handling, processing, and storage are important aspects since these characteristics can have a tremendous impact on the results of the analysis. The awareness of clinical practices in medical laboratories and the current knowledge allow for identification of specific variables that affect the results of a proteomic study. The knowledge of preanalytical variables is a prerequisite to understand and control their impact.
Development of an experimental animal model for reactive arthritis induced by Yersinia enterocolitica infection (1987)

We attempted to induce experimental arthritis in rats by systematically testing the effect of Yersinia infections in five strains of rats, using the intragastric, intraperitoneal, and intravenous routes of inoculation. We observed that Lewis rats which were given 10(4) to 10(5) Yersinia enterocolitica WA organisms via the intravenous route consistently developed arthritis. The arthritis was most severe at 3 weeks and subsided at 6 weeks. No arthritis was observed when this bacterial strain was administered to Buffalo, Fisher, DA, and LDA rats. No replicable bacteria were detected in the joints. This aseptic characteristic parallels that seen in the human condition and establishes this as an animal model of Yersinia-induced arthritis. The probable reason for arthritis development in only the Lewis rats became apparent when we analyzed the numbers of live bacteria in the spleens and livers of these infected animals. The arthritis-susceptible Lewis rats harbored 10-fold more bacteria than the arthritis-resistant rat strains, and this systemic infection also persisted for a significantly longer period. Speculations as to why human subjects who develop Yersinia-induced arthritis are genetically predisposed have been centered principally around the role of the HLA-B27 histocompatibility antigens. The present study reveals a heretofore unrecognized critical factor: the susceptibility of the hosts to the virulence of the infectious organisms. In addition, the present animal model will provide the necessary tool for the investigation of this and other important host and bacterial factors.
Water Gas Shift Reaction on Cu and Au Nanoparticles Supported on CeO2(111) and ZnO(000$\bar 1$): Intrinsic Activity and Importance of Support Interactions (2007)

A cerious contender: The catalytic activity in the water gas shift reaction of Au and Cu nanoparticles supported on CeO2(111) is superior to that of these nanoparticles on a ZnO(000) support or of the bulk metals (the diagram shows the results depending on the Au nanoparticle coverage). These results illustrate the essential role that an oxide can have in the activity of supported Au nanocatalysts.
Local control for mesh morphing (2002)

Mesh morphing techniques are capable of producing a sequence of meshes, gradually changing from a source to a target shape. However, current techniques do not allow to describe the local behavior of the morph. A solution to this problem is presented. The main idea is to describe mesh geometry in a differential way, thus, insertion of local features from one shape into another does not suffer from difference in absolute coordinates. Besides interesting possibilities for animation the technique proves to be a powerful modeling tool.
Enantioselective Syntheses and Cytotoxicity of N,O-Nucleosides (2003)

Enantiomers of 4'-aza-2',3'-dideoxynucleosides have been prepared by two different synthetic approaches, on the basis of 1,3-dipolar cycloaddition of a chiral nitrone. Cytotoxicity and apoptotic activity have been investigated. (5'S)-5-Fluoro-1-isoxazolidin-5-yl-1H-pyrimidine-2,4-dione [(-)-AdFU], while showing low level of cytotoxicity, is a good inductor of apoptosis on lymphoid and monocytoid cells, acting as a strong potentiator of Fas-induced cell death.
Comprehensive Controller for Super Sonic Molecular Beam Gas Chromatograph Mass Spectrometer (2022)

This paper presents a new, comprehensive digital circuit used for the control of a novel gas chromatograph mass spectrometer (GC-MS) interface that is based on supersonic molecular beam (SMB). The circuit includes a Texas Instruments 150 MHz digital signal controller (DSC), high voltage amplifiers for 8 independent channels and 4 independent channels of high resolution pulse width modulation (PWM). The circuit, along with a sophisticated embedded program and a custom made personal computer (PC) application, control all aspects of the interface: smart filament emission-current stabilization, static and scanning mass-dependent ion-source voltages, transfer-line heater proportional integral differential (PID) controls with thermocouple feedbacks, on/off valves, relays and several peripheral device controls that enable the full operation of a turbo-molecular vacuum pump, and of gas flow and pressure controllers. All aspects of this comprehensive controller were successfully tested. The signal for the 450 Th ion (C32H66) for example increased by 123% which is a significant increase. It is obvious that correctly tuned dynamic voltages can guarantee the optimal signal for each mass.
Leveraging publicly available coronavirus data to identify new therapeutic targets for COVID-19 (2021)

Many important questions remain regarding severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the viral pathogen responsible for COVID-19. These questions include the mechanisms explaining the high percentage of asymptomatic but highly infectious individuals, the wide variability in disease susceptibility, and the mechanisms of long-lasting debilitating effects. Bioinformatic analysis of four coronavirus datasets representing previous outbreaks (SARS-CoV-1 and MERS-CoV), as well as SARS-CoV-2, revealed evidence of diverse host factors that appear to be coopted to facilitate virus-induced suppression of interferon-induced innate immunity, promotion of viral replication and subversion and/or evasion of antiviral immune surveillance. These host factors merit further study given their postulated roles in COVID-19-induced loss of smell and brain, heart, vascular, lung, liver, and gut dysfunction.
Semi-supervised model personalization for improved detection of learner's emotional engagement (2016)

Affective states play a crucial role in learning. Existing Intelligent Tutoring Systems (ITSs) fail to track affective states of learners accurately. Without an accurate detection of such states, ITSs are limited in providing truly personalized learning experience. In our longitudinal research, we have been working towards developing an empathic autonomous 'tutor' closely monitoring students in real-time using multiple sources of data to understand their affective states corresponding to emotional engagement. We focus on detecting learning related states (i.e., 'Satisfied', 'Bored', and 'Confused'). We have collected 210 hours of data through authentic classroom pilots of 17 sessions. We collected information from two modalities: (1) appearance, which is collected from the camera, and (2) context-performance, that is derived from the content platform. The learning content of the content platform consists of two section types: (1) instructional where students watch instructional videos and (2) assessment where students solve exercise questions. Since there are individual differences in expressing affective states, the detection of emotional engagement needs to be customized for each individual. In this paper, we propose a hierarchical semi-supervised model adaptation method to achieve highly accurate emotional engagement detectors. In the initial calibration phase, a personalized context-performance classifier is obtained. In the online usage phase, the appearance classifier is automatically personalized using the labels generated by the context-performance model. The experimental results show that personalization enables performance improvement of our generic emotional engagement detectors. The proposed semi-supervised hierarchical personalization method result in 89.23% and 75.20% F1 measures for the instructional and assessment sections respectively.
Influence of Oxygen and Nitrogen in the Intrinsic Layer of a-Si:H Solar Cells (1996)

The effects of oxygen and nitrogen on hydrogenated amorphous silicon (a-Si:H) films and solar cells are systematically studied in the initial and light-soaked states. The oxygen and nitrogen concentrations were varied from 10 18 to 10 21 cm -3 and 10 16 to 10 19 cm -3 , respectively. In the initial state, dark conductivity and photoconductivity increase, and the activation energy of dark conductivity decreases with increase in the oxygen and nitrogen concentrations, because of the creation of donorlike states. These film properties after light-soaking, however, are independent of the oxygen and nitrogen concentrations, probably because they are dominated by light-induced states. On the other hand, the conversion efficiency of solar cells in both the initial and light-soaked states drops as the oxygen and nitrogen concentrations increase. Collection efficiency measurements show that the electric field distribution in the i-layer is affected by the donorlike states even after light-soaking. The photovoltaic properties of solar cells more sensitively reflect the effect of oxygen and nitrogen incorporation than the film properties.
A specific antibiofilm protein-asymmetric release system for chronic wounds (2019)

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