gebhart/patrepeval huggingface dataset:
Design of multiple reaction systems for genetic analysis (2002)

Heat-transfer considerations significantly constrain design of multiple reaction microdevices. We present a new methodology for design and fabrication of multiple reaction systems using the concept of heat integration. Heat integration is a design concept that strikes a balance between complete thermal isolation of individual thermal operations and power consumption in a multiple reaction device. It relies on the use of steady-state temperature gradients developed in the substrate, by the actuation of a single reaction chamber, to initiate several reactions at progressively lower temperatures. The use of thermal gradients in this manner eliminates power requirements to heat individual reactions, active temperature control of "passive" reaction chambers and power requirement for cooling. Complete thermal isolation on the other hand, requires higher power for device cooling but, unlike the case of heat integration, geometry of component placement is relatively unconstrained.
CoCo: Interactive Exploration of Conformance Constraints for Data Understanding and Data Cleaning (2021)

Data profiling refers to the task of extracting technical metadata or profiles and has numerous applications such as data understanding, validation, integration, and cleaning. While a number of data profiling primitives exist in the literature, most of them are limited to categorical attributes. A few techniques consider numerical attributes; but, they either focus on simple relationships involving a pair of attributes (e.g., correlations) or convert the continuous semantics of numerical attributes to a discrete semantics, which results in information loss. To capture more complex relationships involving the numerical attributes, we developed a new data-profiling primitive called conformance constraints, which can model linear arithmetic relationships involving multiple numerical attributes. We present CoCo, a system that allows interactive discovery and exploration of Conformance Constraints for understanding trends involving the numerical attributes of a dataset, with a particular focus on the application of data cleaning. Through a simple interface, CoCo enables the user to guide conformance constraint discovery according to their preferences. The user can examine to what extent a new, possibly dirty, dataset satisfies or violates the discovered conformance constraints. Further, CoCo provides useful suggestions for cleaning dirty data tuples, where the user can interactively alter cell values, and verify by checking change in conformance constraint violation due to the alteration. We demonstrate how CoCo can help in understanding trends in the data and assist the users in interactive data cleaning, using conformance constraints.
ChemInform Abstract: O‐WURSTER RADICAL CATIONS AND ANIONS (1976)

Abstract Verschiedene ringsubstituierte 1,2‐Phenylendiamine, wie z.B. (I) und (II), und ihre Dihydrochloride lassen sich elektrolytisch oder durch Einwirkung von Bleidioxid zu stabilen paramagnetischen Zwischenprodukten oxidieren, die anhand ihrer ESR‐Spektren als Radikalkationen vom Typ der o‐Wursterschen Salze identifiziert werden.
A utility-theoretic approach to privacy and personalization (2008)

Online services such as web search, news portals, and e-commerce applications face the challenge of providing high-quality experiences to a large, heterogeneous user base. Recent efforts have highlighted the potential to improve performance by personalizing services based on special knowledge about users. For example, a user's location, demographics, and search and browsing history may be useful in enhancing the results offered in response to web search queries. However, reasonable concerns about privacy by both users, providers, and government agencies acting on behalf of citizens, may limit access to such information. We introduce and explore an economics of privacy in personalization, where people can opt to share personal information in return for enhancements in the quality of an online service. We focus on the example of web search and formulate realistic objective functions for search efficacy and privacy. We demonstrate how we can identify a near-optimal solution to the utility-privacy tradeoff. We evaluate the methodology on data drawn from a log of the search activity of volunteer participants. We separately assess users' preferences about privacy and utility via a large-scale survey, aimed at eliciting preferences about peoples' willingness to trade the sharing of personal data in returns for gains in search efficiency. We show that a significant level of personalization can be achieved using only a small amount of information about users.
A novel form of human neuropsin, a brain‐related serine protease, is generated by alternative splicing and is expressed preferentially in human adult brain (1999)

We have cloned cDNAs encoding two isoforms of a human novel serine protease. They encoded sequences of 260 and 305 amino acids, and both showed significant homology to mouse neuropsin. Mouse neuropsin has been reported to be involved in hippocampal plasticity, therefore we designated the proteins as type 1 and type 2 neuropsin, respectively. The amino acid sequences of the two types of human neuropsin were identical, except that type 2 carried an insert of 45 amino acids at the C-terminus of the leader sequence. The essential three amino acids in the active site triad, His, Asp, and Ser, and the single putative N-glycosylation site were conserved in human and mouse neuropsin. Sequence analysis of the 946 bp genomic DNA spanning the region encoding the insertion sequence revealed that two isoforms were generated in human brain by alternative splicing. However, the mouse genomic sequence did not conserve the 3' acceptor consensus sequence at the corresponding position, suggesting that type 2 neuropsin was a species-specific splice variant. When the open reading frames of human neuropsin were expressed in insect cells, both types of neuropsin were detected in the conditioned media by western blot analysis using anti-human neuropsin serum. Northern blot hybridization and reverse transcription-polymerase chain reaction showed predominant expression of type 1 neuropsin in pancreas. Type 2 neuropsin was preferentially expressed in human adult brain and hippocampus, although both types were expressed in fetal brain and placenta in comparable amounts. Dot blot hybridization showed that neuropsin was expressed in various regions of adult brain, including the hippocampus and cerebral cortex, and also in various fetal tissues. These results suggest that human type 2 neuropsin may be important to the adult brain plasticity, although both types may be necessary for the development of the nervous system.
Interconnect scaling implications for CAD (1999)

Interconnect scaling to deep submicron processes presents many challenges to today's CAD flows. A recent analysis by Sylvester and Keutzer examined the behavior of average length wires under scaling, and controversially concluded that current CAD tools are adequate for future module-level designs. In our work, we show that average length wire scaling is sensitive to the technology assumptions, although the change in their behavior is small under all reasonable scaling assumptions. However, examining only average length wires is optimistic, since long wires are the ones that primarily cause CAD tool exceptions. In a module of fixed complexity, under both optimistic and pessimistic scaling assumptions, the number of long wires will increase slowly with scaling. More importantly, as the overall die capacity grows exponentially, the number of modules and thus the total number of wires in a design, will also increase exponentially. Thus, if the design team size and per-designer workload is to remain relatively constant, future CAD tools will need to handle long wires much better than current tools to reduce the percentage of wires that require designer intervention.
Dual-frequency broad-band stacked microstrip patch antenna (2003)

A microstrip antenna formed by two stacked patches is proposed for dual-frequency and broad-band performance. Different E-plane and H-plane arrangements are studied to achieve an isolation between bands better than 30 dB. A prototype operating at the 1.8 GHz and 3.5 GHz bands has been simulated and tested.
Flow rate dependent ex vivo deheparinization with immobilized cationic ligand. (1998)

The Heparin Removal Device is a deheparinization system that provides a good alternative when adverse reaction to protamine is suspected or when a heparin coated device is employed for cardiopulmonary bypass. In a bovine model, after systemic heparinization with 300 IU/kg body wt, the authors investigated the rate of deheparinization using this plasmapheresis system that allows exposition of heparinized plasma to an immobilized cationic ligand. Blood was shunted through a heparin coated veno-venous circuit to the plasma separator at a flow rate of 500 ml/min (n = 3, body wt 68 +/- 4 kg) or 1,000 ml/min (n = 3, body wt 57 +/- 4 kg). All plasma separators remained patent without any failure of the devices. Blood samples were drawn at regular intervals for coagulation parameters. The evolution of the activated coagulation time (ACT) was measured during the first 60 min of the deheparinization procedure, and results were compared with spontaneous evolution in a control group (n = 3, body wt 73 +/- 5 kg) without reversal of heparinization. After heparin administration, mean ACT was longer than 1,000 sec in the three groups. Fifteen minutes later it was still > 1,000 sec in the control group, whereas it was 427 +/- 8 sec in the slow flow group (500 ml/min) and 340 +/- 26 sec in the high flow group (1,000 ml/min). At 30 min it was 1,000, 367 +/- 26, and 200 +/- 24 sec, respectively, in the three groups. A regression curve was calculated for each group, and areas under the curves were compared. Ex vivo deheparinization was efficient in normalization of ACT, but removal of heparin appeared to be flow rate dependent. Increased blood flow from 500 to 1,000 ml/min across the deheparinization system resulted in significant acceleration of ACT normalization (p < 0.05).
Effect of the Amide Bond Diamine Structure on the CO2, H2S, and CH4 Transport Properties of a Series of Novel 6FDA-Based Polyamide–Imides for Natural Gas Purification (2012)

A series of higher permeability polyamide–imides based on 2,2′-bis(3,4-dicarboxyphenyl) hexafluoropropane dianhydride with comparable plasticization resistance to Torlon were synthesized and formed into dense film membranes. Polymers possessing 2,4-diamino mesitylene (DAM) were stable up to 56 atm of pure CO2, which is due to enhanced charge transfer complex formation compared to polymers containing 4,4′-(hexafluoroisopropylidene) dianiline (6FpDA) and 2,3,5,6-tetramethyl-1,4-phenylenediamine (TmPDA). The new polymers containing DAM and TmPDA showed ideal CO2/CH4 selectivities of near 50 with CO2 and H2S permeabilities over an order of magnitude higher than Torlon. CO2 and CH4 sorption in the DAM- and TmPDA-based materials was reduced, whereas H2S sorption was enhanced relative to membranes containing fluorinated 6FpDA. Consequently, DAM- and TmPDA-based membranes showed increased stability toward high pressure CO2 but lower plasticization resistance toward pure H2S. These results highlight the differences between CO2 and H2S that challenge the rational design of materials targeting simultaneous separation of both contaminants.
EPR Spectroscopy of Nitrite Complexes of Methemoglobin (2010)

The chemical interplay of nitrogen oxides (NO's) with hemoglobin (Hb) has attracted considerable recent attention because of its potential significance in the mechanism of NO-related vasoactivity regulated by Hb. An important theme of this interplay-redox coupling in adducts of heme iron and NO's-has sparked renewed interest in fundamental studies of FeNO(x) coordination complexes. In this Article, we report combined UV-vis and comprehensive electron paramagnetic resonance (EPR) spectroscopic studies that address intriguing questions raised in recent studies of the structure and affinity of the nitrite ligand in complexes with Fe(III) in methemoglobin (metHb). EPR spectra of metHb/NO(2)(-) are found to exhibit a characteristic doubling in their sharper spectral features. Comparative EPR measurements at X- and S-band frequencies, and in D(2)O versus H(2)O, argue against the assignment of this splitting as hyperfine structure. Correlated changes in the EPR spectra with pH enable complete assignment of the spectrum as deriving from the overlap of two low-spin species with g values of 3.018, 2.122, 1.45 and 2.870, 2.304, 1.45 (values for samples at 20 K and pH 7.4 in phosphate-buffered saline). These g values are typical of g values found for other heme proteins with N-coordinated ligands in the binding pocket and are thus suggestive of N-nitro versus O-nitrito coordination. The positions and shapes of the spectral lines vary only slightly with temperature until motional averaging ensues at approximately 150 K. The pattern of motional averaging in the variable-temperature EPR spectra and EPR studies of Fe(III)NO(2)(-)/Fe(II)NO hybrids suggest that one of two species is present in both of the alpha and beta subunits, while the other is exclusive to the beta subunit. Our results also reconfirm that the affinity of nitrite for metHb is of millimolar magnitude, thereby making a direct role for nitrite in physiological hypoxic vasodilation difficult to justify.
A robust prognostic signature for hormone-positive node-negative breast cancer (2013)

RFRS allows flexibility in both the number and identity of genes utilized from thousands to as few as 17 or eight genes, each with multiple alternatives. The RFRS reports a probability score strongly correlated with risk of relapse. This score could therefore be used to assign systemic chemotherapy specifically to those high-risk patients most likely to benefit from further treatment.
On-Chip Power Noise Measurements of Cryptographic VLSI Circuits and Interpretation for Side-Channel Analysis (2013)

International audience
Generation of submillimeter radiation by strong plasma turbulence at electron beam &#x2014; Plasma interaction (2010)

Paper presents results of investigations of electromagnetic radiation emission in a submillimeter range at strong Langmuir turbulence pumped by a relativistic electron beam. Radiation at double plasma frequency is generated due to plasmon-plasmon merging. Results of radiation power measurements are compared with theoretical estimations.
Isolation, Diversity and Potential Use of Endophytes in the Biomass and Bioenergy Crop Miscanthus (2019)

Endophytes have the potential to contribute to the sustainable production of bioenergy crops such as the perennial rhizomatous grass Miscanthus. They can improve plant growth on marginal land that is otherwise unsuitable for conventional agriculture and can also reduce the need for environmentally damaging chemical inputs including fertilisers and pesticides. This chapter outlines current knowledge of Miscanthus endophytes and presents new data on the diversity of root and shoot fungal endophytes isolated from three Miscanthus species (M. sacchariflorus, M. sinensis and M. ×giganteus). Malt extract, potato dextrose and Czapek Dox media were compared for isolation and growth of the endophytes. The endophytes were then identified using DNA barcoding with three DNA loci (nrITS, nrLSU and TEF). nrITS and nrLSU were found to be the most reliable and consistent barcoding regions. Internal transcribed spacer (ITS) had the highest discriminating potential and is thus recommended for single locus barcoding of endophytes in Miscanthus. Most new isolates were Ascomycota belonging to Pezizomycotina with representatives from Dothideomycetes, Eurotiomycetes and Sordariomycetes. One Basidiomycota species was recovered (a known soil yeast Rhodotorula). Comparisons between Miscanthus endophyte species composition and its better-known sister genus Saccharum (including sugarcane) are provided.
Polarimetric Signatures of Coronary Thrombus in Patients With Acute Coronary Syndrome (2021)

Intravascular PS-OFDI offers the opportunity to quantitatively assess the polarimetric properties of fresh and organizing coronary thrombus, providing new insights into vascular healing and plaque stability.
Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex (2021)

ABSTRACT The plastid caseinolytic protease (Clp) complex plays essential roles in maintaining protein homeostasis and comprises both plastid-encoded and nuclear-encoded subunits. Despite the Clp complex being retained across green plants with highly conserved protein sequences in most species, examples of extremely accelerated amino acid substitution rates have been identified in numerous angiosperms. The causes of these accelerations have been the subject of extensive speculation but still remain unclear. To distinguish among prevailing hypotheses and begin to understand the functional consequences of rapid sequence divergence in Clp subunits, we used plastome transformation to replace the native clpP1 gene in tobacco ( Nicotiana tabacum ) with counterparts from another angiosperm genus ( Silene ) that exhibits a wide range in rates of Clp protein sequence evolution. We found that antibiotic-mediated selection could drive a transgenic clpP1 replacement from a slowly evolving donor species ( S. latifolia ) to homoplasmy but that clpP1 copies from Silene species with accelerated evolutionary rates remained heteroplasmic, meaning that they could not functionally replace the essential tobacco clpP1 gene. These results suggest that observed cases of rapid Clp sequence evolution are a source of epistatic incompatibilities that must be ameliorated by coevolutionary responses between plastid and nuclear subunits.
Improving the scalability of fault-tolerant database clusters (2003)

Replication has become a central element in modem information systems playing a dual role: increase availability and enhance scalability. Unfortunately, most existing protocols increase availability at the cost of scalability; This paper presents architecture, implementation and performance of a middleware based replication tool that provides both availability and better scalability than existing systems. Main characteristics are the usage of specialized broadcast primitives and efficient data propagation.
Thermo-/hydrodynamic in supercritical fluids (2019)

Invited talk
Comparison of an HXH Three-Center Hydrogen Bond with Alternative Two-Center Hydrogen Bonds in a Model System (1999)

Little information is available on the stability of three-center hydrogen bonds relative to two-center hydrogen bonds. In an XHX three-center hydrogen bond, two donors interact with one acceptor; here, we compare an HXH interaction with the component two-center hydrogen bonds (H−X and X−H) in a small depsipeptide, 1. The results show that there is negative cooperativity between the two components of the HXH interaction.
Activation of the grp78 and grp94 Promoters by Hepatitis C Virus E2 Envelope Protein (1999)

The hepatitis C virus E1 and E2 envelope proteins are targeted to the endoplasmic reticulum, but instead of being secreted, they are retained in a pre-Golgi compartment, at least partly in a misfolded state. Since secretory proteins which are retained in the endoplasmic reticulum frequently can activate the transcription of intraluminal chaperone proteins, we measured the effect of the E1 and E2 proteins on the promoters of two such chaperones, GRP78 (BiP) and GRP94. We found that E2 but not E1 protein activates these two promoters, as assayed by a reporter gene system. Furthermore, E2 but not E1 protein induces the synthesis of GRP78 from the endogenous cellular gene. We also found that E2 but not E1 protein expressed in mammalian cells is bound tightly to GRP78. This association may explain the ability of E2 protein to activate transcription, since GRP78 has been postulated to be a sensor of stress in the endoplasmic reticulum. Since overexpression of GRP78 has been shown to decrease the sensitivity of cells to killing by cytotoxic T lymphocytes and to increase tumorigenicity and resistance to antitumor drugs, this activity of E2 protein may be involved in the pathogenesis of hepatitis C virus-induced diseases.
HostSeq: a Canadian whole genome sequencing and clinical data resource (2023)

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.
The Lagrangian kinematics of three-dimensional Darcy flow (2021)

Abstract
Functional characterization of urate transport via a novel urate efflux transporter URATv1. (2009)

ヒト腎臓の尿酸輸送は，その排泄低下が高尿酸血症発症と関連するため臨床的に重要である．2008年に，我々はグルコーストランスポーターファミリーSLC2A9の遺伝子産物が電位依存性尿酸排出トランスポーターURATv1であることを見出した．同遺伝子に変異を有する患者が腎性低尿酸血症を示すこと，またヒト腎臓においてURATv1は主に近位尿細管基底側膜に存在することから,管腔側でURAT1が尿細管中から取込んだ尿酸の基底側における血管側への出口がURATv1であることを示唆した．そこで我々はURATv1を標的とする新規高尿酸血症治療薬創製を目指し，URATv1による尿酸輸送特性の更なる解析を行った．In vitro 転写法により作成したURATv1 cRNAを，アフリカツメガエル卵毋細胞に発現させURATv1による尿酸の細胞内取込みを測定した．RI標識尿酸の卵母細胞からの排出実験には，cRNA発現卵毋細胞へのマイクロインジェクション法による基質の注入を行い，一定時間経過後の細胞内外の尿酸量を測定し，排泄率を計算した．URATv1による尿酸取込みは，細胞内の酸性化およびアルカリ化により増加したのに対し，その尿酸排出は細胞外pH変化による有意な変化を認めなかった．しかしURATv1による尿酸排出は，細胞外溶液のイオン組成をNa+からK+に置換することにより，またCl-からグルコン酸に置換することにより減少した．またURATv1による尿酸輸送は，尿酸降下薬のベンズブロマロンとNSAIDのインドメタシンによる強い抑制を受け，尿酸降下薬のプロベネシドの抑制は軽度であった．ベンズブロマロンによるIC50は44.4μM，インドメタシンによるそれは56.0μMであった．URATv1の尿酸輸送特性は，URAT1のそれとは異なることから，URATv1は新規尿酸降下薬の分子標的となる可能性が示唆された.
Luminescent nanoparticles for molecular medicine (2007)

Novel optical labels based on nanophosphor materials like LaPO<sub>4</sub>:Ce,Tb and CePO<sub>4</sub>:Tb-LaPO<sub>4</sub> core-shell nanophosphors were presented. Core particles could be synthesised smaller than 10nm and stabilized in aqueous media. Polymer coatings of individual nanoparticles increased long term stability and introduced functional groups of interest for bioconjugation chemistry. A new strategy for conjugation of bioligands via His-tags was given. In feasibility studies for in-vitro diagnostic applications these dnanophosphors featured their advantage over organic dyes. As an example the detection of hybridization and thermal induced denaturation events of DNA strands read out by FRET processes was presented.