gebhart/patrepeval huggingface dataset:
A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance (2022)

Detailed knowledge on how bacteria evade antibiotics and eventually develop resistance could open avenues for novel therapeutics and diagnostics. It is thereby key to develop a comprehensive genome-wide understanding of how bacteria process antibiotic stress, and how modulation of the involved processes affects their ability to overcome said stress. Here we undertake a comprehensive genetic analysis of how the human pathogen Streptococcus pneumoniae responds to 20 antibiotics. We build a genome-wide atlas of drug susceptibility determinants and generated a genetic interaction network that connects cellular processes and genes of unknown function, which we show can be used as therapeutic targets. Pathway analysis reveals a genome-wide atlas of cellular processes that can make a bacterium less susceptible, and often tolerant, in an antibiotic specific manner. Importantly, modulation of these processes confers fitness benefits during active infections under antibiotic selection. Moreover, screening of sequenced clinical isolates demonstrates that mutations in genes that decrease antibiotic sensitivity and increase tolerance readily evolve and are frequently associated with resistant strains, indicating such mutations could be harbingers for the emergence of antibiotic resistance.
Proteomic analysis reveals a biosignature of decreased synaptic protein in cerebrospinal fluid of major depressive disorder (2020)

Major depressive disorder (MDD) is a leading cause of morbidity with a lifetime prevalence of 10%. There is increasing evidence suggesting synaptic dysfunction and impaired integrity of certain brain circuits in MDD. Here we investigate the cerebrospinal fluid proteome of psychiatric patients focusing on MDD by deep proteomic profiling approach combined with a further validation step using targeted mass spectrometry. We demonstrate profound CSF proteomic changes during on-going depression episodes in MDD patients (n = 40) in comparison to controls (n = 27), schizophrenia spectrum disorder (n = 13), and bipolar disorder patients (n = 11). The discovery analysis with isobaric tags for relative and absolute quantitation (iTRAQ) reveals changes in proteins associated with synaptic transmission, myelination, and Wnt signaling in CSF of MDD. The multiple reaction monitoring (MRM) validation analysis confirms significantly decreased levels of eight proteins including the membrane synaptic proteins neurexin 3 (NRXN3), contactin-associated protein-like 4 (CNTNAP4), and glutamate ionotropic receptor AMPA type subunit 4 (GRIA4) in the CSF of MDD patients in comparison to the controls. Overall, the study demonstrates proteins that constitute an MDD biosignature for further validation studies and provides insight into the pathophysiology of MDD and other psychiatric disorders.
Corrigendum to : Genetic mapping of commercially significant starch characteristics in wheat crosses (2002)

Starch properties were measured on the doubled haploid progeny of 2 crosses, one between Cranbrook and Halberd and the other between CD87 and Katepwa. Properties studied included starch peak and final viscosity measured by Rapid Visco Analyser, starch granule size distribution measured by laser light scattering, starch gelatinisation temperature by differential scanning calorimetry, and flour swelling volume. In the Cranbrook Halberd cross (samples from 2 environments), a highly significant quantitative trait locus (QTL) was located on chromosome 4A for both starch peak viscosity and starch/flour swelling volume, centred around the Wx-B1 locus. In previous studies, this locus has been found to be linked to Japanese noodle quality. The increases in starch peak viscosity and flour swelling volume are derived from the Halberd parent, consistent with the fact that Halberd is null for the Wx-B1 locus on chromosome 4A and is missing the respective granule-bound starch synthase protein, whereas Cranbrook is a wheat line carrying the normal 3 Wx loci. The final starch viscosity also showed an association with the Wx-B1 locus. In the CD87 Katepwa cross, the progeny showed an association between peak viscosity and a marker on chromosome 7A. This appeared to be near the Wx-A1 locus. In some experiments, flour viscosity showed a highly significant QTL on chromosome 7B, apparently at the same locus as the late maturity - amylase derived from the Cranbrook parent. Starch gelatinisation onset temperature indicated a significant QTL on chromosomes 2B and 7A (LOD = 2.58 and 3.66, respectively, in interval analyses). Starch gelatinisation peak temperatures indicated a QTL on chromosome 7A, which, although not in the significant ( P = 0.05) class based on regression analyses, indicated a LOD score of 3.06 in interval analyses. Heat of gelatinisation (H) indicated a suggestive QTL (LRS = 14.5 with a threshold of 14.7 for P &amp;lt; 0.05, LOD = 2.65 for interval analysis), on chromosome 4A, at the Wx-B1 locus with an increased effect coming from the Halberd parent. The A:B granule ratio analysis indicated a significant QTL on chromosome 4B, but this was not observed in all environments and may be due to the fact that the QTL corresponded to the position of a major QTL controlling plant growth.
Probabilistic unification-based integration of syntactic and semantic preferences for nominal compounds (1990)

In this paper, we describe a probabilistic framework for unification-based grammars that facilitates integrating syntactic and semantic constraints and preferences. We share many of the concerns found in recent work on massively-parallel language interpretation models, although the proposal reflects our belief in the value of a higher-level account that is not stated in terms of distributed computation. We also feel that inadequate learning theories severely limit existing massively-parallel language interpretation models. A learning theory is not only interesting in its own right, but must underlie any quantitative account of language interpretation, because the complexity of interaction between constraints and preferences makes ad hoc trial-and-error strategies for picking numbers infeasible, particularly for semantics in realistically-sized domains.
Resource configurable spoken query detection using Deep Boltzmann Machines (2012)

In this paper we present a spoken query detection method based on posteriorgrams generated from Deep Boltzmann Machines (DBMs). The proposed method can be deployed in both semi-supervised and unsupervised training scenarios. The DBM-based posteriorgrams were evaluated on a series of keyword spotting tasks using the TIMIT speech corpus. In unsupervised training conditions, the DBM-approach improved upon our previous best unsupervised keyword detection performance using Gaussian mixture model-based posteriorgrams by over 10%. When limited amounts of labeled data were incorporated into training, the DBM-approach required less than one third of the annotated data in order to achieve a comparable performance of a system that used all of the annotated data for training.
Thixotropic Colloidal Suspension and Flow curves with Minimum: Identification of Flow Regimes and Rheometric Consequences (1996)

International audience
Polymodal activation of the TREK-2 K2P channel produces structurally distinct open states (2016)

The TREK subfamily of two-pore domain (K2P) K(+) channels exhibit polymodal gating by a wide range of physical and chemical stimuli. Crystal structures now exist for these channels in two main states referred to as the "up" and "down" conformations. However, recent studies have resulted in contradictory and mutually exclusive conclusions about the functional (i.e., conductive) status of these two conformations. To address this problem, we have used the state-dependent TREK-2 inhibitor norfluoxetine that can only bind to the down state, thereby allowing us to distinguish between these two conformations when activated by different stimuli. Our results reconcile these previously contradictory gating models by demonstrating that activation by pressure, temperature, voltage, and pH produce more than one structurally distinct open state and reveal that channel activation does not simply involve switching between the up and down conformations. These results also highlight the diversity of structural mechanisms that K2P channels use to integrate polymodal gating signals.
Synthesis and Characterization of Aflatoxin B1 Mercapturic Acids and Their Identification in Rat Urine (1997)

Biologic effects of the hepatocarcinogenic mycotoxin aflatoxin B1 are principally induced by one of its metabolites, the exo-aflatoxin B1 epoxide which produces both DNA and protein adducts in vivo. Detoxication of the exo-aflatoxin B1 epoxide can be mediated in part by glutathione S-transferases whose induction could be important in chemoprotection interventions. Thus, biomarkers of the enzymatic conjugation of exo-aflatoxin B1 epoxide with glutathione may be important indices of protection against the toxic effects of this agent. Since glutathione conjugates undergo further metabolic processing in vivo to yield mercapturic acids, increased urinary excretion of exo-aflatoxin B1 mercapturate could be expected during chemoprotection intervention. To determine if this mercapturic acid could be used as a biomarker, techniques for its specific measurement were developed using monoclonal antibody immunoaffinity chromatography and reverse phase high-performance liquid chromatography with ultraviolet absorbance and mass spectral detection. First, a synthetic exo-aflatoxin B1 mercapturate was characterized using mass spectrometry, ultraviolet absorbance, circular dichroism spectrometry, and chemical derivatization. In vivo metabolite characterization was then facilitated by comparison with the synthetically prepared exo-aflatoxin B1 mercapturate and both aflatoxin B1-glutathione conjugate diastereoisomers. In rats, 1% of the aflatoxin dose was excreted as exo-aflatoxin B1 mercapturate within 24 h. The finding that exo-aflatoxin B1 mercapturate was excreted in urine in a dose-dependent manner provides the basis for investigating its applicability as a biomarker of glutathione S-transferase status in aflatoxin chemoprotection studies.
An azimuthally polarizing photonic crystal fibre with a central gold nanowire (2011)

An air–silica photonic crystal fibre with a gold nanowire at core centre is shown to support a low-loss azimuthally polarized mode. Since all the other modes have very high attenuation, the fibre effectively supports only this mode, acting as a single-polarization fibre with an extinction ratio >20 dB cm−1 over a broad range of wavelengths (550–1650 nm in the device reported). It can be used as an effective azimuthal mode filter.
Effects of interrupting the renin‐angiotensin system on sodium excretion in man. (1988)

1. Twelve normal volunteers were studied on 2 separate days, having taken a range of diets providing 50-300 mmol sodium per day for 3 days and having been dehydrated overnight. Each volunteer received a background intravenous infusion of arginine vasopressin (5 x 10(-7) i.u. kg-1 min-1) on both days, and also received 6 mg captopril orally on one day and a placebo tablet on the other. The ensuing changes in arterial pressure, and in urinary solute and solute-free water excretion were recorded. 2. Captopril did not significantly alter arterial pressure. It increased the rate of excretion of sodium but not of potassium, and it did not significantly change urinary osmolality or creatinine clearance. 3. Captopril increased the rate of solute-free water reabsorption and did so in direct proportion to its effect of increasing sodium excretion. 4. A further twelve normal, dehydrated volunteers on free diets were studied on each of 2 days, after taking 500 mg lithium carbonate on the previous evening. On each day, they also received a loading dose and maintenance infusion of inulin. On one day they received 50 mg captopril orally, and, on the other, they received a placebo tablet. The arterial pressure, urinary excretion of electrolytes, and inulin clearance were recorded. 5. Captopril increased the rates of excretion of sodium, lithium and potassium, but there were no significant changes in inulin clearance or arterial pressure. 6. The natriuretic effect of captopril in either group of twelve volunteers was not significantly less in those volunteers who were already excreting more sodium, at least over the range of dietary sodium loading to which the volunteers were subjected. 7. Six normal volunteers were studied on a further 2 days, having taken a diet supplying 30 mmol sodium per day for 3 days and being dehydrated overnight. Each volunteer received a background intravenous infusion of arginine vasopressin (5 x 10(-7) i.u. kg-1 min-1) on both days and also received an intravenous infusion of saralasin acetate (50 ng kg-1 min-1) plus carrier on one day and carrier alone on the other. The ensuing changes in arterial pressure, and in urinary solute and solute-free water excretion were recorded. 8. There was a small but significant fall in systolic arterial pressure during the infusion of saralasin.(ABSTRACT TRUNCATED AT 400 WORDS)
Magnetophoretic Measurements of Interfacial Magnetic Susceptibility of Micro-Organic Droplet (2010)

ナノ·マイクロメートルサイズの微粒子を非侵襲で分析し，個々の微粒子の違いを観測する手法が現在求められている。筆者らの研究グループでは，物理的外場による微小作用力を利用した微粒子の新規な分離分析法の開発を行なってきている。小さい微粒子では，その表面に存在する分子が微粒子全体の物性に大きく寄与する。これは，微粒子のサイズに依存する。ここでは，このサイズ依存性に着目し，外部場として不均一磁場を用いた磁気泳動法により，水相中に分散した2-フルオロトルエン液滴の界面に吸着したDy(III)-カルボン酸錯体の検出法について解説する。
K‐Oxyma: a Strong Acylation‐Promoting, 2‐CTC Resin‐Friendly Coupling Additive (2013)

Abstract Here we present a new formulation of the recently introduced OxymaPure additive for peptide bond formation, in which the N ‐hydroxylamine group is replaced by a potassium salt. The complete suppression of its acidity converts K‐Oxyma into the most suitable coupling choice when peptides are assembled on highly acid‐labile solid‐supports. The coupling efficiency and diminished prospects for epimerization are conserved relative to OxymaPure. In addition, K‐Oxyma displays excellent solubility in a variety of organic solvents and undergoes safer decomposition than classical 1‐hydroxybenzotriazole additives.
Ferroelectric electron emission flat panel display (1996)

Ferroelectric electron emission observed under periodic spontaneous polarization switching is the basis for the development of a new type of flat panel display. Electron emission occurs from individually operated ferroelectric domains. It is shown that ferroelectric displays may be fabricated in ‘‘plane-to-plane’’ geometry which is not possible for field emission displays.
5-aminolevulinate synthase: catalysis of the first step of heme biosynthesis. (2009)

5-Aminolevulinate synthase is a homodimeric pyridoxal 5'-phosphate-dependent enzyme that catalyzes the first step of the heme biosynthetic pathway in animals, fungi, and the alpha-subclass of the photosynthetic purple bacteria. The reaction cycle involves condensation of glycine with succinyl-coenzyme A to yield 5-aminolevulinate, carbon dioxide, and CoA. Mutations in the human erythroid-specific aminolevulinate synthase gene are associated with the erythropoietic disorder X-linked sideroblastic anemia. Recent kinetic and crystallographic data have facilitated an unprecedented understanding of how this important enzyme produces 5-aminolevulinate, and suggest possible directions for future research that may lead to treatments not only for X-linked sideroblastic anemia, but also other diseases.
NEW TRENDS AND RESEARCHES IN PNEUMATICS AT POLITECNICO DI TORINO (1996)

New trends in pneumatics are described, with reference to valves, seals, actuators, controls and application.
SHORT COMMUNICATION - Presence of American Cutaneous LeishmaniasisVectors Surrounding the City of Medellín, Colombia (2002)

The presence of Lutzomyia (Helcocyrtomyia) hartmanni, as a vector of Leishmania colombiensis and L. columbiana (Verrucarum group), recently incriminated in the transmission of leishmaniasis, and L. pia (Verrucarum group) are reported for the first time in a periurban area of Medellín city. There is thus a risk of leishmaniasis transmission in this town.
Polystyrene and PMMA surface modification by electron beam generated plasma in argon and oxygen - effect of increased ion energy on polymer surface characteristics (2009)

The present study investigates the polymer surface changes when the incident ion energy is increased to levels comparable to conventional, low pressure plasma discharges (20 eV). This allows for a study of polar groups incorporation, topography, and surface energy analysis over a range of ion energies not easily achieved in plasmas. The use of inert gas environments (Ar) would permit us to compare the influence of ion energy, while the addition of reactive gases (02) adds a chemical component to the studies.
ChemInform Abstract: Aryl N‐Methyliminodiacetic Acid (MIDA) Boronates from Cyclotrimerization of Ethynyl MIDA Boronate with Diynes. (2013)

ChemInformVolume 45, Issue 2 Organoelement Compounds ChemInform Abstract: Aryl N-Methyliminodiacetic Acid (MIDA) Boronates from Cyclotrimerization of Ethynyl MIDA Boronate with Diynes. Silje Melnes, Silje Melnes Dep. Chem., Norw. Univ. Sci. Technol., N-7491 Trondheim, NorwaySearch for more papers by this authorAnnette Bayer, Annette Bayer Dep. Chem., Norw. Univ. Sci. Technol., N-7491 Trondheim, NorwaySearch for more papers by this authorOdd R. Gautun, Odd R. Gautun Dep. Chem., Norw. Univ. Sci. Technol., N-7491 Trondheim, NorwaySearch for more papers by this author Silje Melnes, Silje Melnes Dep. Chem., Norw. Univ. Sci. Technol., N-7491 Trondheim, NorwaySearch for more papers by this authorAnnette Bayer, Annette Bayer Dep. Chem., Norw. Univ. Sci. Technol., N-7491 Trondheim, NorwaySearch for more papers by this authorOdd R. Gautun, Odd R. Gautun Dep. Chem., Norw. Univ. Sci. Technol., N-7491 Trondheim, NorwaySearch for more papers by this author First published: 19 December 2013 https://doi.org/10.1002/chin.201402178Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume45, Issue2January 14, 2014 RelatedInformation
A study of thunderstorm microphysical properties and lightning flash counts associated with terrestrial gamma‐ray flashes (2015)

Abstract The terrestrial gamma ray flash (TGF) is an emission of highly energetic radiation produced by or at least in close association with lightning. Previous investigations attempted to isolate the production mechanisms and production altitude(s) of TGFs as well as macrophysical characteristics, while thunderstorm microphysical characteristics were largely ignored. This investigation into thunderstorms and their hydrometeor and flash characteristics utilize temporal and spatial coincident satellite passes between the Reuven Ramaty High Energy Solar Spectroscopic Imager and the Tropical Rainfall Measuring Mission to determine the bulk (or footprint) microphysical properties of two types of study events, the thunderstorm complexes which are associated with TGFs (TGF case) and the thunderstorm complexes which did not produce a TGF detected by Reuven Ramaty High Energy Solar Spectroscopic Imager during the pass (non‐TGF case). Results are presented for two different comparison methods. The first case utilizes geographic region weighted by TGF distribution, and the second is based on TGF percentage of occurrence when compared to total flash count of data set. Results show that the associated storms around the TGF location possess differences in the hydrometeor concentrations: cloud liquid water, cloud ice, precipitation water, and precipitation ice. These results take place at different levels of the atmosphere, including the mixed phase region. Additionally, results will show that TGFs are a consistent percentage of observed flashes as the rate of TGFs as a function of Lightning Imaging Sensor flash count is relatively constant.
One-Shot Double Amination of Sondheimer–Wong Diynes: Synthesis of Photoluminescent Dinaphthopentalenes (2015)

Photoluminescent diamino-substituted dinaphthopentalenes were synthesized successfully by the treatment of in situ prepared dinaphthocyclooctadiyne with lithium amide. This reaction involves a series of transformations including the nucleophilic addition of the lithium amide to a triple bond of the cyclooctadiyne moiety, transannulation, protonation of the resulting pentalene anion, and the nucleophilic substitution of the pentalene core with the lithium amide. In this procedure, a novel double amination step plays a key role. When the diamino-substituted dinaphthopentalenes were irradiated with UV light in toluene, fluorescence was observed at around 580 nm (ΦF < 0.03).
Knowledge Is Out There: A New Step in the Evolution of Music Digital Libraries (2016)

Musicological knowledge is spread between the lines of thousands of texts stored in hundreds of music libraries. Technology, and more recently semantic technologies, may play a key role in the way information is retrieved. In this article, an analysis of the evolution of music digital libraries from a technological perspective is presented. Then, a methodology to exploit implicit knowledge present in collections of text documents is proposed. The described methodology is applied over a set of 16,707 artist biographies gathered from Grove Music Online. A knowledge graph is then created after applying a process of information extraction. Several insights are extracted from the data to illustrate the possibilities of the proposed methodology for musicologists. Finally, an extension of the methodology is proposed to combine different data sources, and illustrated with the creation of a flamenco music knowledge base.
End-to-end object detection and recognition in forward-looking sonar images with convolutional neural networks (2016)

Object detection and recognition are typically stages that form part of the perception module of Autonomous Underwater Vehicles, used with different sensors such as Sonar and Optical imaging, but their design is usually separate and they are only combined at test time. In this work we present a convolutional neural network that does both object detection (through detection proposals) and recognition in Forward-Looking Sonar images and is trained with bounding boxes and class labels only. Convolutional layers are shared and a 128-element feature vector is shared between both tasks. After training we obtain 93% correct detections and 75% accuracy, but accuracy can be improved by fine-tuning the classifier sub-network with the generated detection proposals. We evaluated fine-tuning with a SVM classifier trained on the shared feature vector, increasing accuracy to 85%. Our detection proposal method can also detect unlabeled and untrained objects, and has good generalization performance. Our unified method can be used in any kind of sonar image, does not make assumptions about an object's shadow, and learns features directly from data.
AbnormalNMDAreceptor function exacerbates experimental autoimmune encephalomyelitis (2012)

Our data, showing both sensitization of NMDA receptors and their involvement in the progression of the EAE disease, supggest that pharmacological impairment of NMDA receptor signalling would be a component of a neuroprotection strategy in MS.