gebhart/patrepeval huggingface dataset:
A microarray‐assisted screen for potential Hap1 and Rox1 target genes in Saccharomyces cerevisiae (2002)

Saccharomyces cerevisiae adapts to altered oxygen availability by differentially expressing a number of genes. Under aerobic conditions oxygen control of gene expression is exerted through the activator Hap1 and the repressor Rox1. The Hap1 transcription factor senses cellular heme status and increases expression of aerobic genes in response to oxygen. The repression of hypoxic genes under normoxic conditions results from Hap1-mediated activation of ROX1 transcription. To allow the identification of additional Hap1 and Rox1 target genes, genome-wide expression was analysed in aerobically, chemostat-cultivated hap1 and rox1 null mutants. The microarray results show that deletion of HAP1 causes a lower transcript level of 51 genes. Transcription of 40 genes was increased in rox1 mutant cells compared to wild-type cells. Combining these results with our previously described transcriptome data of aerobically and anaerobically grown cells and with computational analysis of the promoters identified 24 genes that are potentially regulated by Hap1, and 38 genes satisfied the criteria of being direct targets of Rox1. In addition, this work provides further evidence that Rox1 controls transcription of anaerobic genes through repression under normoxic conditions.
Isolation and characterization of a polyol-responsive monoclonal antibody useful for gentle purification of Escherichia coli RNA polymerase (1992)

A modified enzyme-linked immunosorbent assay (ELISA) was used to screen monoclonal antibodies (MAbs) that react with Escherichia coli RNA polymerase for the ability to release the RNA polymerase in the presence of a low molecular weight polyhydroxylated compound (polyol) and a non-chaotropic salt. This assay, termed the ELISA-elution assay, identified 19 presumptive "polyol-responsive" MAbs out of a total of 218 antigen-specific MAbs screened. One of these MAbs, designated NT73, was examined in detail for the ability to release the antigen in response to various combinations of polyol and salt. Using NT73 conjugated to Sepharose, highly active RNA polymerase could be prepared rapidly by a single immunoaffinity chromatography step, replacing two lengthy chromatographic steps in our conventional purification procedure. Because NT73 reacts with the beta' subunit of RNA polymerase, a mixture of the core polymerase and holoenzyme was recovered from the immunoaffinity column. The holoenzyme (E sigma 70) could be separated from the core polymerase by subsequent chromatography on a Mono Q column. This demonstrates that polyol-responsive MAbs can be easily identified and characterized by the ELISA-elution assay. The use of polyol-responsive MAbs provides a means of adapting immunoaffinity chromatography to the purification of labile proteins.
Transient receptor potential family members PKD1L3 and PKD2L1 form a candidate sour taste receptor (2006)

Animals use their gustatory systems to evaluate the nutritious value, toxicity, sodium content, and acidity of food. Although characterization of molecular identities that receive taste chemicals is essential, molecular receptors underlying sour taste sensation remain unclear. Here, we show that two transient receptor potential (TRP) channel members, PKD1L3 and PKD2L1, are coexpressed in a subset of taste receptor cells in specific taste areas. Cells expressing these molecules are distinct from taste cells having receptors for bitter, sweet, or umami tastants. The PKD2L1 proteins are accumulated at the taste pore region, where taste chemicals are detected. PKD1L3 and PKD2L1 proteins can interact with each other, and coexpression of the PKD1L3 and PKD2L1 is necessary for their functional cell surface expression. Finally, PKD1L3 and PKD2L1 are activated by various acids when coexpressed in heterologous cells but not by other classes of tastants. These results suggest that PKD1L3 and PKD2L1 heteromers may function as sour taste receptors.
Unpinning of the Fermi level at erbium silicide/silicon interfaces (1997)

Fermi-level positions at nearly perfect interfaces of epitaxial erbium silicide on silicon are measured by internal photoemission as a function of the thickness and oxygen contamination of the silicide. Thicknesses in excess of 30 silicide monolayers (about 120 \AA{}) and oxygen concentration lower than 0.3% are necessary to obtain the lowest value of 0.28 eV for the barrier height on $n$-type Si. For thinner silicide films or higher oxygen contents, the barrier height increases and shifts the Fermi level downwards across 45% of the Si band gap. Such an unpinning of the Fermi level is believed to be the consequence of the simultaneous occurrence of the high structural perfection of these interfaces, of the low electronegativity of the silicide, and of the low density of metal-induced gap states near the Fermi level.
Binge eating disorder revisited: what’s new, what’s different, what’s next (2019)

Binge eating disorder (BED) is the most common type of eating disorder. According to the most recent data available, the estimated lifetime prevalence of BED among US adults in the general population is 0.85% (men 0.42% and women 1.25%). Among psychiatric treatment populations, prevalence is several-fold higher. Although many people with BED are obese (BMI ≥ 30 kg/m2), roughly half are not. In the DSM-5, BED is defined by recurrent episodes of binge eating (eating in a discrete period of time, an amount of food larger than most people would eat in a similar amount of time under similar circumstances and a sense of lack of control over eating during the episode), occurring on average at least once a week for 3 months, and associated with marked distress. BED often goes unrecognized and thus untreated; in one study, 344 of 22,387 (1.5%) survey respondents met DSM-5 criteria for BED, but only 11 out of the 344 had ever been diagnosed with BED by a health-care provider. Psychiatric comorbidities are very common, with most adults with BED also experiencing anxiety disorders, mood disorders, impulse control disorders, or substance use disorders, suggesting that clinicians have patients in their practice with unrecognized BED. Multiple neurobiological explanations have been suggested for BED, including dysregulation in reward center and impulse control circuitry. Additionally, there is interplay between genetic influences and environmental stressors. Psychological treatments such as cognitive behavioral interventions have been recommended as first line and are supported by meta-analytic reviews; however, access to such treatments may be limited because of local availability and/or cost, and these treatments generally lead to little to no weight loss, although successfully eliminating binge eating can protect against future weight gain. Routine medication treatments for anxiety and depression do not necessarily ameliorate the symptoms of BED, but there are approved and emerging medication options, lisdexamfetamine and dasotraline, respectively, that specifically address the core drivers behind binge eating, namely obsessive thoughts and compulsive behaviors regarding food, resulting in marked decreases in binge eating behaviors as well as weight loss.
Spectroscopic techniques in the study of human tissues and their components. Part II: Raman spectroscopy (2012)

Among the currently used methods of monitoring human tissues and their components many types of research are distinguished. These include spectroscopic techniques. The advantage of these techniques is the small amount of sample required the rapid process of recording the spectra, and most importantly in the case of biological samples - preparation of tissues is not required. In this work vibrational spectroscopy: ATR-FTIR and Raman spectroscopy will be used. Studies are carried out on tissues: tendons, blood vessels, skin, red blood cells and biological components: amino acids, proteins, DNA, plasma, and deposits.
Direct Stereocontrolled Synthesis of Polyoxygenated Hydrobenzofurans and Hydrobenzopyrans from p-Peroxy Quinols (2007)

An acidic-basic tandem catalytic process on p-peroxy quinols with hydroxy alkyl chains at C-4 allowed the one-pot synthesis of hydrobenzofuran and hydrobenzopyran tricyclic epoxides. In this transformation, two new cycles and four new stereogenic centers are created in a highly stereocontrolled manner. The usefulness of the strategy is illustrated with the first total synthesis and structural revision of natural product Cleroindicin D.
Systematic review of factors affecting the ratios of morphine and its major metabolites (1998)

In a systematic review of 57 studies with information on 1232 patients we examined the effect of age, renal impairment, route of administration, and method of analysis on the ratios of morphine-3-glucuronide:morphine (M3G:M) and morphine-6-glucuronide:morphine (M6G:M) and the relative concentrations of M3G and M6G. Across all studies the range of the ratios of metabolites to morphine was wide (0.001-504 for M3G:M, and 0-97 for M6G:M). Neonates produced morphine glucuronides at a lower rate than older children or adults. Metabolite ratios were higher in renal impairment. Routes of administration which avoided first pass metabolism (intravenous, transdermal, rectal, intramuscular, epidural and intrathecal) resulted in lower metabolite production than oral, buccal or sublingual. Metabolite production was similar for single and multiple dosing. There was no evidence of differences between methods of assay. There was a high correlation between the two glucuronide metabolites in spite of the different situations studied, supporting a single glucuronidating enzyme. Morphine was present in CSF at a fourfold higher concentration than the glucuronide metabolites.
Echographic measurement of the optic nerve in patients with intracranial hypertension (1987)

Measurement of the optic nerve diameter by echographic technique has been performed in 40 patients with intracranial hypertension syndromes of various origin. In all the cases examined the diameter was always increased. Postoperative checks revealed a decrease of the nerve thickness until it reached the normal values. The changes in the optic nerve diameter reflect the variations of the intracranial pressure and they appear earlier than any changes in the fundus oculi. This simple and non-invasive echographic technique is very useful in following patients with an intracranial hypertension syndrome.
Introduction (2015)

Ces deux dernières décennies ont vu les données géographiques intervenir de manière de plus en plus fréquente dans nos vies. Le gps en tout premier lieu, application dérivée de la localisation de personnes et de choses à usage militaire, a connu un vaste déploiement commercial. Nous avons délaissé nos vieilles cartes Michelin au profit des petits appareils qui nous guident magiquement jusqu’à notre destination, quoique parfois encore par d’improbables chemins de campagne. Le tourisme, le comm...
Aurora B couples chromosome alignment with anaphase by targeting BubR1, Mad2, and Cenp-E to kinetochores (2003)

The Aurora/Ipl1 family of protein kinases plays multiple roles in mitosis and cytokinesis. Here, we describe ZM447439, a novel selective Aurora kinase inhibitor. Cells treated with ZM447439 progress through interphase, enter mitosis normally, and assemble bipolar spindles. However, chromosome alignment, segregation, and cytokinesis all fail. Despite the presence of maloriented chromosomes, ZM447439-treated cells exit mitosis with normal kinetics, indicating that the spindle checkpoint is compromised. Indeed, ZM447439 prevents mitotic arrest after exposure to paclitaxel. RNA interference experiments suggest that these phenotypes are due to inhibition of Aurora B, not Aurora A or some other kinase. In the absence of Aurora B function, kinetochore localization of the spindle checkpoint components BubR1, Mad2, and Cenp-E is diminished. Furthermore, inhibition of Aurora B kinase activity prevents the rebinding of BubR1 to metaphase kinetochores after a reduction in centromeric tension. Aurora B kinase activity is also required for phosphorylation of BubR1 on entry into mitosis. Finally, we show that BubR1 is not only required for spindle checkpoint function, but is also required for chromosome alignment. Together, these results suggest that by targeting checkpoint proteins to kinetochores, Aurora B couples chromosome alignment with anaphase onset.
Influence of ghrelin on gastric emptying and meal‐related symptoms in idiopathic gastroparesis (2005)

In idiopathic gastroparesis, administration of ghrelin enhances gastric emptying and improves meal-related symptoms. These observations suggest a potential for ghrelin receptor agonists in the treatment of gastroparesis.
Bacillus Infections in Patients With Cancer (1988)

Eighteen febrile patients experienced 24 episodes of Bacillus bacteremias from January 1978 to June 1986. Bacillus species isolated included Bacillus cereus (eight cases), Bacillus circulans (three), Bacillus subtilis (two), Bacillus pumilus (two), Bacillus licheniformis (one), Bacillus sphaericus (one), Bacillus coagulans (one), and six that could not be speciated. Fifteen patients had lymphoma or leukemia and three had breast cancer. Nine patients were neutropenic (polymorphonuclear neutrophil count, less than 1.0 x 10(9)/L), seven patients had a Hickman catheter in place, and 14 had recently received chemotherapy. Twelve of the bacteremic episodes were clinically significant, and four of these 12 involved Hickman catheters. Catheter removal was ultimately necessary in all four patients. Scanning and transmission electron microscopy was performed on one of the removed Hickman catheters and showed Bacillus organisms embedded in a biofilm composed of gram-positive cocci and glycocalyx. Bacillus species were uniformly susceptible to vancomycin, imipenem, and aminoglycosides, with penicillin susceptibilities being variable. Bacillus appears to be another gram-positive organism now being recognized as a bacterial pathogen for compromised hosts. When such infections involve long-term indwelling venous access devices, treatment should include immediate catheter removal as well as antibiotic therapy.
Optimal inner cladding shapes for double-clad fiber lasers (1996)

Summary form only given. Double-clad fiber lasers typically consist of a doped single-mode core carrying and amplifying a laser signal in the 10-W cw range, a large (100-400 /spl mu/m) inner cladding carrying the pump radiation and confining the signal, and an outer cladding confining the pump radiation. Due to the small area ratio the coupling of the pump radiation from the inner cladding to the core is relatively weak. Achieving high laser efficiency depends on optimizing this coupling, which in turn depends on the cross-sectional shape of the inner cladding. We have determined the optimizing condition for this cladding shape.
RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure (2018)

Abstract Antimicrobial-resistant Neisseria gonorrhoeae is an urgent public-health threat, with continued worldwide incidents of infection and rising resistance to antimicrobials. Traditional culture-based methods for antibiotic susceptibility testing are unacceptably slow (1–2 days), resulting in the use of broad-spectrum antibiotics and the further development and spread of resistance. Critically needed is a rapid antibiotic susceptibility test (AST) that can guide treatment at the point-of-care. Rapid phenotypic approaches using quantification of DNA have been demonstrated for fast-growing organisms (e.g. E . coli ) but are challenging for slower-growing pathogens such as N . gonorrhoeae . Here, we investigate the potential of RNA signatures to provide phenotypic responses to antibiotics in N . gonorrhoeae that are faster and greater in magnitude compared with DNA. Using RNA sequencing, we identified antibiotic-responsive transcripts. Significant shifts (&gt;4-fold change) in transcript levels occurred within 5 min of antibiotic exposure. We designed assays for responsive transcripts with the highest abundances and fold changes, and validated gene expression using digital PCR. Using the top two markers ( porB and rpmB ) we correctly determined the antibiotic susceptibility and resistance of 49 clinical isolates after 10 min exposure to ciprofloxacin. RNA signatures are therefore promising as an approach on which to build rapid AST devices for N . gonorrhoeae at the point-of-care, which is critical for disease management, surveillance, and antibiotic stewardship efforts.
SP6 RNA polymerase containing vaccinia virus for rapid expression of cloned genes in tissue culture. (1993)

A hybrid transient expression system, in which tissue culture cells are infected with a recombinant vaccinia virus encoding bacteriophage DNA-dependent RNA polymerase and transfected with a plasmid containing a cloned gene behind the bacteriophage promoter, allows rapid high-level expression in nearly 100% of the cells. In order to extend this system to clones from libraries containing SP6 promoters, a new vaccinia virus was constructed encoding bacteriophage SP6 RNA polymerase.
Direct mode coding for bi-predictive pictures in the JVT standard (2003)

The direct mode can considerably improve coding efficiency of Bi-predictive pictures within the JVT standard since, by exploiting the correlation that may exist between pictures, it can effectively represent block motion without having to transmit any motion information. Until recently the only correlation that was exploited was temporal correlation which, unfortunately, implies that the motion and timestamp information for previous pictures are available in both the encoder and decoder. In this document we introduce an alternative method for calculating the direct mode parameters using spatial correlation. Our method can achieve similar coding efficiency to the temporal method, while at the same time reducing memory requirements and without requiring timestamp information. In addition, improvements on the existing Rate Distortion Optimization related to Bi-predictive pictures within the JVT coded are also presented.
ATR inhibition induces synthetic lethality and overcomes chemoresistance in TP53- or ATM-defective chronic lymphocytic leukemia cells (2015)

TP53 and ataxia telangiectasia mutated (ATM) defects are associated with genomic instability, clonal evolution, and chemoresistance in chronic lymphocytic leukemia (CLL). Currently, therapies capable of providing durable remissions in relapsed/refractory TP53- or ATM-defective CLL are lacking. Ataxia telangiectasia and Rad3-related (ATR) mediates response to replication stress, the absence of which leads to collapse of stalled replication forks into chromatid fragments that require resolution through the ATM/p53 pathway. Here, using AZD6738, a novel ATR kinase inhibitor, we investigated ATR inhibition as a synthetically lethal strategy to target CLL cells with TP53 or ATM defects. Irrespective of TP53 or ATM status, induction of CLL cell proliferation upregulated ATR protein, which then became activated in response to replication stress. In TP53- or ATM-defective CLL cells, inhibition of ATR signaling by AZD6738 led to an accumulation of unrepaired DNA damage, which was carried through into mitosis because of defective cell cycle checkpoints, resulting in cell death by mitotic catastrophe. Consequently, AZD6738 was selectively cytotoxic to both TP53- and ATM-defective CLL cell lines and primary cells. This was confirmed in vivo using primary xenograft models of TP53- or ATM-defective CLL, where treatment with AZD6738 resulted in decreased tumor load and reduction in the proportion of CLL cells with such defects. Moreover, AZD6738 sensitized TP53- or ATM-defective primary CLL cells to chemotherapy and ibrutinib. Our findings suggest that ATR is a promising therapeutic target for TP53- or ATM-defective CLL that warrants clinical investigation.
Ecdysone‐modulated response of Drosophila cytosolic malate dehydrogenase to juvenile hormone (1997)

Recently, we found that the activity of malate dehydrogenase (MDH), one of the key enzymes in the biosynthesis of lipids, is regulated in Drosophila melanogaster by juvenile hormone (JH) and JH analogues. Here we report that the response of MDH to JH, however, depends on the developmental stage of the animal in relation to its endogenous titre of ecdysteroids. During the interecdysial period of the last instar, when endogenous ecdysteroids are low, MDH rapidly responded to JH by increasing activity, while little or no response was monitored in wandering (post-feeding) larvae, i.e., after a pulse of ecdysteroids. Activity of MDH in ecd1 and su(f)ts67g, two ecdysteroid-deficient mutants of Drosophila, increased during a temperature shift to 29°C as compared to wild-type controls, and was sensitive to administration of JH. In contrast, when ecd1 or su(f)ts67g larvae during restrictive conditions were fed on a 20-hydroxyecdysone diet, JH was unable to increase the activity of the MDH enzyme. However, when JH was applied prior to 20-hydroxyecdysone feeding, the activity of MDH was significantly stimulated. Two phases of MDH response to JH, dependent on ecdysteroids, could be observed. The first phase was short and independent of RNA and protein syntheses. But activation of MDH in later stages of the response was inhibited by actinomycin D and cycloheximide, indicating that MDH might be regulated by JH at the transcriptional and/or translational level. Arch. Insect Biochem. Physiol. 35:71–83, 1997. © 1997 Wiley-Liss, Inc.
A reduced common mode hysteresis current regulation strategy for multilevel inverters (2003)

This paper presents a new hysteresis current regulation technique with reduced common mode switching for three-phase multilevel inverters. The proposed technique uses three independent multilevel hysteresis current regulators to generate three sets of complementary gating signals through the comparison of the measured current errors with implemented hysteresis limits. These gating signals are then distributed to each complementary switch pair of the multilevel inverter structure to switch with reduced common mode voltage. Additionally, by intelligently compensating for transition delays during dead-times, common mode voltage can essentially be eliminated completely. Two versions of the common mode regulation technique are derived by using either the line currents or differences between the line currents, known as delta currents, as the control variables. A detailed investigation is presented to determine that the delta currents are the optimal control variables. The performance of the proposed strategy is confirmed through both simulation and experimental investigations.
How to “Root” a Rootkit That Supports Root Processes Using Strider GhostBuster Enterprise Scanner (2005)

Some rootkits that hide resources through user-mode API interception support the notion of “root processes” (or “privileged processes”), which are exempt from being hooked for API interception and so can see all hidden entries. In this paper, we use Hacker Defender (1.00 and older) as an example and describe a simple technique to “root” such a rootkit (i.e., to run our program as a root process of the rootkit) using the Strider GhostBuster quick scanner for the enterprise.