gebhart/patrepeval huggingface dataset:
Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia (2022)

Low levels of high density lipoprotein-cholesterol (HDL-C) are associated with an elevated risk of arteriosclerotic coronary heart disease. Heritability of HDL-C levels is high. In this research discovery study, we used whole-exome sequencing to identify damaging gene variants that may play significant roles in determining HDL-C levels. We studied 204 individuals with a mean HDL-C level of 27.8 ± 6.4 mg/dl (range: 4-36 mg/dl). Data were analyzed by statistical gene burden testing and by filtering against candidate gene lists. We found 120 occurrences of probably damaging variants (116 heterozygous; four homozygous) among 45 of 104 recognized HDL candidate genes. Those with the highest prevalence of damaging variants were ABCA1 (n = 20), STAB1 (n = 9), OSBPL1A (n = 8), CPS1 (n = 8), CD36 (n = 7), LRP1 (n = 6), ABCA8 (n = 6), GOT2 (n = 5), AMPD3 (n = 5), WWOX (n = 4), and IRS1 (n = 4). Binomial analysis for damaging missense or loss-of-function variants identified the ABCA1 and LDLR genes at genome-wide significance. In conclusion, whole-exome sequencing of individuals with low HDL-C showed the burden of damaging rare variants in the ABCA1 and LDLR genes is particularly high and revealed numerous occurrences in HDL candidate genes, including many genes identified in genome-wide association study reports. Many of these genes are involved in cancer biology, which accords with epidemiologic findings of the association of HDL deficiency with increased risk of cancer, thus presenting a new area of interest in HDL genomics.
Serum amyloid A: high-density lipoproteins interaction and cardiovascular risk (2015)

The acute-phase protein SAA modifies the biological effects of HDL-C in several clinical conditions. The concomitant measurement of SAA is a simple, useful, and clinically applicable surrogate for the vascular functionality of HDL.
Amine Basicity (p<i>K</i><sub>b</sub>) Controls the Analyte Binding Energy on Single Walled Carbon Nanotube Electronic Sensor Arrays (2008)

A wide range of analytes adsorb irreversibly to the surfaces of single walled carbon nanotube electronic networks typically used as sensors or thin-film transistors, although to date, the mechanism is not understood. Using thionyl chloride as a model electron-withdrawing adsorbate, we show that reversible adsorption sites can be created on the nanotube array via noncovalent functionalization with amine-terminated molecules of pKa < 8.8. A nanotube network comprising single, largely unbundled nanotubes, near the electronic percolation threshold is required for the effective conversion to a reversibly binding array. By examining 11 types of amine-containing molecules, we show that analyte adsorption is largely affected by the basicity (pKb) of surface groups. The binding energy of the analyte is apparently reduced by its adsorption on the surface chemical groups instead of directly on the SWNT array itself. This mediated adsorption mechanism is supported by X-ray photoelectron spectroscopy (XPS) and molecular potential calculations. Reversible detection with no active regeneration at the parts-per-trillion level is demonstrated for the first time by creating a higher adsorption site density with a polymer amine, such as polyethyleneimine (PEI). Last, we demonstrate that this transition to reversibility upon surface functionalization is a general phenomenon.
Anytime Algorithm of Database Tuning Advisor for Microsoft SQL Server (2020)

This article provides an overview of the algorithm used by the Database Engine Tuning Advisor (DTA) in Microsoft SQL Server. While many aspects of these algorithms have been described in published papers, in this article we capture the algorithm end-to-end and include a few additional details. One goal of this article is to share with the database community the algorithm and make it easier for researchers intending to compare different approaches to physical design tuning. Note that several patents have been issued to Microsoft that protects its intellectual rights for commercial use of this algorithm.
Analytical interference model for two-dimensional (time-wavelength) asynchronous O-CDMA systems using various receiver structures (2005)

This paper gives a probabilistic model for the interference in optical code-division multiple access (O-CDMA) systems using a conventional and hard-limiting receiver that relates the code parameters to the system performance. It is shown that for a specified number of wavelengths and chip times, the code weight and maximum collision parameter (MCP) of the code can be optimized in order to maximize the numbers of active and/or potential users. Design rules to maximize the number of active users under certain system constraint are also provided. In this study, the spectral efficiency limits in the O-CDMA system using conventional and hard-limiting receivers are studied. It is worth mentioning that the models offered in this paper do not require the knowledge of the specific codes in the code set and provide the full statistics of the interference under the random code assumption.
Reading (2020)

“Reading” is one of the most provocative terms in literary theory, in part because it connotes both an activity and a product: on the one hand, an effort to comprehend a text or object of knowledge, and on the other, a more formal response. Both senses of the term originate in the premise that literary and other cultural texts—including performances, scripted or not—require a more deliberative parsing than weather reports and recipes, or sentences like “rain is expected today” and “add one cup of flour.” At the same time, reading serves as an explanatory trope across various sites of 21st-century culture; in a tennis match, players “read” the strengths and weaknesses of their opponents and strategize accordingly; a cab driver “reads” a GPS when plotting an efficient route to convey a passenger. But an engagement with literary and cultural texts is a different matter. In its former sense as a set of protocols or procedures, reading resides at the center of disciplinary debates as newly formed schools, theories, or methods rise to challenge dominant notions of understanding literature, film, painting, and other forms. Frequently, these debates focus on tensions between binary oppositions (real or presumed): casual versus professional reading (or fast vs. slow), surface reading versus symptomatic reading, close reading versus distant reading, and others. Like the term “reading,” readers are variously described as “informed,” “ideal,” “implied,” and more. In some theoretical formulations, they are anticipated by texts; in others, readers produce or complete them by filling lacunae or conducting other tasks. Complicating matters further, reading also exists in close proximity to several other terms with which it is often associated: interpretation, criticism, and critique. Issues of “textuality” introduce yet another factor in disagreements about the priorities of critical reading, as notions of a relatively autonomous or closed work or object have been supplanted by a focus on both historical context and a work’s “intertextuality,” or its inevitable relationship to, even quotation of, other texts. In the latter sense of a reading as an intellectual or scholarly product, more variables inform definitions. Every reading of a text, as Paul Ricouer describes, “takes place within a community, a tradition, or a living current of thought.” The term “reading” is complicated not only because of the thing studied but also because of both the historically grounded human subject undertaking the activity and the disciplinary expectations shaping and delimiting the interpretations they produce. And, in the 21st century, technologies and practices have emerged to revise these conversations, including machine learning, computational modeling, and digital textuality.
2D TCAD Simulation of High Efficiency n-Type c-Si Solar Cell: Correlation between the Screen-Printing Metallization and the Loss in the Cell Voc (2012)

N-type silicon solar cells are very promising in the short-term since high conversion efficiencies can be reached with a low-cost process. An industrially-compatible process has been developed, providing 19.2% efficiency with a Voc of 634 mV, and an implied Voc of ~670 mV before the screen-printing step. In order to understand the cell performance limitations and determine ways of improvements, two-dimensional TCAD simulations have been developed. It was shown that such physically-based simulations were able to reproduce experimental behaviors, and to address some technological issues. Taking into consideration the metal penetration into the front and back diffused layer, allowed us to simulate precisely the spectral response and the I(V) characteristics of our fabricated samples. This model was used in order to determine different ways of improvements. Simulation results indicated that the formation of deep diffusion profiles (&gt; 1 μm) at the front and at the back side of the solar cells can reduce the drop of the Voc and thus lead to final efficiency around 20%.
Functional Magnetic Resonance Imaging-Assessed Brain Responses during an Executive Task Depend on Interaction of Sleep Homeostasis, Circadian Phase, and PER3 Genotype (2009)

Cognition is regulated across the 24 h sleep-wake cycle by circadian rhythmicity and sleep homeostasis through unknown brain mechanisms. We investigated these mechanisms in a functional magnetic resonance imaging study of executive function using a working memory 3-back task during a normal sleep-wake cycle and during sleep loss. The study population was stratified according to homozygosity for a variable-number (4 or 5) tandem-repeat polymorphism in the coding region of the clock gene PERIOD3. This polymorphism confers vulnerability to sleep loss and circadian misalignment through its effects on sleep homeostasis. In the less-vulnerable genotype, no changes were observed in brain responses during the normal-sleep wake cycle. During sleep loss, these individuals recruited supplemental anterior frontal, temporal and subcortical regions, while executive function was maintained. In contrast, in the vulnerable genotype, activation in a posterior prefrontal area was already reduced when comparing the evening to the morning during a normal sleep-wake cycle. Furthermore, in the morning after a night of sleep loss, widespread reductions in activation in prefrontal, temporal, parietal and occipital areas were observed in this genotype. These differences occurred in the absence of genotype-dependent differences in circadian phase. The data show that dynamic changes in brain responses to an executive task evolve across the sleep-wake and circadian cycles in a regionally specific manner that is determined by a polymorphism which affects sleep homeostasis. The findings support a model of individual differences in executive control, in which the allocation of prefrontal resources is constrained by sleep pressure and circadian phase.
Fusion d'avis d'experts et caractérisation de l'expertise. Application à la détection de transitoires dans les signaux physiologiques (2001)

International audience
ChemInform Abstract: Synthesis of Xenon(VI) Fluoroargentate(III). (1987)

Abstract AgF 2 reacts with an excess of the strong fluorinating agent KrF 2 in the presence of the fluoride‐ion donor XeF 6 in anhydrous HF to yield the light yellow diamagnetic fluoroargentate (IV).
Somatostatin: Central Nervous System Actions on Glucoregulation (1979)

Somatostatin (SRIF) has been tested for its actions on the central nervous system to affect glucoregulation. In doses ineffective when given systemically , SRIF and SRIF analogs given intracisternally (ic) reduce hyperglycemia and hyperglucagonemia after ic bombesin administration. The SRIF analog, des-AA1, 2, 4, 5, 12, 13-[D-Trp8]SRIF, decreases plasma insulin and elevates plasma glucose and glucagon when given systemically. However, when given ic, this peptide prevents the rise in glucose and glucagon after ic bombesin administration and is 10 times more potent than SRIF in reducing bombesin-induced hyperglycemia. Other analogs of SRIF and various unrelated peptides were found to be ineffective in reducing bombesin-induced hyperglycemia. des-AA1, 2, 4, 5, 12, 13-[D-Trp]SRIF prevented the hyperglycemia induced by surgical stress or by ic administration of beta-endorphin or carbacol. des-AA1, 2, 4, 5, 12, 13-[D-Trp]SRIF given ic did not prevent hyperglycemia induced by systemic administration of epinephrine, arginine, or glucagon. These studies suggest that SRIF and its analogs may act within the brain to affect glucoregulation.
Dental trauma after cardiac syncope in a patient with long QT syndrome. (2007)

Dental trauma secondary to a syncopal episode occurs rarely in the pediatric population. Although the majority of these events occurs in patients with a benign medical history, a subset of these cases occur in patients with a genetic predisposition to cardiac arrhythmia. Long QT syndrome, characterized by prolonged cardiac ventricular repolarization, represents one genetic condition in which patients sustain events of seizure, syncope, and sudden cardiac death in response to precipitating physical, mental, or emotional stressors. In this case report, extensive dental injuries occurred after an episode of cardiac syncope in a patient with a dual presentation of long QT syndrome and Pierre Robin sequence. The purpose of this paper was to highlight the potentially malignant course of symptomatic long QT syndrome and emphasize the importance of warning sign recognition and multidisciplinary medical management of pediatric patients with this condition.
Ontology for Scenarios for the Assessment of Automated Vehicles (2020)

The development of assessment methods for the performance of Automated Vehicles (AVs) is essential to enable and speed up the deployment of automated driving technologies, due to the complex operational domain of AVs. As traditional methods for assessing vehicles are not applicable for AVs, other approaches have been proposed. Among these, real-world scenario-based assessment is widely supported by many players in the automotive field. In this approach, test cases are derived from real-world scenarios that are obtained from driving data. 
To minimize any ambiguity regarding these test cases and scenarios, a clear definition of the notion of scenario is required. In this paper, we propose a more concrete definition of scenario, compared to what is known to the authors from the literature. This is achieved by proposing an ontology in which the quantitative building blocks of a scenario are defined. An example illustrates that the presented ontology is applicable for scenario-based assessment of AVs.
The Anticancer Activity for the Bumetanide-Based Analogs via Targeting the Tumor-Associated Membrane-Bound Human Carbonic Anhydrase-IX Enzyme (2020)

The membrane-bound human carbonic anhydrase (hCA) IX is widely recognized as a marker of tumor hypoxia and a prognostic factor within several human cancers. Being undetected in most normal tissues, hCA-IX implies the pharmacotherapeutic advent of reduced off-target adverse effects. We assessed the potential anticancer activity of bumetanide-based analogues to inhibit the hCA-IX enzymatic activity and cell proliferation of two solid cancer cell lines, namely kidney carcinoma (A-498) and bladder squamous cell carcinoma (SCaBER). Bumetanide analogues efficiently inhibit the target hCA-IX in low nanomolar activity (IC<sub>50</sub> = 4.4-23.7 nM) and have an excellent selectivity profile (SI = 14.5-804) relative to the ubiquitous hCA-II isoform. Additionally, molecular docking studies provided insights into the compounds' structure-activity relationship and preferential binding of small-sized as well as selective bulky ligands towards the hCA-IX pocket. In particular, 2,4-dihydro-1,2,4-triazole-3-thione derivative <b>9c</b> displayed pronounced hCA-IX inhibitory activity and impressive antiproliferative activity on oncogenic A-498 kidney carcinoma cells and is being considered as a promising anticancer candidate. Future studies will aim to optimize this compound to fine-tune its anticancer activity as well as explore its potential through in-vivo preclinical studies.
Cotton Breeding in Australia: Meeting the Challenges of the 21st Century (2022)

The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program is the sole breeding effort for cotton in Australia, developing high performing cultivars for the local industry which is worth∼AU$3 billion per annum. The program is supported by Cotton Breeding Australia, a Joint Venture between CSIRO and the program's commercial partner, Cotton Seed Distributors Ltd. (CSD). While the Australian industry is the focus, CSIRO cultivars have global impact in North America, South America, and Europe. The program is unique compared with many other public and commercial breeding programs because it focuses on diverse and integrated research with commercial outcomes. It represents the full research pipeline, supporting extensive long-term fundamental molecular research; native and genetically modified (GM) trait development; germplasm enhancement focused on yield and fiber quality improvements; integration of third-party GM traits; all culminating in the release of new commercial cultivars. This review presents evidence of past breeding successes and outlines current breeding efforts, in the areas of yield and fiber quality improvement, as well as the development of germplasm that is resistant to pests, diseases and abiotic stressors. The success of the program is based on the development of superior germplasm largely through field phenotyping, together with strong commercial partnerships with CSD and Bayer CropScience. These relationships assist in having a shared focus and ensuring commercial impact is maintained, while also providing access to markets, traits, and technology. The historical successes, current foci and future requirements of the CSIRO cotton breeding program have been used to develop a framework designed to augment our breeding system for the future. This will focus on utilizing emerging technologies from the genome to phenome, as well as a panomics approach with data management and integration to develop, test and incorporate new technologies into a breeding program. In addition to streamlining the breeding pipeline for increased genetic gain, this technology will increase the speed of trait and marker identification for use in genome editing, genomic selection and molecular assisted breeding, ultimately producing novel germplasm that will meet the coming challenges of the 21st Century.
Assembly of Bioactive, Heparin-Derivatized Polymer Hydrogels for Protein Delivery (2006)

Polymeric materials that can deliver therapeutic molecules and provide a desired biological response have proven critical in drug delivery and tissue engineering applications. Polysaccharide-derivatized polymers offer unique opportunities for the design of such materials, given the importance of polysaccharides in sequestering bioactive proteins in the extracellular matrix. Accordingly, we have synthesized low molecular weight heparin (LMWH)-modified star poly(ethylene glycol) (PEG-LMWH) that can undergo spontaneous association with heparin binding peptide (HBP)-modified star poly(ethylene glycol) (PEG-HBP) to form assembled hydrogels. Rheological characterization of the noncovalently assembled hydrogels shows that the hydrogels exhibit moderate storage moduli (ca. 200 Pa) that exceed the loss moduli from frequencies from 0.1 to 100 Hz and increase monotonically with increasing molar ratio of the PEG-HBP. The assembled hydrogels are demonstrated to be competent for the sequestration and delivery of bFGF.
ChemInform Abstract: MAGNESIUM IN METHANOL: SUBSTITUTE FOR SODIUM AMALGAM IN DESULFONYLATION REACTIONS (1985)

Abstract Die Desulfonylierung des Bis‐sulfons (V), das aus Vinylidenchlorid (I) in der angegebenen Weise hergestellt wird, kann glatt mit Magnesium in Methanol vorgenommen werden und führt zu einem Gemisch aus (VI) und seiner Dihydro‐Form (VII).
Abnormality of dominant oncogenes and recessive oncogenes in human bone and soft tissue tumors (1989)

Osteosarcoma is a malignant bone tumor which usually occurs in the metaphysis of long bones in adolescents or young adults, but the mechanism of disease occurrence is unknown. To examine alterations in the dominant oncogenes in the osteosarcoma and other bone and soft tissue tumors, DNA extracted from 12 bone tumors, 12 soft part tumors and 2 cells lines was hybridized with c-oncogene (c-myc, c-sis, c-raf-1, c-fos, K-ras2, c-erbB, c-fms, c-fos). DNA extracted from the same samples was examined with Rb cDNA (p0.9R, p3.8R) probes, the retinoblastoma gene (Rb gene) localized at 13q14, to analize whether a recessive mutation is a target in osteosarcoma, and other bone and soft tissue tumors. Amplification of c-myc was observed in 3 cases from 7 osteosarcomas and abnormalities in structure of the Rb gene were found in 4 from 7 osteosarcomas, 2 from 4 MFH, and 1 from 2 Ewing's sarcomas. Both amplification of the c-myc and abnormalities of the Rb gene were observed in 3 osteosarcoma cases. The results indicated that both the Rb gene and c-myc oncogene may be involved in the initiation of osteosarcoma.
AN IMPROVED APPROACH FOR REAL-TIME DETECTION OF SLEEP APNEA (2011)

The traditional diagnosis of sleep apnea and hypopnea syndrome (SAHS) requires an expensive and complex overnight procedure called polysomnography (PSG). Recently, finding valid alternatives for SAHS diagnosis has attracted much research attention. This paper focuses on the real-time monitoring and detection of SAHS based on the arterial oxygen saturation signal measured by pulse oximetry (SpO2). We develop a more comprehensive feature set and a more appropriate annotation criterion, if compared to the existing approaches in the literature. To enjoy competitiveness in computational complexity, we also propose a reduced feature set which provides a higher sensitivity and better adaptivity to distinct databases. The performances of 15 commonly used classifiers with different cost matrixes are assessed on different databases, offering detailed insights on the diagnostic abilities of these methods.
Efficient Ex Vivo Stimulation of<i>Mycobacterium tuberculosis</i>-Specific T Cells by Genetically Detoxified<i>Bordetella pertussis</i>Adenylate Cyclase Antigen Toxoids (2005)

Mycobacterium tuberculosis is a significant threat to global health. Mycobacterium bovis BCG vaccine provides only partial protection, and the skin test reagent used to aid diagnosis of both active and latent tuberculosis, purified protein derivative (PPD), lacks specificity and sensitivity. The use of genetically detoxified Bordetella pertussis adenylate cyclase toxin (CyaA) as a delivery system for two immunodominant proteins of M. tuberculosis that are of greater specificity than PPD, early-secreted antigenic target 6-kDa protein (ESAT-6) and culture filtrate protein 10 (CFP-10), was therefore investigated. CyaA toxoids incorporating these antigens were able to restimulate T cells from more than 91% tuberculosis patients and healthy sensitized donors. Delivery of antigen by CyaA decreased by 10-fold the amount of ESAT-6 and CFP-10 required to restimulate T cells, and in low responders, the overall frequency of gamma interferon-producing cells detected by enzyme-linked immunospot assay was increased (P < 0.01 for both antigens). Delivery of ESAT-6 and CFP-10 by CyaA enabled the detection of both CD4(+) and CD8(+) T cells: these responses could be blocked by inhibition of major histocompatibility complex class II or class I, respectively. Covalent linkage of antigen to the CyaA vector was required for enhancement to occur, as a mixture of mock CyaA toxoid plus recombinant ESAT-6 did not lead to enhancement. In a simplified whole-blood model to detect tuberculosis infection, the frequency of positive responses to CFP-10 was increased by CyaA delivery, a potentially important attribute that could facilitate the identification of latent infection.