gebhart/patrepeval huggingface dataset:
A Possible Role for Cathepsins D, E, and B in the Processing of β‐amyloid Precursor Protein in Alzheimer's Disease (1997)

Formation of the 4-kDa peptides, which are essential constituents of the extracellular plaques in Alzheimer's disease, involves the sequential cleavage of the amyloid precursor protein (APP) by beta- and gamma-secretases. The carboxy-terminal 99-amino-acid peptide which is liberated from APP by beta-secretase was used as a potential native substrate of the gamma-secretase(s). With the addition of an initiator Met and a FLAG sequence at the C-terminus (betaAPP100-FLAG), it was expressed in Escherichia coli under the control of the T7 promotor. The preferred site(s) of cleavage in the N-terminal 40-amino-acid beta-amyloid peptide and betaAPP100-FLAG by potential gamma-secretase(s) were rapidly identified using matrix-assisted laser-desorption/ionization time-of-flight mass spectroscopy in addition to peptide mapping followed by protein sequence analysis. Since gamma-secretases seem to be active at acidic pH, three cathepsins (D, E and B) were selected for testing. Studies using different detergents indicated that the cleavage preference of cathepsin D for the betaAPP100-FLAG is highly dependent on the surfactant used to solubilize this substrate. All three cathepsins were found to be capable of catabolizing both beta-amyloid peptides and the betaAPP100-FLAG. As cathepsin D was found to cleave the betaAPP100-FLAG in the vicinity of the C-terminus of the beta-amyloid peptides and cathepsin B has a high carboxypeptidase activity at low pH, the possibility cannot be excluded that cathepsins D and B are involved in the amyloidogenic processing of APP.
Detection of Flaviviruses by Reverse Transcriptase‐Polymerase Chain Reaction with the Universal Primer Set (1997)

Using a universal primer set designed to match the sequence of the NS1 gene of flaviviruses, the virus RNA of dengue (DEN), Japanese encephalitis (JEV), powassan and langat of Flaviviridae were successfully amplified by polymerase chain reaction (PCR) via cDNA; and with different internal primers, the serotypes of the dengue viruses were identified. Of the 78 clinically diagnosed dengue fever patients, 18 patients were positive for DEN 1, 48 patients for DEN 2 and 8 patients concurrently infected with DEN 4. Of the 52 patients admitted with Japanese encephalitis (JE), 45 were determined to be JEV infections. By nested PCR, we completed the identification of flaviviruses within 2 days. The results show that seven primers have a potential value for rapid clinical diagnosis of flavivirus infections.
Understanding Long-Term Cycling Performance of Li1.2Ni0.15Mn0.55Co0.1O2–Graphite Lithium-Ion Cells (2013)

Lithium-ion cells containing lithium– and manganese– rich layered-oxides (LMR-NMC) have gained significant attention in recent years because of their ability to deliver high energy densities. In this article we report on a comprehensive performance and degradation study of cells, containing Li1.2Ni0.15Mn0.55Co0.1O2–based positive electrodes and graphite–based negative electrodes, on extended cycling. In addition to electrochemical measurements on full cells, characterization data on harvested electrodes by techniques that include scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), Raman spectroscopy, and secondary ion mass spectrometry (SIMS) are discussed. Our data show that cell capacity fade mainly results from lithium trapping in the solid electrolyte interphase (SEI) of the negative electrode. In addition, cell impedance rise and voltage fade mainly arise at the positive electrode and result from degradation processes in its oxide and carbon constituents. Processes that include the accumulation of transition metal elements at the negative electrode, and increasing misalignment of electrode capacity windows on extended cycling, also have a deleterious effect on cell performance. Identifying sources of performance degradation has enabled strategies to extend cell life, which include improved cell fabrication protocols, positive electrode coatings, and bifunctional electrolyte additives.
Composable semantics for model-based notations (2002)

We propose a unifying framework for model-based specification notations. Our framework captures the execution semantics that are common among model-based notations, and leaves the distinct elements to be defined by a set of parameters. The basic components of a specification are non-concurrent state-transition machines which are combined by composition operators to form more complex, concurrent specifications. We define the step-semantics of these basic components in terms of an operational semantics template whose parameters specialize both the enabling of transitions and transitions' effects. We also provide the operational semantics of seven composition operators, defining each as the concurrent execution of components, with changes to their shared variables and events to reflect inter-component communication and synchronization; the definitions of these operators use the template parameters to preserve in composition notation-specific behaviour. By separating a notation's step-semantics from its composition and concurrency operators, we simplify the definitions of both. Our framework is sufficient to capture the semantics of basic transition systems, CSP, CCS, basic LOTOS, ESTELLE, a subset of SDL88, and a variety of statecharts notations. We believe that a description of a notation's semantics in our framework can be used as input to a tool that automatically generates formal analysis tools.
Direct, Androgen Receptor-Mediated Regulation of the FKBP5 Gene via a Distal Enhancer Element (2005)

Androgen signaling via the androgen receptor (AR) transcription factor is crucial to normal prostate homeostasis and prostate tumorigenesis. Current models of AR function are predominantly based on studies of prostate-specific antigen regulation in androgen-responsive cell lines. To expand on these in vitro paradigms, we used the mouse prostate to elucidate the mechanisms through which AR regulates another direct target, FKBP5, in vivo. FKBP5 encodes an immunophilin that has been previously implicated in glucocorticoid and progestin signaling pathways and that likely influences prostate physiology in the presence of androgens. In this work, we show that androgens directly regulate FKBP5 via an interaction between the AR and a distal enhancer located 65 kb downstream of the transcription start site in the fifth intron of the FKBP5 gene. We have found that AR selectively recruits cAMP response element-binding protein to this enhancer. These interactions, in turn, result in chromatin remodeling that affects the enhancer proper but not the FKBP5 locus as a whole. Furthermore, in contrast to prostate-specific antigen-regulatory mechanisms, we show that transactivation of the FKBP5 gene does not rely on a single looping complex to mediate communication between the distal enhancer and proximal promoter. Rather, the distal enhancer complex and basal transcription apparatus communicate indirectly with one another, implicating a regulatory mechanism that has not been previously appreciated for AR target genes.
Cloning and Sequence Determination of Six Staphylococcus aureus -Lactamases and Their Expression in Escherichia coli and Staphylococcus aureus (1989)

The plasmid-encoded beta-lactamase genes of six strains of Staphylococcus aureus were cloned and shown to be expressed in Escherichia coli. The cloned genes were re-introduced into S. aureus via a shuttle vector, and expressed beta-lactamase. However, clones containing only the small amount of DNA found necessary for expression of ampicillin resistance in E. coli did not express beta-lactamase in S. aureus. Much larger pieces of DNA from the original plasmid were necessary to obtain expression in S. aureus. Some of the six strains of S. aureus synthesized beta-lactamase constitutively and some released only a small proportion of the enzyme into the medium. Both these characteristics were maintained in the clones so it is concluded that they are features either of the gene itself or of the surrounding DNA. The cloned genes were sequenced and the putative amino acid sequences of the beta-lactamases were compared. There are several differences between the sequences and in particular one change in the N-terminal region, at a position believed to be especially important for export of proteins from the cell, is thought to have a key effect on whether or not the enzyme is found in the medium.
Corticosteroids Are Associated with Repression of Adaptive Immunity Gene Programs in Pediatric Septic Shock (2014)

Administration of corticosteroids in pediatric septic shock is associated with additional repression of genes corresponding to adaptive immunity. These data should be taken into account when considering the benefit to risk ratio of adjunctive corticosteroids for septic shock.
High Resolution “Ultra Performance” Liquid Chromatography Coupled to oa-TOF Mass Spectrometry as a Tool for Differential Metabolic Pathway Profiling in Functional Genomic Studies (2005)

The combination of a new 1.7 mum reversed-phase packing material, and a chromatographic system, operating at ca. 12,000 psi, (so-called ultra performance liquid chromatography, UPLC) has enabled dramatic increases in chromatographic performance to be obtained for complex mixture separation. This increase in performance is manifested in improved peak resolution, together with increased speed and sensitivity. Here, we show that UPLC offers significant advantages over conventional reversed-phase HPLC amounting to a more than doubling of peak capacity, an almost 10-fold increase in speed and a 3- to 5-fold increase in sensitivity compared to that generated with a conventional 3.5 microm stationary phase. The first functional genomic application of UPLC-MS technology is illustrated here with respect to multivariate metabolic profiling of urines from males and females of two groups of phenotypically normal mouse strains (C57BL19J and Alpk:ApfCD) and a "nude mouse" strain. We have also compared this technology to conventional HPLC-MS under similar analytical conditions and show improved phenotypic classification capability of UPLC-MS analysis together with increased ability to probe differential pathway activities between strains as a result of improved analytical sensitivity and resolution.
SOGC clinical practice guidelines. Hirsutism: evaluation and treatment. (2002)

Hirsutism can be slowly but dramatically improved with a three-pronged approach to treatment: mechanical hair removal, suppression of androgen production, and androgen receptor blockade. Lifestyle changes including weight loss and exercise will lower serum androgen levels and improve self-esteem. The patient should be educated regarding associated health problems or long-term medical consequences of hyperandrogenism, including obesity, irregular menses, anovulation, infertility, pregnancy-induced hypertension, diabetes, hyperlipidemia, hypertension, and heart disease.
Detection of group A streptococci in the laboratory or physician's office. Culture vs antibody methods (1986)

Much controversy has existed concerning the clinical significance of small numbers of group A streptococci (eg, one to ten or even 50 colonies) recovered in culture. The relative quantity of streptococci recovered is, in part, technique dependent. This review documents the need for sensitive throat culture technology, addresses technical problems associated with the culture procedure, and, in light of these problems, explores the need for very carefully performed studies on streptococcal antigen detection kits before their implementation as a routine test either in physicians' offices or in microbiology laboratories. (<i>JAMA</i>1986;255:2638-2642)
Mechanism of High Gain in GaAs Photoconductive Detectors under Low Excitation (1984)

Very high photoconductive gain of about 10 4 –10 5 is observed in GaAs photoconductive detectors for low photon flux density of 10 15 –10 17 photons/(cm 2 ·s). This high gain decreases with increasing photon flux density. A model is proposed which includes carrier separation by surface band dending and surface recombination of photogenerated carriers controlled by surface barrier height. This model is shown to quantitatively explain the photon flux density dependence of both high gain and response time.
Functionally graded copper – steel using laser engineered net shaping™ process (2002)

Laser Engineered Net Shaping™ (LENS™) is an emerging Solid Freeform Fabrication (SFF) process capable of producing fully dense metallic parts with complex shapes directly from a computer-aided drawing (CAD) without the need for molding or tooling. The LENS™ process also shows promise in producing components with graded compositions. One potential application is the production of steel – copper die casting materials. Copper is currently being considered for deposition on dies made out of steel to enhance thermal management. However, difficulties can occur at the Fe-Cu interface, such as, solidification cracking, formation of undesirable phases, and differences in coefficient of thermal expansion. The current research goal is to develop LENS™ processing parameters to optimize the deposition of functionally graded steel - Copper alloys. Dilution control experiments were carried out to determine the cracking susceptibility of Steel - Cu alloys of varying compositions. The resulting microstructures were characterized by various microscopy techniques. The influence of composition on the resultant cracking susceptibility and microstructure will be discussed. This information is useful for successful deposition of crack-free copper layers onto steel for die casting applications.
Reveal, a general reverse engineering algorithm for inference of genetic network architectures. (1998)

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.
Identification of a Novel Cat Allergen – Cystatin (2001)

A newly identified allergen, cystatin, has been cloned from cat skin and is a member of the cysteine protease inhibitor family.
Force-Feedback Surgical Teleoperator: Controller Design and Palpation Experiments (2008)

In this paper, we develop and test a 6-degree-of-freedom surgical teleoperator that has four possible modes of operation: (1) direct force feedback, (2) graphical force feedback, (3) direct and graphical force feedback together, and (4) no force feedback. In all cases, visual feedback of the: environment is provided via a head-mounted display. A position-position controller with local dynamic compensators provides the direct force feedback. The graphical force feedback is overlaid on the environment image, and displays a bar whose height and color is related to the environment force estimated using the current applied to the actuators of the patient-side arm. We evaluate the performance of the teleoperator modes in assisting a user to find the location of stiff objects hidden inside a soft material, similar to a calcified artery hidden in heart tissue and a tumor in the prostate. Seven people used the teleoperator t:o perform palpation in these materials. Results showed that direct force feedback mode minimizes palpation task error for the heart model.
Mapping of the Gene Coding for the Major Late Structural Polypeptide on the Frog Virus 3 Genome (1986)

The gene encoding the major capsid polypeptide (MCP 48) of frog virus 3 (FV 3) has been mapped on the viral DNA. Late FV 3 messenger RNA, hybrid-selected by the SalI-F fragment or a subset of these sequences, BamHI-L and -W fragments, directed the synthesis in vitro of a 48 000 mol. wt. (48K) polypeptide. This product was recognized by monospecific antibodies raised against the major capsid polypeptide. The RNA complementary to these DNA sequences was about 1350 nucleotides in size. This transcript, encoding MCP 48, was precisely located; S1 nuclease analysis indicated that its 5' end mapped at 1250 nucleotides to the right and its 3' end at 160 nucleotides to the left of the BamHI site at the junction between the BamHI-W and -L fragments.
Novel Approach to Aminocarboranes by Mild Amidation of Selected Iodo-carboranes (2010)

A mild protocol for the palladium-catalyzed Buchwald-Hartwig amidation of icosahedral carboranes is described. Employing 2-dicyclohexylphosphino-2'-(N,N-dimethylamino)biphenyl (1) as a ligand and K(3)PO(4) as a base, benzamide, trifluoroacetamide, acetamide, and formamide were coupled to a series of mono- and di-iodo carboranes furnishing the respective carborane derivatives in good to excellent yields. Subsequent base-mediated saponification of the trifluoroacetamide derivatives was shown to provide the free aminocarboranes. The structures of N-(1,7-dicarba-closo-dodecaboran-9-yl)benzamide (8a), N-(1,7-dicarba-closo-dodecaboran-9-yl)trifluoroacetamide (8b), N-(1,12-dicarba-closo-dodecaboran-2-yl)benzamide (10a), N-(1,2-dicarba-closo-dodecaboran-9-yl)benzamide (12a), N-(1,2-dicarba-closo-dodecaboran-9-yl)acetamide (12c), N-(1,2-dicarba-closo-dodecaboran-9-yl)formamide (12d), N-(1,2-dicarba-closo-dodecaboran-3-yl)benzamide (13a), N,N'-(1,7-dicarba-closo-dodecaboran-9,10-diyl)dibenzamide (15a), and N,N'-(1,7-dicarba-closo-dodecaboran-9,10-diyl)bis(trifluoroacetamide) (15b) have been established through X-ray single-crystal diffraction studies.
SYSTEMIC ACQUIRED RESISTANCE (2004)

Systemic acquired resistance (SAR) is a mechanism of induced defense that confers long-lasting protection against a broad spectrum of microorganisms. SAR requires the signal molecule salicylic acid (SA) and is associated with accumulation of pathogenesis-related proteins, which are thought to contribute to resistance. Much progress has been made recently in elucidating the mechanism of SAR. Using the model plant Arabidopsis, it was discovered that the isochorismate pathway is the major source of SA during SAR. In response to SA, the positive regulator protein NPR1 moves to the nucleus where it interacts with TGA transcription factors to induce defense gene expression, thus activating SAR. Exciting new data suggest that the mobile signal for SAR might be a lipid molecule. We discuss the molecular and genetic data that have contributed to our understanding of SAR and present a model describing the sequence of events leading from initial infection to the induction of defense genes.
Advanced water soluble BODIPY dyes : synthesis and application (2011)

[...]Nous nous sommes intéressés au développement de nouvelles méthodes permettant de synthétiser des fluorophores hydrosolubles émettant dans le visible ou le proche infrarouge pour des applications en marquage biologique. Dans un premier temps nous avons effectué une étude méthodologique sur les modifications des boradiazaindacènes (BODIPYs) pour les rendre hydrosolubles et ceci tout en gardant leurs propriétés optiques. Dans un deuxième temps, en utilisant ces nouvelles méthodes nous avons développé une série de BODIPYs hydrosolubles émettant dans le rouge pour le marquage biologique. Le projet s est ensuite orienté vers la synthèse de systèmes push-pull à partir d un BODIPY. Les propriétés optiques et électrochimiques des nouveaux chromophores ont été étudiées.[...]
Granulomatous rosacea-like demodicidosis (2007)

Demodicidosis may present as pityriasis folliculitis, papulopustular lesions, rosacea-like eruptions, and granulomatous rosacea-like eruptions. We report a case of demodex granuloma presenting with recurrent granulomatous rosacea-like papules on the face in a middle-aged woman. The diagnosis of demodicidosis was made by finding extrafollicular mites in the perifollicular inflammatory infiltrate. The papules resolved after 3 weeks of systemic and topical metronidazole, and low-dose oral prednisolone therapy. In summary, demodex granuloma may be mistaken for granulomatous rosacea-like papules. Correct diagnosis can be facilitated by finding extrafollicular demodex mites in skin biopsy specimens.
Epstein-Barr Virus BamHI W Repeat Number Limits EBNA2/EBNA-LP Coexpression in Newly Infected B Cells and the Efficiency of B-Cell Transformation: a Rationale for the Multiple W Repeats in Wild-Type Virus Strains (2011)

The genome of Epstein-Barr virus (EBV), a gammaherpesvirus with potent B-cell growth-transforming ability, contains multiple copies of a 3-kb BamHI W repeat sequence; each repeat carries (i) a promoter (Wp) that initiates transformation by driving EBNA-LP and EBNA2 expression and (ii) the W1W2 exons encoding the functionally active repeat domain of EBNA-LP. The W repeat copy number of a virus therefore influences two potential determinants of its transforming ability: the number of available Wp copies and the maximum size of the encoded EBNA-LP. Here, using recombinant EBVs, we show that optimal B-cell transformation requires a minimum of 5 W repeats (5W); the levels of transforming ability fall progressively with viruses carrying 4, 3, and 2 W repeats, as do the levels of Wp-initiated transcripts expressed early postinfection (p.i.), while viruses with 1 copy of the wild-type W repeat (1W) and 0W are completely nontransforming. We therefore suggest that genetic analyses of EBV transforming function should ensure that wild-type and mutant strains have equal numbers (ideally at least 5) of W copies if the analysis is not to be compromised. Attempts to enhance the transforming function of low-W-copy-number viruses, via the activity of helper EBV strains or by gene repair, suggested that the critical defect is not related to EBNA-LP size but to the failure to achieve sufficiently strong coexpression of EBNA-LP and EBNA2 early postinfection. We further show by the results of ex vivo assays that EBV strains in the blood of infected individuals typically have a mean of 5 to 8 W copies, consistent with the view that evolution has selected for viruses with an optimal transforming function.