gebhart/patrepeval huggingface dataset:
Use of Recombinant ESAT-6:CFP-10 Fusion Protein for Differentiation of Infections of Cattle by <i>Mycobacterium bovis</i> and by <i>M. avium</i> subsp. <i>avium</i> and <i>M. avium</i> subsp. <i>paratuberculosis</i> (2004)

Immunological diagnosis of Mycobacterium bovis infection of cattle is often confounded by cross-reactive responses resulting from exposure to other mycobacterial species, especially Mycobacterium avium. Early secretory antigenic target 6 (ESAT-6) and culture filtrate protein 10 (CFP-10) are dominant gamma interferon (IFN-gamma)-inducing antigens of tuberculous mycobacteria, and they are absent from many environmental nontuberculous mycobacteria. Because M. avium exposure is the primary confounding factor in the diagnosis of M. bovis-infected animals, in vitro responses to a recombinant ESAT-6:CFP-10 (rESAT-6:CFP-10) fusion protein by blood leukocytes from cattle naturally exposed to M. avium or experimentally challenged with Mycobacterium avium subsp. avium or Mycobacterium avium subsp. paratuberculosis were compared to responses by M. bovis-infected cattle. Responses to heterogeneous mycobacterial antigens (i.e., purified protein derivatives [PPDs] and whole-cell sonicates [WCSs]) were also evaluated. Tumor necrosis factor alpha (TNF-alpha), IFN-gamma, and nitric oxide responses by M. bovis-infected cattle to rESAT-6:CFP-10 exceeded (P < 0.05) the corresponding responses by cattle naturally sensitized to M. avium. Experimental infection with M. bovis, M. avium, or M. avium subsp. paratuberculosis induced significant (P < 0.05) IFN-gamma and nitric oxide production to WCS and PPD antigens, regardless of the mycobacterial species used for the preparation of the antigen. Responses to homologous crude antigens generally exceeded responses to heterologous antigens. Nitric oxide and IFN-gamma responses to rESAT-6:CFP-10 by blood leukocytes from M. bovis-infected calves exceeded (P < 0.05) the corresponding responses of noninfected, M. avium-infected, and M. avium subsp. paratuberculosis-infected calves. Despite the reported potential for secretion of immunogenic ESAT-6 and CFP-10 proteins by M. avium and M. avium subsp. paratuberculosis, it appears that use of the rESAT-6:CFP-10 fusion protein will be useful for the detection of tuberculous cattle in herds with pre-existing sensitization to M. avium and/or M. avium subsp. paratuberculosis.
Visualisation of needle position using ultrasonography (2006)

Anaesthetists and intensivists spend a considerable proportion of their working time inserting needles and catheters into patients. In order to access deeper structures like central veins and nerves, they have traditionally relied on surface markings to guide the needle into the correct position. However, patients may present challenges due to anatomical abnormalities and size. Irrespective of the skill of the operator, there is the ever-present risk of needle misplacement with the potential of damage to structures like arteries, nerve bundles and pleura. Repeated attempts, even if ultimately successful, cause patient suffering and probably increase the risk of infection and other long term complications. Portable and affordable, high-resolution ultrasound scanners, has accelerated the interest in the use of ultrasound guidance for interventional procedures. Ultrasound guidance offers several advantages including a greater likelihood of success, fewer complications and less time spent on the procedure. Even if the target structure is identified correctly there is still the challenge to place the needle or other devices in the optimum site. The smaller and deeper the target, the greater the challenge and potential usefulness of ultrasound guidance. As a result of limited training in the use of ultrasound we believe that many clinicians fail to use it to its full potential. A lack of understanding, with regard to imaging the location of the needle tip remains a major obstacle. Needle visualisation and related topics form the basis for this review.
Pharmacotherapy of Borderline Personality Disorder (1988)

Sixteen female outpatients with borderline personality disorder and prominent behavioral dyscontrol, but without a current episode of major depression, were studied in a double-blind, crossover trial of placebo and the following four active medications: alprazolam (average dose, 4.7 mg/d); carbamazepine (average dose, 820 mg/d); trifluoperazine hydrochloride (average dose, 7.8 mg/d); and tranylcypromine sulfate (average dose, 40 mg/d). Each trial was designed to last six weeks. Tranylcypromine and carbamazepine trials had the highest completion rates. Physicians rated patients as significantly improved relative to placebo while receiving tranylcypromine and carbamazepine. Patients rated themselves as significantly improved relative to placebo only while receiving tranylcypromine. Patients who tolerated a full trial of trifluoperazine showed improvement, those receiving carbamazepine demonstrated a marked decrease in the severity of behavioral dyscontrol, and those receiving alprazolam had an increase in the severity of the episodes of serious dyscontrol. As an adjunct to psychotherapy, pharmacotherapy can produce modest but clinically important improvement in the mood and behavior of patients with borderline personality disorder. As a research tool, patterns of pharmacological response may provide clues to biological mechanisms underlying dysphoria and behavioral dyscontrol.
A novel fluorescent probe for protein binding and folding studies: <i>p</i>‐cyano‐phenylalanine (2006)

Recently, it is has been shown that the C=N stretching vibration of a non-natural amino acid, p-cyano-phenylalanine (PheCN), could be used as an infrared reporter of local environment. Here, we further showed that the fluorescence emission of PheCN is also sensitive to solvent and, therefore, could be used as a novel optical probe for protein binding and folding studies. Moreover, we found that the fluorescence quantum yield of PheCN is nearly five times larger than that of phenylalanine and, more importantly, can be selectively excited even when other aromatic amino acids are present, thus making it a more versatile fluorophore. To test the feasibility of using PheCN as a practical fluorescent probe, we studied the binding of calmodulin (CaM) to a peptide derived from the CaM-binding domain of skeletal muscle myosin light chain kinase (MLCK). The peptide (MLCK3CN) contains a single PheCN residue and has been shown to bind to CaM with high affinity. As expected, addition of CaM into a MLCK3CN solution resulted in quenching of the PheCN fluorescence. A series of stochiometric titrations further allowed us to determine the binding affinity (Kd) of this peptide to CaM. Taken together, these results indicated that the PheCN fluorescence is sensitive to environment and could be applicable to a wide variety of biological problems.
Lectin Histochemistry Shows Fucosylated Glycoconjugates in the Primordial Germ Cells of <i>Xenopus</i> Embryos (2003)

Previous works have shown that glycoconjugates with terminal fucose (Fuc) are located in the primordial germ cells (PGCs) of some mammals and might play a role in the migration and adhesion processes during development. The aim of this work was to identify the terminal Fuc moieties of Xenopus PGCs by means of three Fuc-binding lectins: from asparagus pea (LTA), gorse seed (UEA-I), and orange peel fungus (AAA). The histochemical procedures were also carried out after deglycosylation pretreatments: beta-elimination with NaOH to remove O-linked oligosaccharides; incubation with PNGase F to remove N-linked carbohydrate chains; and incubation with alpha(1,2)- and alpha(1,6)-fucosidase. The PGCs were always negative for LTA and UEA-I, two lectins that have the highest affinity for Fuc alpha(1,2)-linked. However, the PGCs were strongly labeled with AAA, which preferentially binds to Fuc with alpha(1,3) or alpha(1,4) linkages and to Fuc alpha(1,6)-linked to the proximal N-acetylglucosamine. There was fainter labeling with AAA when the sections were preincubated with alpha(1,6)-fucosidase, but the labeling remained strong when the sections were pretreated with alpha(1,2)fucosidase. When the beta-elimination procedure was carried out, the PGC labeling with AAA was slight. If the PNGase F incubation was performed, the PGCs remained moderately positive for AAA. These data suggest that the Xenopus PGCs have Fuc moieties in O- and N-linked oligosaccharides, including Fuc alpha(1,6) linked to the innermost GlcNAc, and that the Fuc was not in alpha(1,2)-linkage.
6‐Substituted Purines as Inhibitors of 15‐Lipoxygenase; a Structure‐Activity Study (2005)

15-lipoxygenase (15-LO) has been implicated in oxidation of low-density lipoproteins (LDL), a process believed to be important for the development of atherosclerosis, as well as other pathogenic conditions. Potent and selective inhibitors of 15-LO may have a drug potential. In this study, purines with a variety of substituents have been examined as inhibitors of 15-lipoxygenase (15-LO) from soybeans. Several 6-substitued purines where the purine ring and a phenyl ring in the substituent were separated by a "spacer" were synthesized and their ability to inhibit the enzyme was explored. Sepa ration of the purine and the phenyl rings with none, one or two sp3-carbons resulted in essentially inactive compounds, trans-styrylpurines and phenylethynylpurines, on the other hand, they exhibited activity close to the well-known 15-LO inhibitor quercetin. High activity was also found when the "spacer" was a trans-cyclopropyl ring. The shape of the spacer was important; a corresponding cis-cyclopropylpurine exhibited much less affinity for the enzyme. Only minor differences in inhibitory activity against 15-LO were found regardless of whether an N-substituent was situated on N-9 or N-7, even when the N-substituent was relatively large. Also, a variety of substituents in the purine 2- and 8-position were well tolerated.
Molecular Crystal Microcapsules: Formation of Sealed Hollow Chambers via Surfactant‐Mediated Growth (2020)

Abstract Hollow organic molecular cocrystals comprised of 9‐methylanthracene‐1,2,4,5‐tetracyanobenzene (9MA‐TCNB) and naphthalene‐1,2,4,5‐tetracyanobenzene (NAPH‐TCNB) were fabricated using a surfactant‐mediated co‐reprecipitation method. The crystals exhibit a narrow size distribution that can be easily tuned by varying the concentration of surfactant and incubation temperature. The rectangular crystals possess symmetrical twinned cavities with an estimated storage volume on the order of 10 −10 L. An aqueous dye solution can be incorporated into the cavities during crystal growth and stored inside for up to several hours, confirming the sealed nature of the hollow chambers. Our results demonstrate that it is possible to harness non‐classical crystal growth to fabricate organic molecular crystals with novel topologies.
Aircraft De-Icing System Using Thermal Conductive Fibers (2015)

The accumulation of ice on the leading edges of aircraft wing poses complications for flight control as drag is increased with a tendency for higher relative turbulence over the wing. Pre-emptive and reactive ice removal techniques have been employed in the past by electromechanical, thermal, chemical and pneumatic methods. In this thesis, a carbon fiber fabric is utilized as a heating de-icer for composites aircraft wing surface structures. Two prototypes are constructed, tested to generate temperature profiles, and an appropriate heating voltage is selected for effective de-icing via distinct avenues of heating system configurations. The heat transfer efficiency of the system is theoretically analyzed and validated through experimental results. The advantages of the carbon-fiber based de-icing system are addressed in terms of weight, flexibility, coverage area, safety and easiness of installation.
Towards ontology-driven interoperability for simulation-based applications (2009)

This paper describes an ontology-driven approach for the design and execution of interoperable simulation applications. The premise of the research described in this paper is that ontologies provide the foundation for determining semantic interoperability and information exchange requirements. Two fundamental problems are inherent to simulation application integration: (i) Semantic Inaccessibility: caused by the failure to explicitly specify the semantic content of the information contained within each simulation subsystem; and (ii) Logical Disconnectedness: caused by the failure to explicitly represent constraints between the information managed by the different simulation subsystems. The paper will (i) describe the technical challenges that motivate our research; (ii) describe how ontologies enable effective simulation application mediation and interoperability; (iii) describe an automation approach for ontology creation from simulation system description data; and (iv) present a real world application example to illustrate the practical benefits of the solution ideas.
An approach to the adaptation of estimated cost parameters in the COSYMA system (1994)

Hardware/software partitioning is one of the key issues in hardware/software co-design. The system COSYMA (cosynthesis of embedded architectures) uses simulated annealing based on estimated costs. Deviations between estimations and real costs seem unavoidable due to synthesis, compiler and communication effects. The paper describes an approach to adapt the estimation. The results show fast convergence of estimated to real costs. >
Elimination of redundant array subscript range checks (1995)

This paper presents a compiler optimization algorithm to reduce the run time overhead of array subscript range checks in programs without compromising safety. The algorithm is based on partial redundancy elimination and it incorporates previously developed algorithms for range check optimization. We implemented the algorithm in our research compiler, Nascent, and conducted experiments on a suite of 10 benchmark programs to obtain four results: (1) the execution overhead of naive range checking is high enough to merit optimization, (2) there are substantial differences between various optimizations, (3) loop-based optimizations that hoist checks out of loops are effective in eliminating about 98% of the range checks, and (4) more sophisticated analysis and optimization algorithms produce very marginal benefits.
Real-time analysis of breath using an atmospheric pressure ionization mass spectrometer (1979)

A new technique is reported resulting in the direct, instantaneous analyses of trace compounds in breath. The analyses were performed using a commercial atmospheric pressure chemical ionization mass spectrometer (TAGA TM2000 APCI mass spectrometer). A known flow of breath sample is introduced into the ionization region of the mass spectrometer. The study includes the measurement and monitoring in real-time, of breath ammonia during a 24 hour and a 48 hour period. The ammonia profiles indicate a personalized daily pattern associated with each subject. This method appears to be of potential value in routine detection and treatment of hyperammonemia patients. Results also show that it is possible to obtain instantaneous analyses of several naturally occurring metabolites and other substances on breath in the ppm to ppt range, suggesting a number of diagnostic research applications.
Clinical presentation of metabolic liver disease (1991)

Some clinical clues should alert paediatricians to the possibility of metabolic liver diseases. They can be classified into three categories: (i) Manifestations due to hepatocellular necrosis, acute or subacute, which can reveal galactosaemia, hereditary fructose intolerance, tyrosinaemia type I, Wilson disease and alpha 1-antitrypsin deficiency. Symptoms and signs suggestive of Reye syndrome should lead to a study of fatty acid oxidation and urea cycle enzymes. All these manifestations may necessitate a rapid diagnosis and treatment when liver dysfunction is severe. (ii) Cholestatic jaundice can reveal alpha 1-antitrypsin deficiency, Byler's disease, cystic fibrosis, Niemann-Pick disease and some disorders of peroxisome biogenesis. (iii) Hepatomegaly can reveal disorders with liver damage but also storage diseases such as glycogen storage diseases, cholesteryl ester storage disease and, when associated with splenomegaly, lysosomal storage diseases. Appropriate investigations for recognizing all these entities are proposed.
Gabor wavelets for 3-D object recognition (2002)

This paper presents a model-based object recognition approach that uses a hierarchical Gabor wavelet representation. The key idea is to use magnitude, phase and frequency measures of Gabor wavelet representation in an innovative flexible matching approach that can provide robust recognition. A Gabor grid a topology-preserving map, efficiently encodes both signal energy and structural information of an object in a sparse multi-resolution representation. The Gabor grid subsamples the Gabor wavelet decomposition of an object model and is deformed to allow the indexed object model match with the image data. Flexible matching between the model and the image minimizes a cost function based on local similarity and geometric distortion of the Gabor grid. Grid erosion and repairing is performed whenever a collapsed grid, due to object occlusion, is detected. The results on infrared imagery are presented. Where objects undergo rotation, translation, scale, occlusion and aspect variations under changing environmental conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Compaction of Single-Chain DNA by Histone-Inspired Nanoparticles (2005)

We elaborated a versatile experimental model of chromatin which consists of a single chain of long duplex DNA that interacts with well-defined cationic nanoparticles of various sizes. We found that the DNA compaction by nanoparticles is stepwise and progressive at the single-chain level. It is controlled by the ability of DNA to wrap nanoparticles, which is more efficient for larger particles and, similar to DNA-histone interaction, is optimal at a physiological salt concentration.
Effects of C-reactive protein on platelet endothelial nitric oxide synthase activity (2007)

Objective To observe the effect of C-reactive protein (CRP) on platelet endothelial nitric oxide synthase (eNOS) activity. Methods Peripheral venous blood was collected, platelets were isolated with gel-filtration chromatography and incubated with histamine, L-NAME and different concentrations of CRP(5, 10, 25, 50, 100μg) for 30 min, then eNOS activity was measured as formation of 3H-L-citrulline from 3H-L-arginine. Results Platelet
The Stilbene Scintillation Crystal as a Spectrometer for Continuous Fast-Neutron Spectra (1960)

A method is described for measuring neutron spectra in the energy range 1 to 10 Mev. The pulse-height spectrum of scintillations produced in a stilbene crystal by recoil protons originating in the crystal is analyzed to yield the incident neutron energy distribution. Insensitivity to gamma rays and electrons is achieved by utilizing differences in the pulse shapes of light pulses produced by electrons and protons. This spectrometer is useful for both group and continuous spectra and has been tested by measurement of the spectra from a Pu-Be neutron source and from the spontaneous fission of Cf252. Both measurements are consistent with previous data. The Pu-Be data definitely confirm a peak at 9.7 Mev that was suggested by previous data.
Surgical resection and reconstruction for advanced and recurrent gynecologic malignancies (2008)

The treatment of gynecologic malignancies entails surgery, systemic therapy and radiation therapy. Depending on the primary disease site and extent of the disease, the treatment strategies are applied alone or in combination. Over the past few decades, specialist knowledge and understanding of the pathophysiology and behavior of gynecologic neoplasms has led to a significant improvement in the relevant treatment modalities. The surgical management of gynecologic malignancies has evolved from the simple hysterectomy to more comprehensive staging procedures that are of pivotal importance for improving and estimating the prognosis and guiding the treatment of affected patients. These sometimes complex procedures encompass radical pelvic and upper abdominal surgery, including the associated urologic and intestinal procedures that are required to adequately resect the neoplasm. In this article, we will review and summarize the literature on the surgical resection and reconstruction of advanced and recurrent gynecologic malignancies with a focus on ovarian, endometrial and cervical cancers.
Heterogeneity-aware Distributed Parameter Servers (2017)

We study distributed machine learning in heterogeneous environments in this work. We first conduct a systematic study of existing systems running distributed stochastic gradient descent; we find that, although these systems work well in homogeneous environments, they can suffer performance degradation, sometimes up to 10x, in heterogeneous environments where stragglers are common because their synchronization protocols cannot fit a heterogeneous setting. Our first contribution is a heterogeneity-aware algorithm that uses a constant learning rate schedule for updates before adding them to the global parameter. This allows us to suppress stragglers' harm on robust convergence. As a further improvement, our second contribution is a more sophisticated learning rate schedule that takes into consideration the delayed information of each update. We theoretically prove the valid convergence of both approaches and implement a prototype system in the production cluster of our industrial partner Tencent Inc. We validate the performance of this prototype using a range of machine-learning workloads. Our prototype is 2-12x faster than other state-of-the-art systems, such as Spark, Petuum, and TensorFlow; and our proposed algorithm takes up to 6x fewer iterations to converge.
Resin-to-Resin Acyl- and Aminoacyl-Transfer Reactions Using Oxime Supports (1999)

We describe a convergent approach to solid-phase synthesis in which two fragments of a molecule are synthesized on independent supports and then condensed in a key resin-to-resin transfer reaction. This approach has been utilized for the synthesis of amides and ureas by transferring acyl groups and aminoacyl groups from p-nitrophenyl(polystyrene)ketoxime resin to amino acid-functionalized Wang resins. Oxime resin-derived esters of peptides undergo transacylation to a solution-phase nucleophilic activator which then transfers the peptide to another resin bearing a nucleophilic amine terminus, resulting in amide bond formation. Likewise, oxime resin-derived carbamates, prepared from phosgenated p-nitrophenyl(polystyrene)ketoxime resin, undergo thermolytic isocyanate liberation in solution, which reacts with a second resin bearing a nucleophilic amino terminus resulting in urea bond formation.
Demographic Trends in Arthroscopic SLAP Repair in the United States (2012)

Our analysis illustrates that surgeons are performing significantly more arthroscopic SLAP repairs each year. The highest incidence of repair is in the 20-29- and 40-49-year age groups, and a significant gender difference exists, with men having a threefold higher incidence of repair.