gebhart/patrepeval huggingface dataset:
Enhanced flux pinning in MOCVD-YBCO films through Zr additions: systematic feasibility studies (2009)

Systematic effects of Zr additions on the structural and flux pinning properties of YBa2Cu3O7−δ (YBCO) films deposited by metal–organic chemical vapor deposition (MOCVD) have been investigated. Detailed characterization, conducted by coordinated transport, x-ray diffraction, scanning and transmission electron microscopy analyses, and imaging Raman microscopy have revealed trends in the resulting property/performance correlations of these films with respect to varying mole percentages (mol%) of added Zr. For compositions ≤7.5 mol%, Zr additions lead to improved in-field critical current density, as well as extra correlated pinning along the c-axis direction of the YBCO films via the formation of columnar, self-assembled stacks of BaZrO3 nanodots.
All-epitaxial mode- and current-confined GaAs-based vertical-cavity surface-emitting lasers (2005)

Oxide-confined vertical-cavity surface-emitting laser (VCSEL) emerged as a very attractive light source due to its optical mode-confinement, simultaneous current-confinement, and the resulting low threshold.However, oxideconfinement has serious drawbacks due to the reliability issue and the strain problem among others.In this dissertation, a new all-epitaxial VCSEL with allsemiconductor structure and simultaneous mode-and current-confinement is introduced and aims at attacking the oxide-confined VCSEL limitations.The benefits of the new technology include high performance, reliability, uniformity and the capacity for intracavity patterning.VCSEL performance is mainly determined by how effectively photons and carriers are confined.A lithographically defined intracavity phase-shifting mesa is used for mode confinement.Mesa height and placement in the cavity are carefully considered to achieve excellent optical loss control including both the vi diffraction loss and the scattering loss.A specially designed VCSEL incorporating the intracavity phase-shifting mesa successfully demonstrates mode-confinement.Selective interfacial Fermi-level pinning is used for currentconfinement.Regrowth on oxidized AlGaAs off the intracavity mesa results in Fermi-level pinning at the interface and a valance band barrier for holes, providing current blocking.Regrowth on oxidized AlGaAs is challenging.Factors considered for surface protection and controlling regrowth surface roughness are: (a) sacrificial layers, (b) the Al ratio in the AlGaAs to be regrown on, and (c) the regrowth temperature.An all-epitaxial mode-and current-confined GaAs-based VCSEL is fabricated and device performance is discussed.The ability to incorporate the intracavity patterns for perfect gain/mode matching and optical mode engineering in the all-epitaxial mode-and currentconfined VCSEL could greatly improve the lasing threshold and mode control.An all-epitaxial VCSEL incorporating the intracavity circular gratings is presented and the device performance is compared to a single intracavity mesa VCSEL fabricated on the same wafer.vii
Dendritic cell-based immunotherapy of prostate cancer: immune monitoring of a phase II clinical trial. (2000)

We assessed both non- and peptide-specific immune responses in prostate cancer patients before and after immunotherapy with dendritic cells exogenously pulsed with the prostate-specific membrane antigen-derived peptides, PSM-P1 and PSM-P2. For all subjects, we observed that clinical responses were strongly associated with two indicators of immunocompetence: skin test responses to recall antigens and cytokine secretion by T cells after nonspecific stimulation. In a subset of responders, we observed cytokine secretion or cytotoxicity against the immunizing peptides or an immunodominant epitope from an influenza recall antigen. The clinical results support the use of monitoring for overall immunocompetence to help determine why a patient has or has not responded to therapy. Moreover, it could be useful as an inclusion criterion to select those more likely to benefit from treatment.
Effect of inactivity and passive stretch on protein turnover in phasic and postural rat muscles (1986)

A state of hypokinesia and hypodynamia has been induced in the hindlimb muscles of the rat (100 g) using a suspension model. The ensuing muscle atrophy was assessed by reference to muscles in fully mobile control animals, which were either fed ad libitum or fed the same lower food intake of the suspended animals. Over a total of 7 days of suspension the slow-twitch postural soleus muscle underwent a much greater atrophy than the fast-twitch phasic extensor digitorum longus. Changes with respect to the position of the suspended foot, and hence muscle length, necessitate caution in comparing the extent of the atrophy between different muscle types. After 3 days of inactivity the atrophy of the soleus muscle was explained by a 21% decrease in the fractional rate of synthesis (measured in vivo) and a 100% increase in the rate of protein breakdown. The reduction in the synthetic rate was associated with a net loss (23%) of RNA and hence muscle ribosomes. In contrast when this inactive soleus muscle was permanently stretched the RNA content (44%) and protein synthetic rate increased (59%) markedly above control values. Although protein breakdown remained elevated in this stretched muscle, the extent of the atrophy in response to hypokinesia and hypodynamia was greatly reduced.
Purification and characterization of dihydropyrimidine dehydrogenase from pig liver (1989)

Dihydropyrimidine dehydrogenase was isolated from cytosolic pig liver extracts and purified 3100-fold to apparent homogeneity. Purification made use of ammonium sulfate fractionation, precipitation with acetic acid and chromatography on DEAE-cellulose and 2',5'-ADP-Sepharose with 28% recovery of total activity. The native enzyme has a molecular mass of 206 kDa and is apparently composed of two similar, if not identical, subunits. Proteolytic cleavage reveals two fragments with apparent molecular masses of 92 kDa and 12 kDa. The C-terminal 12-kDa fragment seems to be extremely hydrophobic. The enzyme contains tightly associated compounds including four flavin nucleotide molecules and 32 iron atoms/206-kDa molecule. The iron atoms are probably present in iron-sulfur centers. The flavins released from the enzyme were identified as FAD and FMN in equal amounts. An isoelectric point of 4.65 was determined for the dehydrogenase. Apparent kinetic parameters were obtained for the substrates thymine, uracil, 5-aminouracil, 5-fluorouracil and NADPH.
Learning method for hierarchical behavior controller (2003)

Complex behavior is difficult to obtain using an unsupervised leaning method because of the enormous search space required. In this paper, we propose the hierarchical behavior controller which consists of three types of modules: behavior coordinator, behavior controller and feedback controller. We also propose a new learning algorithm for the behavior coordinator and the behavior controller that consists of some sub-coordinators and some sub-controllers, respectively. This algorithm selects a deficient one by evaluating each sub-coordinator or sub-controller using multiple regression analysis based on previously obtained evaluation values. This can reduce the search area and the learning times by avoiding the necessity of trying to tune good sub-coordinators or sub-controllers. The hierarchical behavior controller is applied to the problem of controlling a seven-link brachiation robot, which moves dynamically from branch to branch like gibbon swinging its body.
Amino Acid Deprivation Inhibits TORC1 Through a GTPase-Activating Protein Complex for the Rag Family GTPase Gtr1 (2013)

The Rag family of guanosine triphosphatases (GTPases) regulates eukaryotic cell growth in response to amino acids by activating the target of rapamycin complex 1 (TORC1). In humans, this pathway is often deregulated in cancer. In yeast, amino acids promote binding of GTP (guanosine 5'-triphosphate) to the Rag family GTPase Gtr1, which, in combination with a GDP (guanosine diphosphate)-bound Gtr2, forms the active, TORC1-stimulating GTPase heterodimer. We identified Iml1, which functioned in a complex with Npr2 and Npr3, as a GAP (GTPase-activating protein) for Gtr1. Upon amino acid deprivation, Iml1 transiently interacted with Gtr1 at the vacuolar membrane to stimulate its intrinsic GTPase activity and consequently decrease the activity of TORC1. Our results delineate a potentially conserved mechanism by which the Iml1, Npr2, and Npr3 orthologous proteins in humans may suppress tumor formation.
Linguini: Language Identification for Multilingual Documents (1999)

Abstract:Given the vast and still growing availability of electronic documents from around the world, it is becoming increasingly important for managers of the information systems on which these documents are stored to sort or tag these documents so that their end users can most readily access those documents that are of most interest and use to them, which in our context means in a language they can understand. Linguini is a vector-space-based categorizer tailored for high-precision language identification. This paper determines the functional dependencies of Linguini's performance and demonstrates that it can identify the language of documents as short as 5 to 10 percent of the size of average Web documents with 100 percent accuracy. It also describes how to determine if a document is in two or more languages, without incurring any appreciable extra computational overhead. This approach can be applied equally to subject-categorization systems to distinguish between cases where, when the system recommends two or more categories, the document belongs strongly to all or really to none.Key Words and Phrases: categorizationinformation retrievallanguage identificationvector-space models Additional informationNotes on contributorsJohn M. PragerJohn M. Prager is a Research Staff Member at the IBM Thomas J. Watson Research Center. He is working in the area of information retrieval, with special interests in question answering, categorization, taxonomy formation, and statistical analysis of linguistic data. From 1979 to 1992 Dr. Prager was at the IBM Cambridge Scientific Center where he was a project leader. He worked initially on some of the earliest desktop publishing systems, subsequently concentrating on the development of user interfaces for powerful personal workstations using techniques from artificial intelligence. Dr. Prager is the author of nine patents in the areas of intelligent help systems and information retrieval, and he is a member of the Association for Computing machinery. He received a B.A. in computer science and an M.A. from the University of Cambridge, and a Ph.D. in computer science from the University of Massachusetts, Amherst.
Role of zinc in bone formation and bone resorption (1998)

Zinc is essential for the growth of the human and other animals. Bone growth retardation is a common finding in various conditions associated with zinc deficiency, suggesting a physiological role of zinc in the growth and mineralization of bone tissue. Bone zinc content is decreased by development with aging, skeletal unloading, and postmenopausal conditions. Zinc deficiency may play a pathophysiological role in the deterioration of bone metabolism. Zinc has been demonstrated to have a stimulatory effect on bone formation and mineralization; the metal directly activates aminoacyl-tRNA synthetase in osteoblastic cells, and it stimulates cellular protein synthesis. Moreover, zinc inhibits osteoclastic bone resorption by inhibiting osteoclast-like cell formation from marrow cells. Zinc may act on the process of bone-resorbing factors-induced protein kinase C activation, which is involved in Ca2+ signaling in osteoclastic cells. Zinc plays a role in the preservation of bone mass. AHZ is a zinc compound, in which zinc is chelated to β-alanyl-L-histidine. The stimulatory effect of AHZ on bone formation was more intensive than that of zinc sulfate. It is confirmed that bone-forming effect of AHZ is a greater than that of various bone-regulating hormones and other factors. The oral administration of AHZ has a fine restorative effect on osteopenia with various pathophysiological conditions. Zinc compound may be a new drug in the therapy of osteoporosis. J. Trace Elem. Exp. Med. 11:119–135, 1998. © 1998 Wiley-Liss, Inc.
A fully integrated active inductor with independent voltage tunable inductance and series-loss resistance (2001)

A fully integrated GaAs MESFET active inductor is presented in this paper with independent voltage tunable inductance and series-loss resistance. The measured inductance is tunable from 65 to 110 nH in the frequency range from 100 MHz to 1.0 GHz. The measured loss resistance is independently tunable over a -5.6- to +20.8-/spl Omega/ range corresponding to a 0.26 and 0.65 V change in dc tuning voltages, respectively.
2D Oculomotor Plant Mathematical Model for eye movement simulation (2008)

This paper builds a two dimensional oculomotor plant mathematical model (2DOPMM) that is capable of generating eye movement trace on a two dimensional plane. The key difference between the proposed model and the models presented previously is a design that is geared towards linearity and capability of integration into a real-time human computer interaction system while providing force output for each extraocular muscle with values close to physiological measurements. The model is represented as a twelve order system created by a set of linear mechanical components representing major anatomical properties of extraocular muscles and the eye globe: muscle location, elasticity, viscosity, eye-globe rotational inertia, muscle active state tension, length tension and force velocity relationships. Linearity is a key point ensuring a real-time performance in an online implementation of the model with twelve order representation providing close match to the eye anatomical structure. Practical applications of the proposed model lie in the area of extraocular muscle effort estimation and human computer interaction.
Efficient multi-tone distortion analysis of analog integrated circuits (2002)

This paper introduces a novel approach to analyze distortion behavior in analog integrated circuits using a nonlinear frequency-domain method. This approach circumvents the difficulties and inaccuracies associated with device modeling required for the traditional Volterra series method and can handle circuits operating in more strongly nonlinear regimes. The efficiency of the method renders the analysis of large analog blocks practical. We present examples of multi-tone distortion analyses of industrial amplifiers and continuous time filters. The trend towards higher levels of integration, particularly for wireless applications, renders this method especially useful.
Efficient, generalized indoor WiFi GraphSLAM (2011)

The widespread deployment of wireless networks presents an opportunity for localization and mapping using only signal-strength measurements. The current state of the art is to use Gaussian process latent variable models (GP-LVM). This method works well, but relies on a signature uniqueness assumption which limits its applicability to only signal-rich environments. Moreover, it does not scale computationally to large sets of data, requiring O (N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) operations per iteration. We present a GraphSLAM-like algorithm for signal strength SLAM. Our algorithm shares many of the benefits of Gaussian processes, yet is viable for a broader range of environments since it makes no signature uniqueness assumptions. It is also more tractable to larger map sizes, requiring O (N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) operations per iteration. We compare our algorithm to a laser-SLAM ground truth, showing it produces excellent results in practice.
Inhibition by Pentosan Polysulfate (PPS) of Heparin-Binding Growth Factors Released From Tumor Cells and Blockage by PPS of Tumor Growth in Animals (1992)

PPS could become a novel treatment tool targeting tumor growth factors.
Therapeutic Effects of Sodium Butyrate on Glioma Cells in Vitro and in the Rat C6 Glioma Model (2001)

These data support further consideration of direct interstitial infusion of sodium butyrate in a Phase I clinical study for patients with recurrent glioblastoma multiforme.
Study of Antiretroviral Drug???Resistant HIV-1 Genotypes in Northern Thailand: Role of Mutagenically Separated Polymerase Chain Reaction as a Tool for Monitoring Zidovudine-Resistant HIV-1 in Resource-Limited Settings (2004)

As the number of HIV-1-infected individuals receiving antiretroviral drugs has been rapidly increasing in developing countries, there is an urgent need for drug resistance genotype information of non-B subtype HIV-1 and for the establishment of a practical system of monitoring drug-resistant viruses. This study first sequenced the reverse transcriptase region of HIV-1 in 112 infected individuals who had been treated with zidovudine (AZT)/didanosine or AZT/zalcitabine as dual therapy at a government hospital in northern Thailand and then compared the above sequence method with mutagenically separated polymerase chain reaction (MS-PCR) for detecting M41L and K70R mutations. Concordant rates of detecting M41L and K70R mutations by the 2 methods were 96.9% (93/96) and 92.7% (89/96), respectively. The M41L and K70R MS-PCR could detect 86.4% of AZT-resistant strains with any resistance mutation, which was determined by the sequencing method. Then 292 drug-naive individuals were screened for the presence of drug-resistant HIV-1 by the MS-PCR assay and it was found that 2 individuals (0.7%) carried viruses with either the M41L or K70R mutation. It is feasible to test a large number of samples with MS-PCR, which is sensitive, cheap, and easy to perform and does not require sophisticated equipment. The M41L and K70R MS-PCR is potentially a useful tool to monitor the spread of AZT-resistant HIV-1 in resource-limited countries.
EFFECTS OF SPECIFIC NEUTROPHIL ELASTASE INHIBITOR, SIVELESTAT SODIUM HYDRATE, IN MURINE MODEL OF SEVERE PNEUMOCOCCAL PNEUMONIA (2007)

An excessive amount of neutrophil elastase (NE) released from neutrophils accumulated in the lung can cause tissue damage, despite its importance to host defense against microbial pathogens in severe pneumonia. Therefore, NE inhibitors may reduce tissue damage in lungs with severe pneumonia. In this study, the efficacy of a specific NE inhibitor, sivelestat sodium hydrate (sivelestat), was examined using a murine model of severe pneumonia with Streptococcus pneumoniae. Male mice (CBA/JNCrj, aged 5 weeks) were inoculated intranasally with penicillin-susceptible S. pneumonia (1.0 x 10(5) CFU/mouse). Sivelestat (3 mg/kg) or physiological saline was administered every 12 hours beginning at 12 hours after inoculation. Survival was primarily evaluated. Bronchoalveolar lavage fluid (BALF) and blood were collected at 30 hours after inoculation. Thus, cell counts in BALF and numbers of viable bacteria in blood were determined. Histopathological analysis was also performed. Sivelestat significantly prolonged survival when compared with the control group (P < .05), although all animals died within 4 days. Cell count and histopathological analysis indicated that sivelestat prevented the progression of lung inflammation, such as alveolar neutrophil infiltration and hemorrhage. Furthermore, the number of viable bacteria in blood was significantly lower in the sivelestat group than in the control group (5.69 +/- 0.27 and 6.75 +/- 0.32 log CFU/mL, respectively; mean +/- SEM, P < .01). Sivelestat prolonged survival in this model. A possible explanation for the improved survival is that sivelestat prevents tissue damage by inhibiting NE activity in the lung. Therefore, NE inhibitors may be useful for treating with patients with severe pneumonia.
Activation of the Complement System During and After Cardiopulmonary Bypass Surgery (1997)

Cardiac surgery with CPB causes a biphasic complement activation. The first phase occurs during CPB and results from the interaction of blood with the extracorporeal circuit. The second phase, which occurs during the first 5 days after surgery, involves CRP, is related to baseline CRP levels, and is associated with clinical symptoms such as arrhythmia.
Quantification of Urinary Albumin by Using Protein Cleavage and LC-MS/MS (2009)

Urinary albumin can be quantified by a protein cleavage LC-MS/MS method using a (15)NrHSA internal standard. This method provides improved analytical performance in the clinically relevant range compared to a commercially available immunoturbidometric assay.
Discovery of Tankyrase Inhibiting Flavones with Increased Potency and Isoenzyme Selectivity (2013)

Tankyrases are ADP-ribosyltransferases that play key roles in various cellular pathways, including the regulation of cell proliferation, and thus, they are promising drug targets for the treatment of cancer. Flavones have been shown to inhibit tankyrases and we report here the discovery of more potent and selective flavone derivatives. Commercially available flavones with single substitutions were used for structure-activity relationship studies, and cocrystal structures of the 18 hit compounds were analyzed to explain their potency and selectivity. The most potent inhibitors were also tested in a cell-based assay, which demonstrated that they effectively antagonize Wnt signaling. To assess selectivity, they were further tested against a panel of homologous human ADP-ribosyltransferases. The most effective compound, 22 (MN-64), showed 6 nM potency against tankyrase 1, isoenzyme selectivity, and Wnt signaling inhibition. This work forms a basis for rational development of flavones as tankyrase inhibitors and guides the development of other structurally related inhibitors.
Inhibition of vagally mediated immune-to-brain signaling by vanadyl sulfate speeds recovery from sickness (2005)

To the ill patient with diabetes, the behavioral symptoms of sickness such as fatigue and apathy are debilitating and can prevent recuperation. Here we report that peripherally administered insulin-like growth factor 1 (IGF-1) attenuates LPS-dependent depression of social exploration (sickness) in nondiabetic (db/+) but not in diabetic (db/db) mice. We show that the insulin/IGF-1 mimetic vanadyl sulfate (VS) is effective at augmenting recovery from sickness in both db/+ and db/db mice. Specifically, peak illness was reached at 2 h for both VS and control animals injected with LPS, and VS mice recovered 50% faster than non-VS-treated animals. Examination of the mechanism of VS action in db/+ mice showed that VS paradoxically augmented peritoneal macrophage responsivity to LPS, increasing both peritoneal and ex vivo macrophage production of IL-1beta and IL-6 but not TNF-alpha. The effects of VS in promoting recovery from sickness were not restricted to LPS, because they were also observed after direct administration of IL-1beta. To explore the possibility that VS impairs immune-to-brain communication via vagal afferents, the vagally mediated satiety-inducing effects of cholecystokinin 8 were tested in db/+ mice. Cholecystokinin decreased food intake in saline-injected mice but not in VS-treated mice. VS also inhibited LPS-dependent up-regulation of IL-1beta and IL-6 mRNA in the brain, while increasing by 50% the cerebral expression of transcripts of the specific antagonist of IL-1 receptors IL-1RA and IL-1R2. Taken together, these data indicate that VS improves recovery from LPS-induced sickness by blocking vagally mediated immune-to-brain signaling and by up-regulating brain expression of IL-1beta antagonists.