gebhart/patrepeval huggingface dataset:
Complete Structural Elucidation of Triacylglycerols by Tandem Sector Mass Spectrometry (1998)

We developed a method to elucidate the complete structure of triacylglycerols by means of high-energy collisional activation tandem mass spectrometry (MS/MS). Both ESI- and FAB-produced [M + NH4]+ and [M + met.]+ ions (where met. = Li, Na, and Cs) of triacylglycerols undergo charge-remote and charge-driven fragmentations. We emphasize the study of fragment ions from ESI-produced [M + NH4]+ and [M + Na]+ ions and FAB-produced [M + Na]+ ions. ESI-produced [M + NH4]+ ions fragment to produce four types of ions, [M + NH4 - RnCOONH4]+, [RnCO + 128]+, [RnCO + 74]+, and RnCO+ ions, from which the carbon number and the degree of unsaturation of each acyl group are obtained. In addition, three series of ions are produced by charge-remote fragmentations (CRFs), and analysis of their patterns gives the position and the number of double bonds on the acyl groups. Information about the position of each acyl group on the glycerol backbone, however, is not provided by collisionally activated dissociation of [M + NH4]+ ions. On the other hand, ESI- and FAB-produced [M + Na]+ ions fragment to form eight types of ions (named A-J ions) that, like those produced by CRF, are highly structurally informative. The absence of certain series members also carries useful structural information. Interpretation of these patterns enables one to obtain the number of carbons, degrees of unsaturation, and location of double bonds, as well as the positions of acyl groups on the glycerol backbone.
An efficient array structure to characterize the impact of through silicon vias on FET devices (2011)

We present a test structure to measure the impact of 3D processing, especially through silicon vias, on FET devices. We also show proven techniques for enabling large numbers of devices to be accessed from a limited number of pads. We will show that through silicon via (TSV) proximity and FET channel length impact the device's behavior. We will show behavior can be predicted by symmetry. Through measurement, analsysis, and correlation with mechanical stress models, we demonstrate that our structure can predict how FET devices will behave in 3D stacked products.
A mouse model of Rubinstein-Taybi syndrome: Defective long-term memory is ameliorated by inhibitors of phosphodiesterase 4 (2003)

Mice carrying a truncated form of cAMP-responsive element binding protein (CREB)-binding protein (CBP) show several developmental abnormalities similar to patients with Rubinstein-Taybi syndrome (RTS). RTS patients suffer from mental retardation, whereas long-term memory formation is defective in mutant CBP mice. A critical role for cAMP signaling during CREB-dependent long-term memory formation appears to be evolutionarily conserved. From this observation, we reasoned that drugs that modulate CREB function by enhancing cAMP signaling might yield an effective treatment for the memory defect(s) of CBP+/- mice. To this end, we designed a cell-based drug screen and discovered inhibitors of phosphodiesterase 4 (PDE4) to be particularly effective enhancers of CREB function. We extend previous behavioral observations by showing that CBP+/- mutants have impaired long-term memory but normal learning and short-term memory in an object recognition task. We demonstrate that the prototypical PDE4 inhibitor, rolipram, and a novel one (HT0712) abolish the long-term memory defect of CBP+/- mice. Importantly, the genetic lesion in CBP acts specifically to shift the dose sensitivity for HT0712 to enhance memory formation, which conveys molecular specificity on the drug's mechanism of action. Our results suggest that PDE4 inhibitors may be used to treat the cognitive dysfunction of RTS patients.
Spoken language translation (2008)

In this article we have reviewed state-of-the-art speech translation systems. We have discussed issues of performance as well as deployment, and we reviewed the history and technical underpinnings of this growing and challenging research area. The field provides a plethora of fascinating research challenges for scientists as well as opportunities for true impact in the society of tomorrow.
Critical Role for Env as well as Gag-Pol in Control of a Simian-Human Immunodeficiency Virus 89.6P Challenge by a DNA Prime/Recombinant Modified Vaccinia Virus Ankara Vaccine (2002)

Cellular immune responses against epitopes in conserved Gag and Pol sequences of human immunodeficiency virus type 1 have become popular targets for candidate AIDS vaccines. Recently, we used a simian-human immunodeficiency virus model (SHIV 89.6P) with macaques to demonstrate the control of a pathogenic mucosal challenge by priming with Gag-Pol-Env-expressing DNA and boosting with Gag-Pol-Env-expressing recombinant modified vaccinia virus Ankara (rMVA). Here we tested Gag-Pol DNA priming and Gag-Pol rMVA boosting to evaluate the contribution of anti-Env immune responses to viral control. The Gag-Pol vaccine raised frequencies of Gag-specific T cells similar to those raised by the Gag-Pol-Env vaccine. Following challenge, these rapidly expanded to counter the challenge infection. Despite this, the control of the SHIV 89.6P challenge was delayed and inconsistent in the Gag-Pol-vaccinated group and all of the animals underwent severe and, in most cases, sustained loss of CD4(+) cells. Interestingly, most of the CD4(+) cells that were lost in the Gag-Pol-vaccinated group were uninfected cells. We suggest that the rapid appearance of binding antibody for Env in Gag-Pol-Env-vaccinated animals helped protect uninfected CD4(+) cells from Env-induced apoptosis. Our results highlight the importance of immune responses to Env, as well as to Gag-Pol, in the control of immunodeficiency virus challenges and the protection of CD4(+) cells.
The Use of Large Allografts for Tumor Reconstruction and Salvage of the Failed Total Hip Arthroplasty (1988)

Large bone defects have become a more common orthopedic problem in recent year. This is due to the increased enthusiasm for limb salvage surgery as a technique to manage patients with primary bone tumors and for patients who have had multiple joint arthroplasties with subsequent bone loss. One technique that has proven successful for this difficult problem is the use of fresh frozen allografts to reconstruct these skeletal defects. From January 1981 until January 1987, 60 large fragment fresh frozen allografts were used for skeletal reconstruction. These grafts were divided into three basic groups: intercalary, 15; osteoarticular, 16; and allograft-prosthetic composite, 29. The diagnoses included 43 bone tumors, 16 failed total hip arthroplasties, and one traumatic bone loss. The average patient age was 39.7 years and had an average follow-up period of 24 months. The average length of allograft was 12.4 cm. Using the Enneking Functional Evaluation System, the final functional analysis revealed excellent or good results in 86% of the patients and fair or poor results in 14% of the patients. Roentgenological union at the allograft-host bone junction was achieved in 90% of the patients in a mean time of 5.8 months after surgery. An additional three patients obtained union after autogeneic bone grafting. At the time of follow-up evaluation, 92.3% of the patients were free of tumor; they had no local recurrences. The use of fresh frozen allografts represents an acceptable alternative for the reconstruction of large skeletal defects. One can expect good or excellent function for the majority of patients. The best functional results were obtained with the intercalary allografts and the allograft-prosthetic composites.
Cytokine regulation of endothelial cell function (1992)

Endothelial cells have long been viewed as a passive lining of blood vessels endowed essentially with negative properties such as that of being nonreactive to blood components. It is now evident that upon exposure to environmental signals, cytokines in particular, vascular cells undergo profound changes in gene expression and function that allow these cells to participate actively in inflammatory reactions, immunity, and thrombosis. Different mediators (e.g., interleukin-1 [IL-1] and interferon-gamma) activate relatively distinct sets of functions. These functional programs expressed in activated endothelial cells include the production by the same cells of cytokines (e.g., IL-1, IL-6, chemotactic cytokines, and colony-stimulating factors), which regulate hematopoiesis, the differentiation and proliferation of T and B lymphocytes, and the extravasation of leukocytes. The identification of cytokine circuits through which vascular cells participate to thrombotic, inflammatory, and immune reactions provides novel targets for therapeutic intervention.
Weekly 24-Hour Infusion of High-dose 5-Fluorouracil and Leucovorin in Patients with Advanced Colorectal Cancer: Taiwan Experience (1998)

Between January 1994 and November 1995, 41 patients with metastatic colorectal carcinoma were enrolled in this study. All these patients had recurrent disease after a prior 5-fluorouracil based adjuvant chemotherapy or failed to achieve response by prior chemotherapy that included 5-fluorouracil. 5-Fluorouracil, 2600 mg/m2, was administered concurrently with 100 mg/m2 leucovorin over 24 hours of continuous intravenous infusion. The treatment was repeated every week until progressive disease was documented. Forty-one patients received a total of 810 courses of treatment. The overall response rate was 17.1% (95% confidence interval 5.6-28.6%). In two patients who achieved complete response, the liver was the metastatic site. The median survival was 18.4 months for responders and 12.6 months for non-responders. Gastrointestinal toxicities including diarrhea, stomatitis, nausea and vomiting were the major side-effects. Sixteen incidences (39.0%) of grade 2-3 gastrointestinal toxicities were observed. One patient (2.4%) developed a grade 3 cardiac toxicity, and another one (2.4%) had a grade 2 neurotoxicity. Hematological toxicities were minimal with no evidence of severe (grade 2 or more) leukopenia or thrombocytopenia. We conclude that in patients with pretreated metastatic colorectal cancer, weekly 24-hour infusion of high-dose 5-fluorouracil and leucovorin is associated with higher efficacy and tolerable toxicity. This regimen is a good option as a second-line treatment for those whose diseases are recurrent from or refractory to prior 5-fluorouracil, and deserves a longer period of follow-up.
Wafer-Scale Nanopatterning and Translation into High-Performance Piezoelectric Nanowires (2010)

The development of a facile method for fabricating one-dimensional, precisely positioned nanostructures over large areas offers exciting opportunities in fundamental research and innovative applications. Large-scale nanofabrication methods have been restricted in accessibility due to their complexity and cost. Likewise, bottom-up synthesis of nanowires has been limited in methods to assemble these structures at precisely defined locations. Nanomaterials such as PbZr(x)Ti(1-x)O(3) (PZT) nanowires (NWs)--which may be useful for nonvolatile memory storage (FeRAM), nanoactuation, and nanoscale power generation--are difficult to synthesize without suffering from polycrystallinity or poor stoichiometric control. Here, we report a novel fabrication method which requires only low-resolution photolithography and electrochemical etching to generate ultrasmooth NWs over wafer scales. These nanostructures are subsequently used as patterning templates to generate PZT nanowires with the highest reported piezoelectric performance (d(eff) ∼ 145 pm/V). The combined large-scale nanopatterning with hierarchical assembly of functional nanomaterials could yield breakthroughs in areas ranging from nanodevice arrays to nanodevice powering.
All-epitaxial growth of orientation-patterned gallium phosphide (OPGaP) (2012)

Significant advances have been made in the quality of orientation-patterned gallium phosphide quasi-phasematched structures grown by MBE through the use of improved phosphorus and silicon cells, and preliminary bulk HVPE growth results are promising.
Software Tools for Dynamic and Kinematic Modeling of Human Emotion (1989)

Human body modeling has been undertaken in both the fields of biomechanics and computer graphics. Historically, each approach has lacked some of the advantages of the the other. This project further develops one model used for human task studies and computer animation by improving motion realism and facilitating user interaction with the model. Realism is provided by an interface that links a general purpose mechanism simulator with the JACK graphics environment and a prototype human figure with realistic mass and joint properties based on studies in the biomechanics literature. Improved interaction is achieved through software tools which can position several of the figures joints simultaneously. Also, a tool is developed for calculating the mass and inertia properties of an arbitrary polyhedron based on its geometry and an assumption of constant density. Finally, suggestions are offered for future study.
Use of quantitative polymerase chain reaction to monitor residual disease in chronic myelogenous leukemia during treatment with interferon. (1995)

Interferon-alpha (IFN-alpha) has become a widely used treatment modality in chronic myelogenous leukemia (CML) and was shown to induce complete hematologic responses in about 70% of the patients. In a minority of cases, complete suppression of the Philadelphia (Ph)-positive clone has been observed by cytogenetic investigation or by Southern blot analysis. In most instances, however, analyses by the highly sensitive two-step polymerase chain reaction (PCR) reveal the presence of residual leukemic cells despite continuous treatment. Since PCR positivity has not been associated with an increased risk of disease recurrence, the monitoring of cells carrying the characteristic BCR/ABL rearrangement by qualitative PCR may not facilitate early identification of patients who are likely to relapse. We have therefore employed a quantitative PCR technique to monitor the BCR/ABL mRNA expression levels during the course of treatment in an attempt to assess the response to IFN-alpha at the molecular level and to provide a basis for early detection of progressive disease. Twenty CML patients who received therapy with IFN-alpha in first chronic phase of the disease were enrolled in the study. In addition, we have monitored two CML patients treated with IFN-alpha for relapse after bone marrow transplantation. Thirteen patients who displayed decreasing, constant or fluctuating levels of BCR/ABL expression during an observation period of up to 4 years (mean 25 months) have remained in hematologic remission. Two patients showed an elevation in the marker gene expression upon discontinuation of treatment, but no further increase in BCR/ABL mRNA has been observed after reinitiation of therapy with IFN, and the patients have remained in hematologic remission. In seven patients, quantitative PCR (Q-PCR) analyses revealed increasing expression of the chimeric gene during treatment with IFN-alpha. In all seven cases, the detection of elevated BCR/ABL transcripts by quantitative PCR preceded signs of hematologic or cytogenetic disease progression by up to 8 months (median 6 months). Our data show that quantitative PCR analysis facilitates the monitoring of the response to IFN-alpha therapy and provides an effective diagnostic tool for the timely detection of recurrent disease. The employment of this technique greatly enhances the diagnostic possibilities in the management of chronic myelogenous leukemia.
Weakly Guiding Fibers (1971)

Thin glass fibers imbedded into a glass cladding of slightly lower refractive index represent a promising medium for optical communication. This article presents simple formulas and functions for the fiber parameters as a help for practical design work. It considers the propagation constant, mode delay, the cladding field depth, and the power distribution in the fiber cross section. Plots vs frequency of these parameters are given for 70 modes.
Graph synopses, sketches, and streams (2012)

Massive graphs arise in any application where there is data about both basic entities and the relationships between these entities, e.g., web-pages and hyperlinks; neurons and synapses; papers and citations; IP addresses and network flows; people and their friendships. Graphs have also become the de facto standard for representing many types of highly structured data. However, the sheer size of many of these graphs renders classical algorithms inapplicable when it comes to analyzing such graphs. In addition, these existing algorithms are typically ill-suited to processing distributed or stream data. Various platforms have been developed for processing large data sets. At the same time, there is the need to develop new algorithmic ideas and paradigms. In the case of graph processing, a lot of recent work has focused on understanding the important algorithmic issues. An central aspect of this is the question of how to construct and leverage small-space synopses in graph processing. The goal of this tutorial is to survey recent work on this question and highlight interesting directions for future research.
Direct and allosteric control of glutamate receptors (1994)

Glutamate Receptors and Their Regulators-An Overview (M.G. Palfreyman). The Molecular Pharmacology of Mammalian AMPA and Kainate Receptors (T.A. Verdoorn). Calcium, Magnesium, and Glutamate Receptors (I.J. Reynolds and S. Rajdev). Desensitization and the Short-Term Modulation of AMPA/Kainate Receptors in Vertebrate Neurons (C.F. Zorumski and S.J. Mennerick). Regulation of Glutamate Receptors by Reversible Phosphorylation (J.F. MacDonald, M.C. Bartlett, B.A. Orser, E.J. Fletcher, M.D. Browning, and L.-Y. Wang). Redox Modulation of the NMDA Receptor (E. Aizenman). Design and Pharmacological Evaluation of Highly Selective Glycine Antagonists (B.M. Baron, J.H. Kehne, S.M. Sorensen, B.L. Harrison, F.G. Saliture, and H.S. White). In Vitro and In Vivo Studies with Glycine Partial Agonists: A Novel Strategy for Preventing NMDA Receptor-Medicated Tissue Damage (K.M. Boje). Neuroprotection in NMDA and Non-NMDA Glutamate Antagonists (B.S. Meldrum). Neuroprotective Potential of the Polyamine Site-Directed NMDA Receptor Antagonists Ifenprodil and Eliprodil (B. Scatton, P. Avenet, J. Benavides, C. Carter, D. Duverger, A. Oblin, G. Perrault, D.J. Sanger, and H. Schoemaker). Conantokin-G and Its Analogs: Novel Probes of the NMDA Receptor Associated Polyamine Site (P. Skolnick, L.-M. Zhou, P. Chandler, N.T. Nashed, M. Pennington, and M.-L. Maccecchini).
Selective excitation of the TE/sub 01/ mode in hollow-glass waveguide using a subwavelength grating (2005)

In this work we demonstrate, for the first time to our knowledge, a novel subwavelength optical element for the selective excitation of the TE/sub 01/ mode inside a 300-μm bore diameter hollow-glass waveguide (HGW) in order to reduce the transmission loss. The device consists of form birefringent gratings, where each section is oriented in a different direction so as to convert a linearly polarized input light to a rotating polarized one matching the TE/sub 01/ mode. Using this polarization converting element, we measured a 1.65-dB decrease in the transmission loss in the HGW at a wavelength of 1.55 μm.
The Effect of the JAK Inhibitor CP-690,550 on Peripheral Immune Parameters in Stable Kidney Allograft Patients (2009)

These findings demonstrate the role of JAK3 in the homeostasis and function of select lymphocyte subpopulations. JAK3 inhibition may provide a novel mechanism for the modulation of allogeneic responses in patients after transplantation.
Increased vascular permeability by a specific agonist of protease‐activated receptor‐2 in rat hindpaw (1998)

The present study examined the effect of intraplantar (i.pl.) administration of a selective agonist of protease-activated receptor (PAR)-2, SLIGRL-NH2(PP6-NH2), on vascular permeability in rat hindpaw. PP6-NH2, administered i.pl. at 10-100 nmol per paw, enhanced vascular permeability and caused oedema formation in rat hindpaw. SLIGRL (PP6-OH) and trypsin, by i.pl. administration, also elicited an increase in vascular permeability, although i.pl. administration of the mixture of constituent amino acids of PP6-OH at an equivalent dose did not. The PP6-NH2-induced increase in vascular permeability was abolished by repeated pretreatment with compound 48/80 to deplete bioactive amines in mast cells. These findings suggest that the activation of PAR-2 induces acute inflammation, at least partially, via mast cell degranulation in rat hindpaw.
iPSC-derived β cells model diabetes due to glucokinase deficiency (2013)

Diabetes is a disorder characterized by loss of β cell mass and/or β cell function, leading to deficiency of insulin relative to metabolic need. To determine whether stem cell-derived β cells recapitulate molecular-physiological phenotypes of a diabetic subject, we generated induced pluripotent stem cells (iPSCs) from subjects with maturity-onset diabetes of the young type 2 (MODY2), which is characterized by heterozygous loss of function of the gene encoding glucokinase (GCK). These stem cells differentiated into β cells with efficiency comparable to that of controls and expressed markers of mature β cells, including urocortin-3 and zinc transporter 8, upon transplantation into mice. While insulin secretion in response to arginine or other secretagogues was identical to that in cells from healthy controls, GCK mutant β cells required higher glucose levels to stimulate insulin secretion. Importantly, this glucose-specific phenotype was fully reverted upon gene sequence correction by homologous recombination. Our results demonstrate that iPSC-derived β cells reflect β cell-autonomous phenotypes of MODY2 subjects, providing a platform for mechanistic analysis of specific genotypes on β cell function.
Principles and Practice of Endocrinology and Metabolism. (1991)

This dynamic CD-ROM provides one-click access to the full text and illustrations of Principles and Practice of Endocrinology and Metabolism, Third Edition, plus over 3,400 multiple-choice self-assessment questions and answers--in an interactive format perfect for consultation, study, or review. Coverage includes new chapters on molecular biology, new therapies for pituitary tumors, pancreatic transplantation, appetite regulation, growth factors and cytokines, endocrine effects on lipids, endocrine blood cells, the endocrine adipocyte, adrenal incidentaloma, endocrine disorders of HIV infection, and more. Also included are quick-access references to aid in clinical decisions--a complete endocrine drug formulary, an extraordinary compendium of normal laboratory values, and a detailed listing of dynamic diagnostic testing. The program allows users to select the most helpful mode of review. Study Mode presents questions with immediate feedback through the chapter list. Quiz Mode displays randomized questions based on settings the user chooses. Exam Mode presents a set number of questions in random order and displays results at the end of the exam. Windows Compatible Compatibility: BlackBerry(r) OS 4.1 or Higher / iPhone/iPod Touch 2.0 or Higher /Palm OS 3.5 or higher / Palm Pre Classic / Symbian S60, 3rd edition (Nokia) / Windows Mobile(t) Pocket PC (all versions) / Windows Mobile Smartphone / Windows 98SE/2000/ME/XP/Vista/Tablet PC