gebhart/patrepeval huggingface dataset:
Reduced expression of the CXC chemokine hIRH/SDF‐1α mRNA in hepatoma and digestive tract cancer (1997)

We isolated human intercrine reduced in hepatomas (hIRH) as a mRNA whose expression was reduced in differential displays from human hepatocellular carcinoma. hIRH is equivalent to the α-chemokine SDF-1α/PBSF. We have previously demonstrated on Northern blot analysis that although hIRH mRNA expression is common in human normal tissues, it is absent from pre-malignant colonic adenomas and from 27 human malignant cell lines. However, there are no reports on the mRNA status of hIRH in other human cancers. The present study was designed to investigate semi-quantitatively the expression of hIRH/SDF-1α mRNA in hepatocellular carcinoma and digestive tract cancers by reverse transcription-polymerase chain reaction (RT-PCR). The expression of hIRH/SDF-1α in the majority of cancer tissues analyzed was markedly reduced compared with that in adjacent non-cancer tissue. RT-PCR was more sensitive than Northern blots in the detection of hIRH mRNA. The average (mean ± SE) tumor/normal (T/N) ratio determined by RT-PCR was 0.40 ± 0.07 in 10 pairs of hepatoma, 0.38 ± 0.09 in 14 pairs of colon cancers, 0.43 ± 0.07 in 10 pairs of esophageal cancers and 0.70 ± 0.09 in 26 pairs of gastric cancers. As a control, the mean G3PDH T/N ratio was 1.16 ± 0.06. The distribution of T/N ratios was significantly different between gastric cancer and the other cancers, but there was no correlation between hIRH/SDF-1α expression and clinico-pathological characteristics in gastric cancer. Our findings demonstrate that hIRH/SDF-1α expression is reduced in the majority of gastrointestinal tumors. Int. J. Cancer 73:656–662, 1997. © 1997 Wiley-Liss, Inc.
An architechture for intelligent assistance in the forecasting process (2002)

The need to effectively integrate decision-making tasks together with knowledge representation and inference procedures has caused recent research efforts towards the integration of decision support systems with knowledge-based techniques. We explore the potential benefits of such an integration in the area of statistical forecasting. In an attempt to clarify the elements of the forecasting process which could be enhanced by intelligent assistance, a generic forecasting process is described and its main functional elements are identified. The paper describes the architecture of such a system (Intelligent Forecasting Information System, IFIS), in which, besides the traditional components of a decision support system, four constituents are included that try to model the expertise required: a process expert, a learning expert, a data expert and a model expert.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intrinsic-Stabilization Uni-Directional Quantum Key Distribution Between Beijing and Tianjin (2004)

Quantum key distribution provides unconditional security for communication. Unfortunately, current experiment schemes are not suitable for long-distance fiber transmission because of instability or backscattering. We present a uni-directional intrinsic-stabilization scheme that is based on Michelson-Faraday interferometers, in which reflectors are replaced with 90 degree Faraday mirrors. With the scheme, key exchange from Beijing to Tianjin over 125 kilometers with an average error rate is below 6% has been achieved and its limited distance exceeds 150 kilometers. Experimental result shows the system is insensitive to environment and can run over day and night without any break even in the noise workshop.
Reduced-intensity preparative regimen and allogeneic stem cell transplantation for advanced solid tumors (2003)

In this prospective multicenter program, we investigated allogeneic stem cell transplantation (ASCT) from HLA-identical siblings following reduced-intensity conditioning (RIC) regimen for patients with refractory metastatic solid tumors (STs). Fifty-seven patients, of whom 39 had a progressive disease (PD) at time of ASCT, received an RIC ASCT combining fludarabine, antithymocyte globulin (ATG), and busulfan. Patients were analyzed in terms of engraftment, transplant-related mortality (TRM), disease response, and outcome. In this setting, RIC was associated with rapid engraftment and low overall TRM (9% [95% confidence interval (CI), 1%-16%]). The cumulative incidence of objective responses (ORs) reached 14% (95% CI, 6%-30%) with this being significantly higher in patients without PD (44% [95% CI, 21%-67%] versus 0; P <.0001) at time of ASCT. Achievement of OR translated into a significantly better overall survival (OS). In multivariate analysis, OS was significantly influenced by disease status at time of ASCT (odds ratio, 4.88; P <.001) and chronic graft-versus-host disease (GVHD) occurrence (odds ratio, 2.86; P <.01). Overall, these results showed that OR can occur after RIC ASCT for resistant ST with a relatively low TRM and potential benefit especially in patients with slowly progressive disease. Further studies are warranted in patients with less advanced ST.
A Synthesis of (+)-Saxitoxin (2006)

An asymmetric synthesis of the bis-guanidinium poison, (+)-saxitoxin (STX), is described. Commencing from an N,O-acetal starting material made readily available through sulfamate ester C-H amination, the completed route to STX showcases the utility of oxathiazinane dioxide heterocycles for the assembly of polyfunctionalized amine derivatives. In the final preparative stages, an unusual nine-membered ring guanidine intermediate is oxidized selectively and made to undergo dehydrative cyclization to afford the tricyclic core of the natural product. Access to STX and related structures will provide unique pharmacological tools for the study of voltage-regulated Na+ ion channel proteins.
Enzymes, Energy, and the Environment: A Strategic Perspective on the U.S. Department of Energy's Research and Development Activities for Bioethanol (1999)

For well over one hundred years, researchers around the world have pursued ways to make ethanol from biomass such as wood, grasses, and waste materials. To distinguish it from ethanol made from starch and sugars in traditional agricultural crops, we refer to ethanol made from biomass as "bioethanol." The effort to develop bioethanol technology gained significant momentum in the late 1970s as a result of the energy crises that occurred in that decade. This article briefly reviews the broader history of bioethanol technology development. With this as a background, we focus our attention on the strategic thinking behind the U.S. Department of Energy's Bioethanol Program, which envisions remarkable advances in cellulase enzyme research and as the basis for significant future process cost reductions.
<title>High-level fault modeling in surface-micromachined MEMS</title> (2000)

MEMS structures rendered defective by particles are modeled a tthe scehamtic-level using existing models of fault-free MEMS primitives within the nodal simulator NODAS. We have compared the results of schematic-level fault simulations with low-level finite element analysis and demonstrated the efficacy of such an approach. Analysis shows that NODAS achieves a 60X speedup over FEA with little accuracy loss in modeling defects caused by particles.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Minimum classification error rate methods for speech recognition (1997)

A critical component in the pattern matching approach to speech recognition is the training algorithm, which aims at producing typical (reference) patterns or models for accurate pattern comparison. In this paper, we discuss the issue of speech recognizer training from a broad perspective with root in the classical Bayes decision theory. We differentiate the method of classifier design by way of distribution estimation and the discriminative method of minimizing classification error rate based on the fact that in many realistic applications, such as speech recognition, the real signal distribution form is rarely known precisely. We argue that traditional methods relying on distribution estimation are suboptimal when the assumed distribution form is not the true one, and that "optimality" in distribution estimation does not automatically translate into "optimality" in classifier design. We compare the two different methods in the context of hidden Markov modeling for speech recognition. We show the superiority of the minimum classification error (MCE) method over the distribution estimation method by providing the results of several key speech recognition experiments. In general, the MCE method provides a significant reduction of recognition error rate.
Light absorption of (oxy-)hemoglobin assessed by spectroscopic optical coherence tomography (2003)

The combination of optical coherence tomography and spectroscopy may allow for highly localized, quantitative measurements of tissue spectral properties. We present, for the first time to our knowledge, quantitative measurements of the absorption coefficients of phantoms and of hemoglobin and oxygenated hemoglobin with spectroscopic optical coherence tomography (SOCT). Our results suggest that SOCT will be able to provide localized, quantitative oxygenation measurements.
CB1 Cannabinoid Receptor Ligands (2005)

The CB1 receptor is expressed in the central nervous system and numerous other tissues including heart, lung and uterus and has been recognized as an important therapeutic target for pain, appetite modulation, glaucoma, multiple sclerosis and other indications. An interesting feature of this GPCR is its ability to be activated by a number of structurally different classes of compounds, thus, raising the possibility of multiple activated forms of the receptor. Understanding of the structure-activity relationships of cannabinergic ligands has paved the road for the development of novel ligands exhibiting receptor subtype selectivity and efficacy. This review highlights the important CB1 cannabinergic ligands developed to date.
PD-L1: PD-1 Interaction Contributes to the Functional Suppression of T-Cell Responses to Human Uveal Melanoma Cells In Vitro (2008)

Expression of PD-L1 by uveal melanoma cells regulates T-cell function by suppressing IL-2 production. The results imply that the presence of IFN-gamma in the tumor local microenvironment promotes upregulation of PD-L1 expression by uveal melanoma, which may, in part, promote immune escape by impairing T-cell function. The selective blockade of PD-L1 is a potential strategy in T-cell-based immunotherapy for uveal melanoma.
Pharmacodynamics of mutant-IDH1 inhibitors in glioma patients probed by in vivo 3D MRS imaging of 2-hydroxyglutarate (2018)

Inhibitors of the mutant isocitrate dehydrogenase 1 (IDH1) entered recently in clinical trials for glioma treatment. Mutant IDH1 produces high levels of 2-hydroxyglurate (2HG), thought to initiate oncogenesis through epigenetic modifications of gene expression. In this study, we show the initial evidence of the pharmacodynamics of a new mutant IDH1 inhibitor in glioma patients, using non-invasive 3D MR spectroscopic imaging of 2HG. Our results from a Phase 1 clinical trial indicate a rapid decrease of 2HG levels by 70% (CI 13%, P = 0.019) after 1 week of treatment. Importantly, inhibition of mutant IDH1 may lead to the reprogramming of tumor metabolism, suggested by simultaneous changes in glutathione, glutamine, glutamate, and lactate. An inverse correlation between metabolic changes and diffusion MRI indicates an effect on the tumor-cell density. We demonstrate a feasible radiopharmacodynamics approach to support the rapid clinical translation of rationally designed drugs targeting IDH1/2 mutations for personalized and precision medicine of glioma patients.
Calculation and Analysis of Stator End-Winding Leakage Inductance of an Induction Machine (2009)

This paper proposes an improved method for calculating the value of and for analyzing the frequency-dependence of the stator end-winding leakage inductance of an induction machine. The method was based on the stored magnetic energy, which was calculated by a 3-D time-harmonic finite element analysis. In this method, there were no rotary parts in the model of the simulated machine. The results of the analysis show that the stator end-winding is capable of influencing the end of the active region of the machine whereas the influence on the central part of the active region is small. In addition, the phenomenon that the stator end-winding leakage inductance, as well as the magnetic energy in the machine, relates to the frequency of the stator current is explored.
<title>Joint source and channel coding for image transmission over lossy packet networks</title> (1996)

We describe a joint source/channel allocation scheme for transmitting images lossily over block erasure channels such as the Internet. The goal is to reduce image transmission latency. Our subband-level and bitplane-level optimization procedures give rise to an embedded channel coding strategy. Source and channel coding bits are allocated in order to minimize an expected distortion measure. More perceptually important low frequency channels of images are shielded heavily using channel codes; higher frequencies are shielded lightly. The result is a more efficient use of channel codes that can reduce channel coding overhead. This reduction is most pronounced on bursty channels for which the uniform application of channel codes is expensive. We derive optimal source/channel coding tradeoffs for our block erasure channel.
Stem cells of the adult lung: their development and role in homeostasis, regeneration, and disease (2012)

The lung has vital functions in gas exchange and immune defense. To fulfill these functions the cellular composition and complex three-dimensional organization of the organ must be maintained for a lifetime. Cell turnover in the adult lung is normally low. However, in response to cellular injury by agents such as infection, toxic compounds, and irradiation there is rapid proliferation and differentiation of endogenous stem and progenitor cells to repair and regenerate the damaged tissue. In the mouse, different populations of epithelial progenitor cells have been identified in different regions of the respiratory system: basal cells in the proximal tracheobronchial region and submucosal glands, and secretory cells in the conducting airways and bronchioalveolar duct junction. The identification of the long-term stem cells in the alveolar region is still under debate, and little is known about resident stem and progenitor cells for the many mesodermal populations. Within this framework information is provided about the origin of lung progenitor cells during development, the microenvironment in which they reside, the experimental injury and repair systems used to promote their regenerative response, and some of the mechanisms regulating their behavior. WIREs Dev Biol 2013, 2:131-148. doi: 10.1002/wdev.58 For further resources related to this article, please visit the WIREs website.
Promoter Structure and Activity of Type 1 Rice Metallothionein-like Gene (1998)

A novel stress-inducible metallothionein-like gene from rice, designated as rgMT-1 (rice genomic metallothionein-like gene-1), was isolated and sequenced. From the sequence analysis of its 5'-flanking region, two putative TATA boxes, one CAAT box, and several short sequences homologous to regulatory cis-elements previously reported were identified. Two direct repeats, one 10 bp in length (CAAAATCAAA) and the other 11 bp (GTGAAAATACT), respectively, were also found. By transient GUS (beta-glucuronidase) assay, the expression of GUS, in vitro, was enhanced by the presence of the rgMT-1 intron. The critical region which controls the basal transcription was shown to lie between -73 and -36 upstream of rgMT-1, in which one of the two putative TATA boxes was located. The promoter activity was lost completely when both putative TATA boxes were deleted. This is the first report describing the genomic structure and regulation of a monocotyledonous metallothionein-like gene critical to the response of stress.
Normal Human Tear pH by Direct Measurement (1981)

• Tear pH was measured in 44 normal subjects by immersing the tip of a microcombination glass pH probe in the tear fluid in the inferior cul-de-sac. The normal pH range was 6.5 to 7.6; the mean value was 7.0. This method provides a rapid and accurate measure of tear pH and may better our understanding of tear physiology and tear buffering capacity.
Genetic manipulation of Kluyveromyces lactis linear DNA plasmids: gene targeting and plasmid shuffles (1999)

Genetic manipulation of yeast linear DNA plasmids, particularly of k1 and k2 from the non-conventional dairy yeast Kluyveromyces lactis, has been advanced by the recent establishment of DNA transformation-mediated one-step gene disruption and allele replacement techniques. These methods provide the basis for a strategy for the functional analysis of plasmid genes and DNA elements. By use of double selection regimens, these single-gene procedures have been extended to effect disruption of individual genes on plasmid k2 and transplacement of a functional copy onto plasmid k1, resulting in the production of yeast strains with an altered plasmid composition. This cytoplasmic gene shuffle system facilitates the introduction of specifically modified alleles into k1 or k2 in order to study the function, expression (from UCS promoters) and regulation of cytoplasmic linear plasmid genes. Additionally, identification, characterization and localization of plasmid gene products of interest are made possible by shuffling GFP-, epitope- or affinity purification-tagged alleles between k2 and k1. The gene shuffle approach can also be used for vector development and heterologous protein expression in order to exploit the biotechnical potential of the K. lactis k1/k2 system in yeast cell factory research.
Mapping and Characterization of a Sequential Epitope on the Rabies Virus Glycoprotein Which Is Recognized by a Neutralizing Monoclonal Antibody, RG719 (1995)

We have established a murine hybridoma cell line RG719 which produces a rabies virus-neutralizing IgM-type monoclonal antibody (referred to as MAb RG719). Immunoblot analysis indicated that the antibody recognized a sequential epitope of G protein. Among four rabies virus strains tested, the antigenicity to MAb RG719 was absent from the Nishigahara strain, while the other three strains (HEP, ERA and CVS) reacted to the MAb. Studies with deletion mutants of the G protein indicated that the epitope was located in a middle region of the primary structure of G protein, ranging from position 242 to 300. By comparing the estimated amino acid sequence of the four strains, we found in this region two amino acids (at positions 263 and 291) which are common to three of those strains but are not shared by the Nishigahara strain. The site-directed point mutagenesis revealed that replacement of phenylalanine-263 by leucine destroyed the epitope of the HEP G protein, while the epitope was generated on the Nishigahara G protein whose leucine-263 was replaced by phenylalanine. These observations suggest that phenylalanine-263 is essential for constructing the epitope for MAb RG719. The synthetic 20-mer peptide produced by mimicking the amino acid sequence (ranging from amino acid positions 249 to 268) of the presumed epitope region was shown to bind specifically to MAb RG719 and also to raise the virus-neutralizing antibodies in rabbits. Vaccination with the HEP vaccine produced in Japan induced in humans and rabbits production of significant amounts of the antibodies which reacted with the 20-mer peptide.
Regulatory Functions of the Vascular Endothelium (1990)

William harvey, when studying the circulation of the blood, must have recognized that "In sound and living vessels the blood remains fluid, but it coagulates in dead ones" (Ernst Brücke, 1857). Joseph Lister (1909) provided further evidence for an active role of blood vessels in maintaining the liquidity of blood. The vascular endothelium, which envelops the circulating blood in a continuous monolayer, is mainly responsible for this function.Over the past 20 years numerous other important functions have been discovered. For instance, the outer surface of the endothelial cell contains angiotensin-converting enzyme, which catalyzes the formation of the vasoconstrictor angiotensin . . .
A tour of accelerated parallel MR imaging from a linear systems perspective (2005)

Parallel MR imaging has become a well-accepted method to improve image acquisition efficiency. Improved efficiency enables one to increase resolution, decrease image acquisition time, or provide some balance of both. It is generally understood that the primary difference between each of the parallel MR methods is the domain in which each reconstruction solution is posed (e.g., the spatial domain [y, x], the k-space domain [ky, kx], or a hybrid domain, [ky, x]). This article presents an alternative approach in which a common analytic framework to comprehensively illustrate the relationship between a number of parallel MRI reconstruction methods is used. With this framework, we demonstrate that the analytic relationship between the various methods is more complex than the domain classification suggests. Furthermore, this framework enables one to identify the strengths of each particular method along with the similarities and contrasts between them. © 2005 Wiley Periodicals, Inc. Concepts Magn Reson Part A 27A: 17–37, 2005.
Learning accurate, compact, and interpretable tree annotation (2006)

We present an automatic approach to tree annotation in which basic nonterminal symbols are alternately split and merged to maximize the likelihood of a training treebank. Starting with a simple X-bar grammar, we learn a new grammar whose nonterminals are subsymbols of the original nonterminals. In contrast with previous work, we are able to split various terminals to different degrees, as appropriate to the actual complexity in the data. Our grammars automatically learn the kinds of linguistic distinctions exhibited in previous work on manual tree annotation. On the other hand, our grammars are much more compact and substantially more accurate than previous work on automatic annotation. Despite its simplicity, our best grammar achieves an F1 of 90.2% on the Penn Treebank, higher than fully lexicalized systems.
Silencing of Aphid Genes by dsRNA Feeding from Plants (2011)

Similar levels of gene silencing were achieved in our plant-mediated RNAi approach and published silencing methods for aphids. Furthermore, the N. benthamiana leaf disk assay can be developed into a screen to assess which genes are essential for aphid survival on plants. Our results also demonstrate the feasibility of the plant-mediated RNAi approach for aphid control.
Comparison of the genomes of the wild-type French viscerotropic strain of yellow fever virus with its vaccine derivative French neurotropic vaccine (1995)

The French neurotropic vaccine, or FNV, was used extensively in Africa to control yellow fever (YF). Although efficacious, the vaccine caused an unacceptable rate of post-vaccinal complications in children and was subsequently replaced by the 17D vaccine. Here we report that the genomes of the wild-type YF virus French viscerotropic virus and its attenuated vaccine derivative, FNV virus from the Institut Pasteur, Paris, (FNV-IP) differ by 77 nucleotides encoding 35 amino acid substitutions. Comparison of FNV-IP and three other isolates of FNV with other YF vaccine strains (17D-204 and 17DD derived from wild-type strain Asibi) revealed that during the two attenuation processes two common nucleotide changes arose that encode two amino acid substitutions: one is in the membrane protein at amino acid 35 (M-35), the other in non-structural (NS) protein 4B at NS4B-95. These common substitutions may be important in the process of attenuation of viscerotropic disease for humans and monkeys, and/or may be involved in loss of mosquito competence of the vaccine viruses.