gebhart/patrepeval huggingface dataset:
Decontamination of the Digestive Tract and Oropharynx in ICU Patients (2008)

In an ICU population in which the mortality rate associated with standard care was 27.5% at day 28, the rate was reduced by an estimated 3.5 percentage points with SDD and by 2.9 percentage points with SOD. (Controlled Clinical Trials number, ISRCTN35176830.)
Spacetime stereo: shape recovery for dynamic scenes (2003)

This paper extends the traditional binocular stereo problem into the spacetime domain, in which a pair of video streams is matched simultaneously instead of matching pairs of images frame by frame. Almost any existing stereo algorithm may be extended in this manner simply by replacing the image matching term with a spacetime term. By utilizing both spatial and temporal appearance variation, this modification reduces ambiguity and increases accuracy. Three major applications for spacetime stereo are proposed in this paper. First, spacetime stereo serves as a general framework for structured light scanning and generates high quality depth maps for static scenes. Second, spacetime stereo is effective for a class of natural scenes, such as waving trees and flowing water, which have repetitive textures and chaotic behaviors and are challenging for existing stereo algorithms. Third, the approach is one of very few existing methods that can robustly reconstruct objects that are moving and deforming over time, achieved by use of oriented spacetime windows in the matching procedure. Promising experimental results in the above three scenarios are demonstrated.
Decoder architecture for array-code-based LDPC codes (2004)

We describe a decoder architecture intended for decoding array-code-based low-density parity-check (LDPC) codes using the sum-product algorithm (SPA). The advantages of the proposed architecture, as compared to the fully parallel implementation of the SPA, are: reduced memory size, avoidance of complex signal interconnect patterns, and ease of programmability to accommodate various code parameters. These advantages are derived from exploiting the well-defined structure of the parity-check matrix of array-code based LDPC codes. Sum-product decoding with modified message-passing schedules are proposed to simplify the decoder implementation further.
The Emergence of lncRNAs in Cancer Biology (2011)

The discovery of numerous noncoding RNA (ncRNA) transcripts in species from yeast to mammals has dramatically altered our understanding of cell biology, especially the biology of diseases such as cancer. In humans, the identification of abundant long ncRNA (lncRNA) >200 bp has catalyzed their characterization as critical components of cancer biology. Recently, roles for lncRNAs as drivers of tumor suppressive and oncogenic functions have appeared in prevalent cancer types, such as breast and prostate cancer. In this review, we highlight the emerging impact of ncRNAs in cancer research, with a particular focus on the mechanisms and functions of lncRNAs.
Combining mTor Inhibitors With Rapamycin-resistant T Cells: A Two-pronged Approach to Tumor Elimination (2011)

Despite activity as single agent cancer therapies, Rapamycin (rapa) and its rapalogs may have their greatest effects when combined with other therapeutic modalities. In addition to direct antitumor activity, rapalogs reverse multiple tumor-intrinsic immune evasion mechanisms. These should facilitate tumor-specific T cell activity, but since rapa directly inhibits effector T cells, this potential immune enhancement is lost. We hypothesized that if T cells were rendered resistant to rapa they could capitalize on its downregulation of tumor immune evasion. We therefore modified T cells with a rapa-resistant mutant of mTor, mTorRR, and directed them to B lymphomas by coexpressing a chimeric antigen receptor (CAR) for CD19 (CAR.CD19-28ζ). T cells expressing transgenic mTorRR from a piggyBac transposon maintain mTor signaling, proliferate in the presence of rapa and retain their cytotoxic function and ability to secrete interferon-γ (IFNγ) after stimulation, effector functions that were inhibited by rapa in control T cells. In combination, rapa and rapa-resistant-CAR.CD19-28ζ-expressing T cells produced greater antitumor activity against Burkitt's lymphoma and pre-B ALL cell lines in vitro than CAR.CD19-28ζ T cells or rapa alone. In conclusion, the combination of rapa and rapa-resistant, CAR.CD19-28ζ-expressing T cells may provide a novel therapy for the treatment of B cell malignancies and other cancers.
Systolic Time Intervals in Heart Failure in Man (1968)

The duration of the systolic time intervals in nondigitalized patients with heart failure was determined from simultaneous fast speed recordings of the electrocardiogram, phonocardiogram, and carotid arterial pulsation. These were compared with the systolic time intervals corrected for heart rate and sex in 211 normal subjects. The failing left ventricle is characterized by a prolongation in the systolic pre-ejection period and a diminution in the left ventricular ejection time while total electromechanical systole remains relatively unaltered. Both components of the pre-ejection period, the Q-1 interval and the isovolumic contraction time, were prolonged. These alterations in the phases of systole occur in the absence of a measurable change in ventricular depolarization time. The prolongation in the pre-ejection period is well correlated with the reduced stroke volume and cardiac output in heart failure and is independently augmented by high levels of arterial pressure. The abbreviation in left ventricular ejection time is also correlated significantly with the stroke volume and cardiac output. It is postulated that a defect in the mechanical performance of the heart is responsible for the abnormal systolic time intervals in human heart failure.
Minireview: Glucagon in Stress and Energy Homeostasis (2012)

Glucagon is traditionally thought of as an antihypoglycemic hormone, for example in response to starvation. However, it actually increases energy expenditure and has other actions not in line with protection from hypoglycemia. Furthermore, it is often found to be elevated when glucose is also raised, for example in circumstances of psychological and metabolic stress. These findings seem more in keeping with glucagon having some role as a hormone enhancing the response to stress.
Selective regulation of mutant K-ras mRNA expression by photo-cross-linking antisense oligonucleotide (2007)

It has been reported that point mutations in genes are responsible for various cancers and the selective regulation of the gene expression is an important issue to develop new types of anticancer drugs. In this report, we report new types of antisense molecules that photo-cross-link to target mRNA having a point mutation site in a sequence specific manner. We designed and synthesized photo-reactive antisense oligonucleotides containing a 2'-O-psoralen-conjugated adenosine (2'-Ps-oligo). They contain a psoralen via an ethoxymethylene linker (2'-Ps-eom), a propoxymethylene linker (2'-Ps-pom) and a buthoxymethylene linker (2'-Ps-bom), respectively. We evaluated the photo-cross-linking efficiency and the sequence specificity toward complementary RNA. 2'-Ps-eom showed the highest photo-cross-linking efficiency among 2'-Ps-oligos.
From classical mutagenesis to nuclease‐based breeding – directing natural DNA repair for a natural end‐product (2016)

Production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damage in an error-prone way. In the case of radiation, multiple double-strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site-directed nucleases (SDNs) - also referred to as sequence-specific nucleases - like the CRISPR/Cas system has enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at pre-defined sites in plant genomes. As these changes are not necessarily associated with the permanent integration of foreign DNA, the obtained organisms per se cannot be regarded as genetically modified as there is no way to distinguish them from natural variants. This applies to changes induced by DSBs as well as single-strand breaks, and involves repair by non-homologous end-joining and homologous recombination. The recent development of SDN-based 'DNA-free' approaches makes mutagenesis strategies in classical breeding indistinguishable from SDN-derived targeted genome modifications, even in regard to current regulatory rules. With the advent of new SDN technologies, much faster and more precise genome editing becomes available at reasonable cost, and potentially without requiring time-consuming deregulation of newly created phenotypes. This review will focus on classical mutagenesis breeding and the application of newly developed SDNs in order to emphasize similarities in the context of the regulatory situation for genetically modified crop plants.
Performance of Human Papillomavirus DNA and mRNA Testing Strategies for Women with and without Cervical Neoplasia (2009)

In the present study we investigated the cross-sectional positivity for DNA and E6/E7 mRNA from high-risk human papillomavirus (HPV) types in 643 women with high-grade cervical neoplasia (135 cases of cervical intraepithelial neoplasia grade 2 [CIN2], 495 cases of CIN3/adenocarcinoma in situ [ACIS], and 13 cases of invasive carcinoma) and in 736 women with normal cytology by using the Amplicor and PreTect HPV-Proofer assays. In addition, genotyping was performed using Linear Array for women with normal cytology and a positive HPV test and in all women with histologically confirmed CIN2+. In women with normal cytology, 8.3% (61/736) were Amplicor positive and 3.3% (24/736) were PreTect HPV-Proofer positive (P < 0.001). Concordant results between the Amplicor and PreTect HPV-Proofer tests were present in 90.3% (665/736). In women with CIN2+ lesions 96.4% (620/643) were positive by Amplicor, 98.4% (633/643) by linear array, and 64.1% (412/643) by PreTect HPV-Proofer. Concordant results for the three HPV assays were present in 63.8%. The genotype profile detected by linear array and PreTect HPV-Proofer showed substantial agreement for HPV types 16, 18, 33, and 45. HPV type 16 and/or 18 was detected in 58.8% (378/643) of the women with high-grade neoplasia. Detection of E6/E7 mRNA by PreTect HPV-Proofer increased with severity of the cervical lesion. Detection of HPV DNA, however, was not associated with histology grade. In conclusion, the detection of HPV varied according to the assay used, and the concordance between the tests was poor. Our results indicate that mRNA testing may be a biomarker for progression of cervical neoplasia, but the optimal genotype mix remains to be determined.
Induction of cyclin D1 overexpression by activated ras. (1994)

Activated ras genes are known to alter control of cell proliferation. This is consistent with the fact that ras proteins are a key component of the biochemical pathway triggered by ligand-bound cell surface receptors that are tyrosine kinases. Although an important part of the ras signaling pathway has been recently uncovered, the molecular target(s) that mediates the effects of ras on cell cycle control remains unknown. Cyclins and cyclin-dependent kinases are key molecules in the control of cell cycle. Cyclin D1, in particular, is a critical target for proliferative signals in G1 and it has been shown that ectopic overexpression of this cyclin can significantly alter cell cycle regulation. Here we report that activated ras induces significant overexpression of cyclin D1 in epithelial cells derived from normal rat intestine and mouse mammary gland. A definitive causal role for activated ras in this overexpression is demonstrated by using intestinal cells transfected with an inducible ras expression vector. Treatment of the ras-transformed intestinal clones with anti-sense cyclin D1 oligonucleotides reduces their rate of cell proliferation indicating that the increment in cyclin D1 expression induced by activated ras is instrumental in the higher rate of cell proliferation conferred by the ras oncogene to the IEC cells. Based on these results we propose that, at least in certain cell types, cyclin D1 can be one of the mediators of the transforming action of activated ras.
Base‐Stabilized Silyleneiron Complexes (1977)

Attempted syntheses of monomeric silylene complexes have so far met with very modest success. The first base-stabilized silyleneiron complexes, e.g. (1), have now been isolated.
Spatially Aware Term Selection for Geotagging (2013)

The task of assigning geographic coordinates to textual resources plays an increasingly central role in geographic information retrieval. The ability to select those terms from a given collection that are most indicative of geographic location is of key importance in successfully addressing this task. However, this process of selecting spatially relevant terms is at present not well understood, and the majority of current systems are based on standard term selection techniques, such as $(\chi^2)$ or information gain, and thus fail to exploit the spatial nature of the domain. In this paper, we propose two classes of term selection techniques based on standard geostatistical methods. First, to implement the idea of spatial smoothing of term occurrences, we investigate the use of kernel density estimation (KDE) to model each term as a two-dimensional probability distribution over the surface of the Earth. The second class of term selection methods we consider is based on Ripley's K statistic, which measures the deviation of a point set from spatial homogeneity. We provide experimental results which compare these classes of methods against existing baseline techniques on the tasks of assigning coordinates to Flickr photos and to Wikipedia articles, revealing marked improvements in cases where only a relatively small number of terms can be selected.
Robot relay: An optimal path planning for multiple client service (2016)

Service robots are being widely implemented to provide specialized services to mankind. Their functionality are widespread among various application domains for providing services related to surveillance, vigilance, accident reporting, mechanical labor and behavior analysis. This paper presents the application of a mobile robot X80SV in a college campus. The robot equipped with a camera makes use of a pre generated map learned by the robot by integrating GPS data and motion sensor information. The map is used for navigating our robot to the desired location for multiple request servicing based on the job specified by the client. The work presents an architecture for efficient handling of the requests for an optimal order of their execution. Optimal path is calculated considering the shortest path; the request order and the processing time required in servicing the client request. The completion of services further depends upon the decision taken after processing the visual data at the end node. The proposed architecture including map based navigation, multiple service handling, optimal service processing and visual data analysis is applied to a subset of services as demonstrated in the result section of the paper. This includes physical transfer of important documents, information about particular region, calling a person and video data transfer.
The intracellular concentration of sialic acid regulates the polysialylation of the neural cell adhesion molecule (2005)

Sialic acids are expressed as terminal sugars in many glycoconjugates and play an important role during development and regeneration, as they are involved as polysialic acid in a variety of cell-cell interactions mediated by the neural cell adhesion molecule NCAM. The key enzyme for the biosynthesis of sialic acid is the UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine-kinase (GNE). Mutations in the binding site of the feedback inhibitor CMP-sialic acid of the GNE leads to sialuria, a disease in which patients produce sialic acid in gram scale. Here, we report on the consequences after expression of a sialuria-mutated GNE. Expression of the sialuria-mutated GNE leads to a dramatic increase of both cellular sialic acid and polysialic acid on NCAM. This could also be achieved by application of the sialic acid precursor N-acetylmannosamine. Our data suggest that biosynthesis of sialic acid regulates and limits the synthesis of polysialic acid.
ECAT: a new computerized tomographic imaging system for position-emitting radiopharmaceuticals (1977)

The ECAT was designed and developed as a complete computerized positron radionuclide imaging system capable of providing high contrast, high resolution, quantitative images in 2 dimensional and tomographic formats. Flexibility, in its various image mode options, allows it to be used for a wide variety of imaging problems.
Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors (2006)

In this article we describe the application of structural biology methods to the discovery of novel potent inhibitors of methionine aminopeptidases. These enzymes are employed by the cells to cleave the N-terminal methionine from nascent peptides and proteins. As this is one of the critical steps in protein maturation, it is very likely that inhibitors of these enzymes may prove useful as novel antibacterial agents. Involvement of crystallography at the very early stages of the inhibitor design process resulted in serendipitous discovery of a new inhibitor class, the pyrazole-diamines. Atomic-resolution structures of several inhibitors bound to the enzyme illuminate a new mode of inhibitor binding.
Synthesis and Enhanced Intercalation Properties of Nanostructured Vanadium Oxides (2006)

Nanomaterials lie at the heart of the fundamental advances in efficient energy storage/conversion and other types of nanodevices in which the surface process and transport kinetics play determining roles. This review describes some recent developments in the synthesis and characterizations of various vanadium oxide nanostructures including nanowires, nanorolls, nanobelts, and ordered arrays of nanorods, nanotubes, and nanocables for significantly enhanced intercalation properties. The major topic of this article is to highlight the lithium ion intercalation properties of nanostructured vanadium oxides for energy storage as well as other applications in sensors, actuators, and transistors.
Miniature mass analyzers (2000)

Increased efforts are being made to develop miniature mass spectrometers, including those which are hand-portable, and to retain the performance characteristics of traditional laboratory instruments as much as possible in the miniature instruments. This review of miniature mass analyzers emphasizes analytical performance and compares the relative merits of each type of miniature mass analyzer. Miniature instruments discussed include sector, Wien filter, time-of-flight, linear quadrupole, quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometers, as well as combinations of and variations on these major types. Special considerations that apply to small mass analyzers are noted and suggestions are made regarding the possible future development of this field. Copyright 2000 John Wiley & Sons, Ltd.
Controlled-release mitochondrial protonophore reverses diabetes and steatohepatitis in rats (2015)

Nonalcoholic fatty liver disease (NAFLD) is a major factor in the pathogenesis of type 2 diabetes (T2D) and nonalcoholic steatohepatitis (NASH). The mitochondrial protonophore 2,4 dinitrophenol (DNP) has beneficial effects on NAFLD, insulin resistance, and obesity in preclinical models but is too toxic for clinical use. We developed a controlled-release oral formulation of DNP, called CRMP (controlled-release mitochondrial protonophore), that produces mild hepatic mitochondrial uncoupling. In rat models, CRMP reduced hypertriglyceridemia, insulin resistance, hepatic steatosis, and diabetes. It also normalized plasma transaminase concentrations, ameliorated liver fibrosis, and improved hepatic protein synthetic function in a methionine/choline-deficient rat model of NASH. Chronic treatment with CRMP was not associated with any systemic toxicity. These data offer proof of concept that mild hepatic mitochondrial uncoupling may be a safe and effective therapy for the related epidemics of metabolic syndrome, T2D, and NASH.
Tec kinase is involved in transcriptional regulation of IL-2 and IL-4 in the CD28 pathway (1999)

The Tec protein tyrosine kinase (PTK) family includes Btk, Itk/Tsk/Emt, Tec, Rlk/Txk and Bmx, which are involved in signals mediated by various surface receptors. We have previously found (W.-C. Yang et al., J. Biol. Chem. 1999. 274 : 607) that Tec is involved in T cell signaling in a way distinct from Itk. However, little is known about the role of Tec in regulation of cytokine expression in the CD28 pathway. Here, we show in heterologous COS-7 cells that co-expression of Src family kinases such as Lck increases Tec activation or CD28-mediated Tec activation, whereas co-expression of kinase-dead Lck blocks Tec activation or CD28-mediated Tec activation. These data suggest that CD28 activates Tec via Src family PTK. As is the case for the IL-2 promoter, transcription of the IL-4 promoter is enhanced by overexpression of wild-type Tec but inhibited by overexpression of a kinase-dead version of Tec following CD28 activation. These results imply that Tec can modulate transcription of Th1 and Th2 cytokines in a kinase-dependent manner. Consistent with the hypothesis postulated above that Lck can regulate Tec activation, overexpression of kinase-dead Lck can block Tec-induced cytokine expression following CD28 ligation.