gebhart/patrepeval huggingface dataset:
α-1-Antitrypsin Ameliorates Cigarette Smoke–induced Emphysema in the Mouse (2003)

Serine elastase inhibitors have been proposed as a treatment for cigarette smoke-induced emphysema, but little is known about whether such agents actually are effective. We recently reported that a synthetic serine elastase inhibitor, ZD0892, provided some protection against emphysema in a guinea pig model. For these experiments, we used transgenic mice that expressed extremely low levels of human alpha-1-antitrypsin (A1AT) but were tolerant of exogenous human A1AT. Mice were exposed to daily cigarette smoke for up to 6 months; some animals received 20 mg of human A1AT (Prolastin) every 48 hours. Treatment with A1AT produced an approximate twofold increase in serum A1AT levels and elastase inhibitory capacity and abolished smoke-induced elevations in lavage neutrophils and matrix breakdown products (desmosine and hydroxyproline) measured from 2 to 30 days of smoke exposure. A1AT oxidized to remove antiproteolytic activity did not increase serum elastase inhibitory capacity but did prevent neutrophil influx. Treatment with A1AT for 6 months provided 63% protection against increased airspace size (emphysema) and abolished smoke-mediated increases in plasma tumor necrosis factor-alpha. We conclude that A1AT therapy ameliorates smoke-induced inflammation and matrix breakdown, possibly via an antiinflammatory mechanism related to tumor necrosis factor-alpha suppression, and provides partial protection against emphysema.
Adenovirus Vectors Expressing Hantavirus Proteins Protect Hamsters against Lethal Challenge with Andes Virus (2009)

Hantaviruses infect humans following aerosolization from rodent feces and urine, producing hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. Due to the high rates of mortality and lack of therapies, vaccines are urgently needed. Nonreplicating adenovirus (Ad) vectors that express Andes hantavirus (ANDV) nucleocapsid protein (AdN) or glycoproteins (AdG(N) and AdG(C)) were constructed. Ad vectors were tested for their ability to protect Syrian hamsters from a lethal ANDV infection that mimics the pulmonary disease seen in humans. When administered once, all three Ad vectors, individually or in combination, elicited a robust immune response that protected hamsters. No vaccinated animal died, and there were no obvious clinical signs of disease. Further, hantavirus RNA was not detected by sensitive reverse transcription-PCR in tissues and blood of hamsters immunized with both AdG(N) and AdG(C). Cellular immunity appeared to be important for protection because the AdN vector completely protected animals. All three Ad vectors produced strong cytotoxic T-lymphocyte responses directed to hantavirus proteins in mice. Moreover, hamsters vaccinated with AdN, AdG(N), or AdG(C) produced no detectable neutralizing antibodies yet were protected. These Ad vectors represent the first vaccines that prevent lethal hantavirus disease and, in some instances (AdG(N) and AdG(C)), provide sterile immunity. These observations set the stage for a more detailed characterization of the types of immunity required to protect humans from hantavirus infections.
The Fbw7 Tumor Suppressor Targets KLF5 for Ubiquitin-Mediated Degradation and Suppresses Breast Cell Proliferation (2010)

Fbw7 is a tumor suppressor frequently inactivated in cancers. The KLF5 transcription factor promotes breast cell proliferation and tumorigenesis through upregulating FGF-BP. The KLF5 protein degrades rapidly through the ubiquitin proteasome pathway. Here, we show that the Skp1-CUL1-Fbw7 E3 ubiquitin ligase complex (SCF(Fbw7)) targets KLF5 for ubiquitin-mediated degradation in a GSK3beta-mediated KLF5 phosphorylation-dependent manner. Mutation of the critical S303 residue in the KLF5 Cdc4 phospho-degrons motif ((303)SPPSS) abolishes the protein interaction, ubiquitination, and degradation by Fbw7. Inactivation of endogenous Fbw7 remarkably increases the endogenous KLF5 protein abundances. Endogenous Fbw7 suppresses the FGF-BP gene expression and breast cell proliferation through targeting KLF5 for degradation. These findings suggest that Fbw7 inhibits breast cell proliferation at least partially through targeting KLF5 for proteolysis. This new regulatory mechanism of KLF5 degradation may result in useful diagnostic and therapeutic targets for breast cancer and other cancers.
Methionine sulfoxide reductase A (MsrA) protects cultured mouse embryonic stem cells from H2O2‐mediated oxidative stress (2010)

Methionine sulfoxide reductase A (MsrA), a member of the Msr gene family, can reduce methionine sulfoxide residues in proteins formed by oxidation of methionine by reactive oxygen species (ROS). Msr is an important protein repair system which can also function to scavenge ROS. Our studies have confirmed the expression of MsrA in mouse embryonic stem cells (ESCs) in culture conditions. A cytosol-located and mitochondria-enriched expression pattern has been observed in these cells. To confirm the protective function of MsrA in ESCs against oxidative stress, a siRNA approach has been used to knockdown MsrA expression in ES cells which showed less resistance than control cells to hydrogen peroxide treatment. Overexpression of MsrA gene products in ES cells showed improved survivability of these cells to hydrogen peroxide treatment. Our results indicate that MsrA plays an important role in cellular defenses against oxidative stress in ESCs. Msr genes may provide a new target in stem cells to increase their survivability during the therapeutic applications.
Mineralization of Synthetic Polymer Scaffolds:  A Bottom-Up Approach for the Development of Artificial Bone (2005)

The controlled integration of organic and inorganic components confers natural bone with superior mechanical properties. Bone biogenesis is thought to occur by templated mineralization of hard apatite crystals by an elastic protein scaffold, a process we sought to emulate with synthetic biomimetic hydrogel polymers. Cross-linked polymethacrylamide and polymethacrylate hydrogels were functionalized with mineral-binding ligands and used to template the formation of hydroxyapatite. Strong adhesion between the organic and inorganic materials was achieved for hydrogels functionalized with either carboxylate or hydroxy ligands. The mineral-nucleating potential of hydroxyl groups identified here broadens the design parameters for synthetic bonelike composites and suggests a potential role for hydroxylated collagen proteins in bone mineralization.
CMOS active pixel image sensors for highly integrated imaging systems (1997)

A family of CMOS-based active pixel image sensors (APSs) that are inherently compatible with the integration of on-chip signal processing circuitry is reported. The image sensors were fabricated using commercially available 2-/spl mu/m CMOS processes and both p-well and n-well implementations were explored. The arrays feature random access, 5-V operation and transistor-transistor logic (TTL) compatible control signals. Methods of on-chip suppression of fixed pattern noise to less than 0.1% saturation are demonstrated. The baseline design achieved a pixel size of 40 /spl mu/m/spl times/40 /spl mu/m with 26% fill-factor. Array sizes of 28/spl times/28 elements and 128/spl times/128 elements have been fabricated and characterized. Typical output conversion gain is 3.7 /spl mu/V/e/sup -/ for the p-well devices and 6.5 /spl mu/V/e/sup -/ for the n-well devices. Input referred read noise of 28 e/sup -/ rms corresponding to a dynamic range of 76 dB was achieved. Characterization of various photogate pixel designs and a photodiode design is reported. Photoresponse variations for different pixel designs are discussed.
Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing (2012)

Clinical management of cancer patients could be improved through the development of noninvasive approaches for the detection of incipient, residual, and recurrent tumors. We describe an approach to directly identify tumor-derived chromosomal alterations through analysis of circulating cell-free DNA from cancer patients. Whole-genome analyses of DNA from the plasma of 10 colorectal and breast cancer patients and 10 healthy individuals with massively parallel sequencing identified, in all patients, structural alterations that were not present in plasma DNA from healthy subjects. Detected alterations comprised chromosomal copy number changes and rearrangements, including amplification of cancer driver genes such as ERBB2 and CDK6. The level of circulating tumor DNA in the cancer patients ranged from 1.4 to 47.9%. The sensitivity and specificity of this approach are dependent on the amount of sequence data obtained and are derived from the fact that most cancers harbor multiple chromosomal alterations, each of which is unlikely to be present in normal cells. Given that chromosomal abnormalities are present in nearly all human cancers, this approach represents a useful method for the noninvasive detection of human tumors that is not dependent on the availability of tumor biopsies.
Nonparametric Estimation from Incomplete Observations (1958)

Abstract In lifetesting, medical follow-up, and other fields the observation of the time of occurrence of the event of interest (called a death) may be prevented for some of the items of the sample by the previous occurrence of some other event (called a loss). Losses may be either accidental or controlled, the latter resulting from a decision to terminate certain observations. In either case it is usually assumed in this paper that the lifetime (age at death) is independent of the potential loss time; in practice this assumption deserves careful scrutiny. Despite the resulting incompleteness of the data, it is desired to estimate the proportion P(t) of items in the population whose lifetimes would exceed t (in the absence of such losses), without making any assumption about the form of the function P(t). The observation for each item of a suitable initial event, marking the beginning of its lifetime, is presupposed. For random samples of size N the product-limit (PL) estimate can be defined as follows: List and label the N observed lifetimes (whether to death or loss) in order of increasing magnitude, so that one has 0≤t 1ǐ≤t 2ǐ≤ … ≤t N ǐ. Then P(t)= II. [(N – r)/(N – r + 1)], where r assumes those values for which tr ≤t and for which tr ǐ measures the time to death. This estimate is the distribution, unrestricted as to form, which maximizes the likelihood of the observations. Other estimates that are discussed are the actuarial estimates (which are also products, but with the number of factors usually reduced by grouping); and reduced-sample (RS) estimates, which require that losses not be accidental, so that the limits of observation (potential loss times) are known even for those items whose deaths are observed. When no losses occur at ages less than t, the estimate of P(t) in all cases reduces to the usual binomial estimate, namely, the observed proportion of survivors.
Antitumor Activity of EBV-specific T Lymphocytes Transduced With a Dominant Negative TGF-β Receptor (2008)

Transforming growth factor (TGF)-beta is produced in most human tumors and markedly inhibits tumor antigen-specific cellular immunity, representing a major obstacle to the success of tumor immunotherapy. TGF-beta is produced in Epstein-Barr virus (EBV)-positive Hodgkin disease and non-Hodgkin lymphoma both by the tumor cells and by infiltrating T-regulatory cells and may contribute the escape of these tumors from infused EBV-specific T cells. To determine whether tumor antigen-specific cytotoxic T lymphocytes (CTLs) can be shielded from the inhibitory effects of tumor-derived TGF-beta, we previously used a hemagglutinin-tagged dominant negative TGF-betaRII expressed from a retrovirus vector to provide CTLs with resistance to the inhibitory effects of TGF-beta in vitro. We now show that human tumor antigen-specific CTLs can be engineered to resist the inhibitory effects of tumor-derived TGF-beta both in vitro and in vivo using a clinical grade retrovirus vector in which the dominant negative TGF-beta type II receptor (DNRII) was modified to remove the immunogenic hemagglutinin tag. TGF-beta-resistant CTL had a functional advantage over unmodified CTL in the presence of TGF-beta-secreting EBV-positive lymphoma, and had enhanced antitumor activity, supporting the potential value of this countermeasure.
Geometric effect on surface enhanced Raman scattering of nanoporous gold: Improving Raman scattering by tailoring ligament and nanopore ratios (2009)

We have synthesized nanoporous gold (NPG) films with a nanostructure consisting of small nanopores and large gold ligaments by the combination of chemical dealloying and electroless plating. The NPG films exhibit dramatic improvement in surface enhanced Raman scattering (SERS) in comparison with the conventional NPG. The superior SERS effect of the NPG films results from the confluence effect of enhanced local surface plasmon fields and electromagnetic coupling between ligaments, as well as the weak plasmon damping with increasing gold ligament sizes.
Novel multi-bit non-uniform channel charge trapping memory device with virtual-source NAND flash array (2010)

In order to overcome the bit-to-bit interference of the traditional multi-level NAND type device, this paper firstly proposes a novel multi-bit non-uniform channel charge trapping memory (NUC-CTM) device with virtual-source NAND-type array architecture, which can effectively restrain the second-bit effect (SBE) and provide 3-bit per cell capability. Owing to the n− buffer region, the SBE induced threshold voltage window shift can be reduced to less than 400 mV and the minimum threshold voltage window between neighboring levels is larger than 750 mV for reliable 3-bit operation. A silicon-rich SiON is also investigated as a trapping layer to improve the retention reliability of the NUC-CTM.
Incorporating Best Practices of Highly Effective Teaching into Common Core-Aligned College Courses (2012)

While aligning the Common Core Standards with Eastern Kentucky University’s General Education and Teacher Preparation courses has been the main focus of Curriculum Alignment for Retention and Transition at Eastern (CARTE), another way we responded to Senate Bill 1 was to identify ways in which to teach this new alignment at the college level. Our solution was to partner with Kentucky’s Council on Postsecondary Education to create a website on best teaching practices and to task each of our Professional Learning Communities with adapting the best teaching practices to its specific discipline (e.g., teacher prep). The result was the creation of Best Practices for Highly Effective Teaching Module Resources, a section of the website of the Kentucky Core Academic Standards for Postsecondary Education. By going beyond the Senate Bill 1 mandate, the website for best practices of highly effective teaching and learning is one more way that Kentucky has positioned itself as a leader in the common core alignment process.
ANALYSIS OF 9 MORTAL CASES CAUSED BY DIHYDROETORPHINE HYDROCHLORIDE ABUSE (1994)

9 addicts died of using dihydroetorphine hydrochloride)DHE)were surveyed and analysed.Most of them began to inhale Huang Pi(a kind of crude heroin)and became addicts.Because of different reasons they inhaled DHE instead of Huang Pi.Their daily dose increased gradually.The highest daily dose was 100-160 tablets)20μg·tab-1).The serious patients often injected intravenously)DHE)by themselves.The body complications were very serious.Most common seen complications were thinness,obvious decrease of body weights)about 10-30 kg),venous inflammation and local abscess.They all died because of respiratory failure.
Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles (2013)

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability.
Understanding the pathophysiology of the arterial wall: which method should we choose? (2002)

Atherosclerosis, the pathological process that underlies myocardial infarction, stroke and other occlusive vascular diseases, is the major cause of death in the Western world. Techniques that accurately and reproducibly detect and measure the early changes that occur in atherosclerosis and/or that identify those who are at highest cardiovascular risk may aid in the development of prevention strategies and may facilitate a decrease in morbidity and mortality from atherosclerosis. Improved understanding of the pathophysiology of early atherosclerosis has allowed development of a number of potential methods for the assessment of early stages in atherosclerosis in humans. These include techniques for assessing early structural changes in the coronary arteries using electron beam computed tomography and magnetic resonance imaging. External vascular ultrasound has also been used to image other circulations as a surrogate marker for coronary atherosclerosis (e.g. measurement of carotid artery intima-media thickness). Early functional changes in atherosclerosis have also been described many years before the development of structural changes. A number of techniques have been developed to measure endothelial dysfunction (one of the earliest changes in atherosclerosis), including non-invasive measurement of endothelial function using external vascular ultrasound. A variety of serum markers have also been described, and may be useful markers of atherosclerosis.
The Xbox One System on a Chip and Kinect Sensor (2014)

The system on a chip (SoC) at the heart of the Xbox One entertainment console is one of the largest consumer designs to date, with five billion transistors. The Xbox One Kinect image sensor uses time-of-flight technology to provide high-resolution, low-latency, lighting-independent 3D image sensing. Together, Kinect and the SoC provide unique voice and gesture interaction with high-performance games and other entertainment applications.
Murine models of liver metastasis. (1995)

Even though the liver is a relevant metastatic site for several human malignant tumors, mechanisms or organ-specific metastasis to the liver remain largely unknown. In the following paper we summarize the results obtained with different murine model systems which have been set up to elucidate the above mechanisms, and describe our own results with two murine models: the F9 teratocarcinoma and the B16 melanoma. While the F9 teratocarcinoma model system underscores the roles of both adhesion and growth stimulation in the target organ, the B16 melanoma model strengthens the relevance of paracrine growth stimulation. Moreover, B16 melanoma cells selected in vivo for increased liver colonization ability appear to depend on cell-to-cell contact with hepatocytes in order to gain efficient growth stimulation. When we next tried to identify the molecule(s) responsible for the growth effect in a liver plasma membrane extract, we found that such activity was mediated by two closely related protein bands. These turned out to be two different forms of transferrin (Tf), one of which is specifically present on the hepatocyte surface. Moreover, when we analyzed the different B16 lines for the expression of c-Met[the receptor for the hepatocyte growth factor-scatter factor (HGF/SF)], we found that liver-specific LS9 had more of this protein than lung-specific F10 or parental F1, suggesting a role for HGF/SF in liver colonization by B16 melanoma cells.
Extracting and Understanding Contrastive Opinion through Topic Relevant Sentences. (2017)

Contrastive opinion mining is essential in identifying, extracting and organising opinions from user generated texts. Most existing studies separate input data into respective collections. In addition, the relationships between the topics extracted and the sentences in the corpus which express the topics are opaque, hindering our understanding of the opinions expressed in the corpus. We propose a novel unified latent variable model (contraLDA) which addresses the above matters. Experimental results show the effectiveness of our model in mining contrasted opinions, outperforming our baselines.
Protective Role of Bacillus anthracis Exosporium in Macrophage-Mediated Killing by Nitric Oxide (2007)

The ability of the endospore-forming, gram-positive bacterium Bacillus anthracis to survive in activated macrophages is key to its germination and survival. In a previous publication, we discovered that exposure of primary murine macrophages to B. anthracis endospores upregulated NOS 2 concomitant with an .NO-dependent bactericidal response. Since NOS 2 also generates O(2).(-), experiments were designed to determine whether NOS 2 formed peroxynitrite (ONOO(-)) from the reaction of .NO with O(2).(-) and if so, was ONOO(-) microbicidal toward B. anthracis. Our findings suggest that ONOO(-) was formed upon macrophage infection by B. anthracis endospores; however, ONOO(-) does not appear to exhibit microbicidal activity toward this bacterium. In contrast, the exosporium of B. anthracis, which exhibits arginase activity, protected B. anthracis from macrophage-mediated killing by decreasing .NO levels in the macrophage. Thus, the ability of B. anthracis to subvert .NO production has important implications in the control of B. anthracis-induced infection.