gebhart/patrepeval huggingface dataset:
Phase I trial of intravenous attenuated vaccinia virus (GL-ONC1) with concurrent chemoradiotherapy (CRT) for locoregionally advanced head and neck carcinoma. (2015)

6026 Background: We aimed to test the safety of GL-ONC1, an attenuated vaccinia virus, delivered intravenously (IV) with concurrent CRT for locoregionally advanced head and neck carcinoma (LA-HNC). Secondary objectives were to test for tumor susceptibility to viral infection in baseline specimens and for tumor infection on mid-treatment biopsies. Methods: This was a 3+3 phase I dose escalation trial for unresected LA-HNC, excluding HPV-positive oropharyngeal cancer (NCT01584284). CRT was given in 33-35 fractions of 2.00-2.12 Gy over 6.5-7 weeks using IMRT with concurrent cisplatin 100 mg/m2 given on days 1, 22, and 43. Escalating doses of GL-ONC1 were given as follows: cohort 1, 3×108 pfu on day 3; cohort 2, 1×109 pfu on day 3; cohort 3, 3×109 pfu on day 3; cohort 4, 3×109 pfu on days 3 and 8; and cohort 5, 3×109pfu on days 3, 8, 15, and 22. Dose-limiting toxicity (DLT) was defined as grade ≥ 4 toxicity or grade ≥ 3 mucositis or skin reaction persisting > 6 weeks after CRT attributed to GL-ONC1. Results: From May 2012 to Dec 2014, 24 patients consented (19 enrolled, 5 screen failures). 18 patients completed CRT, with 1 currently on treatment. Mean age was 56 years. 74% had stage IVA and 26% had stage IVB disease. 26% were HPV-positive. One DLT occurred in cohort 4. Maximum tolerated dose was not reached. Adverse events included grade ≥ 2 rigors (47%), grade ≥ 2 thrombocytopenia (32%), grade ≥ 2 fever (26%) and grade ≥ 1 rash (21%). The rash was confirmed to be viral in origin in 2 patients. Viral tumor infection was confirmed by qPCR for A21L gene in 4 patients. No viral shedding was detected on urine or oral swab 1-2 days post infusion of GL-ONC1. Serious adverse events considered unrelated to GL-ONC1 were myocardial infarction (1), pulmonary embolism (1), syncope (1), grade 3 emesis (1), and grade 3 neutropenia (1). Of 18 patients completing CRT, 78% had 3 cycles of cisplatin and 22% had 2 cycles. With median 17 month follow-up, Kaplan-Meier estimates of 1-year (2-year) PFS and OS were 82% (75%) and 87% (75%) respectively. Conclusions: This is the first trial to establish the safety of IV GL-ONC1 for LA-HNC patients undergoing concurrent CRT. A phase II trial in this population is warranted. Clinical trial information: NCT01584284.
A new text feature extraction model and its application in document copy detection (2004)

Text feature extraction is a common issue in information retrieval, text mining, Web mining, text classification/clustering and document copy etc. The most popular approach is word frequency based scheme, which uses a word frequency vector to represent a document. Cosine function, dot product and proportion function are regular similarity measures of vector. But that is only global semantic feature of a document and loses local feature and structural information so that it prevents us to distinguish text well, especially in copy detection. In this paper we present a new text feature extraction model: semantic sequence model (SSM) that based on the concepts of word distance, word density and semantic sequence. The semantic sequences of a document contain not only local semantic features but also global feature and structural information, on which we get excellent accuracy of text copy detection. At the end of the paper, we contrast SSM with VSM and RFM and the experimental results show SSM is a superior model.
Maintaining stereo calibration by tracking image points (2002)

An important problem in active 3-D vision is updating the camera calibration matrix as the focus, aperture, zoom or vergence angle of the cameras changes dynamically. Techniques are presented to compute the projection matrix from five-and-a-half points in a scene without matrix inversion, and to correct the projective transformation matrix by tracking reference points. The authors' experiments show that a change of focus can be corrected by an affine transform obtained by tracking three points. For a change in camera vergence, a projective correction, based on tracking four image points, is slightly more precise than an affine correction matrix. It is shown how stereo reconstruction makes it possible to 'hop' a reference frame from one object to another. Any set of four non-coplanar points in the scene may define such a reference frame. It is shown how to keep the reference frame locked onto a set of four points as a stereo head is translated or rotated. These techniques make it possible to reconstruct the shape of an object in in its intrinsic coordinates without having to match new observations to a partially reconstructed description.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hepatocyte Growth Factor Induces Retinal Vascular Permeability via MAP-Kinase and PI-3 Kinase without Altering Retinal Hemodynamics (2006)

HGF increases RVP in a time- and dose-dependent manner at physiologically relevant concentrations with a magnitude and profile similar to that of VEGF, without affecting retinal hemodynamics. Thus, HGF may represent another clinically significant contributor to retinal edema distinct from the actions of VEGF.
Neural stem/progenitor cells as a promising candidate for regenerative therapy of the central nervous system (2012)

Neural transplantation is a promising therapeutic strategy for neurodegenerative diseases and other disorders of the central nervous system (CNS) such as Parkinson and Huntington diseases, multiple sclerosis or stroke. Although cell replacement therapy already went through clinical trials for some of these diseases using fetal human neuroblasts, several significant limitations led to the search for alternative cell sources that would be more suitable for intracerebral transplantation.Taking into account logistical and ethical issues linked to the use of tissue derived from human fetuses, and the immunologically special status of the CNS allowing the occurrence of deleterious immune reactions, neural stem/progenitor cells (NSPCs) appear to be an interesting cell source candidate. In addition to their ability for replacing cell populations lost during the pathological events, NSPCs also display surprising therapeutic effects of neuroprotection and immunomodulation. A better knowledge of the mechanisms involved in these specific characteristics will hopefully lead in the future to a successful use of NSPCs in regenerative medicine for CNS disorders.
Modeling and detection techniques for Counter-Terror Social Network Analysis and Intent Recognition (2009)

In this paper, we describe our approach and initial results on modeling, detection, and tracking of terrorist groups and their intents based on multimedia data. While research on automated information extraction from multimedia data has yielded significant progress in areas such as the extraction of entities, links, and events, less progress has been made in the development of automated tools for analyzing the results of information extraction to ldquoconnect the dots.rdquo hence, our counter-terror social network analysis and intent recognition (CT-SNAIR) work focuses on development of automated techniques and tools for detection and tracking of dynamically-changing terrorist networks as well as recognition of capability and potential intent. In addition to obtaining and working with real data for algorithm development and test, we have a major focus on modeling and simulation of terrorist attacks based on real information about past attacks. We describe the development and application of a new Terror Attack Description Language (TADL), which is used as a basis for modeling and simulation of terrorist attacks. Examples are shown which illustrate the use of TADL and a companion simulator based on a hidden Markov model (HMM) structure to generate transactions for attack scenarios drawn from real events. We also describe our techniques for generating realistic background clutter traffic to enable experiments to estimate performance in the presence of a mix of data. An important part of our effort is to produce scenarios and corpora for use in our own research, which can be shared with a community of researchers in this area. We describe our scenario and corpus development, including specific examples from the September 2004 bombing of the Australian embassy in Jakarta and a fictitious scenario which was developed in a prior project for research in social network analysis. The scenarios can be created by subject matter experts using a graphical editing tool. Given a set of time ordered transactions between actors, we employ social network analysis (SNA) algorithms as a filtering step to divide the actors into distinct communities before determining intent. This helps reduce clutter and enhances the ability to determine activities within a specific group. For modeling and simulation purposes, we generate random networks with structures and properties similar to real-world social networks. Modeling of background traffic is an important step in generating classifiers that can separate harmless activities from suspicious activity. An algorithm for recognition of simulated potential attack scenarios in clutter based on support vector machine (SVM) techniques is presented. We show performance examples, including probability of detection versus probability of false alarm tradeoffs, for a range of system parameters.
Proceedings of the Twenty-Second International Conference on Architectural Support for Programming Languages and Operating Systems (2017)

Welcome! It has been my pleasure and privilege to serve as Program Chair for ASPLOS 2017. We received a record 320 submissions, demonstrating the continued popularity of ASPLOS's focus on multidisciplinary research spanning computer architecture, programming languages, compilers, operating systems, networking, and applications. Reflecting recent trends in systems research, popular topics included memory systems (54 submissions), programming models and languages (50), multicore (47) and heterogeneous (43) architectures, power management (41), security (33), cloud (31), virtualization (28), and GPUs (25). Review Process: All reviewing and discussion, including at the PC meeting, was double blind. As in past ASPLOS conferences, I used a 2-phase review process. In the first phase, each paper received 3 reviews, after which the reviewers discussed the papers online. Papers with at least one review that clearly advocated acceptance or two reviews that were mildly supportive, 162 of the 320 submissions, received at least two additional second round reviews. I monitored reviews to track quality and correct any expertise mismatch. After the second round of reviews were in, all authors were given the opportunity to provide rebuttal feedback. After the rebuttal phase, I assigned each paper a discussion lead to carefully read all the reviews, the rebuttal, and the online comments, and initiate a discussion to decide whether the paper should be accepted, rejected, or discussed at the PC meeting. For a few papers, I solicited post-rebuttal reviews to provide additional insights. The program committee met at the J.J. Pickle Research Center in Austin, Texas on November 7th, 2016. PC members had access to the reviews for all papers for which they had no declared conflict. Paper authors were not revealed during the PC meeting. PC papers were not explicitly identified. Before the title or paper number of any paper being discussed was revealed, conflicted PC members were asked to leave the room. We ultimately accepted a record 53 papers for publication and presentation at this year's ASPLOS, a 16.6% acceptance rate.
Influence of Zinc, Sodium Bicarbonate, and Citric Acid on the Antibacterial Activity of Ovotransferrin Against Escherichia coli O157:H7 and Listeria monocytogenes in Model Systems and Ham (2008)

The influence of NaHCO(3) and citric acid on the antibacterial activity of apo-ovotransferrin in model systems and ham was investigated. The antibacterial activity of 20 mg/mL of ovotransferrin solution with added NaHCO(3) (0, 25, 50, or 100 mM) or citric acid (0.25 or 0.5%) was evaluated against Escherichia coli O157:H7 and Listeria monocytogenes in brain heart infusion broth. The antimicrobial activity of ovotransferrin saturated with Fe(2+) or Zn(2+) against both pathogens was also measured. In addition, ovotransferrin solutions containing either 100 mM NaHCO(3) or 0.5% citric acid were applied to commercial hams inoculated with E. coli O157:H7 or L. monocytogenes and stored at 4 degrees C for 4 wk. The antimicrobial activity of ovotransferrin increased as the concentration of added NaHCO(3) increased. Sodium bicarbonate (100 mM) significantly improved the antibacterial activity of ovotransferrin against E. coli O157:H7 and L. monocytogenes. Citric acid (0.5%) combined with ovotransferrin resulted in a synergistic antibacterial effect against E. coli O157:H7, and L. monocytogenes was susceptible to 0.5% citric acid alone. Sodium bicarbonate diminished the strong antibacterial activity of ovotransferrin + citric acid against E. coli O157:H7, and use of sodium citrate instead of citric acid did not produce any antibacterial activity against the pathogens. The antimicrobial activity of ovotransferrin increased significantly under acidic conditions. The Zn-bound ovotransferrin prevented the growth of L. monocytogenes as detected in the apo-ovotransferrin combined with 100 mM NaHCO(3) treatment, but Fe-bound ovotransferrin had little or no inhibitory activity against E. coli O157:H7 and L. monocytogenes. Ovotransferrin + 100 mM NaHCO(3) did not exhibit any antibacterial activity against the 2 pathogens in commercial hams, whereas ovotransferrin + 0.5% citric acid suppressed the growth of L. monocytogenes in irradiated hams. In conclusion, combinations of ovotransferrin with NaHCO(3), citric acid, or Zn(2+) enhanced the antibacterial activity of ovotransferrin against E. coli and L. monocytogenes, but there are some limitations as discussed for applying ovotransferrin to meat or meat products.
Femtomolar Detection of Prostate-Specific Antigen:  An Immunoassay Based on Surface-Enhanced Raman Scattering and Immunogold Labels (2003)

A novel reagent for low-level detection in immunoadsorbent assays is described. The reagent consists of gold nanoparticles modified to integrate bioselective species (e.g., antibodies) with molecular labels for the generation of intense, biolyte-selective surface-enhanced Raman scattering (SERS) responses in immunoassays and other bioanalytical applications. The reagent is constructed by coating gold nanoparticles (30 nm) with a monolayer of an intrinsically strong Raman scatterer. These monolayer-level labels are bifunctional by design and contain disulfides for chemisorption to the nanoparticle surface and succinimides for coupling to the bioselective species. There are two important elements in this label design; it both minimizes the separation between label and particle surface and maximizes the number of labels on each particle. This approach to labeling also exploits several other advantages of SERS-based labels: narrow spectral bandwidth, resistance to photobleaching and quenching, and long-wavelength excitation of multiple labels with a single excitation source. The strengths of this strategy are demonstrated in the detection of free prostate-specific antigen (PSA) using a sandwich assay format based on monoclonal antibodies. Detection limits of approximately 1 pg/mL in human serum and approximately 4 pg/mL in bovine serum albumin have been achieved with a spectrometer readout time of 60 s. The extension of the method to multianalyte assays (e.g., the simultaneous determination of the many complexed forms of PSA) is discussed.
Animal Models for Adult Dermal Wound Healing (2005)

Wound healing in adult mammals proceeds by a series of overlapping highly coordinated events. Dermal wound repair commences with the arrest of hemorrhage followed by an inflammatory response, re-epithelialization of the wound, and formation of granulation tissue within the wound space, culminating in the production of a scar. In order to study the processes involved in the repair of wounded tissue, we have developed a rodent model utilizing full thickness incisional and excisional dermal wounds, which allow for macroscopic observations and also provide tissue for the histological and immunocytochemical analysis of acute wounds and scarring.
Future mapping: A new approach to managing strategic uncertainty (1987)

We must expect the future to surprise us. Our worst pratfalls occur when we become overly proud of our ability to manage the future. Just when we finally learn to live with inflation, we're plagued by deflation. The oil price trends of the 1970s caught everyone by surprise, but no sooner did industry invest to conserve, than the glut struck. Government budget deficits have reached staggering proportions, but even the most wide‐eyed optimists didn't forecast inflation rates of just 3–4 percent, and interest rates gradually floating downward.
cis- andtrans-Linalool 3,7-Oxides and Methyl Salicylate Glycosides and (Z)-3-Hexenylβ-D-Glucopyranoside as Aroma Precursors from Tea Leaves for Oolong Tea (1996)

Two new alcoholic aroma precursors, cis- and trans-linalool, 3,7-oxides 6-O-beta-D-apiofuranosyl-beta-D-glucopyranosides (1 and 2), as well as two already known compounds, (Z)-3-hexenyl beta-D-glucopyranoside (3) and methyl salicylate 6-O-beta-D-xylopyranosyl-beta-D-glucopyranoside (beta-primeveroside: 4), and another new monoterpendiol glycoside, 8-hydroxygeranyl beta-primeveroside (5) have recently been isolated as aroma precursors in tea leaves (Camellia sinensis var. sinensis cv. Maoxie) ready for oolong tea processing.
Activation of Src-like protein-tyrosine kinase Lyn and its association with phosphatidylinositol 3-kinase upon B-cell antigen receptor-mediated signaling. (1992)

Crosslinking of membrane-bound immunoglobulins, which are B-cell antigen receptors, causes proliferation and differentiation of B cells or the inhibition of their growth. The receptor-mediated signaling involves tyrosine phosphorylation of cellular proteins. The Src-like protein-tyrosine kinase Lyn is expressed preferentially in B cells and is an intracytoplasmic constituent of the B-cell antigen receptor complex. Crosslinking of membrane-bound immunoglobulin M with antibody induced rapid increases in the kinase activities of Lyn and Lyn-associated phosphatidylinositol 3-kinase. Crosslinking of B-cell antigen receptor also induced association of Lyn with an 85-kDa noncatalytic subunit of phosphatidylinositol 3-kinase. Thus, Lyn is functionally associated with membrane-bound immunoglobulin M and seems likely to participate in B-cell antigen receptor-mediated signaling.
Supporting reference and dirty bits in SPUR's virtual address cache (1989)

Virtual address caches can provide faster access times than physical address caches, because translation is only required on cache misses. However, because we don't check the translation information on each cache access, maintaining reference and dirty bits is more difficult. In this paper we examine the trade-offs in supporting reference and dirty bits in a virtual address cache. We use measurements from a uniprocessor SPUR prototype to evaluate different alternatives. The prototype's built-in performance counters make it easy to determine the frequency of important events and to calculate performance metrics.
High performance cache replacement using re-reference interval prediction (RRIP) (2010)

Practical cache replacement policies attempt to emulate optimal replacement by predicting the re-reference interval of a cache block. The commonly used LRU replacement policy always predicts a near-immediate re-reference interval on cache hits and misses. Applications that exhibit a distant re-reference interval perform badly under LRU. Such applications usually have a working-set larger than the cache or have frequent bursts of references to non-temporal data (called scans). To improve the performance of such workloads, this paper proposes cache replacement using Re-reference Interval Prediction (RRIP). We propose Static RRIP (SRRIP) that is scan-resistant and Dynamic RRIP (DRRIP) that is both scan-resistant and thrash-resistant. Both RRIP policies require only 2-bits per cache block and easily integrate into existing LRU approximations found in modern processors. Our evaluations using PC games, multimedia, server and SPEC CPU2006 workloads on a single-core processor with a 2MB last-level cache (LLC) show that both SRRIP and DRRIP outperform LRU replacement on the throughput metric by an average of 4% and 10% respectively. Our evaluations with over 1000 multi-programmed workloads on a 4-core CMP with an 8MB shared LLC show that SRRIP and DRRIP outperform LRU replacement on the throughput metric by an average of 7% and 9% respectively. We also show that RRIP outperforms LFU, the state-of the art scan-resistant replacement algorithm to-date. For the cache configurations under study, RRIP requires 2X less hardware than LRU and 2.5X less hardware than LFU.
Effects of acamprosate on memory in healthy young subjects. (1999)

The present study supports the hypothesis that acamprosate impairs memory functions. This is in keeping with the concept of acamprosate acting as NMDA receptor antagonist. The limitations of the study are discussed.
O-GlcNAcase Uses Substrate-assisted Catalysis (2005)

The post-translational modification of serine and threonine residues of nucleocytoplasmic proteins with 2-acetamido-2-deoxy-d-glucopyranose (GlcNAc) is a reversible process implicated in multiple cellular processes. The enzyme O-GlcNAcase catalyzes the cleavage of beta-O-linked GlcNAc (O-GlcNAc) from modified proteins and is a member of the family 84 glycoside hydrolases. The family 20 beta-hexosaminidases bear no apparent sequence similarity yet are functionally related to O-GlcNAcase because both enzymes cleave terminal GlcNAc residues from glycoconjugates. Lysosomal beta-hexosaminidase is known to use substrate-assisted catalysis involving the 2-acetamido group of the substrate; however, the catalytic mechanism of human O-GlcNAcase is unknown. By using a series of 4-methylumbelliferyl 2-deoxy-2-N-fluoroacetyl-beta-D-glucopyranoside substrates, Taft-like linear free energy analyses of these enzymes indicates that O-GlcNAcase uses a catalytic mechanism involving anchimeric assistance. Consistent with this proposal, 1,2-dideoxy-2'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2'-thiazoline, an inhibitor that mimics the oxazoline intermediate proposed in the catalytic mechanism of family 20 glycoside hydrolases, is shown to act as a potent competitive inhibitor of both O-GlcNAcase (K(I) = 0.070 microm) and beta-hexosaminidase (K = 0.070 microm). A series of 1,2-dideoxy-2'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2'-thiazoline analogues were prepared, and one inhibitor demonstrated a remarkable 1500-fold selectivity for O-GlcNAcase (K(I) = 0.230 microm) over beta-hexosaminidase (K(I) = 340 microm). These inhibitors are cell permeable and modulate the activity of O-GlcNAcase in tissue culture. Because both enzymes have vital roles in organismal health, these potent and selective inhibitors of O-GlcNAcase should prove useful in studying the role of this enzyme at the organismal level without generating a complex chemical phenotype stemming from concomitant inhibition of beta-hexosaminidase.
Pravastatin Attenuates Left Ventricular Remodeling and Diastolic Dysfunction in Angiotensin II-Induced Hypertensive Mice (2008)

The beneficial effects of pravastatin on DHF and structural remodeling are through cholesterol- independent mechanism of statins or "pleiotropic" effects of statins involving improving or restoring endothelial function and decreasing vascular inflammation. These findings suggest the potential involvement of ROCK1. Thus, treatment with pravastatin might be beneficial in patients with DHF.