gebhart/patrepeval huggingface dataset:
Taurolidine-Fibrin-Sealant-Matrix using spray application for local treatment of brain tumors. (2004)

Malignant gliomas tend to recur in the vast majority of cases. Recurrent gliomas may arise from vital tumor cells present in this zone around the resection margin. It appears promising to combine tumor resection with local chemotherapy using an antineoplastic, but non-toxic agent. Taurolidine exerts a selective antineoplastic effect by induction of programmed cell death and has anti-angiogenic activity. Fibrin sealant is completely degradable and firmly adheres to brain tissue, suggesting that it would provide a suitable matrix for taurolidine delivery--a Taurolidine-Fibrin-Sealant-Matrix (TFM)--in the local treatment of brain tumors. The potential of local delivery of taurolidine out of a fibrin sealant matrix was investigated. Taurolidine could be suspended homogeneously in both the thrombin and the procoagulant protein components of the fibrin sealant. The fibrin sealant matrix was a suitable carrier for the suspension of taurolidine at a concentration that ensured the release of therapeutically effective amounts of the drug over a period of 2 weeks in vitro. The antineoplastic action of taurolidine was not affected by embedding in the fibrin sealant matrix. The described drug delivery system may be suitable for local taurolidine treatment of brain tumors following complete or partial resection or of tumors that are non-resectable because of their location.
Modeling the Effects of prl Mutations on the Escherichia coli SecY Complex (2005)

The apparatus responsible for translocation of proteins across bacterial membranes is the conserved SecY complex, consisting of SecY, SecE, and SecG. Prior genetic analysis provided insight into the mechanisms of protein export, as well as the interactions between the component proteins. In particular, the prl suppressor alleles of secE and secY, which allow export of secretory proteins with defective signal sequences, have proven particularly useful. Here, we report the isolation of novel mutations in secE and secY, as well as the phenotypic effects of combinations of prl mutations. These new alleles, as well as previously characterized prl mutations, were analyzed in light of the recently published crystal structure of the archaeal SecY complex. Our results support and expand a model of Prl suppressor activity that proposes that all of the prlA and prlG alleles either destabilize the closed state of the channel or stabilize the open form. These mutants thus allow channel opening to occur without the triggering event of signal sequence binding that is required in a wild-type complex.
THE METABOLISM OF TUMORS IN THE BODY (1927)

In this contribution we discuss the question of whether tumor cells in living animals can be killed off through lack of energy, and the related question of how the tumors are supplied with oxygen and glucose in the body.
CD146 Protein as a Marker to Predict Postoperative Liver Metastasis in Colorectal Cancer (2013)

CD146 protein may be a potential biomarker for the postoperative liver metastasis of colorectal cancer.
Lithiation of 2-Heterosubstituted Pyridines with BuLi−LiDMAE:  Evidence for Regiospecificity at C-6 (2001)

The determination of the initial deprotonation site of 2-chloro- and 2-methoxypyridine during reaction with BuLi-LiDMAE has been investigated. A series of experiments on deuterated regioisomers revealed a direct lithiation at C-6 excluding a potential first classical ortholithiation and lithium equilibration in the reaction medium. These results suggested that the formation of lithium aggregates at the neighboring of the pyridinic nitrogen atom favored BuLi delivery at C-6 as well as 6-lithio intermediate stabilization.
Feedback controversy stops here (2009)

In this issue of Blood, Kravtsov and colleagues provide conclusive evidence for factor XII-independent activation of factor XI in plasma.
Superiority of Electrocautery Over the Suture Method for Achieving Cervical Cone Bed Hemostasis (2003)

In Brief OBJECTIVE To compare the efficacy of electrocautery with that of the suture method for achieving hemostasis of the cervical cone bed. METHODS We performed a retrospective chart review of all patients who underwent cold-knife conization of the cervix over a 5-year period. Patients were categorized into two groups: the cautery group, in which the cone bed was electrocauterized with a hand-held electrocoagulation device; and the suture group, in which hemostasis was achieved by a continuous locking suture placed circumferentially around the cone bed. Outcome measures evaluated include estimated blood loss, operative time, and incidence of complications, including secondary hemorrhage, cervicitis, and cervical stenosis. Data were analyzed by Student t test, χ2 test, linear regression, and multiple logistic regression where appropriate. RESULTS There were 156 women in the cautery group and 35 in the suture group. The cautery group had significantly lower estimated blood loss (27 mL versus 101 mL; P < .01) and shorter operative time (34 versus 43 minutes; P < .01) than the suture group. The procedure-related complication rate was 6.4% in the cautery group, compared with 14.3% in the suture group (P = nonsignificant). A higher use of lateral sutures, vasopressors, and thrombotic agents was seen in the cautery group. However, even after adjusting for these variables, mean estimated blood loss (33 mL, P < .01) and mean operative time (34 minutes, P < .01) were significantly less in the cautery group than in the suture group. CONCLUSIONS Cauterization of the cone bed is superior to suture as a method of achieving hemostasis, with significantly less blood loss and shorter operative time. Electrocautery of the cervical cone bed provides effective hemostasis and requires shorter operative time compared with the suture method after cold-knife cervical conization.
Biochemistry and Clinical Role of Trypsinogens and Pancreatic Secretory Trypsin Inhibitor (2006)

Trypsinogens and PSTI/TATI/SPINK1 are expressed, usually together, at high levels by the pancreas but also by many other normal and malignant tissues. The present review describes studies on the expression and putative functions of trypsinogens and PSTI/TATI/SPINK1 in the human body. The clinical aspects are discussed, including the correlations between expression of trypsinogens and PSTI/TATI/SPINK1 in tissues, serum, and urine of patients with pancreatitis or cancer and clinicopathological characteristics, i.e., the roles of trypsinogens and PSTI/TATI/SPINK1 in spontaneous and hereditary pancreatitis, tumor progression, and prognosis.
Efficient exploitation of similar subexpressions for query processing (2007)

Complex queries often contain common or similar subexpressions, either within a single query or among multiple queries submitted as a batch. If so, query execution time can be improved by evaluating a common subexpression once and reusing the result in multiple places. However, current query optimizers do not recognize and exploit similar subexpressions, even within the same query. We present an efficient, scalable, and principled solution to this long-standing optimization problem. We introduce a light-weight and effective mechanism to detect potential sharing opportunities among expressions. Candidate covering subexpressions are constructed and optimization is resumed to determine which, if any, such subexpressions to include in the final query plan. The chosen subexpression(s) are computed only once and the results are reused to answer other parts of queries. Our solution automatically applies to optimization of query batches, nested queries, and maintenance of multiple materialized views. It is the first comprehensive solution covering all aspects of the problem: detection, construction, and cost-based optimization. Experiments on Microsoft SQL Server show significant performance improvements with minimal overhead.
Vascular MAD s: Two novel MAD -related genes selectively inducible by flow in human vascular endothelium (1997)

Vascular endothelium is an important transducer and integrator of both humoral and biomechanical stimuli within the cardiovascular system. Utilizing a differential display approach, we have identified two genes, Smad6 and Smad7, encoding members of the MAD-related family of molecules, selectively induced in cultured human vascular endothelial cells by steady laminar shear stress, a physiologic fluid mechanical stimulus. MAD-related proteins are a recently identified family of intracellular proteins that are thought to be essential components in the signaling pathways of the serine/threonine kinase receptors of the transforming growth factor beta superfamily. Smad6 and Smad7 possess unique structural features (compared with previously described MADs), and they can physically interact with each other, and, in the case of Smad6, with other known human MAD species, in endothelial cells. Transient expression of Smad6 or Smad7 in vascular endothelial cells inhibits the activation of a transfected reporter gene in response to both TGF-beta and fluid mechanical stimulation. Both Smad6 and Smad7 exhibit a selective pattern of expression in human vascular endothelium in vivo as detected by immunohistochemistry and in situ hybridization. Thus, Smad6 and Smad7 constitute a novel class of MAD-related proteins, termed vascular MADs, that are induced by fluid mechanical forces and can modulate gene expression in response to both humoral and biomechanical stimulation in vascular endothelium.
SCsafe: Logging sequential consistency violations continuously and precisely (2016)

Sequential Consistency Violations (SCV) in relaxed consistency machines cause programs to malfunction and are hard to debug. While there are proposals for detecting and recording SCVs, they are limited in that they end program execution after detecting the first SCV because the program is now non-SC. Therefore, they cannot be used in production runs. In addition, such proposals rely on complicated hardware. To address these problems, this paper proposes the first architecture that detects and logs SCVs in a continuous manner, while retaining SC. In addition, the scheme is precise and uses substantially simpler hardware. The scheme, called SCsafe, operates continously because, after SCV detection and logging, it recovers and resumes execution while retaining SC. As a result, it can be used in production runs. In addition, SCsafe is precise in that it identifies only true SCVs - rather than dependence cycles due to false sharing. Finally, SCsafe's hardware is mostly local to each processor, and uses known recovery techniques. We evaluate SCsafe using simulations of 16-processor multicores with Total Store Order or Release Consistency. In codes with SCVs, SCsafe detects and reports SCVs while enforcing SC during the execution. In codes with few SCVs, it adds a negligible performance overhead. Finally, SCsafe is scalable with the processor count.
Wedge transducer design for two-dimensional ultrasonic manipulation in a microfluidic chip (2008)

We analyze and optimize the design of wedge transducers used for the excitation of resonances in the channel of a microfluidic chip in order to efficiently manipulate particles or cells in more than one dimension. The design procedure is based on (1) theoretical modeling of acoustic resonances in the transducer–chip system and calculation of the force fields in the fluid channel, (2) full-system resonance characterization by impedance spectroscopy and (3) image analysis of the particle distribution after ultrasonic manipulation. We optimize the transducer design in terms of actuation frequency, wedge angle and placement on top of the chip, and we characterize and compare the coupling effects in orthogonal directions between single- and dual-frequency ultrasonic actuation. The design results are verified by demonstrating arraying and alignment of particles in two dimensions. Since the device is compatible with high-resolution optical microscopy, the target application is dynamic cell characterization combined with improved microfluidic sample transport.
Molecular Pathways in Prostate Cancer (2013)

The identification of specific molecular markers for prostate cancer may lead to its earliest detection and better prediction of its behavior. The better understanding of the molecular events affecting prostate cancer progression may result in the introduction of new drugs to target these events thus providing a potential cure and a tool for prevention of this very common disease.
mTOR: A Potential Therapeutic Target in Osteoarthritis? (2015)

Osteoarthritis (OA) is a chronic degenerative joint disease characterized by the progressive loss of articular cartilage, remodeling of the subchondral bone, and synovial inflammation. Mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase that controls critical cellular processes such as growth, proliferation, and protein synthesis. Recent studies suggest that mTOR plays a vital role in cartilage growth and development and in altering the articular cartilage homeostasis as well as contributing to the process of cartilage degeneration associated with OA. Both pharmacological inhibition and genetic deletion of mTOR have been shown to reduce the severity of OA in preclinical mouse models. In this review article, we discuss the roles of mTOR in cartilage development, in maintaining articular cartilage homeostasis, and its potential as an OA therapeutic target.
Regional Magnetic Resonance Imaging Lesion Burden and Cognitive Function in Multiple Sclerosis (2001)

<h3>Objective</h3> To investigate the relationship between magnetic resonance imaging regional lesion burden and cognitive performance in multiple sclerosis (MS) over a 4-year follow-up period. <h3>Design</h3> Twenty-eight patients with MS underwent magnetic resonance imaging and took the Brief, Repeatable Battery of Neuropsychological Tests in Multiple Sclerosis at baseline, 1-year, and 4-year follow-up. An automated 3-dimensional lesion detection method was used to identify MS lesions within anatomical regions on proton density T2-weighted images. The relationship between magnetic resonance imaging regional lesion volumes and the Brief, Repeatable Battery of Neuropsychological Tests in Multiple Sclerosis results was examined using regression analyses. <h3>Results</h3> At all time points, frontal lesion volume represented the greatest proportion of total lesion volume, and the percentage of white matter classified as lesion was also highest in frontal and parietal regions. On neuropsychological testing, when compared with age- and educational level–matched control subjects, patients with MS showed significant impairment on tests of sustained attention, processing speed, and verbal memory (<i>P</i>&lt;.001). Performance on these measures was negatively correlated with MS lesion volume in frontal and parietal regions at baseline, 1-year, and 4-year follow-up (<i>R</i>= −0.55 to −0.73,<i>P</i>&lt;.001). <h3>Conclusions</h3> Multiple sclerosis lesions show a propensity for frontal and parietal white matter. Lesion burden in these areas was strongly associated with performance on tasks requiring sustained complex attention and working verbal memory. This relationship was consistent over a 4-year period, suggesting that disruption of frontoparietal subcortical networks may underlie the pattern of neuropsychological impairment seen in many patients with MS.
Run-time hardware trojan detection using performance counters (2017)

There has been a growing trend in recent years to outsource various aspects of the semiconductor design and manufacturing flow to different parties spread across the globe. Such outsourcing increases the risk of adversaries adding malicious logic, referred to as hardware Trojans, to the original design. In this paper, we introduce a run-time hardware Trojan detection method for microprocessor cores. This approach uses Half-space trees to detect the activation of Trojans that introduce abnormal patterns in the data streams obtained from performance counters. It does not require any additional hardware or the monitoring of a large number of internal signals. We evaluate our method by detecting the activation of Trojans that cause denial-of-service, the degradation of system performance, and change in functionality of a microprocessor core. Results obtained using the OpenSPARC T1 core and an FPGA prototyping framework show that Trojan activation is detected with true positive ratio of above 0.9 and a false positive ratio of below 0.1 for most of the implemented Trojans.
Alterations at the carboxyl terminus change assembly and secretion properties of the B subunit of Escherichia coli heat-labile enterotoxin (1987)

The gene encoding the B subunit of heat-labile enterotoxin (etxB) was mutated at its 3' end by targeted addition of random nucleotide sequences. Gene products from five mutated etxB genes, all of which were shown to encode B subunits with short carboxy-terminal amino acid extensions, were analyzed with respect to a range of functional and structural properties. One class of altered B subunits, exemplified by EtxB124 and EtxB138, which both have seven extra amino acid residues, were found to be specifically defective in their ability to stably associate with A subunits and form holotoxin. Other altered B subunits were less subtlely affected by extensions at their C termini and were, in addition to their failure to associate with A subunits, unable to translocate into the periplasm of Escherichia coli, to pentamerize, or to bind to GM1 ganglioside. This suggests that the carboxy-terminal domain of EtxB mediates A subunit-B subunit interaction.
CD4+ T-cell death induced by infectious and noninfectious HIV-1: role of type 1 interferon-dependent, TRAIL/DR5-mediated apoptosis (2005)

It has been proposed that direct and indirect mechanisms contribute to the unresolved issue of CD4(+) T-cell depletion that results from HIV-1 infection. We recently reported that plasma levels of tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) are elevated in HIV-1-infected patients and that they correlate with viral load. The present study investigates the expression of TRAIL death receptor 5 (DR5) in the peripheral-blood mononuclear cells (PBMCs) of HIV-1-infected patients and its role in CD4(+) T-cell death. DR5 expression was elevated and associated with the apoptotic marker annexin V. Apoptosis was reduced in CD4(+) T cells when cultured with anti-DR5 antibody. CD4(+), but not CD8(+), T cells from uninfected donors expressed TRAIL, DR5, and activated caspase-3 when cultured with infectious or noninfectious HIV-1, resulting in preferential apoptosis of CD4(+) T cells. TRAIL, caspase-3 expression, and apoptosis were type 1 interferon (IFN) dependent. Induction of apoptosis and DR5 expression required glycoprotein 120 (gp120)-CD4 interaction. Finally, we analyzed DR5 expression by CD4(+) T cells in highly active antiretroviral therapy (HAART)-treated patients. The decreased viral loads and increased CD4 counts of HAART-responsive patients were associated with a decrease in DR5 mRNA expression by CD4(+) T lymphocytes. We propose a novel model in which a type 1 IFN-regulated TRAIL /DR5 mechanism induces apoptosis of HIV-1-exposed CD4(+) T cells.
Evolution of Lipidic Structures during Model Membrane Fusion and the Relation of This Process to Cell Membrane Fusion (1997)

The sequence of events involved in poly(ethylene glycol)-mediated fusion of small unilamellar vesicles (SUVs) has been studied. Fusion events were monitored using light scattering for vesicle aggregation, the fluorescence lifetime of membrane probe lipids (DPHpPC and NBD-PS) for membrane mixing, the aqueous fluorescent marker (Tb3+/DPA and H+/HPTS) for contents mixing; and quasi-elastic light scattering for the change in the size of vesicles. Poly(ethylene glycol) is a highly hydrated polymer that can bring vesicle membranes to near molecular contact but is unable to induce vesicle fusion without manipulations that reduce packing density and encourage molecular motions in the backbone regions of both contacting membrane leaflets. Once this condition is achieved, the sequence of events involved in vesicle fusion is shown here to be (1) outer leaflet mixing accompanied by (2) transient pore formation, both occurring on a time scale of approximately 10 s and leading to an initial, reversible intermediate; (3) a 1-3 min delay leading to formation of a fusion-committed second intermediate; (4) inner leaflet mixing on a time scale of ca. 150 s; and (5) contents mixing on a time scale of 150-300 s. Inner leaflet mixing, which has never before been shown to be distinct from outer leaflet mixing, begins simultaneously with, but is completed before, contents mixing. Fusion products, which seem to be large vesicles, are estimated to be formed from four to six SUVs. The fusion intermediates are shown to have merged outer leaflets and distinct inner leaflets prior to formation of fusion pores. Using quasi-elastic light scattering, the initial intermediate was shown to revert to SUVs upon removal of PEG, while the second intermediate irreversibly continued to a fusion pore in the presence or absence of PEG. The sequence of events for this pure lipid bilayer fusion process shows remarkable homology to what is known about the sequence of protein-mediated cell membrane fusion events, suggesting a commonality between these two processes.
Robust recovery of camera rotation from three frames (1996)

Computing camera rotation from image sequences can be used for image stabilization, and when the camera rotation is known the computation of translation and scene structure are much simplified as well. A robust approach for recovering camera rotation is presented, which does not assume any specific scene structure (e.g. no planar surface is required), and which avoids prior computation of the epipole. Given two images taken from two different viewing positions, the rotation matrix between the images can be computed from any three homography matrices. The homographies are computed using the trilinear tensor which describes the relations between the projections of a 3D point into three images. The entire computation is linear for small angles, and is therefore fast and stable. Iterating the linear computation can then be used to recover larger rotations as well.