gebhart/patrepeval huggingface dataset:
Morphological Characterization of Intracranial Aneurysms Using 3-D Moment Invariants (2007)

Rupture of intracranial saccular aneurysms is the most common cause of spontaneous subarachnoid hemorrhage, which has significant morbidity and mortality. Although there is still controversy regarding the decision on which unruptured aneurysms should be treated, this is based primarily on their size. Nonetheless, many large lesions do not rupture whereas some small ones do. It is commonly accepted that hemodynamical factors are important to better understand the natural history of cerebral aneurysms. However, it might not always be practical to carry out a detailed computational analysis of such factors if a prompt assessment is required. Since shape is likely to be dependent on the balance between hemodynamic forces and the aneurysmal surrounding environment, an appropriate morphological 3-D characterization is likely to provide a practical surrogate to quickly evaluate the risk of rupture. In this paper, an efficient and novel methodology for 3-D shape characterization of cerebral aneurysms is described. The aneurysms are isolated by taking into account a portion of their adjacent vessels. Two methods to characterize the morphology of the aneurysms models using moment invariants have been considered: geometrical moment invariants (GMI) and Zernike moment invariants (ZMI). The results have been validated in a database containing 53 patients with a total of 31 ruptured aneurysms and 24 unruptured aneurysms. It has been found that ZMI indices are more robust than GMI, and seem to provide a reliable way to discriminate between ruptured and unruptured aneurysms. Correct rupture prediction rates of approximately equal to 80% were achieved in contrast to 66% that is found when the aspect ratio index is considered.
Reverse time migration using vector offset output to improve subsalt imaging — A case study at the Walker Ridge GOM (2011)

Technology advances, such as WAZ/FAZ acquisition, reverse time migration (RTM) and iterative salt imaging in model building, have greatly improved subsalt image quality. However subsalt imaging under complex salt overburden is still challenging. The fundamental issue lies with the imperfect illumination from limited acquisition. In the poor illumination zones, the migration artifacts and coherent noises, such as residual multiples and converted waves, become prevalent and can severely contaminate the images and mislead the interpretation. Migration vector offset output provides a domain in which the true imaging energy and noise can be separated as the imaging contributions focus in different vector offset tiles according to the subsurface structure orientation (azimuth and dip). Thus selective stacking the migration vector offset outputs based on the structural interpretation can achieve migration noise reduction and improve subsalt images.
Order-parameter-based Monte Carlo simulation of crystallization (2006)

A Monte Carlo simulation method is presented for simulation of phase transitions, with emphasis on the study of crystallization. The method relies on a random walk in order parameter Phi(q(N)) space to calculate a free energy profile between the two coexisting phases. The energy and volume data generated over the course of the simulation are subsequently reweighed to identify the precise conditions for phase coexistence. The usefulness of the method is demonstrated in the context of crystallization of a purely repulsive Lennard-Jones system. A systematic analysis of precritical and critical nuclei as a function of supercooling reveals a gradual change from a bcc to a fcc structure inside the crystalline nucleus as it grows at large degrees of supercooling. The method is generally applicable and is expected to find applications in systems for which two or more coexisting phases can be distinguished through one or more order parameters.
Issues in secure distributed operating system design (2003)

Recent advances in the design of secure distributed operating systems are discussed. The two major design approaches for building a secure distributed operating system are outlined. Issues pertaining to the selection of the security model, design of mandatory access checks, design of discretionary access checks, and network security are discussed. Finally, examples of projects in the area of secure distributed operating systems are surveyed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The anthropomorphic flutist robot WF-4R: from mechanical to perceptual improvements (2005)

One of the earliest motivations for developing humanoid robots centered on creating robots that may coexist with humans in environments created for human beings. For several years, at Waseda University, the development of the anthropomorphic flutist player has been focused on improving the musical interaction between the human and the robot to clarify the human flute playing and to propose novel assisted music teaching tools. In this paper, a new architecture for autonomously transferring skills from robot to human using the flutist robot is introduced. Furthermore, the new version of the flutist robot, the WF-4R (Waseda Flutist No.4 Refined) is presented; where the arm system was added to assure the positioning accuracy of the flute and the development of a melody recognition system to enable the robot to interact with students at the same logical level of perception. An experimental setup has been performed in order to verify the effectiveness of both mechanical and perceptual systems. As a result, using the arms system, we have assured the repetitiveness of the flute positioning. Furthermore, the implemented music recognition system was able to recognize the melody of flutist players (an overall recognition rate of 90%); demonstrating that HMM (usually used for speech recognition) is also effective for flute melody identification.
Describing Mimo Designs For Rapid Prototyping In The Bee Environment (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Phase I Pharmacokinetic and Pharmacodynamic Study of Recombinant Human Endostatin in Patients With Advanced Solid Tumors (2003)

Endostatin given daily as a 1-hour intravenous infusion was well tolerated without dose-limiting toxicity at doses up to 300 mg/m2.
Fatty Acid and Carotenoid Composition of Gac (<i>Momordica cochinchinensis</i> Spreng) Fruit (2003)

In this study, we analyzed fatty acid and carotenoid composition of fruit tissues, including seed (which are surrounded by a bright red, oily aril) of Momordica cochinchinensis Spreng, known as gac in Vietnam. Carotenoid content was analyzed by reversed-phase HPLC, using a C(30) column and a method separating cis- and trans-isomers of the major carotenoids in this fruit. Mean values obtained in aril tissues were 1342 microg trans-, 204 microg cis-, and 2227 microg total lycopene; 597 microg trans-, 39 microg cis-, and 718 microg total beta-carotene; and 107 microg alpha-carotene/g FW. Mesocarp contained 11 microg trans-, 5 microg cis-beta-carotene/g FW, trace amounts of alpha-carotene, and no lycopene. Gac aril contained 22% fatty acids by weight, composed of 32% oleic, 29% palmitic, and 28% linoleic acids. Seeds contained primarily stearic acid (60.5%), smaller amounts of linoleic (20%), oleic (9%), and palmitic (5-6%) acids, and trace amounts of arachidic, cis-vaccenic, linolenic, and palmitoleic, eicosa-11-enoic acids, and eicosa-13-enoic (in one fruit only) acids.
Changing the institutional and policy environment for small enterprise development in Africa (1994)

The changes faced by African business people over recent years have provided opportunities in the form of increased export markets and threats in the form of competition from new labour-force entrants. This article, which is adapted from the keynote speech of the conference of donor agencies for small and medium enterprises in Abidjan in 1993, outlines some of the changes that have taken place in many African countries following structural adjustment programmes. It describes changes in the markets in which firms operate, in the business environment and in the institutions affecting small enterprises.
Simulation and experiment research on human riding comfort for vehicle vibration in dynamic environment (2008)

According to the needs of simulation research of human riding comfort for vehicle vibration in dynamic environment, the mathematical model of random road is established using white noise. The model has been subsequently introduced into Matlab/Simulink to simulate several different incentive forms of random road, and the time-domain model of random road excitation-according with Chinese Highway Standard is developed. Moreover, vehicle dynamics model is set up in dynamics analysis software ADAMS, and human biological structure model-coincident with Chinese body characteristics is done alike in ADAMS/LifeMOD. These two models are assembled to construct a biomechanical simulation model of human-vehicle system. Aimed to get vertical vibration response of vehicle and human at different speeds and different road levels, the biomechanical simulation model of human-vehicle system is imitatively analyzed by introduction of random road excitation model. Furthermore, an evaluation study on human riding comfort for vehicle vibration in dynamic environment is presented on the basis of national standard GB/T4970. The objective evaluation test on human vibration comfort is carried out on random vibration platform SA30-S802/ST, the experimental results showed that the results of the objective evaluation test basically tally with the simulation results. The research above provides an important method for the design and analysis of vehicle man-machine interface in dynamic environment and has important technical significance for rapid evaluation of human driving comfort.
Ten-Year Results of a Comparison of Conservation with Mastectomy in the Treatment of Stage I and II Breast Cancer (1995)

In the management of stage I and II breast cancer, breast conservation with lumpectomy and radiation offers results at 10 years that are equivalent to those with mastectomy.
Modulatory effects of dextran sulfate and fucoidan on binding and channel properties of AMPA receptors isolated from rat brain (2006)

Abstract Previous work showed that the glycosaminoglycan (GAG) dextran sulfate (500 kDa) altered the binding and channel properties of α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPA)‐type glutamate receptors. The current study compared the effects of dextran sulfate with another GAG, fucoidan (100–180 kDa), to determine whether GAG‐mediated changes in high‐affinity binding of AMPA receptors have a concomitant influence on specific channel properties. Dextran sulfate was more potent in inhibiting high‐affinity AMPA binding to solubilized receptors (EC 50 of 7 nM) compared to fucoidan (EC 50 of 124 nM). Similarly, dextran sulfate was more potent in modulating the channel properties of purified and reconstituted AMPA receptors. Dextran sulfate, at 1 μg/ml (2 nM), produced a three to fourfold increase in open channel probability and a threefold increase in mean burst duration of channel activity elicited by 283 nM AMPA. The mean open time was increased by two to threefold and closed times were decreased by two to eightfold. Fucoidan produced similar effects at a concentration many times higher than that of dextran sulfate. Dextran sulfate and fucoidan had no effect on the single channel conductance or the ability of a specific antagonist to block AMPA channels. The effects of GAGs on multichannel patches showed an interactive channel gating behavior resulting in macroscopic currents with long lived open channel life times. These findings suggest that GAG components of proteoglycans can interact with and alter the binding affinity of AMPA receptors and modulate their functional properties. Synapse 60:456–464, 2006. © 2006 Wiley‐Liss, Inc.
Toward a new generation of vaccines: The anti-cytokine therapeutic vaccines (2001)

Pathological conditions, such as cancers, viral infections, and autoimmune diseases, are associated with abnormal cytokine production, and the morbidity associated with many medical disorders is often directly a result of cytokine production. Because of the absence of negative feedback control occurring in some pathophysiologic situations, a given cytokine may flood and accumulate in the extracellular compartment of tissues or tumors thereby impairing the cytokine network homeostasis and contributing to local pathogenesis. To evaluate whether the rise of anti-cytokine Abs by vaccination is an effective way to treat these pathological conditions without being harmful to the organism, we have analyzed each step of the cytokine process (involving cytokine production, target response, and feedback regulation) and have considered them in the local context of effector--target cell microenvironment and in the overall context of the macroenvironment of the immune system of the organism. In pathologic tissues, Abs of high affinity, as raised by anti-cytokine vaccination, should neutralize the pool of cytokines ectopically accumulated in the extracellular compartment, thus counteracting their pathogenic effects. In contrast, the same Abs should not interfere with cytokine processes occurring in normal tissues, because under physiologic conditions cytokine production by effector cells (induced by activation but controlled by negative feedback regulation) does not accumulate in the extracellular compartment. These concepts are consistent with results showing that following animal and human anti-cytokine vaccination, induction of high-affinity Abs has proven to be safe and effective and encourages this approach as a pioneering avenue of therapy.
Dietary fatty acids and susceptibility to multiple sclerosis (2018)

Dietary SCFAs constitute interesting candidates as safe and potent add-on therapy in the immunomodulatory treatment armamentarium for relapsing-remitting MS.
Growth- and differentiation-associated expression of bcl-2 in B-chronic lymphocytic leukemia cells (1992)

The bcl-2 gene is translocated into the Ig loci in about 80% of human follicular lymphomas and in 10% of B-type chronic lymphocytic leukemias (B-CLL), resulting in a high level of expression. We have compared the expression of bcl-2 transcripts and protein in B-CLL cells in their normal equivalent CD5+ B cells and in normal B-cell populations representative of different in vivo and in vitro stages of activation and proliferation. We report here that bcl-2 was expressed in 11 of 11 cases of CD5+ B-CLL clones, contrasting with the absent expression in normal CD5+ B cells. Activation of 173 and 183 B-CLL cells by phorbol esters (12-O-tetradecanoylphorbol-13-acetate [TPA]) to IgM secretion without concomitant DNA synthesis resulted in a rapid but transient downregulation of bcl-2 expression. In contrast, the reduction of bcl-2 at both the messenger RNA and protein levels was sustained after mitogenic stimulation, suggesting that bcl-2 expression and proliferation are inversely related in these cells. This notion was further supported by immunocytochemical analysis showing that bcl-2 was primarily expressed in small resting lymphocytes and in cells differentiating to the plasma cell stage, but less expressed in Ki67-positive proliferating B blasts. Moreover, it was also supported by the low level of bcl-2 in exponentially growing Epstein-Barr virus-carrying lymphoblastoid and B-CLL cell lines. The regulation of bcl-2 expression in B-CLL resembled that of normal tonsillar follicular B cells, in which a high level of expression was found in resting mantle zone B cells but not in the proliferating germinal center B cells. Based on these findings and the role of bcl-2 in maintaining B-cell memory, we propose that the phenotype of B-CLL cells corresponds to a mantle zone memory-type B cell.
Oral Amphotericin for Candidiasis in Patients With Hematologic Neoplasms (1979)

Autopsy examinations were conducted in 72 patients with hematologic malignant neoplasms who received antibacterial therapy before their deaths. These patients were participants in a large double-blind study designed to assess the efficacy of oral amphotericin B in decreasing the incidence of candidal infection. The patients received either 50 mg of amphotericin B orally four times a day, or they received a matching placebo. Eight of 33 patients (24%) who had received placebo and two of 39 (5%) who had received amphotericin had histopathologic evidence of disseminated candidiasis. We conclude that in these patients with hematologic malignant neoplasms who received antibiotics within two weeks of death, the concomitant oral administration of amphotericin was effective in decreasing the incidence of systemic candidal infections, indicating that the gastrointestinal tract serves as a portal of entry for Candida albicans.
INTRINSIC EVALUATION OF TEXT MINING TOOLS MAY NOT PREDICT PERFORMANCE ON REALISTIC TASKS (2007)

Biomedical text mining and other automated techniques are beginning to achieve performance which suggests that they could be applied to aid database curators. However, few studies have evaluated how these systems might work in practice. In this article we focus on the problem of annotating mutations in Protein Data Bank (PDB) entries, and evaluate the relationship between performance of two automated techniques, a text-mining-based approach (MutationFinder) and an alignment-based approach, in intrinsic versus extrinsic evaluations. We find that high performance on gold standard data (an intrinsic evaluation) does not necessarily translate to high performance for database annotation (an extrinsic evaluation). We show that this is in part a result of lack of access to the full text of journal articles, which appears to be critical for comprehensive database annotation by text mining. Additionally, we evaluate the accuracy and completeness of manually annotated mutation data in the PDB, and find that it is far from perfect. We conclude that currently the most cost-effective and reliable approach for database annotation might incorporate manual and automatic annotation methods.
Campylobacter pylori-associated gastritis: a double-blind placebo-controlled trial with amoxycillin. (1988)

We randomly assigned 45 adult patients with Campylobacter pylori-confirmed antral gastritis to 8 days of treatment with 1 g amoxycillin suspension twice a day, or placebo, according to a double-blind study design. At the end of therapy, 91% of patients treated with amoxycillin demonstrated clearance of the organism from the antrum, compared with 16% in the placebo group (p less than 0.001). Active antral gastritis resolved in 68% of patients in the amoxycillin group versus only 9% in the placebo group (p less than 0.001). No significant difference was observed when looking at the evolution of chronic only gastritis. No significant improvement was observed in the assessment of clinical symptoms and endoscopic appearance. Reappearance of C. pylori and significant worsening of the histological score of active gastritis was observed after 2 wk in all patients. In a second study phase, 18 patients initially not cleared of their bacteria received amoxycillin single blind for 14 days. Clearance of bacteria associated with improvement or resolution of active gastritis was observed in 72% of the cases. In this subgroup, all patients investigated after 1 month were recolonized with C. pylori and, again, had histological active gastritis. We conclude that amoxycillin is effective in treating active antral gastritis associated with C. pylori, but not in preventing relapses, which occur in all cases within 1 month after therapy.
Prostaglandin D<sub>2</sub> and Reproduction (2002)

This review highlights recent studies investigating the role of prostaglandin (PG)D2 in reproduction. PGD2 induces sleep, allergic responses, inhibition of platelet aggregation, and relaxation of vascular and non-vascular smooth muscle, and has some roles in reproduction. Two types of PGD2 synthase are known. Lipocalin-type PGD synthase is present in cerebrospinal fluid, seminal plasma and may play an important role in male reproduction. Another PGD synthase, hematopoietic PGD synthase is present in the spleen, fallopian tube, endometrial gland cells, extravillous trophoblasts and villous trophoblasts, and perhaps plays an important role in female reproduction. Recent studies demonstrate that PGD2 is probably involved in multiple aspects of inflammation through its dual receptor systems, DP and CRTH2. CRTH2 but not DP is a chemo-attractant receptor for PGD2. Interestingly, CRTH2 is a most reliable marker for the detection of human T helper type 2 (Th2) and T cytotoxic type 2 (Tc2) cells, and the percentages of CRTH expressing CD4+-T cells and CD8+-T cells were significantly higher in the decidua especially at the implantation site, suggesting that Th2 and Tc2 cells recruit into the materno-fetal interface, in a PGD2-mediated manner. PGD2 has a very unique effect to inhibit antigen presentation by inhibition of dendritic cell (DC) migration through DP but not CRTH2. PGD2 might appear to contribute to the maintenance of pregnancy by controlling the Th1/Th2 balance and antigen presentation by DCs through its dual receptor systems, CRTH2 and DP.
DNase I Footprint Analysis of Protein‐<scp>DNA</scp> Binding (1989)

Deoxyribonuclease I (DNase I) protection mapping, or footprinting, is a valuable technique for locating the specific binding sites of proteins on DNA. The basis of this assay is that bound protein protects the phosphodiester backbone of DNA from DNase I-catalyzed hydrolysis. Binding sites are visualized by autoradiography of the DNA fragments that result from hydrolysis, following separation by electrophoresis on denaturing DNA sequencing gels. Footprinting has been developed further as a quantitative technique to determine separate binding curves for each individual protein-binding site on the DNA. For each binding site, the total energy of binding is determined directly from that site's binding curve. For sites that interact cooperatively, simultaneous numerical analysis of all the binding curves can be used to resolve both the intrinsic binding and cooperative components of these energies.DNase I footprint titration is described in this unit and involves (1) preparation of a singly end-labeled DNA restriction fragment, (2) equilibration of the protein with DNA, (3) exposure of the equilibrium mixture to DNase I, and (4) electrophoretic separation on gels of the denatured hydrolysis products, followed by autoradiography. A describes (1) densitometric analysis of the autoradiograms to obtain binding data and (2) numerical analysis of the binding data to yield binding curves and equilibrium constants for the interactions at each of the separate sites. An describes the qualitative use of footprinting to identify DNA-binding proteins in crude extracts.