gebhart/patrepeval huggingface dataset:
A Process for Sentinel Case Review to Assess Causal Relationships between Smallpox Vaccination and Adverse Outcomes, 2003–2004 (2008)

The US Department of Defense requested that the Advisory Committee on Immunization Practices-Armed Forces Epidemiological Board joint Smallpox Vaccine Safety Working Group define the likelihood that smallpox vaccination played a causal role in the fatal illness of an Army reservist. Reported serious adverse events for which there was no a priori reason to discount the existence of a causal association with smallpox vaccine were reviewed to assess whether they were signals of constellations of vaccine-associated adverse events. A causal relationship between the immunization experience and the index patient's death was favored, but the implication of an individual vaccine was precluded. No new smallpox vaccine-associated clinical syndromes were identified. The data supported neutrality regarding the hypothesis that dilated cardiomyopathy was causally associated with smallpox vaccine-induced myocarditis. This review of sentinel cases augmented the ongoing safety review process and was transparent, but it shares limitations with other case-based causality-assessment methods.
Steroid and Cytokine Regulation of Matrix Metalloproteinase Expression in Endometriosis and the Establishment of Experimental Endometriosis in Nude Mice (2002)

The cyclic expression of matrix metalloproteinases (MMPs) by human endometrium has been suggested to play a role in the invasive process necessary to establish endometriosis. The ability of progesterone exposure to inhibit endometrial MMP-3 and MMP-7 expression requires the local action of TGF beta and may also be linked to the local production of retinoic acid by stromal cells. A continuous expression of several MMPs in endometriotic lesions has been reported, indicating a failure of progesterone or locally produced factors to suppress these enzymes. To address cell-specific MMP regulation associated with endometriosis, we examined expression of MMP-3 and MMP-7 mRNA in eutopic endometrium and endometriotic lesions acquired during the secretory phase of the menstrual cycle. We examined the in vitro regulation of MMP-3 and MMP-7 protein in similar tissues. We also examined the in vitro regulation of MMP secretion by progesterone, retinoic acid, and TGF beta in endometriosis tissues relative to the establishment of experimental disease. Our studies indicate that either eutopic or ectopic tissue from women with endometriosis exhibit patterns of altered MMP regulation in vivo. A lack of responsiveness to progesterone was demonstrated in vitro, associated with a failure to suppress MMP expression and an enhanced ability of the tissue to establish experimental endometriosis. However, in vitro treatments with retinoic acid and TGF beta restored the ability of progesterone to suppress MMPs in vitro and prevented the establishment of experimental disease.
Two-Photon-Absorption-Enhanced Laser-Assisted Device Alteration and Single-Event Upsets in 28 nm Silicon Integrated Circuits (2013)

Abstract By inducing two-photon absorption within the active layer of a 28nm test chip, we demonstrate nonlinear laser-assisted device alteration and single-event upsets by temporarily perturbing the timing characteristics of sensitive transistors. Individual qualitative and quantitative evaluations are presented for both techniques, with lateral resolutions demonstrated with sub-100nm performance. A simplistic signal response rate comparison analysis of these two technologies is also presented.
Analysis and Design of Monolithic Rectangular Coaxial Lines for Minimum Coupling (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Coupling through holes etched in a common wall between the neighboring surface micromachined rectangular coaxial lines is studied in this paper. Analytical models for single- and multiple-hole structures are developed using Bethe's small aperture theory, and excellent agreement with finite-element and finite-integration simulations is obtained. These models are used in a circuit-level simulator for efficient optimization of the selected multihole structure. An isolation test structure composed of 200-<formula><tex>$\mu$</tex> </formula>m center-to-center separated 300-<formula><tex>$\mu$</tex></formula>m-tall 50-W rectangular coaxial lines is designed, built, and measured. Coupling levels below <formula formulatype="inline"><tex>${-}$</tex> </formula>55 dB over 1-cm-long coupling lengths are achieved throughout the <formula><tex>$Ka$</tex></formula>-band. It is found that the probe radiation is more than 10 dB higher than the coupling through the common wall holes. This radiation severely affects the accuracy of the measurements and has to be considered when the coupling through the common walls is analyzed. </para>
Dual-Driver Networked Fire Truck Simulator with Multimodal Display including Force Feedback Steering and Rotating Motion Platform (2007)

We describe the integration of two pairs of force displays - a force-feedback wheel (FFBW) and the c Shaire ('Share Chair'), a rotary motion platform - in a dual-driver networked driving simulator which navigates through virtual space using CVE (collaborative virtual environment) groupware. We developed a double-driver (long ladder-style) fire-truck simulation with a tiller (rear steering), driven via an integrated pair of networked driving simulator stations. Such a dual-driver system is useful to turn narrow corners rapidly and smoothly in case of (simulated) emergencies. Its FFB steering wheels display simple collision force to both drivers separately when the vehicle collides with walls or other vehicles. The technique of feeding back the effect employs programs using C++ and Directlnput, escaping to an execution file called force-manager from the driving simulator, which is implemented with Java3D. Effect patterns are changed by arguments to forcemanager. The c Shaire is rotated with a servo-motor, the rotation angle controlled via internet through the CVE. A demonstration video is posted at http: //sonic.u-aizu.ac.jp/spatial-media/Videos/DualDrivingSimulator.mov.
The NEURON Book (2006)

The authoritative reference on NEURON, the simulation environment for modeling biological neurons and neural networks that enjoys wide use in the experimental and computational neuroscience communities. This book shows how to use NEURON to construct and apply empirically based models. Written primarily for neuroscience investigators, teachers, and students, it assumes no previous knowledge of computer programming or numerical methods. Readers with a background in the physical sciences or mathematics, who have some knowledge about brain cells and circuits and are interested in computational modeling, will also find it helpful. The NEURON Book covers material that ranges from the inner workings of this program, to practical considerations involved in specifying the anatomical and biophysical properties that are to be represented in models. It uses a problem-solving approach, with many working examples that readers can try for themselves.
De Novo Expression of Macrophage Migration Inhibitory Factor in Atherogenesis in Rabbits (2000)

Macrophage migration inhibitory factor (MIF) has been shown to play an important role in macrophage-mediated diseases. We investigate the potential role of MIF in atherogenesis using a hypercholesterolemic rabbit model. New Zealand White rabbits fed with a 2% cholesterol diet developed hypercholesterolemia and early fatty streaks at 1 month. The lesions became advanced at 3 months and were associated with de novo MIF expression by vascular endothelial cells (VECs) and smooth muscle cells (SMCs), as demonstrated by immunohistochemistry, reverse transcriptase-polymerase chain reaction, and in situ hybridization. By contrast, there was no increase in MIF levels in rabbits fed a normal diet. In early atherogenesis, marked upregulation of MIF mRNA and protein by VECs and some intimal cells were closely associated with CD68(+) monocyte adhesion onto and subsequent migration into subendothelial space. Of significance, the accumulation of macrophages was exclusively localized to areas of strong MIF expression, which may be associated with the macrophage-rich fatty streak lesion formation. Upregulation of MIF by SMCs is transient during atherogenesis. Importantly, strong MIF expression by activated macrophages may be responsible for the development of foam cell-rich lesions. Finally, the ability of MIF to induce intercellular adhesion molecule-1 expression by VECs implicates its pathogenic role in atherogenesis. In conclusion, the present study provides the first demonstration that MIF is markedly upregulated during atherogenesis. Upregulation of MIF by VECs and SMCs may play a role in macrophage adhesion, transendothelial migration, accumulation, and, importantly, transformation into foam cells. Furthermore, strong MIF expression by macrophages may both initiate and amplify the atherogenesis process.
Underwater Wireless Optical Communications Using Silicon Photo-Multipliers (2017)

We study the use of Silicon photo-multipliers (SiPMs) for underwater wireless optical communications (UWOC) and discuss their main interests and drawbacks, compared with photo-multiplier tubes. This comparison is mainly based on practical considerations regarding system implementation and the attainable link span. Presenting an appropriate model for signal attenuation in water and considering the simple On-Off keying modulation, we bring clearance on the real interest of using an SiPM in the UWOC context. We also elucidate the main drawbacks of these components in practice, in particular, regarding the limitation on the transmission data rate, as well as the nonlinear distortion caused on the received signal in relatively short ranges, where the signal intensity is too large.
Concurrent AURKA and MYCN Gene Amplifications Are Harbingers of Lethal TreatmentRelated Neuroendocrine Prostate Cancer (2013)

Neuroendocrine prostate cancer (NEPC), also referred to as anaplastic prostate cancer, is a lethal tumor that most commonly arises in late stages of prostate adenocarcinoma (PCA) with predilection to metastasize to visceral organs. In the current study, we explore for evidence that Aurora kinase A (AURKA) and N-myc (MYCN) gene abnormalities are harbingers of treatment-related NEPC (t-NEPC). We studied primary prostate tissue from 15 hormone naïve PCAs, 51 castration-resistant prostate cancers, and 15 metastatic tumors from 72 patients at different stages of disease progression to t-NEPC, some with multiple specimens. Histologic evaluation, immunohistochemistry, and fluorescence in situ hybridization were performed and correlated with clinical variables. AURKA amplification was identified in overall 65% of PCAs (hormone naïve and treated) from patients that developed t-NEPC and in 86% of metastases. Concurrent amplification of MYCN was present in 70% of primary PCAs, 69% of treated PCAs, and 83% of metastases. In contrast, in an unselected PCA cohort, AURKA and MYCN amplifications were identified in only 5% of 169 cases. When metastatic t-NEPC was compared to primary PCA from the same patients, there was 100% concordance of ERG rearrangement, 100% concordance of AURKA amplification, and 60% concordance of MYCN amplification. In tumors with mixed features, there was also 100% concordance of ERG rearrangement and 94% concordance of AURKA and MYCN co-amplification between areas of NEPC and adenocarcinoma. AURKA and MYCN amplifications may be prognostic and predictive biomarkers, as they are harbingers of tumors at risk of progressing to t-NEPC after hormonal therapy.
Analyse dipolaire des paroxysmes intercritiques et critiques en EEG et MEG (2001)

RÉSUMÉ Les méthodes de modélisation dipolaire permettent d'estimer statistiquement la localisation et l'orientation des sources des signaux électroencéphalographiques (EEG) ou magnétoencéphalographiques (MEG). Ces méthodes ont été appliquées aux paroxysmes intercritiques depuis plus de 20 ans et suggèrent que la genèse des paroxysmes intercritiques repose plus sur l'expression d'un réseau de structures anatomiques que sur l'activation d'une région très focale. Nous examinons dans cette revue: (1) l'étendue de ce réseau selon différents types d'épilepsies, (2) les rapports entre ce réseau et les anomalies structurelles identifiées grâce à l'imagerie par résonance magnétique (IRM) ou les anomalies fonctionnelles observées en tomographie par émission de positons (TEP), et (3) la concordance spatiale et temporelle des sources dipolaires des paroxysmes intercritiques et critiques avec les enregistrements intracrâniens simultanés. Les informations issues des données de la modélisation dipolaire des pointes intercritiques sont généralement insuffisantes pour planifier une chirurgie sélective sans enregistrements invasifs. Cependant, les résultats des études examinées dans cette revue montrent que, confrontés aux données des autres techniques non invasives, les résultats de la modélisation dipolaire peuvent s'avérer utiles pour mieux définir la limite de la zone épileptogène ou l'étendue de l'implantation stéréo‐électroencéphalographique (SEEG).
Reconfigurable real-time MIMO detector on GPU (2009)

In a high performance multiple-input multiple-output (MIMO) system, a soft output MIMO detector combined with a channel decoder is often used at the receiver to maximize performance gain. Graphic processor unit (GPU) is a low-cost parallel programmable co-processor that can deliver extremely high computation throughput and is well suited for signal processing applications. We propose and implement a novel soft MIMO detection algorithm and show we meet real-time performance while maintaining flexibility using GPU.
Doped V2O5-Based Cathode Materials: Where Does the Doping Metal Go? An X-ray Absorption Spectroscopy Study (2007)

X-ray absorption spectroscopy (XAS) has been used to probe the local structure of doped vanadium pentoxide materials prepared through sol–gel processes. The doped samples have been analyzed at the vanadium K-edge as well as at the doping metal K-edge (copper and zinc). The presence of two metal sites gives two independent absorption signals, even if we are investigating the same compound; for this reason the reliability of the analysis is enhanced. The strategy in determining the local structure will be discussed. The local structural modifications resulting from low to high doping concentration in the best performing copper-doped V2O5 aerogel like material is reported. Similar measurements were done using zinc as doping metal, in both aerogel-like and xerogel form. The EXAFS analysis shows that the vanadium atomic environment is not altered by the doping metal insertion and that the doping metals (Cu and Zn) are found to be in the same site. Copper and zinc are 4-fold coordinated by almost coplanar oxygens in both xerogel and aerogel-like oxide hosts. The use of the metal–metal interaction while analyzing data concerning sample of high doping level played a key role in the determination of the preferred metal sites.
Respiratory Syncytial Virus: Heterogeneity of Subgroup B Strains (1988)

In order to investigate further possible structural differences among the two subgroups of respiratory syncytial virus (RSV), we analysed the antigenic characteristics and size of structural proteins of 20 subgroup A and 43 subgroup B strains by their reactions with monoclonal antibodies (MAbs) directed against the proteins of RSV using immunofluorescence, ELISA and radioimmunoprecipitation assays. The latter test also enabled determination of the size of different structural components. The 37 MAbs employed were generated by immunization with both subgroup A and B strains. They represented specificities for distinct epitopes on five different structural proteins. The subgroup A strains proved to be relatively uniform. The fusion (F) protein, nucleoprotein (NP) and matrix (M) proteins of all strains tested had the same Mr and all except one strain had a phosphoprotein (P protein) of the same Mr. The F and P proteins were lower in Mr in B strains compared to A strains, which confirmed previous findings. The Mr of the large surface glycoprotein (G protein) of subgroup A strains varied slightly, probably on the basis of differing glycosylation. By contrast, the subgroup B strains exhibited substantial variation in the Mr of the G and also the P proteins and in reactivity with MAbs directed against the G and F proteins. Three size classes of the P protein were identified in B strains: 33K to 34K, 32K to 33K, and 31K to 32K. Twenty-seven subgroup B strains failed to react with four anti-G MAbs representing a single epitope, G2; the remaining 16 strains reacted with these MAbs. We designated these two sets of variants of B strains B1, which lacked the epitope, and B2, which had the epitope. The B1 strains also varied in the size of the G and P proteins. In contrast, all B2 strains had large G proteins and all except two strains had relatively large P proteins (33K to 34K). All subgroup B1 and B2 strains exhibited the same sizes of NP, F and M proteins. We conclude that the subgroup B strains of RSV include two variants, B1 and B2, and that the major difference between them resides in the G and P proteins.
Effect of Genistein on In Vitro and In Vivo Models of Cancer (1995)

In two-thirds of studies on the effect of genistein-containing soy materials in animal models of cancer, the risk of cancer (incidence, latency or tumor number) was significantly reduced. In addition, purified genistein delayed mammary tumor appearance in association with increased cell differentiation in mammary tissue in rats treated with 7, 12-dimethylbenz[a]anthracene when administered neonatally, inhibited phorbol ester-induced H2O2 production in a model of skin cancer, and inhibited aberrant crypt formation in a model of colonic cancer. In in vitro models, genistein inhibited the proliferation of human tumor cell lines in culture with a wide variation in IC50 values (2.6-79 mumol/L, or 1-30 micrograms/mL). In only a few cases was the IC50 below 13.2 mumol/L (5 micrograms/mL), the presumed upper limit for the serum genistein concentration in those on a high soy diet. In future studies, greater emphasis should be placed on the effect of genistein on nontransformed, normal cell lines from the tissues where cancer can occur rather than established tumor cell lines. Similarly, the effect of genistein on the progression and/or promotion of cancer may be more clearly examined using nontransformed cell lines transfected with specific oncogenes thought to be activated during oncogenesis.
In Vivo Pharmacokinetics, Long-Term Biodistribution, and Toxicology of PEGylated Graphene in Mice (2010)

Graphene has emerged as interesting nanomaterials with promising applications in a range of fields including biomedicine. In this work, for the first time we study the long-term in vivo biodistribution of (125)I-labeled nanographene sheets (NGS) functionalized with polyethylene glycol (PEG) and systematically examine the potential toxicity of graphene over time. Our results show that PEGylated NGS mainly accumulate in the reticuloendothelial system (RES) including liver and spleen after intravenous administration and can be gradually cleared, likely by both renal and fecal excretion. PEGylated NGS do not cause appreciable toxicity at our tested dose (20 mg/kg) to the treated mice in a period of 3 months as evidenced by blood biochemistry, hematological analysis, and histological examinations. Our work greatly encourages further studies of graphene for biomedical applications.
Case-control study of SUDEP (2005)

This work lends support to the view that SUDEP is a seizure-related phenomenon and that control of tonic-clonic seizures is important in its prevention. Nocturnal supervision seems to protect against SUDEP.
The role of TAK1 expression in thyroid cancer. (2015)

TAK1 may be an important factor involved in the pathogenesis of thyroid cancer, and targeted down-regulation of TAK1 may improve the prognosis of patients with thyroid cancer.
PI3K/Akt/mTOR Pathway Inhibitors in Cancer: A Perspective on Clinical Progress (2010)

The phosphoinositide 3-kinase (PI3K)/serine-theronine protein kinase Akt (also known as protein kinase B (PKB))/mammalian target of rapamycin (mTOR) pathway is a vital transduction cascade that is connected with many essential cellular activities, such as growth and survival. Along with extensive pharmacological studies validating the therapeutic potential of targeting the PI3K/Akt/mTOR pathway for the treatment of cancer, kinase inhibitors targeting significant knots of this pathway including PI3K, Akt, mTOR, and 3-phosphoinositide-dependent protein kinase-1 (PDK-1) keep arising and entering clinical studies. Herein, we review the most up-to-date landscape on developing small-molecule kinase inhibitors targeting the PI3K/Akt/mTOR pathway, with emphasis on small-molecule inhibitors which have been progressed into clinical studies.
Administration of Purified Human Plasma Cholinesterase Protects Against Cocaine Toxicity in Mice (1996)

Pretreatment with purified human plasma cholinesterase protects mice against the convulsive and lethal effects of cocaine.
Pregnancy outcome following swim up preparation of both fresh and cryopreserved spermatozoa (2017)

This study was designed to assess the impact of swim up preparation of both fresh and cryopreserved sperm on the pregnancy outcome in a private fertility centre in Lagos. A cross-sectional prospective analysis of 34 asthenozoospermic semen samples of men whose wives were undergoing assisted reproduction was studied. The basic semen parameters comprising of the volume, count, and motility of the sperm before and after swim up preparations with pregnancy outcome were measured. For fresh semen (n = 28, mean age = 37.0 ± 1.1 years, mean volume = 2.16 ± 0.1 ml), the sperm count decreased significantly (p&lt;0.01) from the pre swim up value of 55.4 ± 3.10 to 44.6 ± 3.20 x 106/ml post swim up. While, the motility increased significantly (p&lt;0.01) from 39.6 ± 3.84 to 58.5 ± 4.29%. The percentage pregnancy outcome in the fresh semen was 66%. For the cryopreserved semen (n = 6, mean age = 41.0 ± 5.4 years, mean volume = 1.8 ± 0.1 ml), the sperm count decreased significantly (p&lt;0.01) from pre swim up value of 35.6 ± 3.03 to 33.3 ± 4.33 x 106/ml post swim up, while the motility increased significantly (p&lt;0.01) from 25.1 ± 4.01 to 32.8 ± 6.18%. The pregnancy outcome of cryopreserved was 30%. The pregnancy outcome was higher with fresh than the cryopreserved semen. However, the motility was a significant indicator for the successful outcome. Swim up procedure improve the motility of both cryopreserved and fresh semen with a better pregnancy outcome in this study.
Phase II evaluation of topotecan for pediatric central nervous system tumors (1996)

Topotecan administered as a 24-hour infusion every 21 days is inactive in high grade gliomas, medulloblastomas, and brain stem tumors.
STEREOCHEMISTRY AND THE MECHANISM OF ENZYMATIC REACTIONS (1953)

The isolation and purification of an enzyme makes it possible to consider the reaction which it catalyzes from the standpoint of organic chemistry, i.e. as a reaction between organic molecules in which the catalyst happens to be a protein. Such a consideration allows the tools of physical organic chemistry to be applied to the the study of the enzyme mechanism, and, since a number of enzymes have been purified, to obtain correlations of what might otherwise appear to be unrelated processes. One of the particularly powerful tools used in the elucidation of chemical mechanisms is stereochemistry, and it would be expected that similar conditions might lead to a clarification of enzymatic mechanisms and enzyme-substrate intermediates. In this article, the effect of enzymatic reactions on the configuration of the asymmetric carbon atoms involved in the reaction has been examined and the observed changes described by mechanisms which are compatible with both the chemical and biochemical evidence.