gebhart/patrepeval huggingface dataset:
Data from Poor Outcome in Estrogen Receptor–Positive Breast Cancers Predicted by Loss of <i>Plexin B1</i> (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; A common characteristic of mammary carcinomas is an inverse relationship between the estrogen receptor (ER) status and the proliferative activity of the tumor. Yet, a subset of ER-positive breast cancers is characterized by a high proliferation, suggesting malfunctions in ER responsiveness that influence the biological and therapeutic behavior of tumor cells. The expression of several ER-dependent genes seems to be dysregulated among those “uncoupled” tumors. One of those genes is &lt;i&gt;plexin B1&lt;/i&gt;, a cell-surface receptor for the semaphorin Sema4D (CD 100). However, the biological role of plexin B1 in breast cancer is largely unknown.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Expression data of plexin B1 were obtained from Affymetrix microarray analysis of &lt;i&gt;n&lt;/i&gt; = 119 breast cancer specimens. Validation was done by quantitative real-time PCR and protein expression was evaluated by immunohistochemistry. Expression data were compared with clinical characteristics as well as follow-up data of the disease.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Low plexin B1 expression levels characterize a more aggressive tumor phenotype. The expression of plexin B1 is strongly correlated with the ER status. However, even among ER-positive tumors, loss of plexin B1 is associated with an impaired prognosis of breast cancer patients in both univariate (all patients, &lt;i&gt;P&lt;/i&gt; = 0.0062; ER positive, &lt;i&gt;P&lt;/i&gt; = 0.0107) and multivariate analyses (all patients, &lt;i&gt;P&lt;/i&gt; = 0.032; ER positive, &lt;i&gt;P&lt;/i&gt; = 0.022). Immunohistochemistry reveals that the tumor cells themselves and not the endothelial cells are the major source of plexin B1 expression in the tumor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Plexin B1 acts not only as a new important prognostic but should also represent a predictive marker indicating an endocrine resistance. These data give a new insight in markers that could be involved in endocrine dysregulation of breast cancer.&lt;/p&gt;&lt;/div&gt;
Concomitant Endothelin Receptor Subtype-A Blockade During the Progression of Pacing-Induced Congestive Heart Failure in Rabbits (1997)

The results from this study suggest that chronically elevated ET-1 levels and subsequent activation of the ETA receptor play a direct and contributory role in the progression of the CHF process. Thus, specific ETA receptor blockade may provide a new and useful therapeutic modality in the setting of CHF.
Composite Role-Based Monitoring (CRBM) for countering insider threats (2004)

Abstract. Through their misuse of authorized privileges, insiders have caused great damage and loss to corporate internal information assets, especially within the Intelligence Community (IC). Intelligence management has faced increasing complexities of delegation and granular protection as more corporate entities have worked together in a dynamic collaborative environment. We have been confronted by the issue of how to share and simultaneously guard information assets from one another. Although many existing security approaches help to counter insiders ’ unlawful behavior, it is still found at a preliminary level. Effi-ciently limiting internal resources to privileged insiders remains a challenge to-day. In this paper we introduce the CRBM (Composite Role-Based Monitoring) approach by extending the current role-based access control (RBAC) model to overcome its limitations in countering insider threats. CRBM not only inherits the RBAC’s advantages, such as scalable administration, least privilege, and separation of duties, but also provides scalable and reusable mechanisms to monitor insiders ’ behavior in organizations, applications, and operating systems based on insiders ’ current tasks. 1
Chemistry of bacterial endotoxins. Part 6. Synthesis of allyl 5-O-(α-D-mannopyranosyl)-(3-deoxy-α-D-manno-oct-2-ulopyranosid) onic acid and of allyl 5-O-(α-D-mannopyranosyl)-(3-deoxy-α-D-manno-oct-2-ulopyranosid)onic acid 4-phosphate and their copolymers with acrylamide (1991)

A mixture of methyl (allyl-7,8-O-cyclohexylidene-3-deoxy-α-, and -β-D-manno-oct-2-ulopyranosid)onates (3 : 1) was prepared from methyl 2,4,5,7,8-penta-O-acetyl-3-deoxy-α-D-manno-oct-2-ulopyranosonate in 3 steps and the anomers were separated by chromatography. Sequential treatment of the α-glycoside with dibutyltin oxide and tert-butyldimethylsilyl chloride gave the corresponding 4-O-tert-butyldimethylsilyl 1,5-lactone. Transformation of the lactone with MeONa to the corresponding ester, was accompanied by partial migration of the silyl group and yielded a 2:1 mixture of the 4-O-, and 5-O-tert-butyldimethylsilyl derivatives which were separated by chromatography. Condensation of the former with 2,3,4,6-tetra-O-benzoyl-α-D-mannopyranosyl bromide in 1,2-dichloroethane in the presence of N,N,N′,N′-tetramethylurea and under silver trifluoromethanesulphonate catalysis afforded a 71% yield of the protected α-linked disaccharide. The silyl group was removed selectively with tetrabutylammonium fluoride, whereafter deprotection by conventional methods produced the unprotected title disaccharide. The alcohol obtained after the removal of the silyl group was treated with bis(trichloroethyl) phosphorochloridate to afford the corresponding phosphotriester which, after deprotection, gave the phosphorylated title disaccharide. Both were copolymerized with acrylamide. 1H NMR revealed that the phosphorylated disaccharide formed a complex with Ca2+ involving Man 4-O, 6-O, and oxygen atoms of the phosphate group.
Colloidal synthesis and thermoelectric properties of Cu2SnSe3nanocrystals (2012)

Copper-based selenides are attracting increasing interest due to their outstanding optoelectronic and thermoelectric properties. Herein a novel colloidal synthetic route to prepare Cu2SnSe3 nanocrystals with controlled size, shape and composition is presented. The high yield of the developed procedure allowed its up-scaling to the production of grams of colloidal Cu2SnSe3 nanocrystals. These nanocrystals were used as building blocks for the production of Cu2SnSe3 bulk nanostructured materials by spark plasma sintering. The thermoelectric properties of the prepared nanocrystalline Cu2SnSe3 pellets were characterized in the temperature range from 300 to 720 K. The obtained results show the bottom-up production of nanocrystalline materials from solution-processed nanocrystals to be a potentially advantageous alternative to conventional methods of production of efficient thermoelectric materials.
Accounting in the abstract world of figures (2012)

Almost any area that wants to be called a science cannot take action to demonstrate the truths of the reality that it governs and manages without resorting to modelling, to mathematical model and hence to figures. Thus, figures become vectors of transparency and a message about and with relation to the scientific nature of the studied realities; they, the figures, manage to translate into practice, actually to translate behaviours, situations and moments taken, gone through and lived in the evolutionary course, why not calling it that way, science of the surrounding reality.
Process of drug registration in Israel: the correlation between the number of discussions within the Ministry of Health and postapproval variations by EMA and/or FDA (2023)

Multiple ACDR discussions associated with limited supportive data are predictive for major postapproval variations. Moreover, our findings demonstrate that approval by the FDA and/or EMA does not pave the way to automatic approval in Israel. In a substantial per cent of the cases, submission of the same clinical data resulted in different safety and efficacy considerations, requiring additional supporting data in some cases or even rejection of the application in others.
Effects of Processing on Curd Yield and Nutrient Composition of Rapid Hydration Hydrothermal Cooking and Traditionally Processed Soymilk and Soybean Curd (1987)

ABSTRACT Soymilk processed by the Rapid Hydration Hydrothermal Cooking (RHHTC) method had higher thiamin and protein when compared to traditionally extracted soymilk (P&lt;0.0001). Traditionally processed soybean curd had higher protein (P &lt; 0.0001) and fat (P &lt; 0.001) while carbohydrate and ash were lower (P&lt;0.0001) when compared to RHHTC produced soybean curd. Variation in amino acid compositions occurred in soymilks and soybean curds. RHHTC‐produced soybean curd had greater curd yields than traditionally produced soybean curd.
Deuterated Linoleic Acid Attenuates the RBC Storage Lesion in a Mouse Model of Poor RBC Storage (2022)

<b>Background:</b> Long-chain polyunsaturated fatty acids (PUFAs) are important modulators of red blood cell (RBC) rheology. Dietary PUFAs are readily incorporated into the RBC membrane, improving RBC deformability, fluidity, and hydration. However, enriching the lipid membrane with PUFAs increases the potential for peroxidation in oxidative environments (e.g., refrigerated storage), resulting in membrane damage. Substitution of bis-allylic hydrogens with deuterium ions in PUFAs decreases hydrogen abstraction, thereby inhibiting peroxidation. If lipid peroxidation is a causal factor in the RBC storage lesion, incorporation of deuterated linoleic acid (DLA) into the RBC membrane should decrease lipid peroxidation, thereby improving RBC lifespan, deformability, filterability, and post-transfusion recovery (PTR) after cold storage. <b>Study Design and Methods:</b> Mice associated with good (C57BL/6J) and poor (FVB) RBC storage quality received diets containing 11,11-D2-LA Ethyl Ester (1.0 g/100 g diet; deuterated linoleic acid) or non-deuterated LA Ethyl Ester (control) for 8 weeks. Deformability, filterability, lipidomics, and lipid peroxidation markers were evaluated in fresh and stored RBCs. <b>Results:</b> DLA was incorporated into RBC membranes in both mouse strains. DLA diet decreased lipid peroxidation (malondialdehyde) by 25.4 and 31% percent in C57 mice and 12.9 and 79.9% in FVB mice before and after cold storage, respectively. In FVB, but not C57 mice, deformability filterability, and post-transfusion recovery were significantly improved. <b>Discussion:</b> In a mouse model of poor RBC storage, with elevated reactive oxygen species production, DLA attenuated lipid peroxidation and significantly improved RBC storage quality.
Comparison of Nosespace, Headspace, and Sensory Intensity Ratings for the Evaluation of Flavor Absorption by Fat (2003)

The goal of this study was to better understand the correspondence between sensory perception and in-nose compound concentration. Five aroma compounds at three different concentrations increasing by factors of 4 were added to four matrixes (water, skim milk, 2.7% fat milk, and 3.8% fat milk). These were evaluated by nosespace analysis with detection by proton transfer reaction mass spectrometry (PTR-MS), using five panelists. These same panelists evaluated the perceived intensity of each compound in the matrixes at the three concentrations. PTR-MS quantification found that the percent released from an aqueous solution swallowed immediately was between 0.1 and 0.6%, depending on the compound. The nosespace and sensory results showed the expected effect of fat on release, where lipophilic compounds showed reductions in release as fat content increases. The effect is less than that observed in headspace studies. A general correlation between nosespace concentration and sensory intensity ratings was found. However, examples of perceptual masking were found where higher fat milks showed reductions in aroma compound intensity ratings, even if the nosespace concentrations were the same.
Impaired Processing and Presentation of Cytotoxic-T-Lymphocyte (CTL) Epitopes Are Major Escape Mechanisms from CTL Immune Pressure in Human Immunodeficiency Virus Type 1 Infection (2004)

Investigating escape mechanisms of human immunodeficiency virus type 1 (HIV-1) from cytotoxic T lymphocytes (CTLs) is essential for understanding the pathogenesis of HIV-1 infection and developing effective vaccines. To study the processing and presentation of known CTL epitopes, we prepared Epstein-Barr virus-transformed B cells that endogenously express the gag gene of six field isolates by adopting an env/nef-deletion HIV-1 vector pseudotyped with vesicular stomatitis virus G protein and then tested them for the recognition by Gag epitope-specific CTL lines or clones. We observed that two field variants, SLFNTVAVL and SVYNTVATL, of an A*0201-restricted Gag CTL epitope SLYNTVATL, and three field variants, KYRLKHLVW, QYRLKHIVW, and RYRLKHLVW, of an A24-restricted Gag CTL epitope KYKLKHIVW escaped from being killed by the CTL lines, despite the fact that they were recognized when the synthetic peptides corresponding to these variant sequences were exogenously loaded onto the target cells. Thus, their escape is likely due to the changes that occur during the processing and presentation of epitopes in the infected cells. Mutations responsible for this mode of escape were located within the epitope regions rather than the flanking regions, and such mutations did not influence the virus replication. The results suggest that the impaired antigen processing and presentation often occur in HIV-1 field isolates and thus are one of the major mechanisms that enable HIV-1 to escape from CTL recognition. We emphasize the importance of testing HIV-1 variants in an endogenous expression system.
Data supporting "Coherent Phonon Disruption and Lock-In during a Photoinduced Charge-Density-Wave Phase Transition" (2016)

This dataset includes 4D ultrafast electron microscopy (UEM) data and ultrafast selected-area electron diffraction (U-SAED) data supporting the paper "Coherent Phonon Disruption and Lock-In during a Photoinduced Charge-Density-Wave Phase Transition" J. Phys. Chem. Lett., 2021, 12 (27). https://doi.org/10.1021/acs.jpclett.1c01673
A Four-State Scheme for Treating Polymer Crystallization and Melting Suggested by Calorimetric and Small Angle X-ray Scattering Experiments on Syndiotactic Polypropylene (1997)

As shown by time- and temperature dependent SAXS experiments, crystals of s-PP do not change their thickness during isothermal crystallization and a subsequent heating to melting. This allows an accurate determination of the relations between crystallization temperature, crystallite thickness, rate of crystallization, and melting points. There are five main results obtained in a comprehensive SAXS and DSC investigation: (i) Crystals have greatly varying stabilities, in spite of their uniform thickness; the first crystals melt close to the crystallization temperature. (ii) Melting points are affected by the distance to neighboring crystals. (iii) Crystals perfect during heating and annealing. (iv) Recrystallization after melting, as observed for low enough heating rates, starts with crystal growth rates that are at least 2 orders of magnitude higher than for a primary crystallization, and then slows down progressively, being accompanied by an increase in crystal thickness. (v) The dynamic signals observed in a MDSC run are indicative of a smooth change between crystallization and melting at the growth front. Data evaluation yields the average time required for a melting of individual crystallites. A four-state scheme allows a description of the behavior. It is based on the following assumptions: (i) Primary crystallization from the melt produces in a first step imperfect “native” crystals, which are subsequently stabilized by structural relaxation processes. These affect both the interior and the surface region. Crystallization proceeds under a small driving force, near to the equilibrium between melt and native crystals. (ii) The amount of structural relaxation is nonuniform thus producing crystals of different stability. (iii) With increasing crystallization temperature, i.e., decreasing growth rate, native crystals continuously approach the equilibrium state. (iv) The main part of fusion takes place near the equilibrium between the relaxed crystals and the disentangled melt.
Arthroscopic "second look" at the GORE-TEX ligament (1989)

We performed an arthroscopic "second look" in 21 knees (20 patients) that had arthroscopic implantation of the GORE-TEX prosthesis for chronic ACL insufficiency. Arthroscopy was done on eight knees at the time of screw removal, eight for knee pain, two for giving way, and three for recurrent effusions. The degree of synovial joint reaction, graft synovial ingrowth, and graft rupture was graded. Microscopic examination was carried out on all biopsies of the GORE-TEX ligament. The average patient age was 30 years and the average time interval from original implantation to second look was 11 months. The GORE-TEX was intact in 11 knees, 10% ruptured in 6, and completely ruptured in 4. There was no correlation between number of GORE-TEX strands ruptured and synovial reaction. No particles of the graft were noted in the synovium if the implant was intact, but particles were noted with graft rupture. We conclude that the intact GORE-TEX ligament is an inert substance and does not cause significant joint reaction. Impingement in the intercondylar notch appeared to be the most common cause of graft failure. Further study is critical to determine the natural history of the GORE-TEX ligament and the knees' response to this prosthetic device.
A wideband integrated piezoelectric bistable generator: Experimental performance evaluation and potential for real environmental vibrations (2014)

International audience
Medium Access Control With Coordinated Adaptive Sleeping for Wireless Sensor Networks (2004)

This paper proposes S-MAC, a medium access control (MAC) protocol designed for wireless sensor networks. Wireless sensor networks use battery-operated computing and sensing devices. A network of these devices will collaborate for a common application such as environmental monitoring. We expect sensor networks to be deployed in an ad hoc fashion, with nodes remaining largely inactive for long time, but becoming suddenly active when something is detected. These characteristics of sensor networks and applications motivate a MAC that is different from traditional wireless MACs such as IEEE 802.11 in several ways: energy conservation and self-configuration are primary goals, while per-node fairness and latency are less important. S-MAC uses a few novel techniques to reduce energy consumption and support self-configuration. It enables low-duty-cycle operation in a multihop network. Nodes form virtual clusters based on common sleep schedules to reduce control overhead and enable traffic-adaptive wake-up. S-MAC uses in-channel signaling to avoid overhearing unnecessary traffic. Finally, S-MAC applies message passing to reduce contention latency for applications that require in-network data processing. The paper presents measurement results of S-MAC performance on a sample sensor node, the UC Berkeley Mote, and reveals fundamental tradeoffs on energy, latency and throughput. Results show that S-MAC obtains significant energy savings compared with an 802.11-like MAC without sleeping.
Pseudo-Random Scrambling for Quasi-Static MIMO Channels (2007)

This paper investigates a blind MIMO precoding technique and benchmarks its performance in a realistic environment. The use of pseudo-random unitary precoding matrices (called "channel scrambling" in this paper) has been proposed to combat quasi- static channels with low diversity, both for the purpose of diversity coding and spatial multiplexing. In this paper we analyse the problem of poor soft output when the channel matrix is almost singular and how channel scrambling can help.The benefits of channel scrambling are quantified in a ray-traced channel and it is shown that substantial gains can be obtained from this simple technique.
Recombinant CD40L Treatment Protects Allogeneic Murine Bone Marrow Transplant Recipients From Death Caused by Herpes Simplex Virus-1 Infection (1998)

Posttransplant infection associated with host immune deficiency is the major cause of nonrelapse mortality of human bone marrow transplant recipients. In a new murine model of posttransplant infection, allogeneic bone marrow transplant recipients were infected with herpes simplex virus-1 (HSV-1) via intraperitoneal inoculation 12 weeks after transplantation. Allogeneic transplant recipients with graft-versus-host disease (GVHD) had significantly increased mortality from HSV-1 encephalitis, with deficiencies of both specific anti-HSV-1 antibody and total serum IgG2a. GVHD mice displayed a Th2 cytokine profile (increased interleukin-4 [IL-4] and decreased interferon-gamma) and decreased lipopolysaccharide (LPS) responses, suggesting that both T-cell and B-cell defects contributed to the impaired production of antibody. Because passive transfer of hyperimmune serum protected mice from HSV-1 infection, we hypothesized that CD40 ligand (CD40L), which induces B-cell maturation, would protect mice from HSV-1 infection. CD40L-treated GVHD mice showed elevated IgG2a levels and increased survival compared with vehicle-treated transplant recipients.
Detailed description of four YAC contigs representing 17 Mb of chromosome 4 of Arabidopsis thaliana ecotype Columbia (1996)

The detailed arrangement of 563 YAC clones comprising four contigs covering approximately 17 Mbp of chromosome 4 is presented. YAC clones were positioned relative to each other and to markers by taking into account marker and end fragment hybridization data and the sizes of all YAC clones. This analysis made it possible to estimate physical distances between the majority of chromosome 4 markers. It also identified a relatively large number of YAC clones containing chimaeric inserts. The YAC contig map of the Columbia ecotype presents an important resource for map-based cloning experiments, rapid mapping of DNA sequences and large-scale genomic sequencing programs.
Factors affecting 30-month survival in lung cancer patients. (2012)

Our results showed that lung cancer in Indians involved younger subjects and associated with poorer survival as compared to other ethnic population. Studies on large sample need to be done to evaluate risk factors in lung cancer patients.
LRRK2 Kinase Inhibition as a Therapeutic Strategy for Parkinson's Disease, Where Do We Stand? (2016)

One of the most promising therapeutic targets for potential disease-modifying treatment of Parkinson's disease (PD) is leucine-rich repeat kinase 2 (LRRK2). Specifically, targeting LRRK2's kinase function has generated a lot of interest from both industry and academia. This work has yielded several published studies showing the feasibility of developing potent, selective and brain permeable LRRK2 kinase inhibitors. The availability of these experimental drugs is contributing to filling in the gaps in our knowledge on the safety and efficacy of LRRK2 kinase inhibition. Recent studies of LRRK2 kinase inhibition in preclinical models point to potential undesired effects in peripheral tissues such as lung and kidney. Also, while strategies are now emerging to measure target engagement of LRRK2 inhibitors, there remains an important need to expand efficacy studies in preclinical models of progressive PD. Future work in the LRRK2 inhibition field must therefore be directed towards developing molecules and treatment regimens which demonstrate efficacy in mammalian models of disease in conditions where safety liabilities are reduced to a minimum.