gebhart/patrepeval huggingface dataset:
Comparing General and Locally-Learned Word Embeddings for Clinical Text Mining (2019)

Dense vector-representations of words, referred to as word embeddings, capture word relations differently depending on the type and the size of the corpus they are trained on. Choosing which word embeddings to use poses a problem when applying machine learning on clinical text which contains many specialized words. In this work, we explore the effects of different embedding sources for clinical text classification using various cohort sizes on three medical prediction tasks: Clostridium Difficile infections, MRSA infections, and in-hospital mortality. We compare three embedding sources: pre-trained embeddings from large and general corpora, pre-trained embeddings from large and domain-related corpora, and locally-learned embeddings trained on the task-specific training data. We experiment with several cohort sizes ranging from 20 patients to 2,500 patients. Our results indicate that pre-trained domain-related embeddings are superior for medium-sized cohorts greater than 150 patients, while locally-learned embeddings become increasingly competitive as cohort size grows.
<i>In situ</i> metrology for adaptive x-ray optics with an absolute distance measuring sensor array (2019)

Adaptive x-ray mirrors are emerging as one of the primary solutions for meeting the performance needs of the next generation of x-ray light sources. Currently, these mirrors operate open loop with intermittent feedback from invasive sensors that measure the beam quality. This paper outlines a novel design for real-time in situ metrology of the shape of these mirrors using an array of interferometric sensors that does not interrupt the x-ray beam. We describe a proof-of-principle demonstration which shows sub-nm agreement over a range of mirror deflection magnitudes and shapes as compared to simultaneous measurements by using a large-aperture Fizeau interferometer.
Finite‐element analysis of ferrite disk resonators by introducing field‐assigned points (1991)

Abstract In this paper, resonant frequencies are calculated by the method of finite elements for resonators with anisotropic ferrite disks. The finite‐element methods with three electric field components are used in general for analyses of ferrite resonators with tensor permeabilities. A new treatment becomes necessary for boundary conditions of the electric fields at the edges of ferrite resonators. By introducing field‐assigned points at resonator edges, it is possible to calculate resonant frequencies. To examine calculated results, the resonant frequencies of resonators with isotropic circular disks were compared. Then the obtained results are compared with calculated results by other methods. It is noted that the authors' method possesses a high level of calculation precision. As a practical example, the resonant frequencies of anisotropic disk resonators loaded inside a below‐cutoff parallel plate waveguide are calculated. Experimentally measured data and the authors' calculated results have been confirmed to show good agreement.
Ca<sub>2</sub>Mg<sub>5</sub>GeN<sub>6</sub> – A Layered Nitridomagnesogermanate (2016)

Abstract The nitridomagnesogermanate Ca 2 Mg 5 GeN 6 was synthesized at 780 °C using a sodium flux in sealed tantalum ampules. Pure metals were used as starting materials and sodium azide NaN 3 was added as nitrogen source. Ca 2 Mg 5 GeN 6 was obtained as a byproduct in the form of colorless platelet‐like crystals. Solution and refinement of the crystal structure [space group P 6 3 / mmc (no. 194), Z = 1, a = 3.453(2), c = 17.506(13) Å and V = 180.8(2) Å 3 ] were performed on the basis of single‐crystal X‐ray diffraction data. Ca 2 Mg 5 GeN 6 represents the first layered nitridogermanate. Its structure is made up of corner‐sharing (Mg/Ge)N 4 tetrahedra and corner‐sharing trigonal planar (Mg/Ge)N 3 units with mixed occupancy of Mg and Ge. Ca 2+ ions are located in between the sheets. The crystal structure is closely related to that of the nitridomagnesoaluminate CaMg 2 AlN 3 as well as to the carbides ScAl 3 C 3 and UAl 3 C 3 .
Apolipoprotein A1 and C-Terminal Fragment of α-1 Antichymotrypsin Are Candidate Plasma Biomarkers Associated With Acute Renal Allograft Rejection (2011)

Together α-1 antichymotrypsin, Apo A1, and the unidentified 5191 Da peptide provide a plasma molecular profile, and this is associated with acute cellular renal allograft rejection.
Phospho-RNA sequencing with CircAID-p-seq (2020)

Abstract Accurate positional information concerning ribosomes and RNA binding proteins with respect to their transcripts is important to understand the global regulatory network underlying protein and RNA fate in living cells. Most footprinting approaches generate RNA fragments bearing a phosphate or cyclic phosphate groups at their 3′ end. Unfortunately, all current protocols for library preparation rely only on the presence of a 3′ hydroxyl group. Here, we developed circAID-p-seq, a PCR-free library preparation for 3′ phospho-RNA sequencing. We applied circAID-p-seq to ribosome profiling, which produces fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast, highly efficient and low-cost sequencing of phospho-RNA fragments from eukaryotic cells and tissues. While assessing circAID-p-seq to portray ribosomes engaged with transcripts, we provide a versatile tool to unravel any 3′-phospho RNA molecules.
Development of a novel mouse model of hepatocellular carcinoma with nonalcoholic steatohepatitis using a high-fat, choline-deficient diet and intraperitoneal injection of diethylnitrosamine (2016)

The nonalcoholic steatohepatitis-hepatocellular carcinoma model we describe here is simple to establish, results in rapid tumor formation, and recapitulates most of the key features of nonalcoholic steatohepatitis. It could therefore facilitate further studies of the development, oncogenic potential, diagnosis, and treatment of this condition.
Electrical Characterization of Low Temperature PECVD Oxides for TSV Applications (2018)

Abstract In the present work we investigate the quality of low temperature Plasma Enhanced Chemical Vapor Deposition (PECVD) and plasma treated Tetraethyl orthosilicate (TEOS)-based TSV-liner films. Different designs of Trough Silicon Via (TSV) Test structures with 10μm and 20μm width and a depth of 100μm have been fabricated. Two differently doped silicon substrates have been used – highly p-doped and moderately doped. The results for break-through, resistivity and capacitance for the 20μm structures show a better performance compared to the 10μm structures. This is mainly due to increased liner thickness in the reduced aspect ratio case. Lower interface traps and oxide charge densities have been observed in the C-V measurements results for the 10μm structures.
Energy-harvesting microsensors: Low-energy task schedule &amp; fast drought-recovery design (2016)

The main challenge with microsensors is limited space, because tiny batteries store little energy. Harvesting energy helps, but only when ambient energy is available. And even then, power is low because miniaturized transducers harness little power. This is why managing how and when to schedule functional tasks is so important. This paper proposes a schedule that requires the battery to hold only the energy necessary to sustain single events and allows the battery to drain across harvesting droughts. When input power returns, an inefficient starter charges a temporary supply that bootstraps the system quickly into an efficient state. This way, when harvested input, idle, and peak load power are 10, 0.5, and 1000 μW, a 0.7% efficient starter and an 87% efficient charger can recharge a 1.8-μF battery to 1 V in 220 ms with a 71-pF temporary supply and in 13 s without the temporary supply. The system therefore wakes 59× faster than without a temporary supply and 1880× faster and with 1800× less capacitance than when forcing the battery to survive a 2-hour power outage.
ChemInform Abstract: Organophosphorus Compounds. Part 52. Phosphatriafulvenes and Their Reaction with Electrophiles. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: The Anodic Dissolution of Copper in Aqueous Acidic Solutions Containing F‐ Ions (1988)

Abstract (pH 1.6‐6, 0.1 M KF) has been investigated by cyclic voltammetry and by some surface sensitive techniques (SEM, XPS, AES).
Cushing's syndrome due to ectopic adrenocorticotropic hormone production by a non-metastatic gastrinoma after long-term conservative treatment of Zollinger-Ellison syndrome. (1998)

This report concerns a case of a Cushing's syndrome 10 years after first diagnosis of a Zollinger-Ellison syndrome within the same patient. In a 69-year-old female patient symptoms of hypergastrinaemia have been successfully treated with a proton pump inhibitor. Cushing's syndrome was the result of ectopic adrenocorticotropic hormone production by a large cystic gastrin-producing tumour of the pancreatic tail. After resection by subtotal pancreatectomy serum adrenocorticotropic hormone, cortisol, gastrin levels and secretin infusion test returned to normal. In contrast to all other previously published cases of ectopic adrenocorticotropic hormone syndrome associated with Zollinger-Ellison syndrome, this tumour had not metastasized into the liver and did not show local invasive growth.
SHOULD WE ABANDON FULL POLY TOTAL KNEE PROSTHESES (2008)

Purpose of the study: The objective of this study was to compare outcome after total knee arthroplasty (TKA) with a metallic tibial base versus full poly prostheses.

Material and methods: This monocentric retrospective study compared 169 Tornier full poly HLS TKA (group A) with 169 TKA with a fixed metallic tibial base (group B). The two series were matched for age, gender and etiology. Mean age was 71 years and female gender predominated, 80%. Mean follow-up was 66 months. Clinical (IKS score) and radiological outcome was assessed. Statview 5.0™ was used for the statistical analysis, Student’s t test for quantitative variables and chi-square test for qualitative variables. Differences were considered significant for p<0.05. The beta factor was 0.2.

Results: The main intraoperative incidents were, weakening of the popliteal tendon (n=1) and supra and inter-condylar fracture of the femur (n=1) in group A patients and weakening of the popliteal tendon (n=2) and secondary fracture line of the medial tibial plateau (n=2) in group B patients. For group A, the knee score was 89±10.82 (mean±SD) and for group B 88.28±11.94. The function score was 68±23.75 for group A and 71±24.05 for group B. Mean flexion in both groups was 113°. Non-progressive tibial lucent lines were observed in 27 patients in group A and in 23 in group B. There were 7 replacements of the TKA in group A and 6 in group B. Survival for group A was 94.5% and 93.64% for group B.

Discussion: There were no significant differences concerning function and knee scores, presence of lucent lines and prosthesis replacement between the two series (p>0.05).

Conclusion: This study did not demonstrate a superiority of the metallic tibial base TKA at five years follow-up. Use of a full poly TKA could decrease the medical cost by more than 30%.
Loss of Cdc13 causes genome instability by a deficiency in replication-dependent telomere capping (2019)

Abstract In budding yeast, Cdc13, Stn1, and Ten1 form a telomere binding heterotrimer dubbed CST. Here we investigate the role of Cdc13/CST in maintaining genome stability, using a Chr VII disome system that can generate recombinants, loss, and enigmatic unstable chromosomes. In cells expressing a temperature sensitive CDC13 allele, cdc13 F684S , unstable chromosomes frequently arise due to problems in or near a telomere. Hence, when Cdc13 is defective, passage through S phase causes Exo1-dependent ssDNA and unstable chromosomes, which then are the source for whole chromosome instability events (e.g. recombinants, chromosome truncations, dicentrics, and/or loss). Specifically, genome instability arises from a defect in Cdc13’s replication-dependent telomere capping function, not Cdc13s putative post-replication telomere capping function. Furthermore, the unstable chromosomes form without involvement of homologous recombination nor non-homologous end joining. Our data suggest that a Cdc13/CST defect in semi-conservative replication near the telomere leads to ssDNA and unstable chromosomes, which then are lost or subject to complex rearrangements. This system defines a links between replication-dependent chromosome capping and genome stability in the form of unstable chromosomes.
PD-1 blockade and vaccination provide therapeutic benefit against SIV by inducing broad and functional CD8 <sup>+</sup> T cells in lymphoid tissue (2021)

During antiretroviral therapy (ART), most of the human immunodeficiency virus (HIV) reservoirs persist in the B cell follicles (BCFs) of lymphoid tissue. Thus, for HIV cure strategies, it is critical to generate cytolytic CD8<sup>+</sup> T cells that home to BCF, reduce the reservoir burden, and maintain strong antiviral responses in the absence of ART. Here, using a chronic simian immunodeficiency virus (SIV)/rhesus macaque model, we showed that therapeutic vaccination under ART using a CD40L plus TLR7 agonist–adjuvanted DNA/modified vaccinia Ankara vaccine regimen induced robust and highly functional, SIV-specific CD4<sup>+</sup> and CD8<sup>+</sup> T cell responses. In addition, the vaccination induced SIV-specific CD8<sup>+</sup> T cells in the lymph nodes (LNs) that could home to BCF. Administration of PD-1 blockade before initiation of ART and during vaccination markedly increased the frequency of granzyme B<sup>+</sup> perforin<sup>+</sup> CD8<sup>+</sup> T cells in the blood and LN, enhanced their localization in germinal centers of BCF, and reduced the viral reservoir. After ART interruption, the vaccine + anti–PD-1 antibody–treated animals, compared with the vaccine alone and ART alone control animals, displayed preservation of the granzyme B<sup>+</sup> CD8<sup>+</sup> T cells in the T cell zone and BCF of LN, maintained high SIV antigen-recognition breadth, showed control of reemerging viremia, and improved survival. Our findings revealed that PD-1 blockade enhanced the therapeutic benefits of SIV vaccination by improving and sustaining the function and localization of vaccine-induced CD8<sup>+</sup> T cells to BCF and decreasing viral reservoirs in lymphoid tissue. This work has potential implications for the development of curative HIV strategies.
Performance Evolution of Mobile Web-Based Services (2009)

The mobile Web's widespread diffusion opens many interesting design and management issues about server infrastructures that must satisfy present and future client demand. Future mobile Web-based services will have growing computational costs. Even requests for the same Web resource will require services to dynamically generate content that takes into account specific devices, user profiles, and contexts. The authors consider the evolution of the mobile Web workload and trends in server and client devices with the goal of anticipating future bottlenecks and developing management strategies.
Application of Recombinant <scp>DNA</scp> Technology in Medicinal Chemistry and Drug Discovery (2003)

Abstract Drug discovery is usually a long and arduous process. However, pharmaceutical industries are making a significant progress in simplifying certain aspects of drug discovery process, especially in the area of target discovery, validation, and lead‐compounds discovery. Advances in recombinant DNA technology are intimately connected with the explosion of newly identified pharmaceutically important targets, and an understanding of how these targets function to regulate biological processes of interest. This is providing new and exciting opportunities for therapeutic intervention in diseases including those diseases that were thought to be untreatable a few years back. In this chapter we describe how each stage of drug discovery, from target identification to lead generation and even clinical trials, have benefited from the tools of recombinant DNA technology.
Increase in BNP in Response to Endothelin-Receptor Antagonist Atrasentan Is Associated With Incident Heart Failure (2022)

In patients with type 2 diabetes and CKD, baseline BNP and early changes in BNP in response to atrasentan were associated with HF hospitalization, highlighting the importance of natriuretic peptide monitoring upon initiation of atrasentan treatment. (Study Of Diabetic Nephropathy With Atrasentan [SONAR]; NCT01858532).
Cellular and genetic control of antibody responses in vitro. III. Immune response gene regulation of accessory cell function (1978)

The possibility was investigated that Ir genes regulate the function of cells other than T or B cells in the primary IgM responses to the synthetic antigens trinitrophenylated poly-L-(Tyr,Glu)-poly-D,L-Ala--poly-L-Lys [TNP-(T,G)-A--L]and trinitrophenylated poly-,-(His,Glu)-poly-D, L-Ala--poly-L-Lys [TNP-(H,G)-A--L]. The primary responses of (B10 x B10.A)F(1) spleen cells to both antigens were abrogated by Sephadex G-10 passage, and restored by the addition of spleen adherent cells. The cell type in the spleen adherent cell population active in reconstituting the responses to TNP-(T,G)-A--L and TNP-(H,G)-A--L was a non-T, non-B, radiation-resistant, glass-adherent spleen cell. The responses of Sephadex G-10-passed (responder x nonresponder)F(1) spleen cells to TNP-(T,G)-A--L or TNP-(H,G)-A--L were reconstituted by spleen adherent cells from only responder strains. Spleen adherent cells from F(1) mice reconstituted the responses to both antigens. Spleen adherent cells from each of the strains tested reconstituted the non- Ir gene-controlled response to a third antigen, TNP-keyhole limpet hemocyanin. The inability of spleen adherent cells from nonresponder strains to reconstitute the responses to either TNP-(T,G)-A--L or TNP-(H,G)-A--L was not a result of active suppression induced by the presence of nonresponder adherent cells, since a mixture of responder and nonresponder spleen adherent cells reconstituted the responses to both antigens. The use of spleen adherent cells from recombinant strains demonstrated that the autosomal dominant genes controlling the ability of spleen adherent cells to function as accessory cells in the responses to TNP-(T,G)-A--L and TNP-(H,G)-A--L are located in the K or I-A regions of the responder H-2 complex, the same region(s) of H-2 as the Ir genes controlling overall in vitro and in vivo responsiveness to these antigens.
<i>American Journal of Physiology-Cell Physiology</i> begins a Theme on “Cellular Processes in Tumor Metastasis: From Basic Research to Translation” (2019)

International audience
Interleukin-4 suppresses inflammatory cytokine gene transcription in porcine macrophages (1994)

Inflammatory cytokines, including interleukin (IL)-1 alpha, IL-1 beta, IL-8, and tumor necrosis factor alpha (TNF-alpha) are produced by macrophages in response to a variety of pathogenic stimuli. We show here that the expression of inflammatory cytokines is suppressed by IL-4 at the transcriptional level. Interleukin-4, when added together with bacterial lipopolysaccharide (LPS), suppressed LPS-induced increases in mRNA levels of IL-1 alpha, IL-1 beta, IL-8, and TNF-alpha in alveolar macrophages. The level of suppression was dependent on dose and time of exposure and reached a maximum of 75-80% of uninduced values for IL-1 alpha, IL-8, and TNF. Interleukin-1 beta expression was completely inhibited by IL-4. The amount of secreted protein, as determined by TNF-alpha bioassay, was also suppressed by IL-4. Half-maximal suppression occurred at IL-4 concentrations between 0.02 and 0.1 ng/ml for all inflammatory cytokines. Nuclear run-on assays showed that IL-4 suppressed transcriptional activity of all inflammatory cytokines. Messenger RNA stability was not changed by IL-4. The data suggest that IL-4 plays an important transcriptional role in the regulation of alveolar macrophage inflammatory activities in respiratory disease and raise the possibility that IL-4 may function in vivo as a coordinator of inflammatory and immune responses.
Electro‐kinetic Separation of Rare Earth Elements Using a Redox‐Active Ligand (2017)

Abstract Purification of rare earth elements is challenging due to their chemical similarities. All of the deployed separation methods rely on thermodynamic properties, such as distribution equilibria in solvent extraction. Rare‐earth‐metal separations based on kinetic differences have not been examined. Herein, we demonstrate a new approach for rare‐earth‐element separations by exploiting differences in the oxidation rates within a series of rare earth compounds containing the redox‐active ligand [{2‐( t BuN(O))C 6 H 4 CH 2 } 3 N] 3− . Using this method, a single‐step separation factor up to 261 was obtained for the separation of a 50:50 yttrium–lutetium mixture.
System for Detecting Driver's Drowsiness Robust Variations of External Illumination (2016)

In this study, a system is proposed for analyzing whether driver's eyes are open or closed on the basis of images to determine driver's drowsiness. The proposed system converts eye areas detected by a camera to a color space area to effectively detect eyes in a dark situation, for example, tunnels, and a bright situation due to a backlight. In addition, the system used a thickness distribution of a detected eye area as a feature value to analyze whether eyes are open or closed through the Support Vector Machine(SVM), representing 90.09% of accuracy. In the experiment for the images of driver wearing glasses, 83.83% of accuracy was obtained. In addition, in a comparative experiment with the existing PCA method by using Eigen-eye and Pupil Measuring System the detection rate is shown improved. After the experiment, driver's drowsiness was identified accurately by using the method of summing up the state of driver's eyes open and closes over time and the method of detecting driver's eyes that continue to be closed to examine drowsy driving.
A More Compact Representation of XTR Cryptosystem (2008)

XTR is one of the most efficient public-key cryptosystems that allow us to compress the communication bandwidth of their ciphertext. The compact representation can be achieved by deploying a subgroup Fq2 of extension field Fq6, so that the compression ratio of XTR cryptosystem is 1/3. On the other hand, Dijk et al. proposed an efficient public-key cryptosystem using a torus over Fq30 whose compression ratio is 4/15. It is an open problem to construct an efficient public-key cryptosystem whose compression ratio is smaller than 4/15. In this paper we propose a new variant of XTR cryptosystem over finite fields with characteristic three whose compression ratio is 1/6. The key observation is that there exists a trace map from Fq6 to Fq in the case of characteristic three. Moreover, the cost of compression and decompression algorithm requires only about 1% overhead compared with the original XTR cryptosystem. Therefore, the proposed variant of XTR cryptosystem is one of the fastest public-key cryptosystems with the smallest compression ratio.