gebhart/patrepeval huggingface dataset:
Transcriptional profiling of hepatocytes infected with the replicative form of the malaria parasite Plasmodium cynomolgi (2022)

ABSTRACT The zoonotic simian parasite Plasmodium cynomolgi develops into replicating schizonts and dormant hypnozoites during the infection of hepatocytes and is used as a model organism to study relapsing malaria. We previously reported the transcriptional profiling of P. cynomolgi liver stages and revealed many important biological features of the parasite (Bertschi et al., Elife, 2018; Voorberg-van der Wel et al., Elife, 2017) but left out the host response to malaria infection. Here, we used our published RNA sequencing data to quantify the expression of host genes in rhesus macaque hepatocytes infected with P. cynomolgi in comparison to either cells from uninfected samples or uninfected bystander cells. Although the dataset could not be used to resolve the transcriptional profile of hypnozoite-infected hepatocytes, it provided a snapshot of the host response to liver stage schizonts and identified specific host pathways that are modulated during malaria infection. This study constitutes a valuable resource characterizing the hepatocyte response to P. cynomolgi infection and provides a framework to build on future research that aims at understanding hepatocyte-parasite interactions during relapsing malaria infection.
Giant electro-mechanical transduction in all-organic MEMS for physical and chemical sensors (2016)

International audience
Characteristics of systemic antibody responses of nonhuman primates to cell envelope and cell wall antigens from periodontal pathogens (1997)

The immune response of the primate, Macaca fascicularis, to cell envelope (CEA) or cell wall (CWA) antigens of several periodontal pathogens was examined to develop a strategy to interfere with ligature-induced periodontitis. Animals were parenterally immunized with CEA of either Porphyromonas gingivalis, Prevotella intermedia or a combination of CEA/CWA of Campylobacter rectus, Fusobacterium nucleatum and Actinomyces viscosus. Serum samples were taken every 2-4 weeks over a 4-month period, which included a 13-week interval with molar teeth ligated. All of the nonhuman primates in the study exhibited baseline levels of IgG, IgM and IgA antibody to formalinized whole cells of the bacteria. These levels increased significantly following immunization and were elevated above baseline throughout the remainder of the experiment. The largest change in antibody responses was seen in IgA antibody levels of P. gingivalis and C. rectus (42-fold above baseline), IgM antibody to P. intermedia, (41-fold increase) and IgG antibody to F. nucleatum and A. viscosus (32 and 63-fold increases). Moreover, the nonhuman primates exhibited differences in isotype response levels to whole microorganisms compared with the cell envelope antigens. These findings demonstrate the capacity of these nonhuman primates to produce an active immune response to microorganisms chronically colonizing the subgingival microbiota. Additionally, it appears that the bacteria may exhibit some unique differences in their immunogenicity as detected by the nonhuman primate and may contribute to the ability of the immune responses to effectively interact with these pathogens.
Intervention of physical exercise in the workplace on work ability, depression, anxiety and job satisfaction in workers with sedentary tasks (2022)

The intervention had an impact on the mental factor of work ability in the workers whose occupations were based on sedentary tasks, and reinforcing this variable with an exercise program in the workplace could contribute to reducing the mental factor of work ability.
P4HA2 induces hepatic ductular reaction and biliary fibrosis in chronic cholestatic liver diseases (2023)

P4HA2 promotes hepatic ductular reaction and biliary fibrosis by regulating the SAV1-mediated Hippo signaling pathway. P4HA2 is a potential therapeutic target for PBC and PSC.
Chemical capacitance of nanoporous-nanocrystalline TiO2in a room temperature ionic liquid (2006)

The electrochemical behaviour of nanoporous TiO2 in a room temperature ionic liquid (RTIL), 1-ethyl-3-methylimidazolium bis((trifluoromethyl)sulfonyl)amide (EMITFSI), was investigated by cyclic voltammetry (CV) and impedance spectroscopy. Exponentially rising currents in voltammetry were attributed to the charging/discharging of electrons in the TiO2 film and a charge transfer mechanism. The main features of the voltammetry and impedance followed the same trends in the ionic liquid as in other organic solvents and also in aqueous electrolytes. In the presence of lithium ions, the onset potential of the charge accumulation increased due to the change of the initial position of the TiO2 conduction band. The results show that substitution of organic solvents contained in solar cells, supercapacitors or other electrochemical devices is in general feasible, though requires some adjustment in the electrolyte composition for optimal performance.
Size measurement of nanostructure using digital super-resolution interference microscopy (2014)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. Ishikawa and Y. Hayasaki, "Size measurement of nanostructure using digital super-resolution interference microscopy," in Imaging and Applied Optics 2014, OSA Technical Digest (online) (Optica Publishing Group, 2014), paper DTh4B.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Abstract 2632: Syrbactin, a novel proteasome inhibitor class, induces apoptosis and autophagy in neuroblastoma (2010)

Abstract Syrbactins belong to a new class of proteasome inhibitors which include syringolins and glidobactins. These small molecules are structurally distinct from other, well-established proteasome inhibitors, and bind the eukaryotic 20S proteasome by a novel mechanism. In this study, we examined the effects of syringolin A (SylA) and glidobactin A (GlbA) as well as two synthetic SylA-analogs (SylA-PEG and SylA-LIP) in human neuroblastoma (SK-N-SH), human multiple myeloma (MM1.S, MM1.RL, and U266), and human ovarian cancer (SKOV3) cells. While all four syrbactins inhibited cell proliferation in a dose-dependent manner, GlbA was most potent in both dexamethasone-sensitive MM1.S cells (IC50: 0.004 µM) and dexamethasone-resistant MM1.RL cells (IC50: 0.005 µM). Syrbactins also inhibited the chymotrypsin-like proteasome activity in a dose-dependent fashion, and GlbA was most effective in SK-N-SH cells (IC50: 0.015 µM). The GlbA-promoted inhibition of proteasomal activity in SK-N-SH cells resulted in the accumulation of ubiquitinated proteins and tumor suppressor protein p53, and led to apoptotic cell death. Strikingly, GlbA treatment also promoted the activation of Akt/PKB via phosphorylation at residue Ser473 and induced autophagy as judged by the presence of the lipidated form of microtubule-associated protein 1 light chain 3 (LC3) and autophagosomes. Collectively, our data suggest that syrbactins belong to a new and effective proteasome inhibitor class which promotes cell death. Proteasome inhibition is a promising strategy for targeted anticancer therapy and syrbactins are a new class of inhibitors which provide a structural platform for the development of novel, proteasome inhibitor-based drug therapeutics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2632.
The top 10 programming languages spectrum's 2014 ranking [dataflow] (2014)

Working with computational journalist Nick Diakopoulos, IEEE Spectrum has weighted and combined 12 metrics from 10 sources (including IEEE Xplore, Google, and GitHub) to rank the most popular programming languages. If you don,t agree with our weighting, want to see more languages, or are interested in what,s dominant in a specific subsector, such as mobile, go to our online interactive version. There you can adjust the weight of each metric and create your own custom ranking.
Ferrocenyl Oligo(phenylene‐vinylene) Thiols for the Construction of Self‐Assembled Monolayers (2007)

Abstract A short and efficient preparation of conjugated oligo(phenylene‐ethylene) thiols bearing redox‐active ferrocene moieties is described. While minimising the number of synthetic steps, the proposed strategy permits the development of sets of oligomers with varying chain length. The redox properties of the compounds in solution are determined. Preliminary studies of self‐assembled monolayers (SAMs) on gold electrodes are discussed, and indicate that electron transfer through the SAMs is indeed rapid.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Reporting Guidelines for Health Care Simulation Research (2016)

We have developed extensions for the CONSORT and STROBE Statements that can help improve the quality of reporting for SBR.
Helicopter flight test demonstration of differential GPS (1985)

An off-line post-mission processing facility is being established by NASA Ames Research Center to analyze differential GPS flight tests. The current and future differential systems are described, comprising an airborne segment in an SH-3 helicopter, a GPS ground reference station, and a tracking system. The post-mission processing system provides for extensive measurement analysis and differential computation. Both differential range residual corrections and navigation corrections are possible. Some preliminary flight tests were conducted in a landing approach scenario and statically. Initial findings indicate the possible need for filter matching between airborne and ground systems (if used in a navigation correction technique), the advisability of correction smoothing before airborne incorporation, and the insensitivity of accuracy to either of the differential techniques or to update rates.
An Algroithm for Finding Best Matches in Logarithmic Expected Time (1976)

An algorithm and data structure are presented for searching a file containing N records, each described by k real valued keys, for the m closest matches or nearest neighbors to a given query record. The computation required to organize the file is proportional to kNlogN. The expected number of records examined in each search is independent of the file size. The expected computation to perform each search is proportional to logN. Empirical evidence suggests that except for very small files, this algorithm is considerably faster than other methods.
Branched Ta nanocolumns grown by glancing angle deposition (2006)

Periodic arrays of Ta nanocolumns, 200nm wide and 600nm tall, were grown by glancing angle sputter deposition onto self-assembled close-packed arrays of 260-nm-diameter silica spheres. Each sphere leads to the development of a single Ta column. As growth progresses, roughening of the column top surfaces causes branching of some columns into subcolumns. The measured fraction of branched columns fb decreases with increasing growth temperature, from 30% at 200°C to 4% at 700°C. This is attributed to the increased adatom mobility at elevated temperatures, leading to a larger average separation of growth mounds and, in turn, lower nucleation probabilities for subcolumns. Branching into 3 and 4 subcolumns exhibits probabilities proportional to fb2 and fb3, respectively. A fit of the data with a simple nucleation model provides an effective activation energy for Ta surface diffusion of 2.0eV.
Traumatic Osteochondral Injury of the Femoral Head Treated by Mosaicplasty: A Report of Two Cases (2010)

The increased risk of symptomatic progression towards osteoarthritis after chondral damage has led to the development of multiple treatment options for cartilage repair. These procedures have evolved from arthroscopic lavage and debridement, to marrow stimulation techniques, and more recently, to osteochondral autograft and allograft transplants, and autogenous chondrocyte implantation. The success of mosaicplasty procedures in the knee has led to its application to other surfaces, including the talus, tibial plateau, patella, and humeral capitellum. In this report, we present two cases of a chondral defect to the femoral head after a traumatic hip dislocation, treated with an osteochondral autograft (OATS) from the ipsilateral knee, and the inferior femoral head, respectively, combined with a surgical dislocation of the hip. At greater than 1 year and greater than 5 years of follow-up, MRI studies have demonstrated good autograft incorporation with maintenance of articular surface conformity, and both patients clinically continue to have no pain and full active range of motion of their respective hips. In our opinion, treatment of osteochondral defects in the femoral head surface using a surgical dislocation combined with an OATS procedure is a promising approach, as full exposure of the femoral head can be obtained while preserving its vasculature, thus enabling adequate restoration of the articular cartilage surface.
Whole Animal Perfusion Fixation for Rodents (2012)

The goal of fixation is to rapidly and uniformly preserve tissue in a life-like state. While placing tissue directly in fixative works well for small pieces of tissue, larger specimens like the intact brain pose a problem for immersion fixation because the fixative does not reach all regions of the tissue at the same rate (5,7). Often, changes in response to hypoxia begin before the tissue can be preserved (12). The advantage of directly perfusing fixative through the circulatory system is that the chemical can quickly reach every corner of the organism using the natural vascular network. In order to utilize the circulatory system most effectively, care must be taken to match physiological pressures (3). It is important to note that physiological pressures are dependent on the species used. Techniques for perfusion fixation vary depending on the tissue to be fixed and how the tissue will be processed following fixation. In this video, we describe a low-cost, rapid, controlled and uniform fixation procedure using 4% paraformaldehyde perfused via the vascular system: through the heart of the rat to obtain the best possible preservation of the brain for immunohistochemistry. The main advantage of this technique (vs. gravity-fed systems) is that the circulatory system is utilized most effectively.
Modeling and analysis of high-speed links (2004)

Very low bit error rate (BER) requirements for the operation of a high-speed link system require a very precise analysis of the link performance in order to prevent unrealistic specifications on both IC design and communication algorithm development. This paper presents the analysis of the noise and distortion sources in a high-speed link system, and their impact on the choice and effectiveness of different communication techniques. Phase-locked loop and clock-and-data recovery loop modeling is also described. It is shown that the most dominant noise and distortion sources are colored and bounded, as opposed to standard unbounded Gaussian white noise assumptions, which yield large errors in the estimation of the link performance and comparison of different signaling techniques. With very low BER requirements, shape of probability distribution of noise and distortion sources and their correlations, are much more important than just their total power, which contrasts the standard analysis in communication systems.
A Stereotactic Head Frame for Use with CT Body Scanners (1979)

A prototype stereotactic head frame has been constructed for use in conjunction with a computed tomographic (CT) body scanner. Interactive software has been developed to allow target delineation using a standard CT scanner computer and image display console. The mathematic equations fundamental to this software are described. In preliminary experiments, it has been demonstrated that this frame can accurately direct a probe to an appropriately delineated target in a series of CT scans. A theoretic method for determining accuracy is presented; results suggest that this system represents a significant improvement over classic methods of neurosurgical stereotactic localization.
Changes in Key Odorants of Raw Coffee Beans during Storage under Defined Conditions (2007)

During storage of raw coffee beans (green coffee) atypical odors may develop, which are suggested to influence the aroma of particularly the coffee beverage. To gain insight into the aroma compounds responsible for such odor changes, a comparative aroma extract dilution analysis was applied on unstored, raw Arabica coffee beans from Colombia (water content=11.75%) and on the same beans with a water content of 13.5%, which were stored for 9 months at 40 degrees C. In combination with the flavor dilution (FD) factors, the results of the identification experiments showed strong increases in (E)-beta-damascenone (cooked apple-like), 2-methoxy-4-vinylphenol (clove-like), and methyl 2-methyl- and methyl 3-methylbutanoate (fruity), whereas others, such as the earthy smelling 3-isopropyl-2-methoxypyrazine as well as 2-phenylethanol and 3-methoxyphenol, remained unchanged during storage. In addition, the previously unknown coffee odorant 2-methoxy-5-vinylphenol (intense smoky odor) increased significantly during storage. Quantitative measurements performed on raw coffee samples stored at various temperatures, water contents, and oxygen availabilities indicated that the significant increase of, in particular, the methyl esters of 2- and 3-methylbutanoic acid were responsible for the pronounced and fruity odor quality perceived in the stored green coffee, whereas the higher concentrations of 2-methoxy-4-vinylphenol and 2-methoxy-5-vinylphenol led to the more pronounced smoky, clove-like odor quality. On the basis of the results obtained, in particular the reduction of the water content in combination with lower temperatures can be suggested to avoid aroma changes in raw coffee beans caused by storage.
Engineering of near infrared fluorescent proteinoid-poly(L-lactic acid) particles for in vivo colon cancer detection (2014)

The results of this study suggest a significant advantage of NIR fluorescence imaging using NIR fluorescent P(EF-PLLA) nanoparticles over colonoscopy. In future work we plan to broaden this study by encapsulating cancer drugs such as paclitaxel and/or doxorubicin, within these biodegradable NIR fluorescent P(EF-PLLA) nanoparticles, for both detection and therapy of colon cancer.
A mutation in the nerve growth factor beta gene (NGFB) causes loss of pain perception (2004)

Identification of genes associated with pain insensitivity syndromes can increase the understanding of the pathways involved in pain and contribute to the understanding of how sensory pathways relate to other neurological functions. In this report we describe the mapping and identification of the gene responsible for loss of deep pain perception in a large family from northern Sweden. The loss of pain perception in this family is characterized by impairment in the sensing of deep pain and temperature but with normal mental abilities and with most other neurological responses intact. A severe reduction of unmyelinated nerve fibers and a moderate loss of thin myelinated nerve fibers are observed in the patients. Thus the cases in this study fall into the class of patients with loss of pain perception with underlying peripheral neuropathy. Clinically they best fit into HSAN V. Using a model of recessive inheritance we identified an 8.3 Mb region on chromosome 1p11.2-p13.2 shared by the affected individuals in the family. Analysis of functional candidate genes in the disease critical region revealed a mutation in the coding region of the nerve growth-factor beta (NGFB) gene specific for the disease haplotype. This NGF mutation seems to separate the effects of NGF involved in development of central nervous system functions such as mental abilities, from those involved in peripheral pain pathways. This mutation could therefore potentially provide an important tool to study different roles of NGF, and of pain control.
New ultraviolet-transport electroconductive oxide, ZnGa2O4 spinel (1994)

ZnGa2O4 having the spinel structure was prepared, and optical and electrical properties of the material were measured. By the measurements of diffuse reflectance spectra, ZnGa2O4 was found to have a wider band gap (∼5 eV) than ITO (indium tin oxide). Electrical conductivity of the H2-annealed ceramic of ZnGa2O4 was 3×101 S cm−1. Thus the ZnGa2O4 spinel was found to be a new UV-transparent electronic conductor.
C2 auditing in the X Display Manager (2002)

This paper describes the implementation of C2 auditing in the MIT X Consortium X Display Manager (XDM) on a Sun Workstation. This custom implementation of XDM audits user logins, attempted logins and logouts by creating a C2 audit trail in the workstation's audit file. Additionally, when a user has exceeded a specified number of failed login attempts, the user's account and/or workstation may be disabled.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Treatment of Chronic Myeloid Leukemia (1980)

Most known chemotherapy agents, used singly, may induce remission of CML. Those that best alleviate symptoms (anemia, splenomegaly, etc) do not change either the Ph' chromosome anomaly in the hemopoietic cells nor the median delay of 3--4 years before fatal blastic transformation. A new goal has recently been formulated in CML therapy, namely complete remission, i.e. disappearance of all signs of leukemia including the Ph' abnormality. This can be achieved in certain cases by the use of aggressive (radio)chemotherapy during the chronic phase of CML. Whether or not it means cure of CML awaits further investigation. Encouraging results with these new therapeutic modalities during the chronic phase, and the possibility of rescuing toxic marrow aplasia by autologous cryopreserved blood stem cells, make it less and less defensible to await CML transformation before using aggressive "eradication" therapy.
Molecular weight dependent structure and charge transport in MAPLE‐deposited poly(3‐hexylthiophene) thin films Part B Polymer physics (2018)

In this work, poly(3‐hexylthiophene) (P3HT) films prepared using the matrix‐assisted pulsed laser evaporation (MAPLE) technique are shown to possess morphological structures that are dependent on molecular weight (MW). Specifically, the structures of low MW samples of MAPLE‐deposited film are composed of crystallites/aggregates embedded within highly disordered environments, whereas those of high MW samples are composed of aggregated domains connected by long polymer chains. Additionally, the crystallite size along the side‐chain (100) direction decreases, whereas the conjugation length increases with increasing molecular weight. This is qualitatively similar to the structure of spin‐cast films, though the MAPLE‐deposited films are more disordered. In‐plane carrier mobilities in the MAPLE‐deposited samples increase with MW, consistent with the notion that longer chains bridge adjacent aggregated domains thereby facilitating more effective charge transport. The carrier mobilities in the MAPLE‐deposited simples are consistently lower than those in the solvent‐cast samples for all molecular weights, consistent with the shorter conjugation length in samples prepared by this deposition technique. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 652–662