gebhart/patrepeval huggingface dataset:
Institutionally Distributed Deep Learning Networks (2017)

Deep learning has become a promising approach for automated medical diagnoses. When medical data samples are limited, collaboration among multiple institutions is necessary to achieve high algorithm performance. However, sharing patient data often has limitations due to technical, legal, or ethical concerns. In such cases, sharing a deep learning model is a more attractive alternative. The best method of performing such a task is unclear, however. In this study, we simulate the dissemination of learning deep learning network models across four institutions using various heuristics and compare the results with a deep learning model trained on centrally hosted patient data. The heuristics investigated include ensembling single institution models, single weight transfer, and cyclical weight transfer. We evaluated these approaches for image classification in three independent image collections (retinal fundus photos, mammography, and ImageNet). We find that cyclical weight transfer resulted in a performance (testing accuracy = 77.3%) that was closest to that of centrally hosted patient data (testing accuracy = 78.7%). We also found that there is an improvement in the performance of cyclical weight transfer heuristic with high frequency of weight transfer.
Supplementary Figure S4 from &lt;i&gt;CCNE1&lt;/i&gt; and &lt;i&gt;PLK1&lt;/i&gt; Mediate Resistance to Palbociclib in HR+/HER2− Metastatic Breast Cancer (2023)

&lt;p&gt;Progression Free Survival analysis on CCNE1 expression levels under palbociclib plus ET treatment&lt;/p&gt;
Abstract 2231: The over-activation of Akt1 oncogene heightens the Glypican-3 (GPC3) effects on metastatic progression of murine mammary tumor cells (2012)

Abstract It is known that Akt kinases 1, 2 and 3 have critical roles in regulating survival, metabolism and other cellular activities. However, their functions on migratory potential and metastasis development are less clear. GPC3 is a proteoglycan downregulated in breast tumors. We have previously shown that GPC3 reexpression inhibits metastatic capacity in vivo of the LM3 murine mammary adenocarcinoma cells. Moreover, this phenomenon was associated with a partial reversion of the epithelial-to-mesenchymal transition as shown in vitro. On the other hand, we have also determined that GPC3 modulates Akt signaling pathway in LM3 cells. The aim of this work was to investigate the role of Akt1 on the invasive/metastatic behavior of GPC3 reexpressing cells. First, we have confirmed that LM3-GPC3 cells present higher Akt1 levels than LM3-vector ones by western blot. To elucidate the function of this isoform, LM3-GPC3 clones were infected with viruses carrying a constitutively active variant of Akt1 (CA Akt1). Although there were no changes in the actin cytoskeleton organization, we could determine by a wound healing assay that LM3-GPC3-CA Akt1 cells were less migrant than their controls (Wound coverage: LM3-GPC3 control=50% vs. LM3-GPC3-CA Akt1=30%, p&amp;lt;0.05). To address an in vivo effect, different clones were injected s.c. into syngeneic female BALB/c mice. We found that these tumors did not differ in their growth rate, reaching a similar size at 30 days post inoculation (LM3-vector= 189±25, LM3-GPC3= 181±40, LM3-GPC3-CA Akt1= 200±51 mm3). No differences were found in either tumor incidence or in tumor latency. In order to study the experimental metastatic ability, all cell lines were i.v. inoculated. We observed that LM3-GPC3-CA Akt1 tumors developed fewer lung metastases than controls (Median [Range]: LM3-GPC3 control=9 [3-29] vs. LM3-GPC3 CA Akt1=0.5 [0-10], p&amp;lt;0.05). Moreover, the LM3-GPC3-CA Akt1 metastatic nodes were also of a smaller size (&amp;lt;0.5 mm). In sum, our results suggest that Akt1 expression and signaling could be mediating GPC3 inhibitory effect on the metastatic dissemination. The over-activation of this oncogene would exacerbate or heighten GPC3 effects, preventing the metastasis progression through the reduction of cell migration. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2231. doi:1538-7445.AM2012-2231
Arachidonic acid drives adaptive responses to chemotherapy-induced stress in malignant mesothelioma (2021)

AA is an early mediator of the adaptive response to pem in chemoresistant MPM and, possibly, other malignancies.
Paired MyoD-binding sites regulate myosin light chain gene expression. (1991)

The muscle-specific enhancer element located downstream of the myosin light chain (MLC) locus encoding MLC1 and MLC3 contains three binding sites (A, B, and C) for the myogenic determination factor MyoD. A 173-base-pair region of the MLC gene enhancer, including these three sites, retains full enhancer function when transfected into muscle cells. Whereas mutation of either upstream MyoD binding site (A or B) has a mild effect on muscle-specific enhancer activity, mutation of the third MyoD binding site (C) substantially weakens the enhancer, both in muscle cells or in nonmuscle cells cotransfected with a MyoD, myogenin, or myf5 expression vector. Site C is necessary but insufficient, since double mutation of two MyoD binding sites (A plus B) abrogates enhancer activity. Thus, site C requires either site A or B for enhancer function. This study shows a hierarchy of function among the three MyoD binding sites in the MLC enhancer. We propose that a protein-DNA complex is formed with at least two of these sites (A and C or B and C) to effect activation of the locus encoding MLC1/3 during myogenesis.
Mutator activity induced by microRNA-155 ( <i>miR-155</i> ) links inflammation and cancer (2011)

Infection-driven inflammation has been implicated in the pathogenesis of ~15-20% of human tumors. Expression of microRNA-155 (miR-155) is elevated during innate immune response and autoimmune disorders as well as in various malignancies. However, the molecular mechanisms providing miR-155 with its oncogenic properties remain unclear. We examined the effects of miR-155 overexpression and proinflammatory environment on the frequency of spontaneous hypoxanthine phosphoribosyltransferase (HPRT) mutations that can be detected based on the resistance to 6-thioguanine. Both miR-155 overexpression and inflammatory environment increased the frequency of HPRT mutations and down-regulated WEE1 (WEE1 homolog-S. pombe), a kinase that blocks cell-cycle progression. The increased frequency of HPRT mutation was only modestly attributable to defects in mismatch repair machinery. This result suggests that miR-155 enhances the mutation rate by simultaneously targeting different genes that suppress mutations and decreasing the efficiency of DNA safeguard mechanisms by targeting of cell-cycle regulators such as WEE1. By simultaneously targeting tumor suppressor genes and inducing a mutator phenotype, miR-155 may allow the selection of gene alterations required for tumor development and progression. Hence, we anticipate that the development of drugs reducing endogenous miR-155 levels might be key in the treatment of inflammation-related cancers.
Inferring artistic intention in comic art through viewer gaze (2012)

Comics are a compelling, though complex, visual storytelling medium. Researchers are interested in the process of comic art creation to be able to automatically tell new stories, and also, summarize videos and catalog large collections of photographs for example. A primary organizing principle used by artists to lay out the components of comic art (panels, word bubbles, objects inside each panel) is to lead the viewer's attention along a deliberate visual route that reveals the narrative. If artists are successful in leading viewer attention, then their intended visual route would be accessible through recorded viewer attention, i.e., eyetracking data. In this paper, we conduct an experiment to verify if artists are successful in their goal of leading viewer gaze. We eyetrack viewers on images taken from comic books, as well as photographs taken by experts, amateur photographers and a robot. Our data analyses show that there is increased consistency in viewer gaze for comic pictures versus photographs taken by a robot and by amateur photographers, thus confirming that comic artists do indeed direct the flow of viewer attention.
[Fc-IgG and Fc-IgM receptor-carrying lymphocytes in human blood. Optimization of determining T(M) lymphocytes]. (1987)

Several methods for enumeration of Fc receptor bearing T lymphocytes and mononuclear cells from human peripheral blood were compared. The detection of Fc receptors is based on the formation of EA rosettes by using bovine erythrocytes and purified rabbit IgG or IgM antibodies. As alternative method the mixed rosette assay (EA rosettes plus sheep erythrocyte rosettes) (3) was applied for determining TG lymphocytes without the need of T cell separation. Independent of the method used for T cell separation (preparative rosetting with sheep erythrocytes stabilized by AET or HSA) the number of TG and TM lymphocytes was found to be identical. TG values obtained by use of the mixed rosette assay were significant lower (10 +/- 2%) than those obtained with the classical test (18 +/- 5%) (EA rosettes after T cell separation). Obviously this difference is due to a contamination of T lymphocyte preparations by non-T cells. On freshly isolated T lymphocytes without overnight culture we obtained 29% and 35%, respectively TM lymphocytes after separation of T cells using sheep erythrocyte rosettes stabilized with AET or HSA. The expression of FcIgM receptors was found to be strongly dependent on the composition and pH value of the culture medium. In the presence of human AB serum the maximum of FcIgM receptor expression on isolated T cells was obtained at pH 8.5. Under optimum conditions we found 63% and 66% respectively TM lymphocytes after T cell separation using AET or HSA stabilized sheep erythrocytes.
ADMET polymerization of biobased monomers deriving from syringaresinol (2016)

Renewable α,ω-dienes have been prepared from syringaresinol, a naturally occurring bisphenol deriving from sinapyl alcohol, and further studied as monomers in ADMET polymerizations.
Detuning-dependent properties and dispersion-induced instabilities of temporal dissipative Kerr solitons in optical microresonators (2017)

A high-accuracy measurement of dissipative Kerr soliton properties in a driven nonlinear microresonator is performed, providing an experimental verification of an approximate ansatz of the Lugiato-Lefever equation. The present work contributes to the understanding and controlling of dissipative solitons and their use as optical frequency combs.
Apprentissage non-linéaire en ligne dans les réseaux de capteurs sans fil (2009)

International audience
Assessing Long-Distance Atmospheric Transport of Soilborne Plant Pathogens (2023)

Pathogenic fungi are a leading cause of crop disease and primarily spread through microscopic, durable spores adapted differentially for both persistence and dispersal. Computational Earth System Models and air pollution models have been used to simulate atmospheric spore transport for aerial-dispersal-adapted (airborne) rust diseases, but the importance of atmospheric spore transport for soil-dispersal-adapted (soilborne) diseases remains unknown. This study adapts the Community Atmosphere Model, the atmospheric component of the Community Earth System Model, to simulate the global transport of the plant pathogenic soilborne fungus Fusarium oxysporum, F. oxy. Our sensitivity study assesses the model's accuracy in long-distance aerosol transport and the impact of deposition rate on long-distance spore transport in Summer 2020 during a major dust transport event from Northern Sub-Saharan Africa to the Caribbean and southeastern U.S. We find that decreasing wet and dry deposition rates by an order of magnitude improves representation of long distance, trans-Atlantic dust transport. Simulations also suggest that a small number of viable spores can survive trans-Atlantic transport to be deposited in agricultural zones. This number is dependent on source spore parameterization, which we improved through a literature search to yield a global map of F. oxy spore distribution in source agricultural soils. Using this map and aerosol transport modeling, we show how viable spore numbers in the atmosphere decrease with distance traveled and offer a novel danger index for viable spore deposition in agricultural zones.
Results of surgical and percutaneous ablative therapy for hepatocellular carcinoma in elderly patients (2010)

Background
Liver resection is a curative treatment for hepatocellular carcinoma (HCC) [1]. Its role for the elderly remains undefined. In addition to surgery, percutaneous procedures have recently been proposed [2,3]. The choice of surgical and non-surgical therapy closely depends on the liver functional reserve and pre-existing co-morbidities.
Cold Atmospheric Plasma Deposition of Diamond (2007)

Abstract Nanocluster diamonds can be synthesized in open air on stainless steel and molybdenum substrates with a hybrid cold atmospheric plasma source using air plasma and an air + alcohol mixture. At microwave powers below 300 W and at gas flow rates below 300 sccm the temperature of a thermally insulated steel substrate placed 1.5 cm from the hollow cathode caused by the air plasma were less than 600 °C. 200 nm thick coatings with nanocluster diamond grains and aggregates exhibiting diamond peaks in the Raman spectra at 1 325 cm −1 on stainless steel and at 1 322 cm −1 on Mo were formed after 1 h on untreated substrates. magnified image
Optical System Based on Nafion Membrane for the Detection of Ammonia in Blood Serum Samples (2022)

The blood ammonia (NH<sub>3</sub>) level is one of the most important hepatic biomarkers for the diagnosis and monitoring of liver pathologies and infections. In this work, we developed an optimized optical biosensing method to extract and quantify the ammonia contained in complex-matrix samples emulating the blood serum. First, the approach was tested with solutions of phosphate-buffered saline (PBS) and ammonia chloride. Then, further trials were carried out with solutions of fetal bovine serum (FBS). The ammonia was extracted from the tested samples through a customized cell, and it was optically quantified by exploiting the indophenol reaction. The extraction cell included a cation-exchange membrane in Nafion, which was chemically pre-treated through cleaning procedures of sulfuric acid and hydrogen peroxide to keep a basic pH in the ammonia solution and to avoid contaminants in the membrane. From the NH<sub>3</sub> solution, the indophenol reaction produced light-reactive indophenol dye molecules, which were used as colorimetric indicators. Through absorbance measurements of the indophenol dye solution at 670 nm wavelength, we were able to detect and quantify the ammonia level in the samples both with a spectrophotometer and a customized miniaturized read-out system, obtaining a detection limit of 0.029 µmol/mL.
Structured Random Linear Codes (SRLC): Bridging the Gap between Block and Convolutional Codes (2014)

Several types of AL-FEC (Application-Level FEC) codes for the Packet Erasure Channel exist. Random Linear Codes (RLC), where redundancy packets consist of random linear combinations of source packets over a certain finite field, are a simple yet efficient coding technique, for instance massively used for Network Coding applications. However the price to pay is a high encoding and decoding complexity, especially when working on $GF(2^8)$, which seriously limits the number of packets in the encoding window. On the opposite, structured block codes have been designed for situations where the set of source packets is known in advance, for instance with file transfer applications. Here the encoding and decoding complexity is controlled, even for huge block sizes, thanks to the sparse nature of the code and advanced decoding techniques that exploit this sparseness (e.g., Structured Gaussian Elimination). But their design also prevents their use in convolutional use-cases featuring an encoding window that slides over a continuous set of incoming packets. In this work we try to bridge the gap between these two code classes, bringing some structure to RLC codes in order to enlarge the use-cases where they can be efficiently used: in convolutional mode (as any RLC code), but also in block mode with either tiny, medium or large block sizes. We also demonstrate how to design compact signaling for these codes (for encoder/decoder synchronization), which is an essential practical aspect.
GaN Photocathodes for UV detection and Imaging (2003)

The nitride-III semiconductors, in particular GaN (band gap energy 3.5 eV), AlN (band gap 6.2 eV) and their alloys AlxGa1-xN are attractive as UV photo-convertors with applications as photocathodes for position sensitive detector systems. These can “fill the gap” in the 150-400nm wavelength regime between alkali halide photocathodes ( 4000A, mutlialkali & GaAs). Currently CsTe photocathodes have fairly low efficiency (Fig. 1) in the 100nm to 300nm regime are sensitive to contamination and have no tolerance to gas exposure. We have prepared and measured a number of GaN photocathodes in opaque and semitransparent modes, achieving >50% quantum efficiency in opaque mode and ~35% in semitransparent mode (Fig. 2). The GaN photocathodes are stable over periods of >1 year and are robust enough to be re-activated many times. The cutoff wavelength is sharp, with a rapid decline in quantum efficiency at ~380-400nm. Application of GaN photocathodes in imaging devices should be feasible in the near future. Further performance improvements are also expected as GaN fabrication and processing techniques are refined.
Recrutement d'ubiquitine-ligases par la protéine de l'adenovirus humain responsable de l'internalisation virale (2004)

Used data from 465 premature, low birth weight children representing three major sociocultural groups (Caucasian, African American, Hispanic) to examine the relation between children's home environments and their adaptive social behavior. Results showed low to moderate associations between scores on the HOME Inventory at 1 and 3 years and scores on two measures of adaptive social behavior at 30 to 36 months, the Adaptive Social Behavior Inventory, and observations of mother-child interaction in a structured laboratory situation. Results indicated that responsive, nurturant care at both 1 and 3 years are related to child adaptive social behavior, as are cognitively stimulating experiences and materials. However, canonical correlational analysis indicated that only Acceptance and Variety of Experience, measured at age 3, and Variety of Experience measured at age 1 accounted for independent amounts of variance in adaptive social behavior as perceived by mothers. Also, only sociocultural group status and Learning Materials at 36 months contributed to the prediction of persistence and enthusiasm as observed in the laboratory setting.
Evidence supporting the enhanced efficacy of pentavalent antimonials with adjuvant therapy for cutaneous leishmaniasis: a systematic review and meta‐analysis (2020)

Cutaneous leishmaniasis (CL) is one of the major neglected disease worldwide. Although many drugs have been used, the pentavalent antimonials (PA) remain as the first-line choice despite their toxicity and limited efficacy. The combination of two drugs has risen as a potential alternative to increase the cure rate while lowering the side-effects caused by pentavalent antimonials (PA). The objective of this study was to critically review and appraise the potential synergism of the adjuvant therapies of PA with other drugs/interventions previously used in the literature. We carried out a search of literature from PubMed, MEDLINE, Embase, Cochrane and clinicaltrials.gov. Articles that described a two-arm or three-arm design in which one of the arms consisted in a combination of a drug/intervention with intralesional or systemic PA were selected. The primary outcome was proportion of complete clearance of the lesions defined as complete re-epithelization and/or negative direct smear. Our literature search identified 554 references. Thirty-one records with a total sample size of 2668 participants met the eligibility criteria. The studies investigated the association of PA with the following: cryotherapy (five studies), allopurinol, imiquimod, pentoxifylline (four studies each), trichloroacetic acid 50% (three studies) and other additional interventions (eleven studies). Overall, the combined therapy of PA with a supplementary intervention was superior to PA monotherapy (RR: 1.23 95% CI: 1.11-1.35, I<sup>2</sup> = 64%). In association with PA, the comparator-specific stratified analysis showed that cryotherapy (RR: 1.50 95% CI: 1.25-1.81, I<sup>2</sup> = 57%) and allopurinol (RR: 1.70 95% CI: 1.37-2.12, I<sup>2</sup> = 28%) were superior to PA in monotherapy. On the contrary, the combined therapy with imiquimod (RR: 1.08 95% CI: 0.88-1.32, I<sup>2</sup> = 40%) and pentoxifylline (RR: 1.14 95% CI: 0.94-1.40, I<sup>2</sup> = 41%) revealed a non-significant result. The application of TCA along with PA did not show significant differences in the clearance rate, although it was close to it (RR: 1.31 95% CI: 0.99-1.73, I<sup>2</sup> = 84%). The present work represents an attempt to find new and reliable treatment modalities to enhance the efficacy based on the adjuvant therapy of pre-existing drugs/interventions with PA. According to our results, the combination of allopurinol-PA is the most effective adjuvant therapy. The application of cryotherapy and TCA stand as useful and encouraging supplementary interventions. The combination of imiquimod-PA and pentoxifylline adds no additional benefit. The results of this work may be helpful in devising and modifying the current guidelines for CL which face major remaining evidence gaps. Triple therapies consisting in cryotherapy-PA-TCA or allopurinol-PA-cryotherapy or allopurinol-PA-TCA can represent promising treatments yet to be confirmed in future trials.
Connexin 43 Hemichannels Regulate Osteoblast to Osteocyte Differentiation (2022)

Connexin 43 (Cx43) is the predominant connexin subtype expressed in osteocytes. Osteocytes, accounting for 90%-95% of total bone cells, function as orchestrators coordinating balanced activity between bone-resorbing osteoclasts and bone-forming osteoblasts. In this study, two newly developed osteocytic cell lines, OCY454 and IDG-SW3, were used to determine the role of Cx43 gap junctions and hemichannels (HCs) in the regulation of osteoblast to osteocyte differentiation. We found that the Cx43 level was substantially increased during the differentiation of IDG-SW3 cells and is also much higher than that of OCY454 cells. We knocked down Cx43 expression using the lentiviral CRISPR/Cas9 approach and inhibition of Cx43 HCs using Cx43 (E2) antibody in IDG-SW3 cells. Cx43 knockdown (KD) or Cx43 HC inhibition decreased gene expression for osteoblast and osteocyte markers, including alkaline phosphatase, type I collagen, dentin matrix protein 1, sclerostin, and fibroblast growth factor 23, whereas increasing the osteoclastogenesis indicator and the receptor activator of nuclear factor kappa-B ligand (RANKL)/osteoprotegerin (OPG) ratio at early and late differentiation stages. Moreover, mineralization was remarkably attenuated in differentiated Cx43-deficient IDG-SW3 cells compared to ROSA26 control. The conditioned medium collected from fully differentiated IDG-SW3 cells with Cx43 KD promoted osteoclastogenesis of RAW264.7 osteoclast precursors. Our results demonstrated that Cx43 HCs play critical roles in osteoblast to osteocyte differentiation process and regulate osteoclast differentiation <i>via</i> secreted factors.