gebhart/patrepeval huggingface dataset:
Learning to segment with limited annotations: Self-supervised pretraining with regression and contrastive loss in MRI (2022)

Obtaining manual annotations for large datasets for supervised training of deep learning (DL) models is challenging. The availability of large unlabeled datasets compared to labeled ones motivate the use of self-supervised pretraining to initialize DL models for subsequent segmentation tasks. In this work, we consider two pre-training approaches for driving a DL model to learn different representations using: a) regression loss that exploits spatial dependencies within an image and b) contrastive loss that exploits semantic similarity between pairs of images. The effect of pretraining techniques is evaluated in two downstream segmentation applications using Magnetic Resonance (MR) images: a) liver segmentation in abdominal T2-weighted MR images and b) prostate segmentation in T2-weighted MR images of the prostate. We observed that DL models pretrained using self-supervision can be finetuned for comparable performance with fewer labeled datasets. Additionally, we also observed that initializing the DL model using contrastive loss based pretraining performed better than the regression loss.
Synthesis, structural, thermal and optical studies of inorganic-organic hybrid semiconductors, R-PbI4 (2013)

Wide varieties of naturally self-assembled two-dimensional inorganic-organic (IO) hybrid semiconductors, (4-ClC6H4NH3)2PbI4, (C6H9C2H4NH3)2PbI4, (CnH2n+1NH3)2PbI4 (where n = 12, 16, 18), (CnH2n-1NH3)2PbI4 (where n = 3, 4, 5), (C6H5C2H4NH3)2PbI4, NH3(CH2)12NH3PbI4, and (C4H3SC2H4NH3)2PbI4, were fabricated by intercalating structurally diverse organic guest moieties into lead iodide perovskite structure. The crystal packing of all these fabricated IO-hybrids comprises of well-ordered organic and inorganic layers, stacked-up alternately along c-axis. Almost all these hybrids are thermally stable upto 200 °C and show strong room-temperature exciton absorption and photoluminescence features. These strongly confined optical excitons are highly influenced by structural deformation of PbI matrix due to the conformation of organic moiety. A systematic correlation of optical exciton behavior of IO-hybrids with the organic/inorganic layer thicknesses, intercalating organic moieties, and various structural disorders were discussed. This systematic study clearly suggests that the PbI layer crumpling is directly responsible for the tunability of optical exciton energy.
Topographical Risk Factor Analysis of New Neurological Deficits Following Precentral Gyrus Resection (2015)

The posterior upper quadrant of the precentral gyrus was vulnerable to post-resective neurological impairment.
A structural voyage toward an understanding of the MHC‐I‐restricted immune response: lessons learned and much to be learned (2012)

T cells that express clonally distributed αβ T-cell receptors (TCRs) corecognize antigenic peptides (p) bound to major histocompatibility complex class I (MHC-I) and class II molecules (MHC-II). Extensive human leukocyte antigen (HLA) polymorphism enables HLA molecules from different haplotypes to capture an array of self- and microbe-derived peptide antigens that is fundamental to adaptive immunity. T cells developing in the thymus are selected for weak binding to self-peptide-HLA complexes generating a vast repertoire of clonally distinct T cells in the periphery. Indeed, diversity within germline loci and the finally assembled TCR genes, coupled with inherent TCR cross-reactivity, enables CD8(+) T cells to survey the multitude of pHLA-I landscapes. Precisely how does the TCR ligate to pHLA-I, and how does knowledge of the detailed structural interactions inform immunobiology? A recent number of our structural studies concerning the TCR-pMHC-I axis, alongside others in the field, have provided insight into HLA-I polymorphism, pMHC-I flexibility, TCR bias, TCR polymorphism, maintenance of self-tolerance, T-cell cross-reactivity, and alloreactivity. Collectively, the data also provide an opportunity to address the structural correlates of MHC-I restriction. Here, we provide our perspective concerning these advances in the field. Although much key information has been gleaned, the structural data show that some of the key concepts surrounding the TCR-pMHC-I interaction remain controversial and unresolved.
Two-Laser Optical Distance-Measuring Instrument that Corrects for the Atmospheric Index of Refraction (1972)

The Wave Propagation Laboratory of the Environmental Research Laboratories of the National Oceanic and Atmospheric Administration has been engaged in the development of dual-wavelength, optical distance- measuring instruments. Recently a new generation of this type of high-accuracy instrument has been completed. Preliminary testing of the new instrument indicates that the original goal of the project, accuracy of better than one part in a million over distances of 5-10 km using averaging times of less than 1 min, is being met. This paper describes the instrument and preliminary test results.
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions (2010)

Protein-protein complexes play key roles in all cellular signal transduction processes. We have developed a fast and accurate computational approach to predict changes in the binding free energy upon alanine mutations in protein-protein interfaces. The approach is based on a knowledge-based scoring function, DrugScore(PPI), for which pair potentials were derived from 851 complex structures and adapted against 309 experimental alanine scanning results. Based on this approach, we developed the DrugScore(PPI) webserver. The input consists of a protein-protein complex structure; the output is a summary table and bar plot of binding free energy differences for wild-type residue-to-Ala mutations. The results of the analysis are mapped on the protein-protein complex structure and visualized using J mol. A single interface can be analyzed within a few minutes. Our approach has been successfully validated by application to an external test set of 22 alanine mutations in the interface of Ras/RalGDS. The DrugScore(PPI) webserver is primarily intended for identifying hotspot residues in protein-protein interfaces, which provides valuable information for guiding biological experiments and in the development of protein-protein interaction modulators. The DrugScore(PPI) Webserver, accessible at http://cpclab.uni-duesseldorf.de/dsppi, is free and open to all users with no login requirement.
Role of Gab1 in Heart, Placenta, and Skin Development and Growth Factor- and Cytokine-Induced Extracellular Signal-Regulated Kinase Mitogen-Activated Protein Kinase Activation (2000)

Gab1 is a member of the Gab/DOS (Daughter of Sevenless) family of adapter molecules, which contain a pleckstrin homology (PH) domain and potential binding sites for SH2 and SH3 domains. Gab1 is tyrosine phosphorylated upon stimulation of various cytokines, growth factors, and antigen receptors in cell lines and interacts with signaling molecules, such as SHP-2 and phosphatidylinositol 3-kinase, although its biological roles have not yet been established. To reveal the functions of Gab1 in vivo, we generated mice lacking Gab1 by gene targeting. Gab1-deficient embryos died in utero and displayed developmental defects in the heart, placenta, and skin, which were similar to phenotypes observed in mice lacking signals of the hepatocyte growth factor/scatter factor, platelet-derived growth factor, and epidermal growth factor pathways. Consistent with these observations, extracellular signal-regulated kinase mitogen-activated protein (ERK MAP) kinases were activated at much lower levels in cells from Gab1-deficient embryos in response to these growth factors or to stimulation of the cytokine receptor gp130. These results indicate that Gab1 is a common player in a broad range of growth factor and cytokine signaling pathways linking ERK MAP kinase activation.
The Double Discontinuous Mode Operation of a Converter: A Method for Soft Switching (2004)

This paper describes a way of ensuring soft switching in a converter without using additional components. This method is called double discontinuous mode (DDM). In particular, it permits any free wheeling diode to switch off at zero current, and for transistors to switch on at zero current and to switch off at zero voltage. The method illustrated here refers to a buck, but this concept may be applied to any type of converter, with or without transformer. Various mathematical models of this method are developed, and its characteristics and fields of application highlighted in this paper.
Silver Plating from Acid Complex Iodide Baths (1938)

Bright, adherent electrodeposits of silver are obtained at a pH of 1.7 from a bath containing 0.24 N silver, 3.47 N potassium iodide and 0.05 N sulfuric acid, with a current efficiency of 95 per cent. The quality of deposit is equivalent to that obtainable from cyanide baths. Baths containing, respectively, citric, acetic, maleic, and hydrochloric in place of the sulfuric acid, give similar results. The acid component functions as a proton donor ; no specific anion reaction is apparent. Both quality and efficiency increase as the pH is decreased from 3.0 to 0.65.
Considerations for the Development of New Antiarrhythmic Drugs (2010)

Several studies over the past few years have investigated the benefits of antiarrhythmic drugs (AADs) for the treatment of atrial fibrillation (AF). Data from key studies comparing rate versus rhythm control show no evidence of superiority in terms of survival benefits with either therapeutic strategy. In terms of AADs, many of the currently available drugs are associated with safety issues, thus the relative risk–benefit ratios of each drug is a major consideration when selecting an AAD in therapy. The safety issues and complications associated with current therapeutic drug options clearly indicate the need for novel drug development in the field of AF. New approaches that have been evaluated include AADs with greater atrial selectivity and novel non-selective multichannelblocking AADs. Trials evaluating new AADs will likely need to demonstrate superior safety profiles over existing drugs. However, in light of the inconclusive results in terms of survival benefits of the major rate versus rhythm studies and the increasing use of nonpharmacological techniques, including direct-current cardioversion and ablative techniques, cardiologists are faced with questions concerning the specific direction of new AAD development to be undertaken in future.
Waveguide stub-line tuning of RF cavities with heavy beam loading (2002)

A method is proposed for using adjustable, waveguide stub-line tuners to match the load impedance of the cavity plus beam to the power source, without the need to detune the cavity. Adjustable stub-line tuners are shown to be able to completely match the resistive and reactive parts of the load impedance to a generator under all conditions of beam loading, ensuring optimum power transfer between generator and cavity. This technique may have advantages in high-current storage rings such as the SLC damping rings and the new PEP II storage rings. The coupled-bunch instability driven by the fundamental mode of the cavity is re-appraised in this coupling scheme in which the cavity is no longer detuned. The consequences of this matching scheme are also considered for the beam loading stability limit.
Cytotoxic CD8+ T cells may be drivers of tissue destruction in Sjögren’s syndrome (2022)

Sjögren's syndrome is a chronic autoimmune disorder whose pathogenesis is poorly understood and that lacks effective therapies. Detailed quantitative and spatial analyses of tissues affected by Sjögren's syndrome were undertaken, including the quantitation of the frequency of selected cell-cell interactions in the disease milieu. Quantitative analyses of CD4<sup>+</sup> T cell subsets and of CD8<sup>+</sup> T cells in the labial salivary glands from untreated patients with primary Sjögren's syndrome revealed that activated CD8<sup>+</sup> cytotoxic T cells (CD8<sup>+</sup>CTLs) were the most prominent T cells in these infiltrates. An accumulation of apoptotic glandular epithelial cells, mainly ductal and acinar cells, was observed, consistent with the impaired salivary secretion often observed in patients with this disease. FasL expressing activated CD8<sup>+</sup> T cells were seen to accumulate around Fas expressing apoptotic epithelial cells. Quantitative analyses of apoptotic cell types and of conjugates between cytotoxic T cells and epithelial cells undergoing apoptosis suggest that Sjögren's syndrome is primarily driven by CD8<sup>+</sup>CTL mediated execution of epithelial cells mainly represented by ductal and acinar cells.
RNA interference of the stress related OsMADS26 transcription factor in rice increases resistance to various pathogens and reduces plant development (2010)

Several transcription factors have been involved in rice response against biotic and abiotic stresses (Khong et al., 2008). In A. thaliana, the MADS box transcription factor AGL12 control cell division in root meristem and is involved in flowering transition (Tapia-Lopez et al., 2008). When over expressed in Catharanthus roseus cell suspension AGL12 promotes tissue like organization and alkaloid biosynthesis (Montiel et al., 2007). OsMADS26, the rice orthologous of AGL12 in A. thaliana was recently over expressed under the control of a DEX inducible promoter and described as a stress related gene Lee et al., 2008). Nevertheless its precise function remains unknown. QPCR analysis revealed that this gene is expressed both in leaves and roots and is upregulated in response to osmotic stress. In order to precise the function of OsMAD26 in stress response or in development, and in absence of insertion mutant, we had generated rice lines RNA interfered for this gene. Interfered lines were obtained with two GST tagging the 5' or the 3' end of the mRNA. Interfered lines were affected in their development (root, tillering, height, dry weight) and were delayed for their flowering time in comparison to control. Roots of interfered lines present a reduced geotropism. Interfered lines were not affected in comparison to control line in their availability to resist to drought stress. But interestingly, interfered lines present an increased resistance against Magnaeporthae grisea, Xanthomonas oryzae and the Rice Yellow Mottle Virus. This suggests that OsMADS26 is a negative regulator of biotic stress response and acts as a general activator of development. In order to identify the genes and the biological pathways regulated by OsMADS26 we have proceeded to a transcriptome comparative analysis of genes expressed in WT and RNA interfered lines. Data analysis is in progress. (Texte intégral)
Search for a correlation length in a simulation of the glass transition (1991)

We have looked for evidence of a correlation length in a molecular-dynamics simulation of the glass transition. We have studied the correlation functions of both the translational order of particle positions and the orientational order of nearest-neighbor bond angles, and have seen no indication of a diverging length scale. We also present data from the simulation, which extend recent laboratory measurements of the frequency-dependent specific heat and thermal conductivity.
Generation of random fiber distributions for unidirectional fiber‐reinforced composites based on particle swarm optimizer (2018)

The stochastic nature of fiber distribution over transversal cross‐section in unidirectional fiber‐reinforced composites has a significant effect on the microscopical distribution of stresses and strains. Towards simulation‐based analysis and design of fiber‐reinforced composite, this paper concentrates on the issue of random fiber distributions and a new approach is developed to effectively generate microstructures of composite material with high fiber volume fraction. The method, named random distribution particle swarm optimization (PSO) algorithm, is proposed based on the particle movement regulation and position updating principle of PSO. The method creates microstructures with different fiber volume fractions conveniently by distributing each single fiber with inter‐fiber distance arrangement. The performance of algorithm is analyzed statistically and the results demonstrate that it is capable of catching the typical distribution of these materials for both low and high fiber volume fractions. Finite‐element analysis is conducted to predict effective properties of the generated microstructures and the simulation results exhibit reasonable agreement with experimental results. The developed algorithm is easily realized and highly efficient without introducing heuristic steps to achieve high volume fraction. The approach provides a valuable alternative to generate random numerical models used in micromechanical analysis of unidirectional fiber‐reinforced composites. POLYM. COMPOS., 40:1643–1653, 2019. © 2018 Society of Plastics Engineers
Umami the Fifth Basic Taste: History of Studies on Receptor Mechanisms and Role as a Food Flavor (2015)

Three umami substances (glutamate, 5'-inosinate, and 5'-guanylate) were found by Japanese scientists, but umami has not been recognized in Europe and America for a long time. In the late 1900s, umami was internationally recognized as the fifth basic taste based on psychophysical, electrophysiological, and biochemical studies. Three umami receptors (T1R1 + T1R3, mGluR4, and mGluR1) were identified. There is a synergism between glutamate and the 5'-nucleotides. Among the above receptors, only T1R1 + T1R3 receptor exhibits the synergism. In rats, the response to a mixture of glutamate and 5'-inosinate is about 1.7 times larger than that to glutamate alone. In human, the response to the mixture is about 8 times larger than that to glutamate alone. Since glutamate and 5'-inosinate are contained in various foods, we taste umami induced by the synergism in daily eating. Hence umami taste induced by the synergism is a main umami taste in human.
Prediction of Readmission and Complications in Pituitary Adenoma Resection via the National Surgical Quality Improvement Program (NSQIP) Database (2021)

Purpose: Pituitary adenomas are common intracranial tumors (incidence 4:100,000 people) with good surgical outcomes; however, a subset of patients show higher rates of worsened perioperative morbidity. Understanding the relevant risk factors and whether outcomes have improved over time would improve understanding of this disease.
Pan-cancer analysis of CD274 (PD-L1) mutations in 314,631 patient samples and subset correlation with PD-L1 protein expression (2021)

Overall, the prevalence of <i>CD274</i> SV mutations was low (0.3%, 1081/314,631) with 577 unique variants. The most common <i>CD274</i> SV mutations were R260H (n=51), R260C (n=18), R125Q (n=12), C272fs*13 (n=11), R86W (n=10), and R113H (n=10). The prevalence of <i>CD274</i> mutations varied depending on tumor type with diffuse large B-cell lymphoma (1.9%, 19/997), cutaneous squamous cell carcinoma (1.6%, 14/868), endometrial adenocarcinoma (1.0%, 36/3740), unknown primary melanoma (0.9%, 33/3679), and cutaneous melanoma (0.8%, 32/3874) having the highest frequency of mutations. Of the R260H cases concurrently tested with PD-L1 IHC, most (81.8%, 9/11) had no PD-L1 expression, which contrasts to the five E237K cases where most (80%, 4/5) had PD-L1 expression. In addition, we saw a significantly lower level of PD-L1 expression in samples with a clonal truncating variant (nonsense or frameshift indel) when compared with samples with a subclonal truncating variants (mean: TPS=1 vs TPS=38; p<0.001), and also in clonal versus subclonal missense mutations (mean: TPS=11 vs TPS=22, respectively; p=0.049) CONCLUSIONS: We defined the landscape of <i>CD274</i> mutations in a large cohort of tumor types that can be used as a reference for examining <i>CD274</i> mutations as potential resistance biomarkers for ICPI. Furthermore, we presented novel data on the correlation of <i>CD274</i> mutations and PD-L1 protein expression, providing important new information on the potential functionality of these mutations and can serve as a basis for future research.
Twice regularized MDPs and the equivalence between robustness and regularization (2021)

Robust Markov decision processes (MDPs) aim to handle changing or partially known system dynamics. To solve them, one typically resorts to robust optimization methods. However, this significantly increases computational complexity and limits scalability in both learning and planning. On the other hand, regularized MDPs show more stability in policy learning without impairing time complexity. Yet, they generally do not encompass uncertainty in the model dynamics. In this work, we aim to learn robust MDPs using regularization. We first show that regularized MDPs are a particular instance of robust MDPs with uncertain reward. We thus establish that policy iteration on reward-robust MDPs can have the same time complexity as on regularized MDPs. We further extend this relationship to MDPs with uncertain transitions: this leads to a regularization term with an additional dependence on the value function. We finally generalize regularized MDPs to twice regularized MDPs (R${}^2$ MDPs), i.e., MDPs with $\textit{both}$ value and policy regularization. The corresponding Bellman operators enable developing policy iteration schemes with convergence and robustness guarantees. It also reduces planning and learning in robust MDPs to regularized MDPs.
Differential Diagnosis between Small Cell Carcinoma and Adenocarcinoma of Lung in Fine Needle Aspiration Cytology. (2006)

Distinguishing small cell carcinoma from other lung malignancies is of great clinico-therapeutic significance. Small cell carcinoma is an aggressive tumor with a tendency to metastasize early. Survival time if untreated is low but this tumor is highly responsive to chemotherapy. We have occasionally experienced difficulties in differentiation between adenocarcinoma and small cell carcinoma of the lung in fine needle aspiration cytology (FNAC). The aim of this study was to investigate the possibility of distinguishing small cell carcinoma from adenocarcinoma of the lung in FNAC. We evaluated cytomorphological features of FNAC specimens from 62 small cell carcinomas and 57 adenocarcinomas from the lung that were confirmed by biopsy and/or immunohistochemistry on cell block. Cytomorphological details of the two tumors were compared. Nuclear smearing and nearly absent cytoplasm were the most distinct findings in small cell carcinoma compared to adenocarcinoma (p
INORA- A Unified Signaling and Routing Protocol in Mobile AdHoc networks (2002)

Mobile Ad hoc NETworks(MANET) are characterized by bandwidthconstrained wireless links, multiple hops and highly dynamic topologies.Providing QoS support in MANETs is hence a challenging task. Thispaper presents the design, implementation and evaluation of INORA,which is a network layer QoS support mechanism that makes use of theINSIGNIA in-band signaling mechanism and TORA routing protocol forMANETs. TORA provides multiple routes between a given source and destination. We present an effective coupling between TORA and INSIGNIA to getroutes that are "best-able" to provide QoS requirements fora flow. INORA also combines congestion control with routing.