gebhart/patrepeval huggingface dataset:
A Coarse-to-Fine Deformable Transformation Framework for Unsupervised Multi-Contrast MR Image Registration with Dual Consistency Constraint (2021)

Multi-contrast magnetic resonance (MR) image registration is useful in the clinic to achieve fast and accurate imaging-based disease diagnosis and treatment planning. Nevertheless, the efficiency and performance of the existing registration algorithms can still be improved. In this paper, we propose a novel unsupervised learning-based framework to achieve accurate and efficient multi-contrast MR image registration. Specifically, an end-to-end coarse-to-fine network architecture consisting of affine and deformable transformations is designed to improve the robustness and achieve end-to-end registration. Furthermore, a dual consistency constraint and a new prior knowledge-based loss function are developed to enhance the registration performances. The proposed method has been evaluated on a clinical dataset containing 555 cases, and encouraging performances have been achieved. Compared to the commonly utilized registration methods, including VoxelMorph, SyN, and LT-Net, the proposed method achieves better registration performance with a Dice score of 0.8397± 0.0756 in identifying stroke lesions. With regards to the registration speed, our method is about 10 times faster than the most competitive method of SyN (Affine) when testing on a CPU. Moreover, we prove that our method can still perform well on more challenging tasks with lacking scanning information data, showing the high robustness for the clinical application.
[Biophysical concept of the human autodiagnostic system]. (2005)

A possible neurophysiological mechanism of the therapeutic effect of weak influences was proposed, which is based on the following assumptions: 1. In the organism, there is an autodiagnostic system, which serves for the accumulation and processing of information on the state of the organs to diagnose a desease. 2. The autodiagnostic disease is a recognizing system, i. e., a neuronet, which is constructed and functions according to the paradigms of neurocomputing. 3. Systemic (psychosomatic) diseases appear to result from erroneous diagnosis due to the defects of the autodiagnostic system. The influence of puncture on biologically active points corrects these defects, providing a positive therapeutic effect. A theoretical model for the structure and functioning of the autodiagnostic system is discussed. It is shown that the structure of the model autodiagnostic system coincides with that of Rexede plates forming the gray substance of the spinal cord. The experimental data on Rexede plates and their connections with organs and corresponding biologically active points are discussed. A relationship between the concept of the autodiagnostic system and the basic principles of alternative eastern medicine is discussed. It is shown that the Chinese model of puncture therapy represents a verbal description of the topological features of the phase space of the mathematical model for the recognizing neuroprocessor.
Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth (2019)

Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type-dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.
Synthesis of carbon nanotubes from bulk polymer (1996)

Carbon nanotubes have been synthesized by heat treating the polymer at 400 °C in air which was obtained by polyesterification between citric acid and ethylene glycol. Transmission electron micrographs and an electron diffraction pattern showed the formation of carbon nanotubes. The diameter of the tubes ranged from 5 to 20 nm, whereas the lengths were less than 1 μm.
Laser Transmitter Aims At Laser Beacon (1993)

Central India witnessed Chikungunya virus (CHIKV) outbreaks in 2016 and 2017. The present report is a hospital based cross-sectional study on the serological and molecular epidemiology of the outbreak. Mutational and phylogenetic analysis was conducted to ascertain the genetic relatedness of the central Indian strains with other Indian and global strains. Chikungunya infection was confirmed in the clinically suspected patients by the detection of anti-CHIKV IgM antibody by ELISA and viral RNA by RT-PCR. A representative set of the RT-PCR positive samples were sequenced for E1 gene and analyzed to identify the emerging mutations and establish their phylogenetic relationship, particularly with other contemporary strains. Phylogenetic analysis revealed the present strains to be of East Central South African (ECSA) genotype. Emergence of a variant strain was observed in the year 2016, which became the predominant strain in this region in 2017. The strains showed significant identity with recent New Delhi strains of 2015 and 2016 and Bangladesh strains of 2017. The epidemic mutation A226V which emerged in 2006 outbreaks of India and Indian Ocean Islands was found to be absent in the current strains. Among the important mutations viz. K211E, M269 V, D284E, I317V & V322A observed in the recent strains. I317V is a novel mutation which has emerged very recently as it was found only in central Indian (2016, 2017), New Delhi strains (2015, 2016) and Bangladesh strains (2017). This study has identified a unique mutation E1:I317V in the Central Indian strains, which is present only in recent New Delhi and Bangladesh strains till date. This study highlights the need for continuous molecular surveillance of circulating CHIKV strains in order to facilitate the prompt identification of novel strains of this virus and enable the elucidation of their clinical correlates.
Transparent and Colorless Dye‐Sensitized Solar Cells Based on Pyrrolopyrrole Cyanine Sensitizers (2022)

The development of transparent solar cells extends the applications of photovoltaics by offering the opportunity to substitute the gigantic surface coverage of windows by solar panels to produce electricity. Herein, we report a new family of NIR-sensitizers based on pyrrolopyrrole cyanine dyes, particularly efficient for the development of fully transparent and colorless dye-sensitized solar cells since a record efficiency of 2.5 % was achieved with an average visible transmittance (AVT) of 76 % and a color rending index (CRI) of 93.
Machine Learning Classification of Cirrhotic Patients with and without Minimal Hepatic Encephalopathy Based on Regional Homogeneity of Intrinsic Brain Activity (2016)

Machine learning-based approaches play an important role in examining functional magnetic resonance imaging (fMRI) data in a multivariate manner and extracting features predictive of group membership. This study was performed to assess the potential for measuring brain intrinsic activity to identify minimal hepatic encephalopathy (MHE) in cirrhotic patients, using the support vector machine (SVM) method. Resting-state fMRI data were acquired in 16 cirrhotic patients with MHE and 19 cirrhotic patients without MHE. The regional homogeneity (ReHo) method was used to investigate the local synchrony of intrinsic brain activity. Psychometric Hepatic Encephalopathy Score (PHES) was used to define MHE condition. SVM-classifier was then applied using leave-one-out cross-validation, to determine the discriminative ReHo-map for MHE. The discrimination map highlights a set of regions, including the prefrontal cortex, anterior cingulate cortex, anterior insular cortex, inferior parietal lobule, precentral and postcentral gyri, superior and medial temporal cortices, and middle and inferior occipital gyri. The optimized discriminative model showed total accuracy of 82.9% and sensitivity of 81.3%. Our results suggested that a combination of the SVM approach and brain intrinsic activity measurement could be helpful for detection of MHE in cirrhotic patients.
Copious Direct Photon Production: A Possible Resolution of the Prompt-Lepton Puzzle (1976)

We propose that all direct leptons not due to vector meson decay can be attributed to the decay of virtual photons. At ${p}_{\ensuremath{\perp}}\ensuremath{\approx}3$ GeV/c, we expect $\frac{\ensuremath{\gamma}}{\ensuremath{\pi}}$, the ratio of direct photons to pions, to be about 10 to 20% for $\sqrt{s}\ensuremath{\approx}20\ensuremath{-}60$ GeV.
Major role of sub-dominant bacteria in mixed cultures producing biohydrogen by dark fermentation (2011)

International audience
From Adaptive Kernel Density Estimation to Sparse Mixture Models (2018)

We introduce a balloon estimator in a generalized expectation-maximization method for estimating all parameters of a Gaussian mixture model given one data sample per mixture component. Instead of limiting explicitly the model size, this regularization strategy yields low-complexity sparse models where the number of effective mixture components reduces with an increase of a smoothing probability parameter $\mathbf{P&gt;0}$. This semi-parametric method bridges from non-parametric adaptive kernel density estimation (KDE) to parametric ordinary least-squares when $\mathbf{P=1}$. Experiments show that simpler sparse mixture models retain the level of details present in the adaptive KDE solution.
Group B Streptococcus circumvents neutrophils and neutrophil extracellular traps during amniotic cavity invasion and preterm labor (2016)

Preterm birth is a leading cause of neonatal morbidity and mortality. Although microbial invasion of the amniotic cavity (MIAC) is associated with the majority of early preterm births, the temporal events that occur during MIAC and preterm labor are not known. Group B Streptococci (GBS) are β-hemolytic, gram-positive bacteria, which commonly colonize the vagina but have been recovered from the amniotic fluid in preterm birth cases. To understand temporal events that occur during MIAC, we utilized a unique chronically catheterized nonhuman primate model that closely emulates human pregnancy. This model allows monitoring of uterine contractions, timing of MIAC and immune responses during pregnancy-associated infections. Here, we show that adverse outcomes such as preterm labor, MIAC, and fetal sepsis were observed more frequently during infection with hemolytic GBS when compared to nonhemolytic GBS. Although MIAC was associated with systematic progression in chorioamnionitis beginning with chorionic vasculitis and progressing to neutrophilic infiltration, the ability of the GBS hemolytic pigment toxin to induce neutrophil cell death and subvert killing by neutrophil extracellular traps (NETs) in placental membranes <i>in vivo</i> facilitated MIAC and fetal injury. Furthermore, compared to maternal neutrophils, fetal neutrophils exhibit decreased neutrophil elastase activity and impaired phagocytic functions to GBS. Collectively, our studies demonstrate how a unique bacterial hemolytic lipid toxin enables GBS to circumvent neutrophils and NETs in placental membranes to induce fetal injury and preterm labor.
Fundamental research on mercuryless rare gas fluorescent lamps at pulsed discharge (2002)

The characteristics of xenon-neon discharge fluorescent lamps with inner electrodes, and xenon discharge lamps with external electrodes are described in this paper. All these lamps were operated at pulsed discharge. In the case of inner electrode type, when the partial pressure of neon is high, the ignition voltage is low because of the Penning effect. Then, the high mixing ratio of neon is desirable for the lower ignition voltage. However, the luminance of phosphor increases as the mixing ratio of xenon increases. Therefore, in order to obtain high luminance, xenon should be filled at high mixing ratio. If only xenon is filled in the lamp of inner electrode type, the cathode is bombed and damaged by the large mass xenon ions. Consequently, the most suitable mixing ratio of xenon and neon or some buffer gas should be found experimentally for inner electrode type. On the other hand, when the lamp filled only with xenon is operated by external electrodes, as the pressure of xenon increases, the afterglow peak of phosphor emission increases. These increases seem to be caused by the UV light of xenon excimers. However, the starting voltage becomes high at high xenon pressure. So, the optimization of some conditions such as electrodes, pulse frequency, etc. is required for external electrode type.
Expression of glycine receptor subunits and gephyrin in single bipolar cells of the rat retina (1995)

We studied the expression of glycine receptor (GlyR) subunits and gephyrin in the adult rat retina. Reverse transcribed RNA was amplified by polymerase chain reaction (RT-PCR) with primers designed to recognize GlyR alpha 1, alpha 2, alpha 3, beta subunits, and gephyrin. Using RNA isolated from the whole retina, signals for all four GlyR subunits and gephyrin could be observed. In rod bipolar cells, in contrast, we detected a subset of GlyR subunits, alpha 1 and beta, and no gephyrin. Patch-clamp recording employing two subtype-specific blockers of the GlyR, picrotoxinin and cyanotriphenylborate (CTB), indicated that the GlyR in rod bipolar cells is a heteromeric protein composed of the alpha 1 and beta subunit. Moreover, the absence of detectable amounts of gephyrin mRNA suggests that the anchor protein is not required for the function of GlyRs in rod bipolar cells.
Long-Range Automatic Detection, Acoustic Signature Characterization and Bearing-Time Estimation of Multiple Ships with Coherent Hydrophone Array (2020)

Three approaches for instantaneous wide-area analysis of ship-radiated underwater sound, each focusing on a different aspect of that sound, received on a large-aperture densely-sampled coherent hydrophone array have been developed. (i) Ship’s narrowband machinery tonal sound is analyzed via temporal coherence using Mean Magnitude-Squared Coherence (MMSC) calculations. (ii) Ship’s broadband amplitude-modulated cavitation noise is examined using Cyclic Spectral Coherence (CSC) analysis that provides estimates for propeller blade pass rotation frequency, shaft rotation frequency, and hence the number of propeller blades. (iii) Mean power spectral densities (PSD) averaged across broad bandwidths are calculated in order to detect acoustically energetic ships. Each of these techniques are applied after beamforming of the received acoustic signals on a coherent hydrophone array, leading to significantly enhanced signal-to-noise ratios for simultaneous detection, bearing-time estimation and acoustic signature characterization of multiple ships over continental-shelf scale regions. The approaches are illustrated with underwater recordings of a 160-element coherent hydrophone array for six ocean vessels, that are located at a variety of bearings and ranges out to 200 km from the array, in the Norwegian Sea in February 2014. The CSC approach is shown to also be useful for automatic detection and bearing-time estimation of repetitive marine mammal vocalizations, providing estimates for inter-pulse-train and inter-pulse intervals from CSC spectra cyclic fundamental and first recurring peak frequencies respectively.
Identification of Hub Genes Associated With Progression and Prognosis of Bladder Cancer by Integrated Bioinformatics Analysis. (2021)

Abstract Background: Bladder cancer (BLCA) is the most popular malignant carcinomas in genitourinary system which has a high incidence and is prone to relapse. However, the molecular mechanism of BLCA remains to be unclear. Moreover, there is still a shortage of effective biomarkers that can predict progression and prognosis of BLCA. The objective of current study is to screen significant genes as biomarkers to forecast the progression and prognosis of BLCA patients. Methods: Gene expression profile downloaded from TCGA database and GEO database was used. Differential gene expression analysis and WGCNA were conducted to identify differential co-expression genes. In addition, GO enrichment analysis and KEGG pathway analysis were used to explore the functions of these genes. Moreover, PPI network, OS and DFS were used to identify survival-related hub genes. Finally, the expression levels of these genes were validated by qRT-PCR and HPA database. Results: About 124 differential co-expression genes were identified. And these genes were mainly enriched in muscle system process and muscle contraction (BP), contractile fiber, myofibril, sarcomere, focal adhesion and cell-substrate junction (CC) and actin binding (MF) in GO enrichment analysis, while enriched in vascular smooth muscle contraction, focal adhesion, cardiac muscle contraction, hypertrophic cardiomyopathy, dilated cardiomyopathy and regulation of actin cytoskeleton in KEGG analysis. Furthermore, five survival-related hub genes (MYH11, ACTA2, CALD1, TPM1, MYLK) were identified via overall OS and DFS. In addition, the expression levels of the five survival-related genes were upregulated with the procession of BLCA, such as grade, stage and TNM stage. Finally, all survival-related hub genes were found to be down-regulated in BLCA via qRT-PCR and HPA database. Conclusions: Our current study verified five new key genes in BLCA, which could help us better understand the pathogenesis of BLCA. And these five hub genes may be involved in the development and progression of BLCA and served as potential biomarkers.
Auditory motion tracking ability of adults with normal hearing and with bilateral cochlear implants (2019)

Adults with bilateral cochlear implants (BiCIs) receive benefits in localizing stationary sounds when listening with two implants compared with one; however, sound localization ability is significantly poorer when compared to normal hearing (NH) listeners. Little is known about localizing sound sources in motion, which occurs in typical everyday listening situations. The authors considered the possibility that sound motion may improve sound localization in BiCI users by providing multiple places of information. Alternatively, the ability to compare multiple spatial locations may be compromised in BiCI users due to degradation of binaural cues, and thus result in poorer performance relative to NH adults. In this study, the authors assessed listeners' abilities to distinguish between sounds that appear to be moving vs stationary, and track the angular range and direction of moving sounds. Stimuli were bandpass-filtered (150-6000 Hz) noise bursts of different durations, panned over an array of loudspeakers. Overall, the results showed that BiCI users were poorer than NH adults in (i) distinguishing between a moving vs stationary sound, (ii) correctly identifying the direction of movement, and (iii) tracking the range of movement. These findings suggest that conventional cochlear implant processors are not able to fully provide the cues necessary for perceiving auditory motion correctly.
Method of locating a leaking fuel element in a fast breeder power reactor (2023)

Leaking fuel elements in a fast reactor are identified by measuring the ratio of .sup.134 Xe to .sup.133 Xe in the reactor cover gas following detection of a fuel element leak, this ratio being indicative of the power and burnup of the failed fuel element. This procedure can be used to identify leaking fuel elements in a power breeder reactor while continuing operation of the reactor since the ratio measured is that of the gases stored in the plenum of the failed fuel element. Thus, use of a cleanup system for the cover gas makes it possible to identify sequentially a multiplicity of leaking fuel elements without shutting the reactor down.
<title>Liquid chromatography combined with visible diode-laser-induced fluorescence detection for photosensitizers</title> (1994)

A combination of conventional-size liquid chromatography and visible diode-laser induced fluorescence (DIO-LIF) detection has been developed and applied for the detection of a model photosensitizer, AlPcS<SUB>2</SUB>, in biological samples. Conventional fluorimetry was found to give unsatisfactory information. A detection limit of 2.1 X 10<SUP>-12</SUP> M (S/N equals 3) was obtained for AlPcS<SUB>2</SUB> in both rat urine and faeces extracts using the DIO-LIF system, 20-fold lower than obtained with a conventional fluorescence detection system, when used in combination with chromatography.
Editorial: Special Issue - IMBioC 2021 (2022)

This special issue is dedicated to dear colleagues, Mojgan Daneshmand (Professor, Electrical and Computer Engineering) and Pedram Mousavi (Professor, Mechanical Engineering) from the University of Alberta, and their daughters, Daria and Dorina. We lost them too early, in a plane crash on January 8, 2020. Their creativity in research and dedication to teaching remain with us through the work they left behind, and students whose career paths they have helped form and inspire.
High Dose Chlorambucil in the Treatment of Lymphoid Malignancies (2003)

High dose chlorambucil has been shown to be an effective single-agent treatment in chronic lymphocytic leukemia (CLL), and to be useful as part of combination chemotherapy in low-grade non-Hodgkin's (NHL) and Hodgkin's disease (HD). In general, it is well tolerated and can be used in an outpatient setting. The optimum dose of chlorambucil has not been defined and there are numerous different dosing schedules available. Pharmacokinetic studies suggest decreased bioavailability with successive cycles, probably due to accelerated metabolism. There is good evidence that regimens which use higher doses of chlorambucil have a better outcome than standard dose therapy. Most of the trials which have compared chlorambucil with fludarabine have not used a higher dose regimen of chlorambucil and cannot truly be described as comparative. There is an increase in the incidence of grade 3 and 4 neutropenia and also of sepsis with fludarabine treatment, compared to chlorambucil. Fludarabine produces a higher initial response rate in CLL but no statistical difference has been shown in long term survival between fludarabine and high dose chlorambucil. In the treatment of lymphoma, single agent chlorambucil does not confer a durable remission. There have been good results with combination chemotherapy regimens such as CID and PECC. The oral route of administration of these combinations makes them particularly useful as part of palliative chemotherapy. A further point to consider is that chlorambucil is very much cheaper than fludarabine and other newer agents. Chlorambucil should not automatically be overlooked in favor of more recently developed drugs such as fludarabine. There is good evidence that the drug is an effective treatment at a suitable dose, and there is a need for randomized trials to compare it fully with other current treatments.