gebhart/patrepeval huggingface dataset:
A Cluster of Major Specific Resistance Genes to Leptosphaeria maculans in Brassica napus (2004)

ABSTRACT Two types of genetic resistance to Leptosphaeria maculans usually are distinguished in Brassica napus: qualitative, total resistance expressed at the seedling stage and quantitative, partial resistance expressed at the adult plant stage. The latter is under the control of many genetic factors that have been mapped through quantitative trait loci (QTL) studies using 'Darmor' resistance. The former usually is ascribed to race-specific resistance controlled by single resistance to L. maculans (Rlm) genes. Three B. napus-originating specific Rlm genes (Rlm1, Rlm2, and Rlm4) previously were characterized. Here, we report on the genetic identification of two novel resistance genes, Rlm3 and Rlm7, corresponding to the avirulence genes AvrLm3 and AvrLm7. The identification of a novel L. maculans- B. napus specific interaction allowed the detection of another putative new specific resistance gene, Rlm9. The resistance genes were mapped in two genomic regions on LG10 and LG16 linkage groups. A cluster of five resistance genes (Rlm1, Rlm3, Rlm4, Rlm7, and Rlm9) was strongly suggested on LG10. The relation between all these specific resistance genes and their potential role in adult-plant field resistance is discussed. These two Rlm-carrying regions do not correspond to major QTL for Darmor quantitative resistance.
Additional file 10: Figure S5. of The antiproliferative ELF2 isoform, ELF2B, induces apoptosis in vitro and perturbs early lymphocytic development in vivo (2017)

Reconstitution efficiency in ELF2+ retrogenic mice. A) Murine stem cell virus-based (MSCV) retroviral vector (pMIG) used for expressing HA-tagged Elf2 isoforms; primer sequences used for detecting specific isoform expression are indicated (arrowheads); a common 5’ primer within the HA-tag and 3’ primer able to detect all Elf2 isoforms were used. B) RT-qPCR of ectopic Elf2a isoform expression in the spleens of retrogenic mice after 3 months reconstitution. Analysis of GFP expression after 4 weeks in peripheral blood mononuclear cells: total C); T cell population D); B cell population E); and granulocytes F). Reconstitution efficiency in the haemopoietic compartment after 3 months. Data represents the mean ± SEM of 3 experiments each performed with 4–5 mice per experimental arm. Statistical analysis performed using Student’s t test (ns, not significant; *, p
Improving the specificity of lung cancer screening CT using deep learning (2018)

PURPOSE Evaluate the utility of deep learning to improve the specificity and sensitivity of lung cancer screening with low-dose helical computed tomography (LDCT), relative to the Lung-RADS guidelines. METHOD AND MATERIALS We analyzed 42,943 CT studies from 14,863 patients, 620 of which developed biopsy-confirmed cancer. All cases were from the National Lung Screening Trial (NLST) study. We randomly split patients into a training (70%), tuning (15%) and test (15%) sets. A study was marked “true” if the patient was diagnosed with biopsy confirmed lung cancer in the same screening year as the study. A deep learning model was trained over 3D CT volumes (400x512x512) as input. We used the 95% specificity operating point based on the tuning set, and evaluated our approach on the test set. To estimate radiologist performance, we retrospectively applied Lung-RADS criteria to each study in the test set. Lung-RADS categories 1 to 2 constitute negative screening results, and categories 3 to 4 constitute positive results. Neither the model nor the Lung-RADS results took into account prior studies, but all screening years were utilized in evaluation. RESULTS The area under the receiver operator curve of the deep learning model was 94.2% (95% CI 91.0, 96.9). Compared to Lung-RADS on the test set, the trained model achieved a statistically significant absolute 9.2% (95% CI 8.4, 10.1) higher specificity and trended a 3.4% (95% CI -5.2, 12.6) higher sensitivity (not statistically significant).Radiologists qualitatively reviewed disagreements between the model and Lung-RADS. Preliminary analysis suggests that the model may be superior in distinguishing scarring from early malignancy. CONCLUSION A deep learning based model improved the specificity of lung cancer screening over Lung-RADS on the NLST dataset and could potentially help reduce unnecessary procedures. This research could supplement future versions of Lung-RADS; or support assisted read or second read workflows. CLINICAL RELEVANCE/APPLICATION While Lung-RADS criteria is recommended for lung cancer screening with LDCT, there is still an opportunity to reduce false-positive rates which lead to unnecessary invasive procedures.
Hybrid Video Codec Based on Flexible Block Partitioning With Extensions to the Joint Exploration Model (2019)

This article describes the main video coding technologies included in a joint proposal submitted by Qualcomm and Technicolor, in response to a Call for Proposals (CfP) issued by ITU-T SG16 WP3 Q.6 (VCEG) and ISO/IEC JTC1/SC29/WG11 (MPEG) in Oct. 2017. The proposal contains the majority of the tools that have been adopted into the Joint Exploration Model (JEM), developed in the exploratory phase that preceded the CfP. A flexible multi-tree type (MTT) block-partitioning scheme is proposed to extend the quadtree and binary tree (QTBT) based partitioning in JEM by including triple tree (TT) and asymmetric binary tree (ABT) partitions. In addition, several JEM tools in intra and inter prediction, transforms and arithmetic coding are modified, and new tools such as sign prediction and motion compensated padding are proposed. Objective standard dynamic range (SDR) gains of 43.1% and 15.5% in terms of average luma BD-rate improvement have been achieved for the CfP constraint set 1 (random-access configuration) relative to HEVC/H.265 (HM) and JEM anchors, respectively. For the CfP constraint set 2 (low-delay configuration), the average luma BD-rate improvements are 33.7% relative to the HM anchor and 12.7% relative to the JEM anchor. The proposed codec scored highly in both subjective evaluations and objective metrics and was among the best-performing CfP proposals.
Pseudo-constant logic optimization (2013)

Constant folding reduces area and enables greater parallelism, but requires circuits with constant inputs. In this work, we extend constant folding to support pseudo-constants, which are values that change with low frequency. We present a method of pseudo-constant logic optimization based on dynamically reconfigurable capabilities of FPGAs, which optimizes logic for different pseudo-constant values and then reconfigures the logic whenever the pseudo-constant changes. Although not beneficial for all logic, we show this optimization achieves up to a 1.25x increase in functional density on Xilinx Virtex 5 FPGAs.
Advances in the Pathogenesis of Cardiorenal Syndrome Type 3 (2015)

Cardiorenal syndrome (CRS) type 3 is a subclassification of the CRS whereby an episode of acute kidney injury (AKI) leads to the development of acute cardiac injury or dysfunction. In general, there is limited understanding of the pathophysiologic mechanisms involved in CRS type 3. An episode of AKI may have effects that depend on the severity and duration of AKI and that both directly and indirectly predispose to an acute cardiac event. Experimental data suggest that cardiac dysfunction may be related to immune system activation, inflammatory mediators release, oxidative stress, and cellular apoptosis which are well documented in the setting of AKI. Moreover, significant derangements, such as fluid and electrolyte imbalance, metabolic acidosis, and uremia, which are typical features of acute kidney injury, may impair cardiac function. In this review, we will focus on multiple factors possibly involved in the pathogenesis issues regarding CRS type 3.
SWORD: scalable and flexible workload generator for distributed data processing systems (2006)

Workload generation is commonly employed for performance characterization, testing and benchmarking of computer systems and networks. Workload generation typically aims at simulating or emulating traffic generated by different types of applications, protocols and activities, such as web browsing, email, chat, as well as stream multimedia traffic. We present a Scalable WORkloaD generator (SWORD) that we have developed for the testing and benchmarking of high-volume data processing systems. The tool is not only scalable but is also flexible and extensible allowing the generation of workload of a variety of types of applications and of contents.
Real-time, functional intra-operative localization of rat cavernous nerve network using near-infrared cyanine voltage-sensitive dye imaging (2020)

Despite current progress achieved in the surgical technique of radical prostatectomy, post-operative complications such as erectile dysfunction and urinary incontinence persist at high incidence rates. In this paper, we present a methodology for functional intra-operative localization of the cavernous nerve (CN) network for nerve-sparing radical prostatectomy using near-infrared cyanine voltage-sensitive dye (VSD) imaging, which visualizes membrane potential variations in the CN and its branches (CNB) in real time. As a proof-of-concept experiment, we demonstrate a functioning complex nerve network in response to electrical stimulation of the CN, which was clearly differentiated from surrounding tissues in an in vivo rat prostate model. Stimulation of an erection was confirmed by correlative intracavernosal pressure (ICP) monitoring. Within 10 minutes, we performed trans-fascial staining of the CN by direct VSD administration. Our findings suggest the applicability of VSD imaging for real-time, functional imaging guidance during nerve-sparing radical prostatectomy.
Nanocrystal Superlattice Embedded within an Inorganic Semiconducting Matrix by in Situ Ligand Exchange: Fabrication and Morphology (2015)

The authors carry out ligand exchange reaction replacing bulky insulating org. ligands with inorg. chalcogenidometallate clusters in nanocrystal assemblies floating at the gas-liq. interface. The mobility of the nanocrystals allows lattice contraction without significantly diminishing the ordering obsd. by grazing incidence X-ray scattering and transmission electron microscopy (TEM). This approach produces inorg. nanocomposite films one to a few nanocrystals in thickness with highly regular arrangements of nanocrystals. Anal. of free-standing nanocrystal membranes by low-dose, aberration-cor. TEM allows direct visualization of the nanocrystal-matrix interface.
5′ CArG degeneracy in smooth muscle α-actin is required for injury-induced gene suppression in vivo (2005)

CC(A/T)6GG-dependent (CArG-dependent) and serum response factor-dependent (SRF-dependent) mechanisms are required for gene expression in smooth muscle cells (SMCs). However, an unusual feature of many SMC-selective promoter CArG elements is that they contain a conserved single G or C substitution in their central A/T-rich region, which reduces binding affinity for ubiquitously expressed SRF. We hypothesized that this CArG degeneracy contributes to cell-specific expression of smooth muscle alpha-actin in vivo, since substitution of c-fos consensus CArGs for the degenerate CArGs resulted in relaxed specificity in cultured cells. Surprisingly, our present results show that these substitutions have no effect on smooth muscle-specific transgene expression during normal development and maturation in transgenic mice. However, these substitutions significantly attenuated injury-induced downregulation of the mutant transgene under conditions where SRF expression was increased but expression of myocardin, a smooth muscle-selective SRF coactivator, was decreased. Finally, chromatin immunoprecipitation analyses, together with cell culture studies, suggested that myocardin selectively enhanced SRF binding to degenerate versus consensus CArG elements. Our results indicate that reductions in myocardin expression and the degeneracy of CArG elements within smooth muscle promoters play a key role in phenotypic switching of smooth muscle cells in vivo, as well as in mediating responses of CArG-dependent smooth muscle genes and growth regulatory genes under conditions in which these 2 classes of genes are differentially expressed.
SN? reactions involving organocuprate reagents (1979)

The allyl halides (1) and (14) and the allyl epoxide (5) react with butylcuprate reagents through an SN′anti process preferentially: with the same reagents the hindered halide (10) gives the product derived from an SN′syn reaction.
Application de la nano-tomographie FIB/SEM à l’étude des propriétés électriques des batteries Lithium-ion (2018)

International audience
MicroRNA-155 contributes to shear-resistant leukocyte adhesion to human brain endothelium in vitro (2016)

Increased leukocyte adhesion to brain endothelial cells forming the blood–brain barrier (BBB) precedes extravasation into the central nervous system (CNS) in neuroinflammatory diseases such as multiple sclerosis (MS). Previously, we reported that microRNA-155 (miR-155) is up-regulated in MS and by inflammatory cytokines in human brain endothelium, with consequent modulation of endothelial paracellular permeability. Here, we investigated the role of endothelial miR-155 in leukocyte adhesion to the human cerebral microvascular endothelial cell line, hCMEC/D3, under shear forces mimicking blood flow in vivo. Using a gain- and loss-of-function approach, we show that miR-155 up-regulation increases leukocyte firm adhesion of both monocyte and T cells to hCMEC/D3 cells. Inhibition of endogenous endothelial miR-155 reduced monocytic and T cell firm adhesion to naïve and cytokines-induced human brain endothelium. Furthermore, this effect is partially associated with modulation of the endothelial cell adhesion molecules VCAM1 and ICAM1 by miR-155. Our results suggest that endothelial miR-155 contribute to the regulation of leukocyte adhesion at the inflamed BBB. Taken together with previous observations, brain endothelial miR-155 may constitute a potential molecular target for treatment of neuroinflammation diseases.
Failure of LIC13435 Protein of Leptospira interrogans Serovar Copenhageni to Confer Protection in Immunized Hamsters (2011)

Leptospirosis is a re-emergent zoonosis characterized by an acute febrile and systemic illness in humans caused by pathogenic spirochetes belonging to the genus Lepstospira.This disease has global distribution, and it is more frequent in tropical and subtropical areas.The complete genomic sequence of Leptospira species offered the possibility to identify potential vaccine candidates for leptospirosis, since environmental control measures are difficult to implement and there is not an ideal vaccine available for human use.Secreted and surface exposed molecules are potential targets for inducing protective immune response in the host.Although we selected six predicted sequences coding for putative outer membrane proteins with unknown function to be analyzed as vaccinal candidates against leptospirosis and for biological characterization, only the lic13435 gene was expressed and purified.The lic13435 gene is specific for pathogenic leptospires suggesting a possible virulence and/or pathogenicity associated function.The recombinant protein was purified and tested as vaccine candidate against leptospirosis.The immunization with the recombinant protein was able to produce a significant immune response in hamsters.Nevertheless, the animals were not protected against leptospirosis.
Enhanced Allergic Inflammation and Airway Responsiveness in Rats with Chronic Cryptococcus neoformans Infection: Potential Role for Fungal Pulmonary Infection in the Pathogenesis of Asthma (2006)

Although Cryptococcus neoformans is recognized for its ability to cause meningoencephalitis and pneumonia among immunocompromised persons, subclinical pulmonary infection is also common among immunocompetent persons. The significance of this infection is unknown. Using a rat model, we explored the potential for pulmonary cryptococcosis to modify allergic responses and airway reactivity. Our findings indicate that localized pulmonary cryptococcal infection (but not disseminated infection) can exacerbate allergic responses to respiratory challenge with ovalbumin, as measured by total immunoglobulin E levels, ovalbumin-specific immunoglobulin E titers, and eosinophil content of bronchoalveolar lavage fluid. Infection-associated enhancement of allergic responses was not dependent on cryptococcal encapsulation and was partially ameliorated by the administration of fluconazole. Increases in both the number of goblet cells and airway responsiveness, which are also features of reactive airway disease, were also present with pulmonary infection. An examination of lung cytokine levels in the context of active pulmonary infection revealed increased expression of interleukin (IL)-10, tumor necrosis factor- alpha , and IL-13, but not IL-12 or interferon- gamma . In contrast, systemic infection was associated with higher levels of interferon- gamma but lower levels of IL-13. Our studies highlight the potential for localized pulmonary C. neoformans infection to potentiate allergic responses and airway reactivity and suggest a potential role for subclinical pulmonary cryptococcosis in the pathogenesis of asthma.
An Instrumented Ultrasound Probe for Shear Wave Elastography With Uneven Force Distribution (2019)

An instrumented ultrasound probe system is designed to estimate the distribution of pressure applied across the probe face during image acquisition. The pressure distribution is used to investigate the effects of varying, and non-uniform, pressure distributions on shear wave elastography measurements in phantoms and ex vivo samples. Pressure distribution has a notable effect on shear wave elastography of ex vivo samples. The gradient in applied pressure across the probe face is mirrored in the gradient of elasticity measurements across the ultrasound elastogram image.
Cobalt–phosphate oxygen-evolving compound (2008)

The utilization of solar energy on a large scale requires efficient storage. Solar-to-fuels has the capacity to meet large scale storage needs as demonstrated by natural photosynthesis. This process uses sunlight to rearrange the bonds of water to furnish O2 and an H2-equivalent. We present a tutorial review of our efforts to develop an amorphous cobalt-phosphate catalyst that oxidizes water to O2. The use of earth-abundant materials, operation in water at neutral pH, and the formation of the catalyst in situ captures functional elements of the oxygen evolving complex of Photosystem II.
Search for anomalous electroweak production of WW/WZ in association with a high-mass dijet system in pp collisions at s=8  TeV with the ATLAS detector (2017)

A search is presented for anomalous quartic gauge boson couplings in vector-boson scattering. The data for the analysis correspond to $20.2\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of $\sqrt{s}=8\text{ }\text{ }\mathrm{TeV}$ $pp$ collisions and were collected in 2012 by the ATLAS experiment at the Large Hadron Collider. The search looks for the production of $WW$ or $WZ$ boson pairs accompanied by a high-mass dijet system, with one $W$ decaying leptonically and a $W$ or $Z$ decaying hadronically. The hadronically decaying $W/Z$ is reconstructed as either two small-radius jets or one large-radius jet using jet substructure techniques. Constraints on the anomalous quartic gauge boson coupling parameters ${\ensuremath{\alpha}}_{4}$ and ${\ensuremath{\alpha}}_{5}$ are set by fitting the transverse mass of the diboson system, and the resulting 95% confidence intervals are $\ensuremath{-}0.024&lt;{\ensuremath{\alpha}}_{4}&lt;0.030$ and $\ensuremath{-}0.028&lt;{\ensuremath{\alpha}}_{5}&lt;0.033$.
Development of a method and software for human motion training based on an inertial measurement units system (2015)

Rehabilitation and training is generally performed under control of a specialist. However the possibility to self-train motion as effectively as it would be done with an expert has clearly many advantages. One can indeed choose time, duration and place of his training. This paper presents the development of a software based on real-time data collecting from IMUs (Inertial Measurement Units) for human motion self-training. By choosing adequate location for the IMUs, and parameters (anatomic angles) of the movement to control, the system will be able to monitor every single motion of the user. The software allows to choose any body segment and to compute angles between any IMUs in 3 dimensions or in projection in anatomical planes. After defining the movement to control, the user needs to record several optimal movements so as to specify the reference and the boundaries of what will be set as the acceptable motion. Then, the software allows the user to repeat the movement as many times as he wants and displays a visual feedback showing the compliance between the reference and the actual motion. Recording the reference motion with the instructions of an expert will allow using it as an efficient tool for self-rehabilitation or self-training.
Isocyanate–epoxy reactions in bulk and solution (1989)

Abstract The reaction between diisocyanates and diepoxides can produce polyoxazolidones. However, the reaction may be accompanied by concurrent cyclization of isocyanate to produce trimeric isocyanurate. Studies were performed with pure phenyl isocyanate or diphenylmethane‐4,4′‐diisocyanate (MDI) and the diglycidyl ether of bisphenol‐A (DGEBA). Reactions were followed by FT‐IR and differential scanning calorimetry in order to determine relative rates of conversion to polyoxazolidone and isocyanurate. Various catalysts were utilized, with the most effective being 2‐ethyl‐4‐methylimidazole (EMI). Bulk reactions between MDI and DGEBA at 150°C resulted in considerable amounts of trimerization, thus giving crosslinked polymers. Solution reactions at 180–185°C in dry N ‐methylpyrrolidone using 0.1% EMI gave soluble and moldable polyoxazolidones.
Sex Differences in Mineralocorticoid Receptor Antagonist Trials: A Pooled Analysis of Three Large Clinical Trials (2020)

In three large MRA RCTs, women were substantially different from men with regard to their clinical features and event rates. Nonetheless, this meta-analysis supports a consistent and beneficial MRA effect regardless of sex.
Power-Efficient Beam Tracking During Connected Mode DRX in mmWave and Sub-THz Systems (2021)

Discontinuous reception (DRX), wherein a user equipment (UE) temporarily disables its receiver, is a critical power saving feature in modern cellular systems. DRX is likely to be aggressively used at mmWave and sub-THz frequencies due to the high front-end power consumption. A key challenge for DRX at these frequencies is blockage-induced link outages: a UE will likely need to track many directional links to ensure reliable multi-connectivity, thereby increasing the power consumption. In this paper, we explore bandit algorithms for link tracking in connected mode DRX that reduce power consumption by tracking only a fraction of the available links, but without adversely affecting the outage and throughput performance. Through detailed, system level simulations at 28 GHz (5G) and 140 GHz (6G), we observe that even sub-optimal link tracking policies can achieve considerable power savings with relatively little degradation in outage and throughput performance, especially with digital beamforming at the UE. In particular, we show that it is feasible to reduce power consumption by 75% and still achieve up to 95% (80%) of the maximum throughput using digital beamforming at 28 GHz (140 GHz), subject to an outage probability of at most 1%.