gebhart/patrepeval huggingface dataset:
Variants near CHRNB3-CHRNA6 are associated with DSM-5 cocaine use disorder: Evidence for pleiotropy (2014)

In the U.S.A., cocaine is the second most abused illicit drug. Variants within the CHRNB3-A6 gene cluster have been associated with cigarette consumption in several GWAS. These receptors represent intriguing candidates for the study of cocaine dependence because nicotinic receptors are thought to be involved in generalized addiction pathways. Using genotypic data from a GWAS of the Study of Addiction: Genetics and Environment (SAGE) dataset, we tested for association of CHRNB3-A6 SNPs with DSM-5 cocaine use disorder. Multiple SNPs in the region were significantly associated with increased risk of cocaine use disorder. Inclusion of the most significant SNP as a covariate in a linear regression model provided evidence for an additional independent signal within this locus for cocaine use disorder. These results suggest that the CHRNB3-A6 locus contains multiple variants affecting risk for vulnerability to cocaine and nicotine dependence as well as bipolar disorder, suggesting that they have pleiotropic effects.
Targeted Next-Generation Sequencing can Replace Sanger Sequencing in Clinical Diagnostics (2013)

Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted next-generation sequencing (NGS), in which a selected fraction of genes is sequenced, may circumvent these shortcomings. We aimed to determine whether the sensitivity and specificity of targeted NGS is equal to those of SS. We constructed a targeted enrichment kit that includes 48 genes associated with hereditary cardiomyopathies. In total, 84 individuals with cardiomyopathies were sequenced using 151 bp paired-end reads on an Illumina MiSeq sequencer. The reproducibility was tested by repeating the entire procedure for five patients. The coverage of ≥30 reads per nucleotide, our major quality criterion, was 99% and in total ∼21,000 variants were identified. Confirmation with SS was performed for 168 variants (155 substitutions, 13 indels). All were confirmed, including a deletion of 18 bp and an insertion of 6 bp. The reproducibility was nearly 100%. We demonstrate that targeted NGS of a disease-specific subset of genes is equal to the quality of SS and it can therefore be reliably implemented as a stand-alone diagnostic test.
Feedback-Assisted Wavefront Shaping for Monitoring Chemical Reactions Inside Opaque Media (2020)

We utilize feedback-assisted wavefront shaping to monitor the fluorescence and Raman spectra of molecular crystals inside opaque media as they undergo chemical reactions. This technique has applications in the study of explosives and novel propellants.
Supplementary Fig 1 from WNT/β-catenin Pathway Activation Correlates with Immune Exclusion across Human Cancers (2023)

&lt;p&gt;Sup Fig 1&lt;/p&gt;
Real time control laws to control HCCI combustion by Ozone addition (2016)

International audience
Management of Nephrolithiasis in Pregnancy: Multi-Disciplinary Guidelines From an Academic Medical Center (2021)

<b>Introduction:</b> The management of nephrolithiasis during pregnancy can be stressful for urologists due to concerns for investigations and treatments that may pose risk of fetal harm, and unfamiliarity with optimal management of these complex patients. In response, we created multi-disciplinary evidence-based guidelines to standardize the care for obstetric patients presenting with flank pain and suspicion for nephrolithiasis. <b>Methods:</b> A multi-disciplinary team involving Urology, Obstetric Anesthesiology, Obstetrics and Gynecology, Diagnostic Radiology, and Interventional Radiology from a single academic medical center was assembled. A PubMed search was performed using keywords of pregnancy/antepartum, nephrolithiasis/calculi/kidney stones, ureteroscopy, non-obstetric surgery, complications, preterm delivery, MRI, computerized tomography, renal bladder ultrasound (RBUS), and anesthesia to identify relevant articles. Team members reviewed their respective areas to create a comprehensive set of guidelines. One invited external expert reviewed the guidelines for validation purposes. <b>Results:</b> A total of 54 articles were reviewed for evidence synthesis. Four guideline statements were constructed to guide diagnosis and imaging, and seven statements to guide intervention. Guidelines were then used to create a diagnostic and intervention flowchart for ease of use. In summary, RBUS should be the initial diagnostic study. If diagnostic uncertainty still exists, a non-contrast CT scan should be obtained. For obstetric patients presenting with a septic obstructing stone, urgent decompression should be achieved. We recommend ureteral stent placement as the preferred intervention if local factors allow. <b>Conclusions:</b> We present a standardized care pathway for the management of nephrolithiasis during pregnancy. Our aim is to standardize and simplify the clinical management of these complex scenarios for urologists.
The Selective Tie2 Inhibitor Rebastinib Blocks Recruitment and Function of Tie2Hi Macrophages in Breast Cancer and Pancreatic Neuroendocrine Tumors (2017)

Tumor-infiltrating myeloid cells promote tumor progression by mediating angiogenesis, tumor cell intravasation, and metastasis, which can offset the effects of chemotherapy, radiation, and antiangiogenic therapy. Here, we show that the kinase switch control inhibitor rebastinib inhibits Tie2, a tyrosine kinase receptor expressed on endothelial cells and protumoral Tie2-expressing macrophages in mouse models of metastatic cancer. Rebastinib reduces tumor growth and metastasis in an orthotopic mouse model of metastatic mammary carcinoma through reduction of Tie2<sup>+</sup> myeloid cell infiltration, antiangiogenic effects, and blockade of tumor cell intravasation mediated by perivascular Tie2<sup>Hi</sup>/Vegf-A<sup>Hi</sup> macrophages in the tumor microenvironment of metastasis (TMEM). The antitumor effects of rebastinib enhance the efficacy of microtubule inhibiting chemotherapeutic agents, either eribulin or paclitaxel, by reducing tumor volume, metastasis, and improving overall survival. Rebastinib inhibition of angiopoietin/Tie2 signaling impairs multiple pathways in tumor progression mediated by protumoral Tie2<sup>+</sup> macrophages, including TMEM-dependent dissemination and angiopoietin/Tie2-dependent angiogenesis. Rebastinib is a promising therapy for achieving Tie2 inhibition in cancer patients. <i>Mol Cancer Ther; 16(11); 2486-501. ©2017 AACR</i>.
The Dark Side of Molecular Catalysis: Diimine–Dioxime Cobalt Complexes Are Not the Actual Hydrogen Evolution Electrocatalyst in Acidic Aqueous Solutions (2016)

The perspective of integrating molecular catalysts for hydrogen evolution into operating devices requires the benchmarking of their activity preferentially in aqueous media. Within a series of cobalt complexes assessed in that way, cobalt diimine–dioxime derivatives were shown to be the most active catalysts with onset overpotential for proton reduction as low as 260 mV in phosphate buffer (pH = 2.2) (McCrory et al. J. Am. Chem. Soc. 2012, 134, 3164–3170). Combining a set of analytical techniques (electrochemistry, gas chromatography, SEM, and XPS), we demonstrate here that the electrochemical wave previously assigned to H2 evolution catalyzed by the molecular complex actually corresponds to low levels of catalytic hydrogen production (≤27% faradaic yield). Instead, we assign this wave to the reductive degradation of the molecular complex and to the formation of a nanoparticulate deposit at the electrode. Actually, this coating is responsible for the high faradaic yields for hydrogen evolution observed at more cathodic potentials. The catalytic nanoparticulate material is metastable and readily redissolves, so that rinse-test experiments were insufficient here to rule out the formation of solid-state materials. This point accounts for the previous misidentification of the active species in H2 evolution mediated by a cobalt diimine–dioxime complex in aqueous phosphate buffer (pH = 2.2). Our finding, exemplified on a cobalt complex, may be extended to other molecular systems and suggests that the routine use of rinse-test experiments may not be sufficient to ascertain the molecular nature of active water-splitting catalytic species.
Ocular hypotensive effect of the novel EP3/FP agonist ONO-9054 versus Xalatan: results of a 28-day, double-masked, randomised study (2016)

NCT02083289, Results.
β-arrestin- but not G protein-mediated signaling by the “decoy” receptor CXCR7 (2009)

Ubiquitously expressed seven-transmembrane receptors (7TMRs) classically signal through heterotrimeric G proteins and are commonly referred to as G protein-coupled receptors. It is now recognized that 7TMRs also signal through beta-arrestins, which act as versatile adapters controlling receptor signaling, desensitization, and trafficking. Most endogenous receptors appear to signal in a balanced fashion using both beta-arrestin and G protein-mediated pathways. Some 7TMRs are thought to be nonsignaling "decoys" because of their inability to activate typical G protein signaling pathways; it has been proposed that these receptors act to scavenge ligands or function as coreceptors. Here we demonstrate that ligand binding to the decoy receptor CXCR7 does not result in activation of signaling pathways typical of G proteins but does activate MAP kinases through beta-arrestins in transiently transfected cells. Furthermore, we observe that vascular smooth muscle cells that endogenously express CXCR7 migrate to its ligand interferon-inducible T-cell alpha chemoattractant (ITAC), an effect that is significantly attenuated by treatment with either a CXCR7 antagonist or beta-arrestin depletion by siRNA. This example of an endogenous "beta-arrestin-biased" 7TMR that signals through beta-arrestin in the absence of G protein activation demonstrates that some 7TMRs encoded in the genome have evolved to signal through beta-arrestin exclusively and suggests that other receptors that are currently thought to be orphans or decoys may also signal through such nonclassical pathways.
From initial segment to cauda: a regional characterization of mouse epididymal CD11c<sup>+</sup> mononuclear phagocytes based on immune phenotype and function (2020)

Successful sperm maturation and storage rely on a unique immunological balance that protects the male reproductive organs from invading pathogens and spermatozoa from a destructive autoimmune response. We previously characterized one subset of mononuclear phagocytes (MPs) in the murine epididymis, CX3CR1<sup>+</sup> cells, emphasizing their different functional properties. This population partially overlaps with another subset of understudied heterogeneous MPs, the CD11c<sup>+</sup> cells. In the present study, we analyzed the CD11c<sup>+</sup> MPs for their immune phenotype, morphology, and antigen capturing and presenting abilities. Epididymides from CD11c-EYFP mice, which express enhanced yellow fluorescent protein (EYFP) in CD11c<sup>+</sup> MPs, were divided into initial segment (IS), caput/corpus, and cauda regions. Flow cytometry analysis showed that CD11c<sup>+</sup> MPs with a macrophage phenotype (CD64<sup>+</sup> and F4/80<sup>+</sup>) were the most abundant in the IS, whereas those with a dendritic cell signature [CD64<sup>-</sup> major histocompatibility complex class II (MHCII)<sup>+</sup>] were more frequent in the cauda. Immunofluorescence revealed morphological and phenotypic differences between CD11c<sup>+</sup> MPs in the regions examined. To assess the ability of CD11c<sup>+</sup> cells to take up antigens, CD11c-EYFP mice were injected intravenously with ovalbumin. In the IS, MPs expressing macrophage markers were most active in taking up the antigens. A functional antigen-presenting coculture study was performed, whereby CD4<sup>+</sup> T cells were activated after ovalbumin presentation by CD11c<sup>+</sup> epididymal MPs. The results demonstrated that CD11c<sup>+</sup> MPs in all regions were capable of capturing and presenting antigens. Together, this study defines a marked regional variation in epididymal antigen-presenting cells that could help us understand fertility and contraception but also has larger implications in inflammation and disease pathology.
Quand le consommateur devient commerçant : motivations et perspectives (2014)

International audience
Electroantennographic responses of Heterotermes tenuis (Isoptera: Rhinotermitidae) to synthetic (3Z,6Z,8E)-Dodecatrien-1-ol (2004)

The subterranean termite Heterotermes tenuis (Isoptera: Rhinotermitidae) is a pest of great importance for the Brazilian economy as it causes serious damages in commercial reforestations of Eucalyptus spp. and sugarcane cultures. (3Z,6Z,8E)-Dodecatrien-1-ol has been identified as a pheromone of some species of subterranean termites. The objective of this research was to synthesize (3Z,6Z,8E)-dodecatrien-1-ol and determine by electroantennographic (EAG) bioassays the selectivity and sensitivity of H. tenius antennae to its whole worker extract and to the synthetic triene alcohol.
A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data (2019)

The new hierarchical integration deep flexible neural forest framework(HI-DFNForest) is an effective method to integrate multi-omics data to classify cancer subtypes.
Management of Biceps Tendon Pathology: From the Glenoid to the Radial Tuberosity (2018)

Management of proximal and distal biceps tendon pathology is evolving. The long head of the biceps tendon, if inflamed, may be a pain-producing structure. In appropriately indicated patients, a symptomatic long head of the biceps tendon can be surgically managed via tenotomy, tenodesis, and/or superior labrum anterior to posterior repair. In some patients, primary superior labrum anterior to posterior pathology can be managed via biceps tenodesis. Determining which procedure is most appropriate and which technique and implant are preferred for a given patient with biceps tendon pathology is controversial. Less debate exists with regard to the timing of distal biceps tendon repair; however, considerable controversy exists with regard to selection of an appropriate surgical technique and implant. In addition, the treatment of patients with a chronic and/or retracted distal biceps tendon tear and patients in whom distal biceps tendon repair fails is extremely challenging. Orthopaedic surgeons should understand the anatomy of, nonsurgical and surgical treatment options for, and outcomes of patients with proximal or distal biceps tendon pathology.
Quantum trajectory approach to circuit QED: Quantum jumps and the Zeno effect (2008)

We present a theoretical study of a superconducting charge qubit dispersively coupled to a transmission line resonator. Starting from a master equation description of this coupled system and using a polaron transformation, we obtain an exact effective master equation for the qubit. We then use quantum trajectory theory to investigate the measurement of the qubit by continuous homodyne measurement of the resonator out field. Using the same polaron transformation, a stochastic master equation for the conditional state of the qubit is obtained. From this result, various definitions of the measurement time are studied. Furthermore, we find that in the limit of strong homodyne measurement, typical quantum trajectories for the qubit exhibit a crossover from diffusive to jumplike behavior. Finally, in the presence of Rabi drive on the qubit, the qubit dynamics is shown to exhibit quantum Zeno behavior.
Design of a widely tunable modulated grating Y-branch laser using the additive Vernier effect for improved super-mode selection (2003)

We present the design of a modulated grating Y-branch semiconductor laser containing a splitter and two multi-peak reflectors. High selectivity is achieved using the additive Vernier effect.
Exploratory social network analysis and gene sequencing in people who inject drugs infected with hepatitis C virus (2016)

Social networks facilitate the transmission of hepatitis C virus (HCV) in people who inject drugs (PWID). The aim of this study was to assess how certain network structural characteristics are related to HCV infections in PWID and to determine the most susceptible individuals for HCV transmission in a network of PWID. PWID (N = 80) from central China were recruited from a previous follow-up case-control study. Demographic and behavioural information was obtained from a computerized database for each group. HCV RNA was extracted from blood specimens. Sequences were used to construct a phylogenetic tree and to determine genetic distances. Socio-metric social links were established between participants. Network measures were calculated using UCINET. Three HCV genotypes were identified, covering five subtypes. The density of the social networks for the whole sample (N = 80), case group (n = 31) and control group (n = 49) was 0.038, 0.054 and 0.008, respectively. PWID infected with HCV were in frequent contact with others within their group. There were four pairs of nodes with genotypic distances of 0.000 that were identified and clustered in subtypes 6a and 1b; each subject pair was linked and found in one clique. Three of the five most active nodes were infected with HCV. These three nodes served as a bridge, contributing to the connection of other nodes. These findings identify susceptible individuals for HCV transmission in PWID based on their frequent contact with others in the network. These results provide data that could be used for modelling HCV transmission patterns and in public health policies.
Highly Regioselective Ruthenium-Catalyzed Allylic Alkylations of Chelated Enolates (2010)

Ru-catalyzed allylic alkylations are a highly interesting alternative to Pd-catalyzed reactions. Ru complexes show a high tendency for regioretention, especially for branched and (Z)-configured substrates, and they do not undergo isomerization of the allyl intermediates formed. Therefore, (Z)-substrates conserve their olefin geometry, and a perfect chirality transfer is observed with optically active substrates.
Semi-Intact Cell Systems - Application to the Analysis of Membrane Trafficking Between the Endoplasmic Reticulum and the Golgi Apparatus and of Cell Cycle-Dependent Changes in the Morphology of These Organelles (2012)

The endoplasmic reticulum (ER) and the Golgi apparatus both maintain their specific morphology, composition, and function in spite of the exchange of proteins and lipids between the two organelles through membrane trafficking. The morphology of the Golgi apparatus is closely linked to the balance between anterograde (ER-to-Golgi) and retrograde (Golgi-to-ER) transport. It has been reported that the inhibition of anterograde transport leads to the redistribution of Golgi components to the cytoplasm or the ER (Storrie et al., 1998; Ward et al., 2001; Miles et al., 2001). Inhibition of anterograde transport at the onset of mitosis also results in the relocation of Golgi enzymes to the ER Thus, in living cells, the rates of anterograde and retrograde transport between the two organelles appear to have a substantial effect on the morphology of the Golgi. The effect of the balance between anterograde and retrograde transport on the morphology of the ER remains to be explored. Recently, increasing evidence has suggested that alteration in Golgi morphology during mitosis is not a passive process but rather an active one, which is highly coordinated with entry into mitosis and its progression. On the basis of the concept that cell cycle-dependent membrane trafficking between the ER and Golgi during mitosis should be tightly coupled with the changes in their morphology, it will be important to elucidate the cell cycle-dependent regulation of membrane trafficking to understand the morphological changes in more detail.
Identification of the adenylyl cyclase‐activating 5‐hydroxytryptamine receptor subtypes expressed in the rat submandibular gland (2000)

1. Serotonin (5-hydroxytryptamine, 5-HT) has been shown to increase cyclic AMP production in dispersed cell aggregates from the major salivary glands of the rat. The goal of the present study was to identify the 5-HT receptor subtypes that mediate these effects in rat submandibular glands (SMG). 2. Among the 5-HT receptor subtypes identified in the rat, 5-HT(4(a,b)), 5-HT(6) and 5-HT(7(a,b,c)) activate adenylyl cyclase (AC). We used subtype specific primers to screen rat SMG by reverse transcription-PCR. Results indicate the presence of mRNA for 5-HT(4(b)) and 5-HT(7(a)) but not for 5-HT(4(a)), 5-HT(6) and 5-HT(7(b,c)). 3. In dispersed SMG cells, 5-carboxyamidotryptamine (5-CT), a 5-HT(7) receptor agonist, stimulated cyclic AMP synthesis with higher potency (EC(50)=27+/-5 nM) but lower efficacy than 5-HT, suggesting a 5-HT(7) component and an additional component in the response to 5-HT. The 5-HT(7) contribution was further supported by antagonism of the 5-CT effect by metergoline, a 5-HT(7) antagonist, which exhibited an affinity (K(i)=50 nM) similar to that obtained at the cloned 5-HT(7) receptor. 4. In the presence of a maximally effective concentration of 5-CT, 5-HT produced an additional increase in cyclic AMP production that was inhibited by the 5-HT(4) receptor antagonist, GR113808, suggesting that the second component of cyclic AMP production is mediated by 5-HT(4) receptors. 5. These findings indicate the presence in rat SMG of both 5-HT(4(b)) and 5-HT(7(a)) receptors positively coupled to AC.
The changing climate and the arctic coastal settlements (2018)

The changing climate has led to increased summer temperatures in the Arctic, later sea ice formation in the fall season and less ice during the winter. Parts of the icecap are thinning and during summer, the area covered by ice has been shrinking. This situation has led to open seas and longer wind fetch, so larger waves build up during the late summer and fall seasons. This situation is then associated with larger waves hitting the Arctic coastline. The larger waves are influencing the shores where melting of permafrost occurs to a larger extent than previously and the consequences are large erosion and retracting of the coastline.
Modeling conduction in host-graft interactions between stem cell grafts and cardiomyocytes (2009)

Cell therapy has recently made great strides towards aiding heart failure. However, while transplanted cells may electromechanically integrate into host tissue, there may not be a uniform propagation of a depolarization wave between the heterogeneous tissue boundaries. A model using microelectrode array technology that maps the electrical interactions between host and graft tissues in co-culture is presented and sheds light on the effects of having a mismatch of conduction properties at the boundary. Skeletal myoblasts co-cultured with cardiomyocytes demonstrated that conduction velocity significantly decreases at the boundary despite electromechanical coupling. In an attempt to improve the uniformity of conduction with host cells, differentiating human embryonic stem cells (hESC) were used in co-culture. Over the course of four to seven days, synchronous electrical activity was observed at the hESC boundary, implying differentiation and integration. Activity did not extend far past the boundary, and conduction velocity was significantly greater than that of the host tissue, implying the need for other external measures to properly match the conduction properties between host and graft tissue.
Pressure support ventilation reduce ventilator-induced diaphragmatic dysfunction (2006)

Constantin, J. M.1; Futier, E.1; Combaret, L.2; Attaix, D.2; Bazin, J. E.1 Author Information