gebhart/patrepeval huggingface dataset:
FrangiPANe, a tool for creating a panreference using left behind reads (2022)

ABSTRACT We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.
Commandes des exosquelettes des membres inférieurs pour l’assistance à la mobilité (2017)

International audience
Target volume delineation in breast conserving radiotherapy: are co-registered CT and MR images of added value? (2014)

The mean volume of the delineated glandular breast tissue based on CT was significantly larger compared to the volume based on CTMR. For patients with a CVS ≥ 4, the mean CIs of the LC were higher compared to CVS<4 for volumes delineated on both CT as well as CTMR images. In our study cohort no significant differences between the CIs of the CTV breast and the LC delineated on CTMR co-registered images were found compared to the CIs on CT images only. Adding MR images does not seem to improve consistency of the delineation of the CTV breast and the LC, even though the volumes were copied from CT images. Since we included only ten patients, caution should be taken with regard to the results of our study.
Interpretable Machine Learning Models to Predict the Resistance of Breast Cancer Patients to Doxorubicin from Their microRNA Profiles (2022)

Doxorubicin is a common treatment for breast cancer. However, not all patients respond to this drug, which sometimes causes life-threatening side effects. Accurately anticipating doxorubicin-resistant patients would therefore permit to spare them this risk while considering alternative treatments without delay. Stratifying patients based on molecular markers in their pretreatment tumors is a promising approach to advance toward this ambitious goal, but single-gene gene markers such as HER2 expression have not shown to be sufficiently predictive. The recent availability of matched doxorubicin-response and diverse molecular profiles across breast cancer patients permits now analysis at a much larger scale. 16 machine learning algorithms and 8 molecular profiles are systematically evaluated on the same cohort of patients. Only 2 of the 128 resulting models are substantially predictive, showing that they can be easily missed by a standard-scale analysis. The best model is classification and regression tree (CART) nonlinearly combining 4 selected miRNA isoforms to predict doxorubicin response (median Matthew correlation coefficient (MCC) and area under the curve (AUC) of 0.56 and 0.80, respectively). By contrast, HER2 expression is significantly less predictive (median MCC and AUC of 0.14 and 0.57, respectively). As the predictive accuracy of this CART model increases with larger training sets, its update with future data should result in even better accuracy.
Structural investigations on a synthetic alkali-free hydrogen-deficient Fe-tourmaline (foitite) (2000)

The crystal structure of a single crystal of foitite, hydrothermally synthesized from a bulk composition of X □ Y (Fe 2 Al) Z Al 6 [Si 6 O 18 |(BO 3 ) 3 |(OH) 3 OH] at 700°C and 200 MPa, has been refined to an R(|F|) index of 0.023 for 950 unique reflections. The compound is trigonal with space group symmetry R 3 m, Z = 3, a = 15.964(1) A, c = 7.119(1) A, V = 1571.2(3) A 3 , and D calc = 3.133 g cm −3 . The crystal-chemical formula of this foitite derived by structure refinement is X □ Y (Fe 1.58 Al 1.42 ) Z Al 6 [Si 6 O 18 |(BO 3 ) 3 |(OH) 3.58 O 0.42 ]. This composition is in very good agreement with the data obtained by electron microprobe analysis. The two main results of the structure analysis are: (1) iron occupies exclusively the Y-position and (2) bond valence calculations clearly indicate a hydrogen-deficiency at the anion site O1 yielding less than 4 OH groups per formula unit.
Expression of decorin in human tissues and cell lines and defined chromosomal assignment of the gene locus (DCN) (1992)

Earlier studies had shown that the expression of the gene coding for one eminent connective tissue proteoglycan, decorin (DCN), is deficient in the fibroblasts of 3 out of 15 Marfan patients (Pulkkinen et al., 1990). To obtain more information on the expression of this gene, various human tissues and cell lines were studied. High mRNA levels of decorin were detected in aorta, lung, skin, kidney, smooth muscle, and placenta, whereas significantly lower mRNA levels were found in the rest of the tissues analyzed. Two sizes of transcripts were observed in all tissues. The two transcripts of decorin most probably do not represent two different genes, since in situ hybridization gave only one strong signal, placing the gene in 12q21----q22. No tissue-specific differences in the two mRNA species of decorin were detected. This is in contrast to the gene of versican, another connective tissue proteoglycan gene, that was analyzed as a control; high expression of a longer transcript of the versican gene was found in brain and smooth muscle, whereas the shorter transcript was predominant in all other tissues studied. DCN was actively transcribed in cultured mesenchymal cells, whereas in cells of endothelial or epithelial origin, the transcription level was undetectable. These tissue- and cell type-specific variations in the expression of DCN may help to explain the complex phenotypic variation typical of individuals with Marfan syndrome.
Analysis of non-coding RNAs in Methylorubrum extorquens reveals a novel small RNA specific to Methylobacteriaceae (2022)

Methylorubrum extorquens metabolizes methanol, a cheap raw material that can be derived from waste. It is a facultative methylotroph, making it a model organism to study the metabolism of one carbon compounds. Despite a considerable interest to exploit this bacteria as a biotechnological tool in a methanol-based bioeconomy, little is known about its non-coding sRNA. Small RNAs play well-documented essential roles in Escherichia coli for post-transcriptional regulation; and have important functions in many bacteria, including other Alphaproteobacteria like Agrobacterium tumefaciens. M. extorquens is expected to contain many sRNAs, especially since it also encodes for the protein Hfq, a chaperone protein important in the interaction between sRNAs and their target, but also critical for the stabilization of sRNAs themselves. Few sRNAs are annotated in the genome of this Alphaproteobacteria and they were never validated. In this study, formerly annotated sRNAs ffh, CC2171, BjrC1505 were confirmed by Northern blot, validating the expression of sRNAs in M. extorquens . Moreover, analysis of RNA-sequencing data established a considerable list of potential sRNAs. Interesting candidates selected after bioinformatic analysis were tested by Northern blot, revealing a novel sRNA specific to Methylobacteriaceae, sRNA Met2624. Its expression patterns and genomic context were analyzed. This research is the first experimental validation of sRNAs in M. extorquens and paves the way for other sRNA discoveries.
Normalization of Hypercalcaemia of Primary Hyperparathyroidism by Treatment with Methallenestril, a Synthetic Oestrogen with Low Oestrogenicity (1983)

The oestrogenic compound methallenestril has a relatively low oestrogenicity but a marked growth-inhibiting property in experimental studies. Methallenestril was administered in a dose of 6 mg daily to 6 postmenopausal women with hypercalcaemia and primary hyperparathyroidism (HPT) for periods between 5 and 24 weeks. In all the patients, serum calcium was normalized during treatment, presumably due to a reduction of bone resorption since fasting urinary calcium and urinary hydroxyproline excretion were lowered as well. This pilot study indicates that certain oestrogenic compounds with high potencies for growth inhibition but with low oestrogenic properties might be worth further investigation in the medical management of primary HPT.
Modification of abdominal sacrocolpopexy using a suture anchor system. (2003)

Use of the Vesica PRESS IN Suture Anchor System for placement of the suture in the mesh that suspends the vaginal vault from the L-5 or S-1 vertebra obviates the need for placement of multiple sutures into the longitudinal ligament of the vertebra. This minimizes the risk of damage to the presacral vessels, inferior vena cava and abdominal aorta. Therefore, this procedure retains the well-documented advantages of preserving the natural vaginal axis, maintaining coital function and offering a lasting solution to the problem of vaginal vault prolapse.
A monochromatic and high-power terahertz source tunable in the ranges of 2.7–38.4 and 58.2–3540 μm for variety of potential applications (2004)

Based on phase-matched collinear difference-frequency generation in a single GaSe crystal, continuously tunable and coherent radiation in the extremely wide ranges of 2.7–38.4 and 58.2–3540 μm has been achieved. This unique source has the additional advantages of high coherence (narrow linewidth) and simple alignment. The peak output power for the terahertz radiation reaches 209 W at the wavelength of 196 μm (1.53 THz), which corresponds to a power conversion efficiency of 0.055%. Moreover, the terahertz transmission spectra on DNA macromolecules and protein were directly measured, demonstrating some potential and important applications of this terahertz source.
Familial prostate cancer and possible associated malignancies: Nation-wide register cohort study in Sweden (1998)

There is a familial aggregation of prostate cancer, and 5 to 10% of all prostate cancers are estimated to be inherited in an autosomal-dominant mode. A population-based cohort study was performed in order to study familial prostate cancer and associated malignancies. A nation-wide register cohort study was conducted using an unselected study population. The cohort of 5,595 sons and 5,089 daughters of Swedish men found to have prostate cancer between 1959 and 1963 was identified. All types of cancer reported between 1958 and 1992 in this cohort were identified through linkage to the Swedish Cancer Registry. The expected number of different cancers was calculated using incidence rates obtained from the Registry. A highly significant increased overall standardized incidence ratio (SIR) of 1.65 (95% CI, 1.49-1.83) was obtained for prostate cancer, with 370 observed cases compared with 224 expected prostate cancers. The SIR was 3.18 among cases 45 to 49 years old at diagnosis, with the risk gradually decreasing to a SIR of 1.45 among cases over 80 years of age. Among sons and daughters with a father whose prostate cancer was diagnosed at an early age (<70 years), an increased risk for colorectal cancer SIR 1.48 (1.10-1.95) was observed. No significant difference in cancer risk for other sites was observed among the daughters and sons of men with prostate cancer. This cohort study confirms earlier studies that a positive family history of prostate cancer is an important risk factor for developing this disease. Though increased risk was found for all ages, it was more pronounced in younger men. Since no other malignancy was significantly associated with prostate cancer, it is most likely that familial prostate cancer is "site-specific".
Effect of Normal Load and Sliding Velocity on Friction and Wear Behavior of Carbon Fiber Reinforced Epoxy Composites (2007)

Friction and dry sliding wear behavior of [0°/90°] S and unidirectionally (UD) oriented carbon-epoxy (C-E) composites has been studied using block-on-roller test set up. The dry sliding wear experiments were conducted for the following C-E composites namely 0°/90°, parallel and anti-parallel surfaces with respect to the sliding direction. The coefficient of friction and wear of the composites for two different loads and various sliding velocities have been determined. It was observed that the wear loss increases linearly with increase in sliding velocity/loads. Besides conventional weighing, determination of the coefficient of friction and examination of worn surface features by scanning electron microscopy (SEM) were undertaken to study the tribological behavior. Disorientation of fibers, fiber fracture, matrix deformation and wear debris damage mechanisms were observed under SEM. Composite wear was accompanied by material transfer onto the counter surface.
IgM, but not IgA rheumatoid factor interferes with anti-cardiolipin and anti-β2 glycoprotein I measurements: a quantitative analysis (2011)

IgM rheumatoid factor (RF) is sometimes referred to as capable of causing interference in the IgM anti-cardiolipin (aCL) testing. Published guidelines are, however, inconsistent, and evidence regarding the interference is limited. Our goal was investigate IgM and IgA RF cross-reactivity and/or interference in IgM and IgA aCL and anti-β2 glycoprotein I (aβ2GPI) testing. Serum specimens with high IgM and IgA RF levels were tested for IgG, IgA and IgM aCL and aβ2GPI antibodies to examine cross-reactivity. Samples containing IgG aCL and aβ2GPI antibodies were spiked with IgM (and IgA) RF, and samples with high RF levels were spiked with IgG aCL antibodies. The mixtures were tested for IgM and IgA aCL and aβ2GPI antibodies. Specimens with high IgM and IgA RF concentrations did not test positive for IgM or IgA aCL and aβ2GPI antibodies (except one weak positive IgA aβ2GPI result), indicating the lack of cross-reactivity. In the spiked specimens, addition of IgM RF caused significant positive bias in the measurement of both aCL and aβ2GPI antibodies of IgM isotype in the presence of IgG aCL and aβ2GPI antibodies. The threshold for triggering significant interference was 318( )IU/ml for IgM RF, and 77 GPLU/ml for IgG aCL. Neither IgM, nor IgA RF, however, affected the IgA antiphospholipid (aPL) antibody testing. IgM RF can cause a false-positive IgM aCL result in the presence of IgG aCL antibodies. In studies on the prevalence and clinical significance of IgM aPL antibodies, RF interference should be considered and RF testing should be performed.
Blockade of Na+and K+Currents by Local Anesthetics in the Dorsal Horn Neurons of the Spinal Cord (1998)

In clinically relevant concentrations, local anesthetics block Na+ and KA currents but not delayed-rectifier K+ currents in spinal dorsal horn neurons. The molecular mechanisms of Na+ and K+ channel block by local anesthetics seem to be different. Characterization of these mechanisms could be an important step in understanding the complexity of local anesthetic action during spinal and epidural anesthesia.
Some Bionomical Aspects of Horn Fly1Populations in Central Texas2 (1972)

At Camp Stanley, Bexar County, Texas, Haematobia irritans (L.) ovipositing on cattle manure during October and November were responsible for the spring buildup of flies on cattle during April and May. The average 0.14 flies per pat that emerged from the subsequent overwintering pupae produced an F l generation that averaged 1.2 flies per pat, an 8-fold increase from the overwintering flies to the F l generation. The average monthly rate of production for the period May–October was 6.6 horn flies per pat when competition from other orthropods was allowed, compared with 66.8 per pat when competition was essentially eliminated.
Appearance of Fucolipid after Conventionalization of Germ-Free Mice (1981)

Incorporation of [6-3H]fucose and [1-14C]glucosamine into the lipid fraction of microvillus membrane (MVM) was studied in germ-free and conventionalized mice after intraperitoneal injection of the radioactive precursors. Incorporation of [6-3H]fucose was clearly detected in conventionalized mice but not detectable in germ-free mice. There was no difference in the incorporation of [1-14C]glucosamine between the two groups. The lipid fraction of MVM labeled with [6-3H]fucose showed a spot of slower mobility than asialo GM1 on TLC with autoradiography and it was confirmed to be a fucolipid on abolishing the radiolabeled original spot by alpha-L-fucosidase treatment. These results suggest that the synthesis of the fucolipid is induced by conventionalization of germ-free mice.
T Cells Are Required for the Production of Blister-Inducing Autoantibodies in Experimental Epidermolysis Bullosa Acquisita (2009)

Epidermolysis bullosa acquisita is a prototypical organ-specific autoimmune disease caused by autoantibodies against type VII collagen of the dermal-epidermal junction. Although mechanisms of autoantibody-induced blister formation were extensively characterized, the initiation of autoantibody production in autoimmune blistering diseases is still poorly defined. In the current study, we addressed the role of T cells for the production of blister-inducing autoantibodies in mice immunized with type VII collagen. To detect autoreactive type VII collagen-specific T cells, lymph node cells from immunized SJL mice were stimulated in vitro with recombinant Ag, and their proliferation was measured by radioactive thymidine incorporation and flow cytometry analysis of CFSE-labeled cells. Interestingly, using synthetic peptides of the immunogen, partly different T and B cell epitopes in mice immunized with type VII collagen were demonstrated. In contrast to wild-type mice, immunization with type VII collagen of SJL athymic nude mice lacking T cells did not induce an autoimmune response and blistering phenotype. Importantly, SJL nude mice repleted with T cells from immunized wild-type mice showed a robust and durable autoantibody production resulting in subepidermal blistering disease in the recipients. Our present results demonstrate that T cells are required for the initiation of autoimmunity against type VII collagen in experimental epidermolysis bullosa acquisita and provide a basis for developing T cell-directed immunomodulatory strategies for this and related autoimmune diseases.
Ultraviolet–visible spectroscopic studies on manganese and rhenium oxide fluorides in low-temperature matrices (1991)

Five high-oxidation-state metal oxide fluorides, MnO3F, ReO3F, ReO2F3, ReOF5 and ReOF4 have been isolated as molecular species in inert-gas matrices at low temperatures, and studied by IR and UV/VIS spectroscopy. In particular, the electronic spectra are described and the principal charge-transfer bands assigned using the optical electronegativity model. This suggested that a new value for χopt(F–) of 3.6 is appropriate for transition-metal oxide fluorides.
SIR JOHN WILLIAM DAWSON: A PROFILE OF A NOVA SCOTIAN SCIENTIST (2010)

This is a summary of the life and work of Sir John William Dawson (1820- 1899), a Nova Scotian who made major contributions to geology, education and the development of science in Canada. His early life and educational work in Nova Scotia, his years as Principal of McGill, his success in developing science, at the community, national, and international level, his prolific written output, and highlights of his geological work are described. Key words: Darwin; Education; Eozoon; Fossils; McGill; Pictou; Royal Society of Canada; Science and Religion
A role for ATP in bronchoconstriction‐induced activation of guinea pig vagal intrapulmonary C‐fibres (2012)

Activation of vagal afferent sensory C-fibres in the lungs leads to reflex responses that produce many of the symptoms associated with airway allergy. There are two subtypes of respiratory C-fibres whose cell bodies reside within two distinct ganglia, the nodose and jugular, and whose properties allow for differing responses to stimuli. We here used extracellular recording of action potentials in an ex vivo isolated, perfused lung-nerve preparation to study the electrical activity of nodose C-fibres in response to bronchoconstriction. We found that treatment with both histamine and methacholine caused strong increases in tracheal perfusion pressure that were accompanied by action potential discharge in nodose, but not in jugular C-fibres. Both the increase in tracheal perfusion pressure and action potential discharge in response to histamine were significantly reduced by functionally antagonizing the smooth muscle contraction with isoproterenol, or by blocking myosin light chain kinase with ML-7. We further found that pretreatment with AF-353 or 2',3'-O-(2,4,6-Trinitrophenyl)-adenosine-5'-triphosphate (TNP-ATP), structurally distinct P2X3 and P2X2/3 purinoceptor antagonists, blocked the bronchoconstriction-induced nodose C-fibre discharge. Likewise, treatment with the ATPase apyrase, in the presence of the adenosine A1 and A2 receptor antagonists 8-cyclopentyl-1,3-dipropylxanthine (DPCPX) and SCH 58261, blocked the C-fibre response to histamine, without inhibiting the bronchoconstriction. These results suggest that ATP released within the tissues in response to bronchoconstriction plays a pivotal role in the mechanical activation of nodose C-fibres.
In Vitro Evaluation of Antibiotic Synergy for Polymyxin B-Resistant Carbapenemase-Producing Klebsiella pneumoniae (2010)

Since carbapenemase-producing Klebsiella pneumoniae strains were first reported in North Carolina, these highly resistant organisms have been isolated with increasing frequency, especially in the New York City area. Polymyxin B is one of the few antimicrobials that retain reliable activity against these organisms. However, polymyxin B MICs are elevated against K. pneumoniae isolates with increasing frequency, leaving clinicians with few therapeutic options. We investigated several antimicrobial agents for potential synergy with polymyxin B against 12 clinical strains of carbapenemase-producing K. pneumoniae. A broth microdilution assay using a 96-well plate was developed in which graded dilutions of polymyxin B and the study drug were incubated with resistant isolates in a checkerboard pattern. Polymyxin B was studied in combination with cefazolin, ceftriaxone, cefepime, imipenem, gentamicin, tigecycline, doxycycline, and rifampin. All K. pneumoniae strains tested positive for K. pneumoniae carbapenemase (KPC) genes by real-time PCR and had elevated polymyxin B MIC values ranging from 16 to 128 μg/ml. Synergy was observed with the combination of polymyxin B and rifampin as well as with polymyxin B and doxycycline, resulting in at least a 4-fold decrease in the polymyxin B MIC. For both combinations, this effect occurred at physiologically achievable concentrations. Less pronounced synergy was noted with tigecycline and polymyxin B. No synergy was observed at physiologic concentrations with the other antimicrobials studied. These results suggest that rifampin, doxycycline, and tigecycline may be useful additions to polymyxin B in the treatment of infections caused by highly resistant carbapenemase-producing K. pneumoniae. Further studies are warranted to determine if these in vitro findings translate into clinical efficacy.