gebhart/patrepeval huggingface dataset:
A new paramutation-like example at the Delta gene of Drosophila (2017)

The hereditary transmission of a phenotype independent from DNA sequence implies epigenetic effects. Paramutation is a heritable epigenetic phenomenon observed in plants and animals. To investigate paramutation in Drosophila, we used the P{ry+t7.2 = PZ}Dl05151 P-element insertion in the Drosophila melanogaster genome that causes a dominant visible phenotype: the presence of characteristic extra-veins in the fly wings. This extra-vein phenotype presents variable expressivity and incomplete penetrance. The insert is a PZ element located 680 bp upstream from the ATG of the Delta (Dl) gene, encoding the Notch ligand involved in wing vein development, and acts as a null allele. In the G2 offspring from a cross between the heterozygous transgenic stock and wild-type flies, we observed the transmission of the extra-vein phenotype to wild-type flies without the transgene, independently of gender and across many generations. This is a "paramutation-like" example in the fly: the heritable transmission of a phenotypic change not linked to a classical genetic mutation. A "paramutagenic" allele in heterozygotes transmits the phenotype of the heterozygotes to the wild-type allele ("paramutant") in a stable manner through generations. Distinct from paramutation events so far described in Drosophila, here we deal with a dominant effect on a single gene involving variable hereditary signals.
Electron spin resonance of TOAC labeled peptides: Folding transitions and high frequency spectroscopy (2000)

The unnatural, conformationally constrained nitroxide amino acid TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) stabilizes helical structure and provides a means for studying rigidly spin labeled peptides by electron spin resonance (ESR). Two new directions in TOAC research are described. The first investigates intermediates formed during α-helix unfolding. Double TOAC labeled α-helical peptides were unfolded at low temperature in aqueous solution with increasing concentrations of guanidine hydrochloride. Comparison of ESR spectra from two doubly labeled peptides suggests that 310-helix emerges as an intermediate. The second research direction involves the use of high frequency ESR (140 GHz) at low temperature to assess dipolar couplings and, hence, distances between TOAC pairs in a series of 310-helical peptides. Preliminary simulations suggest that high frequency ESR is able to extract correct distances between 6 and 11 Å. In addition, the spectra appear to be very sensitive to the relative orientation of the TOAC labels. © 2001 John Wiley & Sons, Inc. Biopolymers (Pept Sci) 55: 479–485, 2000
Dual-targeting of peripheral cannabinoid-1 receptors and inducible NO synthase in pulmonary fibrosis (2017)

<b>Introduction:</b> Idiopathic pulmonary fibrosis (IPF) is a life-threatening disease with limited treatment options that may benefit from simultaneously targeting multiple pathways to improve therapeutic efficacy. Endocannabinoids (ECs) acting via the CB1R promote fibrosis, but their role in IPF has not been established. Activity of the enzyme inducible nitric oxide synthase (iNOS) is also increased in fibrosis and correlates with IPF progression. <b>Aims and objectives:</b> We tested the involvement of the EC/CB1R system and iNOS in the pathogenesis of IPF and the therapeutic impact of their simultaneous targeting using MRI-1867, an orally bioavailable, peripherally restricted CB1R/iNOS hybrid inhibitor in mice. <b>Methods:</b> We used the bleomycin-induced mouse PF (BL-PF) model, as well as BALF and lung tissue samples from patients with IPF and respective controls. <b>Results:</b> The EC anandamide was increased in the lung of bleomycin-treated mice and in BALF samples from IPF patients, in whom its level negatively correlated with pulmonary function tests. CB1R and iNOS protein levels were significantly elevated in lung tissue from patients with severe IPF or from bleomycin-treated mice. Upregulation of these two targets in the fibrotic lung was independent of one another. Moreover, MRI-1867 treatment arrested the progression of established fibrosis in BL-PF and dramatically improved survival rate, compared to vehicle or CB1R antagonism alone. <b>Conclusion:</b> We identified CB1R as a novel therapeutic target in IPF. Dual-targeting of CB1R and iNOS for inhibition offers a novel therapeutic approach with improved efficacy.
Occurrence of odorous compounds in the emission of building materials measured by GC-olfactometry (2009)

International audience
The synthesis of a series of (α‐amino)indol‐3‐yl ketones (1988)

Abstract A series of [(α‐amino)indol‐3‐yl]‐2‐methyl‐1‐propanones and [(α‐amino)indol‐3‐yl]cyclopentylmethanones has been synthesized by a variety of reductive reactions performed on the corresponding series of (α‐azido)‐indol‐3‐yl ketones. One of the more interesting reductive procedures involved the palladium‐catalyzed decomposition of formic acid with the formation of hydrogen in situ. The (α‐azido)ketones were prepared in excellent yield by the displacement of the tertiary bromine atom from the (α‐bromo)ketones using sodium azide in N,N ‐dimethylformamide. Bromination was accomplished by using either cupric bromide in ethyl acetate/chloroform or phenyltrimethylammonium tribromide in tetrahydrofuran.
Impact of Iron Chelation Therapy on Overall Survival and AML Transformation in Lower Risk MDS Patients Treated At the Moffitt Cancer Center (2011)

Abstract Abstract 2776 Background: Elevated serum ferritin levels and red blood cell transfusion dependence are associated with poor outcome in patients with lower risk myelodysplastic syndromes (MDS). Few retrospective and observational studies suggest that iron chelation therapy (ICT) may favorably impact outcome in lower risk MDS. The vast majority of patients in those studies were treated with deferoxamine (Desferal). Two studies reported that oral deferasirox (Exjade) significantly decreases ferritin level over time in MDS. An ongoing randomized placebo-controlled trial (TELESTO) is designed to address the impact of deferasirox on overall survival (OS) in lower risk MDS. We examined the impact of ICT predominantly deferasirox in lower risk MDS patients treated at the Moffitt Cancer Center (MCC). Methods: Patients were retrospectively identified from the MCC database and individual patients' records reviewed. Inclusion criteria included lower risk MDS patients defined as low or intermediate-1 (int-1) risk disease by the international prognostic scoring system (IPSS) and serum ferritin level ≥ 1000 ng/ml. Patients were divided into two comparator groups: ICT vs. no ICT. Baseline characteristics were compared between the two groups; chi square test was used for categorical variables and t-test for continuous variables. The primary endpoint was overall survival compared between the two groups using Kaplan-Meier estimates. Cox regression was used for multivariate analysis. All analyses were conducted using SPSS version 19.0 statistical software. Results: Between July 2001 and July 2009, 97 patients with lower risk MDS and serum ferritin ≥ 1000 ng/ml were identified. Forty five (46.4%) received ICT and 52 did not. The ICT included deferasirox in 35 patients and deferoxamine in 10 patients. The baseline characteristics between the two groups (ICT and no ICT) are summarized in (table-1). No statistically significant difference in baseline characteristics was observed except more patients in the ICT group were transfusion dependent. The median duration of follow up was 85.7 month from time of diagnosis. The median OS was 59 months (95%CI 22–48) for patients who received ICT compared to 33.7 months (95%CI 38–80) for patients who did not receive ICT (P= 0.013). After adjustment for age and cytogenetics in Cox multivariable analysis, ICT was associated with better OS (HR 0.52, 95%CI 0.31–0.87, P= 0.013). The rate of AML transformation was 21.2% in patients who did not receive ICT compared to 15.6% in those who had ICT. (p=0.33). Conclusion: ICT in lower risk MDS patients with elevated serum ferritin ≥ 1000 ng/ml was associated with improved overall survival and a trend to lower AML transformation. Results of ongoing randomized clinical study with deferasirox are needed to confirm the retrospective data. Disclosures: Komrokji: Novartis: Honoraria, Research Funding.
The effectiveness of art therapy for anxiety in adults: A systematic review of randomised and non-randomised controlled trials (2018)

Effectiveness of AT on anxiety has hardly been studied, so no strong conclusions can be drawn. This emphasizes the need for high quality trials studying the effectiveness of AT on anxiety.
Why do we see myocardial edema in acute myocardial infarcts with balanced SSFP imaging? (2010)

Introduction Recent studies have demonstrated that conventional balanced steady-state free precession (b-SSFP) cine imaging can identify regions of myocardial edema in-and-around acute myocardial infarctions (AMI). However, the underlying mechanisms of b-SSFP edema contrast are not well understood. A more detailed understanding of the contrast mechanisms at play may enable opportunities for optimization of SSFP-based edema contrast.
A Light-Modulated Sequence-Specific DNA-Binding Peptide (2000)

Packende Verbindungen! Zwei Monomere eines bZIP-Proteins wurden an den basischen Bereichen über eine photoempfindliche Azobenzoleinheit zu einem Homodimer verknüpft. Dieses Dimer kann nach Bestrahlung mit Licht geeigneter Wellenlänge isomerisiert werden, wobei die beiden Isomere mit einer geringen (trans) oder hohen Affinität (cis) in der großen Furche der DNA binden (siehe Bild). BB=basische Bereiche, ds=Doppelstrang.
Analyzing Real-Time Multimedia Content From Network Cameras Using CPUs\n and GPUs in the Cloud (2018)

Millions of network cameras are streaming real-time multimedia content\n(images or videos) for various environments (e.g., highways and malls) and can\nbe used for a variety of applications. Analyzing the content from many network\ncameras requires significant amounts of computing resources. Cloud vendors\noffer resources in the form of cloud instances with different capabilities and\nhourly costs. Some instances include GPUs that can accelerate analysis\nprograms. Doing so incurs additional monetary cost because instances with GPUs\nare more expensive. It is a challenging problem to reduce the overall monetary\ncost of using the cloud to analyze the real-time multimedia content from\nnetwork cameras while meeting the desired analysis frame rates. This paper\ndescribes a cloud resource manager that solves this problem by estimating the\nresource requirements of executing analysis programs using CPU or GPU,\nformulating the resource allocation problem as a multiple-choice vector bin\npacking problem, and solving it using an existing algorithm. The experiments\nshow that the manager can reduce up to 61\\% of the cost compared with other\nallocation strategies.\n
A PRINTED CIRCUIT BOARD BASED MICROFLUIDIC SYSTEM FOR POINT-OF-CARE DIAGNOSTICS APPLICATIONS (2011)

We propose an alternative approach for fabricating microfluidic devices by using printed circuit board (PCB) as a substrate to produce high precision, highly integrated microfluidic systems. Driven by consumer electronics industry, the PCB manufacturing has reached a high level of maturity and precision, enabling the production of sophisticated electronic substrates at high-resolution and low cost. Lacking the integration capability in current microfluidic technology, PCB makes an ideal platform for producing microfluidics for lab-on-a-chip applications. We report the development of new techniques to integrate microfluidics with PCBs. Isotachophoresis was performed as a demonstration to employ such devices for point-ofcare applications.
Trends in packaging and high density interconnection (2000)

In this paper, some of the main trends in packaging and interconnection technology for microelectronic devices are reviewed. Particular attention is given to the impact of the evolution of microelectronic technology on the requirements for electronic packaging.
Subcellular Mislocalization of Mutant Hepatitis B X Proteins Contributes to Modulation of STAT/SOCS Signaling in Hepatocellular Carcinoma (2008)

Our results suggest that atypical nuclear/perinuclear localization of HBx mutants might be responsible for an enhanced activation of STAT3, inhibition of STAT1 and silencing of SOCS1/SOCS3 expression. This observation points to an active role of HBx mutants in hepatocarcinogenesis that involves dysregulation of STAT/SOCS signaling.
Metabolic and enzymatic elucidation of cooperative degradation of red seaweed agarose by two human gut bacteria (2021)

Various health beneficial outcomes associated with red seaweeds, especially their polysaccharides, have been claimed, but the molecular pathway of how red seaweed polysaccharides are degraded and utilized by cooperative actions of human gut bacteria has not been elucidated. Here, we investigated the enzymatic and metabolic cooperation between two human gut symbionts, Bacteroides plebeius and Bifidobacterium longum ssp. infantis, with regard to the degradation of agarose, the main carbohydrate of red seaweed. More specifically, B. plebeius initially decomposed agarose into agarotriose by the actions of the enzymes belonging to glycoside hydrolase (GH) families 16 and 117 (i.e., BpGH16A and BpGH117) located in the polysaccharide utilization locus, a specific gene cluster for red seaweed carbohydrates. Then, B. infantis extracted energy from agarotriose by the actions of two agarolytic β-galactosidases (i.e., Bga42A and Bga2A) and produced neoagarobiose. B. plebeius ultimately acted on neoagarobiose by BpGH117, resulting in the production of 3,6-anhydro-L-galactose, a monomeric sugar possessing anti-inflammatory activity. Our discovery of the cooperative actions of the two human gut symbionts on agarose degradation and the identification of the related enzyme genes and metabolic intermediates generated during the metabolic processes provide a molecular basis for agarose degradation by gut bacteria.
Process and system for hot and/or cold energy transfer, transport and/or storage (2023)

A thermal conveyance system and process for absorbing, transporting, storing, and recovering thermal energy (both hot and cold energy) over a wide range of temperatures from up to 2,100° F., or higher, or cool energy at subzero temperatures in inert and stable particles without the need to maintain a minimum temperature or requiring high system pressures. The process involving the transferring thermal energy to a first transfer fluid and recovering thermal energy from a second transfer fluid wherein the first and the second transfer fluids comprise a two phase thermal media including a gaseous carrier containing a quantity of micron to millimeter sized solid particles.
Engineering of an insulating buffer and use of AlN interlayers: two optimisations for AlGaN–GaN HEMT-like structures (2003)

The semi-insulating character of GaN epitaxial layers can be achieved by the control of the early stages of growth on the substrate. Adding two low temperature (LT) AlN interlayers is a technique enough powerful to reduce threading dislocation densities by up to one order of magnitude. A compressive strain as high as 2.8 × 10–3 is induced in the uppermost GaN epilayer. The global structure is kept semi-insulating so that it is a perfect template for undoped AlGaN–GaN HEMTs (High Electron Mobility Transistors). HEMTs with interlayers present better two dimensional electron gas (2DEG) properties: up to 20% higher carrier density (nS) and 40% higher mobility. Typically nS is as high as 1.7 × 1013 cm–2 for a record mobility of 1200 cm2/Vs. The improvement of the mobility can be correlated to the reduction of nano-scale V-shaped defects in the AlGaN (less morphological-relaxation). The improvement of nS could be explained by the higher piezo-doping resulting from GaN extra-compression and AlGaN weaker relaxation. As a consequence, the DC transistors characteristics are improved: in 2 μm gate transistors, the maximum current and transconductance are increased by up to 80% and 20%, respectively, and could be extrapolated to values as high as 1500 mA/mm and 250 mS/mm for 0.2 μm gate devices.
BC4GO: a full-text corpus for the BioCreative IV GO task (2014)

Gene function curation via Gene Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this task is considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification of GO terms and supporting information from full text. However, few systems have delivered an accuracy that is comparable with humans. One recognized challenge in developing such systems is the lack of marked sentence-level evidence text that provides the basis for making GO annotations. We aim to create a corpus that includes the GO evidence text along with the three core elements of GO annotations: (i) a gene or gene product, (ii) a GO term and (iii) a GO evidence code. To ensure our results are consistent with real-life GO data, we recruited eight professional GO curators and asked them to follow their routine GO annotation protocols. Our annotators marked up more than 5000 text passages in 200 articles for 1356 distinct GO terms. For evidence sentence selection, the inter-annotator agreement (IAA) results are 9.3% (strict) and 42.7% (relaxed) in F1-measures. For GO term selection, the IAAs are 47% (strict) and 62.9% (hierarchical). Our corpus analysis further shows that abstracts contain ∼ 10% of relevant evidence sentences and 30% distinct GO terms, while the Results/Experiment section has nearly 60% relevant sentences and >70% GO terms. Further, of those evidence sentences found in abstracts, less than one-third contain enough experimental detail to fulfill the three core criteria of a GO annotation. This result demonstrates the need of using full-text articles for text mining GO annotations. Through its use at the BioCreative IV GO (BC4GO) task, we expect our corpus to become a valuable resource for the BioNLP research community. Database URL: http://www.biocreative.org/resources/corpora/bc-iv-go-task-corpus/.
Divergent Roles of PI3K Isoforms in PTEN-Deficient Glioblastomas (2020)

Loss of PTEN, the negative regulator of PI3K activity, is frequent in glioblastomas (GBMs). However, the role of the two major PI3K isoforms, p110α and p110β, in PTEN-deficient gliomagenesis remains unknown. We show that PTEN-deficient GBM largely depends on p110α for proliferation and p110β for migration. Genetic ablation of either isoform delays tumor progression in mice, but only ablating both isoforms completely blocks GBM driven by the concurrent ablation of Pten and p53. BKM120 (buparlisib) treatment only modestly prolongs survival in mice bearing intracranial Pten/p53 null tumors due to partial pathway inhibition. BKM120 extends the survival of mice bearing intracranial tumors in which p110β, but not p110α, has been genetically ablated in the Pten/p53 null glioma, indicating that BKM120 fails to inhibit p110β effectively. Our study suggests that the failure of PI3K inhibitors in GBM may be due to insufficient inhibition of p110β and indicates a need to develop brain-penetrant p110α/β inhibitors.
Stochastic resonance in a bistable SQUID loop (1993)

Stochastic Resonance (SR) is the name given to a statistical nonlinear phenomenon whereby a weak or subthreshold coherent function can be amplified by random forces, or noise, within the system. It was first advanced in the early 1980’s as a possible explanation for the observed periodicities in the recurrences of the Earth’s Ice Ages. The first publication of a modern theory led to an experiment and a flurry of further theoretical activity, an international conference, and a review. In this paper, we describe a demonstration experiment wherein SR is exhibited in a superconducting quantum interference device (SQUID). Here SR is viewed as a noisy information transmission process. It is entirely appropriate, therefore, to look for this dynamics in a widely used sensitive detector in this example, a detector of weak magnetic fields. Using a modern, miniature, thin film SQUID, we hope this demonstration will stimulate further research and development of SR in applied superconductivity.
Détection ultrastructurale du compartiment cellulaire d’accumulation des génomes VIH1 par hybridation in situ avec microscopie électronique (2007)

Le virus VIH1 et les autres lentivirus ont un processus de retrotranscription plus complexe que les oncovirus, durant lequel la presence de deux sequences cis-actives supplementaires, le cPPT (central polypurine tract) et le CTS (central termination sequence), gouvernent a la formation d’un ADN a trois brins au centre du genome, l’ADN Flap [1]. Des mutations dans le cPPT menent a la synthese d’un genome viral lineaire depourvu d’ADN Flap et les virus ont un defaut d’infectivite prononce attribuable a un defaut d’import nucleaire [2]. Ce defaut se caracterise par une accumulation d’ADN viral lineaire a proximite du compartiment nucleaire.
Application of High-Gradient Magnetic Separation for the Recovery of Super-Paramagnetic Polymer Adsorbent Used in Adsorption and Desorption Processes (2023)

This study examined the application of high-gradient magnetic separation (HGMS) for recycling of super-paramagnetic polymer adsorbent (MPA), namely, polyvinyl acetate-iminodiacetic acid. The HGMS can be incorporated with the adsorption and desorption processes (ADPs) with fresh or regenerated desorbed MPAs and exhausted adsorbed MPAs, respectively. This combines the permanent magnet’s advantage of low running costs with the easy operation using the solenoid to flush the filter in place. The effects of the inlet concentration of MPA in solution (CLF,i) and the fluid velocity (v0) or volumetric flow rate (QLF) on the performance of the recovery of MPA via HGMS were assessed. The results indicated that the separation efficiency (η or P0), breakthrough time (tB) and exhaustion time (tE) of HGMS reduce as CLF,i, as well as v0, increases. Further, the filter saturated capture capacity (σS) of HGMS also decreases with increasing v0. The effect of v0 on tB proportional to 1/v02 is more significant than that on σS proportional to 1/v0. A kinetic model of HGMS shows good agreements for the experimental and predicted breakthrough results, with determination coefficients of 0.985–0.995. The information obtained in this study is useful for the rational design and proper operation of a HGMS system for the recycling and reuse of MPA in ADPs.
Bile salt–phospholipid conjugate ursodeoxycholyl lysophosphatidylethanolamide as a hepatoprotective agent # (2009)

UDCA-LPE, which targeted the liver in vivo, elicited potent biological activities in vitro by stimulating hepatocyte growth and by inhibiting TNF-alpha-induced apoptosis. Thus, UDCA-LPE may be suitable for evaluation of treatment efficacy in NASH.
Water-soluble bis(1,10-phenanthroline) octanedioate Cu2+ and Mn2+ complexes with unprecedented nano and picomolar in vitro cytotoxicity: promising leads for chemotherapeutic drug development (2011)

Dinuclear Cu2+ and Mn2+ bis-phenanthroline octanedioate compounds exhibit rapid, unprecedented nano and picomolar in vitro cytotoxicity against human-derived colorectal cancer lines (HT29, SW480 and SW620) and are less cytotoxic toward non-cancerous normal human keratinocyte cells (HaCaT). Both complexes displayed greater in vivo drug tolerance compared to cisplatin when examined using the insect Galleria mellonella. The compounds are potent generators of intracellular reactive oxygen species within HT29 cells, display avid DNA binding and induce O2-dependent cleavage of supercoiled pUC18 DNA. The Cu2+ complex was found to display self-cleaving nuclease activity and a mechanism of deoxyribose C–H bond activation is proposed, based on interactions with the superoxide anion and hydrogen peroxide along with DNA cleavage observations under anaerobic conditions and with an excess of the metal chelator EDTA.