gebhart/patrepeval huggingface dataset:
Physical map of the aromatic amine and m-toluate catabolic plasmid pTDN1 in Pseudomonas putida: location of a unique meta-cleavage pathway (1990)

A restriction endonuclease map was derived for the aromatic amine and m-toluate catabolic plasmid pTDN1 present in Pseudomonas putida UCC22, a derivative of P. putida mt-2. The plasmid is 79 +/- 1 kbp in size and can be divided into a restriction-site-deficient region of 51 +/- 1 kbp and a restriction-site-profuse region of 28 kbp which begins and ends with directly repeating sequences of at least 2 kbp in length. A mutant plasmid isolated after growth of the host on benzoate had lost the restriction-profuse region by a straightforward recombinational loss retaining one copy of the direct repeat. Analysis of clones, deletion and Tn5 insertion mutants strongly suggested that the meta-cleavage pathway of pTDN1 was situated in the region readily deleted. The catechol 2,3-dioxygenase (C23O) gene of pTDN1 showed no hybridization or restriction homology to previously described C23O genes of TOL plasmids pWW0 and pWW15. In addition, there was little homology between intact pTDN1, pWW0 and pWW15, suggesting the presence of a unique meta-cleavage pathway. We also demonstrated that pTDN1 did not originate from P. putida mt-2 chromosome.
Human intestinal tissue tropism in Escherichia coli O157 : H7 – initial colonization of terminal ileum and Peyer's patches and minimal colonic adhesion ex vivo (2007)

Enterohaemorrhagic Escherichia coli (EHEC) are an important cause of diarrhoeal and renal disease in man. Studies of a single prototypic O157 : H7 strain have shown tropism for follicle-associated epithelium (FAE) of distal ileal Peyer's patches without colonization of either small or large intestine. This study determined tropism in a range of Shiga toxin (Stx)-negative EHEC strains and looked for factors that might induce colonic colonization using human in vitro intestinal organ culture (IVOC). An FAE-restricted colonization was confirmed in two strains; four strains additionally colonized ileal villous surfaces, and adhesion to proximal small intestinal FAE was observed. All strains showed minimal adhesion to non-FAE regions of proximal small intestinal and to the transverse colon. Extensive large-bowel IVOC studies using three O157 : H7 strains, an O26 : H11 and an O103 : H2 strain, and tissue from caecum to rectum found colonization and attaching/effacing lesion formation in only 4 of 113 (3.5 %) IVOCs. Colonic adhesion was not enhanced by altering the IVOC technique or environment. Co-incubation of O157 : H7-infected ileal FAE with colonic samples enhanced colonic colonization, producing a novel, non-intimate adhesive phenotype. Thus, in the initial stages of colonization Stx-negative EHEC preferentially infect FAE and villi of the terminal ileal region ex vivo; colonic colonization is infrequently observed as an initial event but may represent a subsequent stage of infection.
Methods for aligning near-continuous railway track inspection data (2019)

Railroads have long used track inspection vehicles that capture data on a defined interval as the vehicle travels longitudinally down the track. These data can be captured on a constant interval, near-constant interval, or temporally. The data are normally evaluated in real time against exception thresholds, which define locations of safety or maintenance concern. In addition, railways evaluate multiple inspection runs of the same track over time to determine the rates of degradation. Since most inspection vehicles rely on the operator input of location events (mile posts, signals, switches, etc.) and tachometer-based distance measurement, the resulting inspection data are often longitudinally misaligned, on occasion by as much as several hundred feet. This paper presents an application of classical and advanced time-series methods for aligning data longitudinally. It also presents a novel methodology for aligning data with a nonconstant sampling interval, utilizing a combination of classical techniques.
An Indoor Emergency Guidance Algorithm Based on Wireless Sensor Networks (2015)

Traditional safety in the important building is noisy, expensive and has big drawbacks in guiding trapped people to the safety exit gate. Hence, a new mechanism is needed to rescue human from the fire building and to guide them to the best safety gate. Wireless Sensor Network (WSN) combined with a proposed guidance algorithm is an important indoor application. This paper proposes an indoor emergence guidance algorithm based on WSN to guide people to a building exit gate while helping them avoid a hazardous area. WSN is responsible for real-time monitoring of the environment, and when emergency event is detected the proposed algorithm will be invoked and a real-time guidance will assist to rescue the trapped people very fast. The proposed guiding mechanism has been successfully studied and verified through real test bed implementation using Telosb motes.
Modulation of the in vitro antimalarial effects of artemisinin by selected extracts: the case of olive leaf water extract (2008)

Within the framework of a larger research project [1] aimed at evaluating the possible synergistic effects in malaria treatment between artemisinins –today the most potent antimalarial agents- and a variety of plant extracts and isolated natural constituents, the specific antiplasmodial properties in vitro of a dried extract of olive leaf alone and in combination with artemisinin were evaluted against 3D7 P. falciparum strains. The extract was prepared by aqueous extraction of olive leaf and purified with membrane techniques as microfiltration, ultrafiltration, nanofiltration and reverse osmosis, both in laboratory scale and in pilot plant experimental apparatus, according to PCT/IT2006/47783 [2]. The extract was characterised by HPLC/DAD as previously reported [3] and HPLC/MS analysis, showing 20% oleuropein and 33% polyphenols. The possible synergism between artemisinin and the single constituents on the parasite growth was investigated adding artemisinin, at sublethal doses, ranging from 0.625 to 40 nM, either in the presence (or in the absence) of 10µM (no reduction of parasitemia) or 50µM (reduction of 12% of parasitemia) concentrations of the individual compounds. The effects of artemisinin tested at different concentrations and both 10 and 50µM olive leaf extract are more than additive implying some moderate synergism between these two substances. The observed synergism by isobologram analysis, between olive leaf extract, expecially at 50µM and artemisinin might be conveniently exploited to determine the constituents responsible of the synergism and design new and/or more effective combination therapies.
Intergeneric Somatic Hybrids between Citrus and Atalantia or Severinia by Electrofusion, and Recombination of Mitochondrial Genomes. (1995)

Two intergeneric hybridizations through protoplast fusion between the embryogenic callus cells of 'Seminole' tangelo (Citrus reticulata Blanco X C. paradisi Macf.) and leaf cells of Indian atalantia (Atalantia monophylla DC.) or Chinese box-orange (Severinia buxifolia (Poir.) Tenore) were performed to overcome the genetic incompatibility. We were successful in regenerating whole plants of 16 somatic hybrids between 'Seminole' tangelo and Indian atalantia, and 46 somatic hybrids between 'Seminole' tangelo and Chinese box-orange, and hybridity was confirmed by Southern blot hybridization with rDNA. The mitochondrial DNA (mtDNA) of the somatic hybrids between 'Seminole' tangelo and Indian atalantia was identical to that of 'Seminole' tangelo, when rrn 26 and cox I were used as probes. However, when atp A was used as a probe, a 'Seminole' tangelo-specific fragment was found missing besides an Indian atalantia-specific fragment. The band pattern obtained by chloroplast DNA (CpDNA) analysis was identical to that of Indian atalantia. On the contrary, somatic hybrids between 'Seminole' tangelo and Chinese box-orange showed the mtDNA band pattern identical to that of 'Seminole' tangelo, when atp A and cox I were used as probes. However, analysis by rrn 26 probe showed the presence of a part of a Chinese box-orange-specific band in addition to a 'Seminole' tangelo-specific band. The cpDNA of the somatic hybrids was identical to that of Chinese boxorange. These results suggest the occurrence of mitochondrial recombination between parents
Analysis Of Thresholds In Rule-Based Antilock Braking Control Algorithms (2020)

An Antilock Braking System (ABS) is an Active Vehicle Safety System (AVSS) employed to prevent wheel lock in road vehicles. Wheel lock is undesirable as it may lead to loss of vehicle steerability and directional stability. These become critical in Heavy Commercial Road Vehicles (HCRVs) as unintentional yaw motion resulting from directional instability may also lead to vehicle roll-over. ABS algorithms are broadly classified as Model-Based Algorithms (MBAs) and Rule-Based Algorithms (RBAs). MBAs are typically physics based and employ vehicle dynamic models. RBAs, which are currently predominantly used in vehicles, are threshold based. RBAs require measurement of wheel speed that is readily available, while MBAs require real time information on vehicle parameters and tire models. Most commercially available RBAs are proprietary and the details are not revealed. This has motivated the present study, and the physical significance of the wheel slip and wheel acceleration thresholds used in RBAs are clearly identified, backed by experiments from a Hardware-in-Loop (HiL) pneumatic brake setup along with IPG TruckMaker®, a software for vehicle dynamic simulation. This study is an important first step in developing an advanced RBA for HCRVs.
Human T Lymphotropic Virus Type I-Associated Myelopathy/Tropical Spastic Paraparesis in Sao Paulo, Brazil (1995)

We conducted a prospective clinical and epidemiologic evaluation of 45 cases of human T lymphotropic virus type I (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in São Paulo, Brazil. All enrolled patients had progressive chronic myelopathy and high titers of HTLV-I and HTLV-II antibodies, as determined by enzyme immunoassay and western blot. In 24 cases, the polymerase chain reaction (PCR) was performed so that HTLV-I could be distinguished from HLTV-II. The clinical and epidemiologic features of the patients from our study were similar to those of patients with HAM/TSP from other areas of endemicity for HTLV-I except that more patients in our study had received a blood transfusion prior to their illness. Despite the presence of HTLV-II virus in Brazil, all patients whose serum was tested by PCR were found to be infected with the HTLV-I virus.
Development of a Multi-Modal Optical Imaging System (2016)

A multi-modal optical imaging system is presented which uses diffuse optical tomography to determine subject-specific, heterogeneous tissue attenuation to increase the quantitative accuracy of bioluminescence tomography.
Fault-tolerant computer for the Automated Transfer Vehicle (2002)

Matra Marconi Space is developing their fourth generation fault-tolerant majority voting computers for use on future spacecraft such as the European Automated Transfer Vehicle, a servicing vehicle for the International Space Station. This paper presents how the computer participates in the spacecraft safety concept with emphasis on the critical on-orbit rendezvous phase. The functional architecture of the computer pool is described addressing fault containment layers, inter-channel synchronisation, communication, failed channel detection and passivation. Lastly, the hardware and software design of the test bench, built up to validate this new computer pool, is presented together with some performance measurements.
Supplementary Figure 3 from Control of HIF-1α Expression by eIF2α Phosphorylation–Mediated Translational Repression (2023)

Supplementary Figure 3 from Control of HIF-1α Expression by eIF2α Phosphorylation–Mediated Translational Repression
Irradiation performance of HTGR fuel in HFIR capsule HT-31 (1979)

The capsule was irradiated in the High Flux Isotope Reactor at ORNL to peak particle temperatures up to 1600/sup 0/C, fast neutron fluences (0.18 MeV) up to 9 x 10/sup 25/ n/m/sup 2/, and burnups up to 8.9% FIMA for ThO/sub 2/ particles. The oxygen release from plutonium fissions was less than calculated, possibly because of the solid solution of SrO and rare earth oxides in UO/sub 2/. Tentative results show that pyrocarbon permeability decreases with increasing fast neutron fluence. Fission products in sol-gel UO/sub 2/ particles containing natural uranium mostly behaved similarly to those in particles containing highly enriched uranium (HEU). Thus, much of the data base collected on HEU fuel can be applied to low-enriched fuel. Fission product palladium penetrated into the SiC on Triso-coated particles. Also the SiC coating provided some retention of /sup 110m/Ag. Irradiation above about 1200/sup 0/C without an outer pyrocarbon coating degraded the SiC coating on Triso-coated particles.
Molecular Testing for Mutations in Improving the Fine-Needle Aspiration Diagnosis of Thyroid Nodules (2009)

These results indicate that molecular testing of thyroid nodules for a panel of mutations can be effectively performed in a clinical setting. It enhances the accuracy of FNA cytology and is of particular value for thyroid nodules with indeterminate cytology.
A piezoresistive based tactile sensor for use in minimally invasive surgery (2011)

In the present paper, a novel tactile sensor is proposed for use in minimally invasive surgery to provide surgeons with tactile information. The sensing element of the sensor relies on a piezoresistive material. The proposed sensor measures contact force as well as the relative hardness of soft contact objects. A prototype of the sensor has been built, calibrated, and tested. Experimental test results confirm the ability of the sensor to distinguish between two different elastomeric materials. Such materials resemble two different biological tissues.
Reconstitution of 50 S ribosomal subunits from Bacillus stearothermophilus with 5 S RNA from spinach chloroplasts and low‐Mr RNA from mitochondria of Locusta migratoria and bovine liver (1984)

Reconstitution experiments with 50 S ribosomal subunits from Bacillus stearothermophilus demonstrate that spinach chloroplast 5 S rRNA can be incorporated into the bacterial ribosome and yield biologically active particles, thereby establishing the eubacterial nature of chloroplast 5 S rRNA. In contrast, mitochondria from Locusta migratoria or bovine liver do not appear to contain discrete, low-Mr RNAs, which can replace 5 S rRNA in the functional reconstitution of B. stearothermophilus ribosomes.
Mutations in α‐helical solvent‐exposed sites of eglin c have long‐range effects: Evidence from molecular dynamics simulations (2005)

Eglin c is a small protease inhibitor whose structural and thermodynamic properties have been well studied. Previous thermodynamic measurements on mutants at solvent-accessible positions in the protein's helix have shown the unexpected result that the data could be best fit by the inclusion of residue- and position-specific parameters to the model. To explore the origins of this surprising result, long molecular dynamics simulations in explicit solvent have been performed. These simulations indicate specific long-range interactions between the solvent-exposed residues in the eglin c alpha-helix and binding loop, an unexpected observation for such a small protein. The residues involved in the interaction are on opposite sides of the protein, about 25 A apart. Simulations of alanine substitutions at the solvent-exposed helix positions, arginine 22, glutamic acid 23, threonine 26, and leucine 27, show both small and large perturbations of eglin c dynamics. Two mutations exhibit large impacts on the long-range helix-loop interactions. Previous stability measurements (Yi et al., Biochemistry 2003;42:7594-7603) had indicated that an alanine substitution at position 27 was less stabilizing than at other solvent-exposed positions in the helix. The L27A mutation effects observed in these simulations suggest that the position-dependent loss of stability measured in wet bench experiments is derived from changes in dynamics that involve long-range interactions; thus, these simulations support the hypothesis that solvent-exposed positions in helices are not always equivalent.
Clinico-pathological correlation of lacrimal caruncle tumors: a retrospective analysis over 22 years at the University Eye Hospital Bonn (2021)

Abstract Purpose The lacrimal caruncle is composed of numerous structures including different glands as well as hair follicles. Accordingly, the spectrum of benign and malignant lesions is broad, and the clinical diagnosis is often challenging. Here we systematically analyzed excised caruncular tumors over the past 22 years with special emphasis on the clinico-pathological correlation to provide a guidance for clinicians. Methods Retrospective evaluation with clinico-pathologic correlation of surgically removed caruncular tumors between 1998 and 2020 at a tertiary referral center. Results Eighty-two caruncular tumors were identified in the respective period. The patients were between 11 and 85 years of age (mean, 46.8 years; median, 49 years). Nevi ( n = 35), cystic lesions ( n = 14), oncocytoma ( n = 9), papilloma ( n = 8), sebaceous gland hyperplasia ( n = 8), and reactive lymphoid hyperplasia ( n = 4) were observed most frequently. Besides, we are the first reporting herniated orbital fat accompanied by a pyogenic granuloma. 2.4% ( n = 2) were malignant tumors (sebaceous gland carcinoma, conjunctival intraepithelial neoplasia with pyogenic granuloma). Conclusion Caruncular tumors show a broad spectrum of mostly benign tumors. They can occur in patients of any age. However, 8/9 oncocytomas and both malignant lesions were detected in patients older than 60 years. Although the clinical diagnosis was confirmed in only 68.3% by the histopathological analysis, the two malignant lesions were identified as such already clinically. Caruncular lesions with a history of growth or other signs of malignancy should be excised followed by detailed histopathological examination to allow a final diagnosis and exclude rare malignant tumors with lethal potential.
Immunodietica: interrogating the role of diet in autoimmune disease (2020)

Abstract Diet is an environmental factor in autoimmune disorders, where the immune system erroneously destroys one’s own tissues. Yet, interactions between diet and autoimmunity remain largely unexplored, particularly the impact of immunogenetics, one’s human leukocyte antigen (HLA) allele make-up, in this interplay. Here, we interrogated animals and plants for the presence of epitopes implicated in human autoimmune diseases. We mapped autoimmune epitope distribution across organisms and determined their tissue expression pattern. Interestingly, diet-derived epitopes implicated in a disease were more likely to bind to HLA alleles associated with that disease than to protective alleles, with visible differences between organisms with similar autoimmune epitope content. We then analyzed an individual’s HLA haplotype, generating a personalized heatmap of potential dietary autoimmune triggers. Our work uncovered differences in autoimmunogenic potential across food sources and revealed differential binding of diet-derived epitopes to autoimmune disease-associated HLA alleles, shedding light on the impact of diet on autoimmunity.
Méthodologie pour le calcul de champ électromagnétique pouvant être rayonné par un panneau solaire réel (2013)

International audience
Human Retroviruses (2009)

This chapter contains sections titled: Introduction Retrovirus Replication and Genomes Taxonomy Human and Zoonotic Retrovirus Infections Retroviral Vectors References
The National Carbon Capture Center: Cost-effective test bed for carbon capture R&D (2013)

The US Department of Energy (DOE) established the National Carbon Capture Center (NCCC) as part of its strategy to address the need for cost-effective CO2 capture technologies. The focus of the NCCC is to conduct research and development to advance emerging CO2 control technologies to commercial scale for effective integration into coal- based Integraged Gasification Combined Cycle (IGCC) and combustion processes. To achieve this goal, the NCCC provides a test-bed for government, industrial, and university projects to conduct meaningful tests in an industrial setting. The NCCC test plan includes both post-combustion and pre-combustion CO2 capture development. A flexible post- combustion test facility, Post-combustion Carbo Plant E.C. Gaston, in Wilsonville, Alabama. The facility, which is managed by Southern Company Services, provides a platform for testing technologies at a wide-range of sizes and process conditions on coal-derived flue gas. Since completing commissioning and baseline testing in early 2011, several technologies have been tested. The PC4 facility includes multiple slipstreams with a range of flue gas throughputs to allow the evaluation of post- combustion CO2 capture technologies. It provides the capability to test modules from technology developers and to test solvents in an absorber/regenerator unit, the pilot solvent test unit (PSTU). In 2011, PSTU baseline tests were completed, using a reference solvent, monoethanol amine (MEA) to characterize its performance and verify the reliability of the data generated. The PSTU was later operated to test a potential commercial solvent developed by Babcock & Wilcox. Aker Carbon Solutions installed a mobile test unit at the site to test its commercial solvent, and Membrane Technology & Research installed and commissioned its 0.05-MW polymeric CO2-separation membrane, which will continue to be tested throughout 2012. Also in 2012, several other developers will test solvents in the PSTU and enzyme-based solvent systems in the bench scale area on coal-derived flue gas. Collaboration with additional developers for future test plans is on-going. The NCCC also generates coal derived syngas which is available for testing technologies related to pre-combustion CO2 capture. Several slipstreams are in place with a range of syngas throughputs. Technologies tested in 2011 include water gas shift catalysts, high-temperature mercury and CO2 sorbents, a hydrocarbon removal system, physical and chemical solvents for CO2 absorption, a polymeric CO2-separation membrane, and three hydrogen- separation membranes (carbon molecular sieve, polymeric, and palladium based). Several of these technologies will be tested further in 2012, and membranes and solvents from other developers will also be tested. Result from NCCC's testing have indicated the facility's usefulness in accelerating the commercialization of advanced CO2 capture technologies. This paper will detail the NCCC's capabilities, test results, and future plans.