gebhart/patrepeval huggingface dataset:
Linguistic Unit Discovery from Multi-Modal Inputs in Unwritten Languages: Summary of the “Speaking Rosetta” JSALT 2017 Workshop (2018)

We summarize the accomplishments of a multi-disciplinary workshop exploring the computational and scientific issues surrounding the discovery of linguistic units (subwords and words) in a language without orthography. We study the replacement of orthographic transcriptions by images and/or translated text in a well-resourced language to help unsupervised discovery from raw speech.
Smart E-textile: Resistance properties of conductive knitted fabric – Single pique (2016)

Wearable electronics textiles are a new emerging phenomenon. These are textiles that incorporate electrical properties, for example heating, light emitting, sensing, etc., and are now being rapidly developed due to the creation of new types of fibers and fiber composites. The different ways that can be used to combine conductive fibers with electronics components have been receiving much attention in wearable electronics research. However, to meet the requirements for both aesthetics and function, textiles technology and the garment design method are important for commercial success. In order to apply electronics to fabrics with the use of conductive fibers, complex and elastic fabric structures both need to be modeled. Therefore, the focus of this study is to examine the resistance properties of single pique, a fabric that is conductive and has a knitted structure that uses tuck stitches, a typical structure in knitting. A planar geometric model is established for a single pique structure based on the loop construction of this knitted fabric. Subsequently, resistive network models are developed for different cases of external voltages to calculate the resistance values of single pique fabrics with different numbers of wales and courses. Corresponding experiments are carried out to verify the proposed resistive network modeling. The newly developed resistance model in this study will provide significant benefits to the industrialization of wearable electronics textiles and the apparel industry as they can offer commercial apparel products that are not only aesthetically pleasing and multi-functional, but also have high added value.
Swelling and Thermal Transitions of Polyelectrolyte Multilayers in the Presence of Divalent Ions (2016)

The effects of CaCl2, MgCl2, and Na2SO4 on the swelling response and the thermal transition of poly(diallyldimethylammonium chloride)/poly(styrenesulfonate) (PDAC/PSS) layer-by-layer (LbL) assemblies are investigated. For MgCl2 and CaCl2, two swelling regimes are observed depending on the salt concentration of the overlying solution. Below 0.17 M MgCl2 or CaCl2, swelling appears to arise from electrostatic repulsion within the multilayer. Above 0.17 M MgCl2 or CaCl2, the multilayer swells linearly with the concentration of the overlying solution due to doping; the degree of swelling in this linear regime depends on the hydration shell of the doping ions. Alternatively, swelling with no concentration dependence was observed for Na2SO4. Unlike the swelling behavior, the thermal transition temperature observed in hydrated films shifts to higher temperatures with increasing concentration of Na2SO4. However, when hydrated with CaCl2 or MgCl2 solutions, the transition remains relatively constant within error. Results are discussed in terms of the salt ion’s hydration shell and Donnan exclusion.
Lipidomics Reveals Dramatic Physiological Kinetic Isotope Effects during the Enzymatic Oxygenation of Polyunsaturated Fatty Acids Ex Vivo (2017)

Arachidonic acid (AA, 20:4) is an omega-6 polyunsaturated fatty acid (PUFA) and the main precursor to the class of lipid mediators known as eicosanoids. The enzymes that catalyze the oxygenation of AA begin by abstracting hydrogen from one of three bis-allylic carbons within 1,4-cis,cis-diene units. Substitution of deuterium for hydrogen has been shown to lead to massive kinetic isotope effects (KIE) for soybean lipoxygenase (sLOX) oxygenation of linoleic acid (LA, 18:2). Yet, experimental determination of the KIE during oxygenation of AA and LA by mammalian enzymes including cyclooxygenase (COX) and lipoxygenase (LOX) has revealed far lower values. All prior studies investigating the KIE of PUFA oxygenation have relied on in vitro systems using purified enzymes and were limited by availability of deuterated substrates. Here we demonstrate the use of macrophages as an ex vivo model system to study the physiological KIE (PKIE) during enzymatic AA oxygenation by living cells using a newly synthesized library of deuterated AA isotopologues. By extending lipidomic UPLC-MS/MS approaches to simultaneously quantify native and deuterated lipid products, we were able to demonstrate that the magnitude of the PKIE measured in macrophages for COX and LOX oxygenation of AA is similar to KIEs determined in previous reports using the AA isotopologue deuterated at carbon 13 (C13). However, for the first time we show that increasing the number of deuterated bis-allylic carbons to include both C10 and C13 leads to a massive increase in the PKIE for COX oxygenation of AA. We provide evidence that hydrogen(s) present at C10 of AA play a critical role in the catalysis of prostaglandin and thromboxane synthesis. Furthermore, we discovered that deuteration of C10 promotes the formation of the resolving lipid mediator lipoxin B4, likely by interfering with AA cyclization and shunting AA to the LOX pathway under physiological conditions.
Automatic Hot Test of Gyrotron-Traveling Wave Tubes by Adaptive PID Feedback Control (2017)

It is of great importance in many applications to provide a stable output power of a gyrotron-traveling wave tube (gyro-TWT) during a long operation time (over several hours). In order to achieve this goal, an automatic hot test platform of gyro-TWTs was set up and the power stabilization was obtained by an adaptive scheme of proportional integral derivative (PID) feedback by the beam current controlled by the filament heating power and cathode-anode beam voltage. With determined operating parameters, the PID controller can adaptively adjust the beam current and voltage, and then maintain the output power on a target. This PID controlling process can effectively eliminate the influence of the power supply voltage surge and cathode emission instability. Automatic hot test of the gyro-TWTs shows that the PID feedback controlling accuracy of the output power is better than 2%.
Eosinophil-mediated bile duct stricture. A case studied by immunohistochemistry. (1992)

Major basic protein accounts for the majority of the protein within the eosinophilic granule. Utilizing immunohistochemical staining for major basic protein, we have demonstrated the dominant role of the eosinophil in a reversible bile duct stricture.
NETWORKS FROM GENE EXPRESSION TIME SERIES: CHARACTERIZATION OF CORRELATION PATTERNS (2007)

We address the problem of finding large-scale functional and structural relationships between genes, given a time series of gene expression data, namely mRNA concentration values measured from genetically engineered rat fibroblasts cell lines responding to conditional cMyc proto-oncogene activation. We show how it is possible to retrieve suitable information about molecular mechanisms governing the cell response to conditional perturbations. This task is complex because typical high-throughput genomics experiments are performed with high number of probesets (10 3 –10 4 genes) and a limited number of observations (&lt; 10 2 time points). In this paper, we develop a deepest analysis of our previous work [Remondini et al., 2005] in which we characterized some of the main features of a gene-gene interaction network reconstructed from temporal correlation of gene expression time series. One first advancement is based on the comparison of the reconstructed network with networks obtained from randomly generated data, in order to characterize which features retrieve real biological information, and which are instead due to the characteristics of the network reconstruction method. The second and perhaps more relevant advancement is the characterization of the global change in co-expression pattern following cMyc activation as compared to a basal unperturbed state. We propose an analogy with a physical system in a critical state close to a phase transition (e.g. Potts ferromagnet), since the cell responds to the stimulus with high susceptibility, such that a single gene activation propagates to almost the entire genome. Our result is relative to temporal properties of gene network dynamics, and there are experimental evidence that this can be related to spatial properties regarding the global organization of chromatine structure [Knoepfler et al., 2006].
Increased Tuberculosis Patient Mortality Associated with Mycobacterium tuberculosis Mutations Conferring Resistance to Second-Line Antituberculous Drugs (2017)

Rapid molecular diagnostics have great potential to limit the spread of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) (M/XDR-TB). These technologies detect mutations in the <i>Mycobacterium tuberculosis</i> genome that confer phenotypic drug resistance. However, there have been few data published regarding the relationships between the detected <i>M. tuberculosis</i> resistance mutations and M/XDR-TB treatment outcomes, limiting our current ability to exploit the full potential of molecular diagnostics. We analyzed clinical, microbiological, and sequencing data for 451 patients and their clinical isolates collected in a multinational, observational cohort study to determine if there was an association between <i>M. tuberculosis</i> resistance mutations and patient mortality. The presence of an <i>rrs</i> 1401G mutation was associated with significantly higher odds of patient mortality (adjusted odds ratio [OR] = 5.72; 95% confidence interval [CI], 1.65 to 19.84]) after adjusting for relevant patient clinical characteristics and all other resistance mutations. Further analysis of mutations, categorized by the associated resistance level, indicated that the detection of mutations associated with high-level fluoroquinolone (OR, 3.99 [95% CI, 1.10 to 14.40]) and kanamycin (OR, 5.47 [95% CI, 1.64 to 18.24]) resistance was also significantly associated with higher odds of patient mortality, even after accounting for clinical site, patient age, reported smoking history, body mass index (BMI), diabetes, HIV, and all other resistance mutations. Specific <i>gyrA</i> and <i>rrs</i> resistance mutations, associated with high-level resistance, were associated with patient mortality as identified in clinical <i>M. tuberculosis</i> isolates from a diverse M/XDR-TB patient population at three high-burden clinical sites. These results have important implications for the interpretation of molecular diagnostics, including identifying patients at increased risk for mortality during treatment. (This study has been registered at ClinicalTrials.gov under registration no. NCT02170441.).
The Average Mappings Problem: Statement, Applications, and Approximate Solution (2006)

Finalist for best paper awards
Highly Luminescent Europium-Based Heteroleptic Coordination Polymers with Phenantroline and Glutarate Ligands (2021)

Isostructural lanthanide-based coordination polymers with general chemical formula [Ln(phen)(glu)(NO<sub>3</sub>)]<sub>∞</sub> with Ln = La-Tm (except Ce and Pm) have been synthesized by hydrothermal methods (H<sub>2</sub>glu stands for glutaric acid and phen stands for 1,10-phenantroline). They crystallize in the monoclinic system with the <i>P</i>2<sub>1</sub>/<i>c</i> (no. 14) space group. The crystal structure has been solved on the basis of the La derivative. It can be described as the superimposition of molecular chains of dimeric La(phen)(NO<sub>3</sub>)-La(phen)(NO<sub>3</sub>) units bridged by glutarate ligands. Luminescent properties have been explored and show that the Eu derivative exhibits the highest luminance observed for Eu-based coordination polymers (85 to 105 cd·m<sup>-2</sup>). Effects of the dilution of the Eu<sup>3</sup><sup>+</sup> and Tb<sup>3</sup><sup>+</sup> luminescent ions by Gd<sup>3</sup><sup>+</sup> optically inactive ions are unexpected and to the best of our knowledge unprecedented. This could be related to the different intermetallic energy-transfer mechanisms in competition and to the nonisotropic distribution of the lanthanide ions in these molecular alloys. The investigation of molecular alloys with general chemical formula [Eu<sub>1-<i>x</i></sub>Tb<sub><i>x</i></sub>(phen)(glu)(NO<sub>3</sub>)]<sub>∞</sub> with 0 ≤ <i>x</i> ≤ 1 highlights a very sizable and constant Eu<sup>3</sup><sup>+</sup> luminescence whatever the <i>x</i> value, which further confirms the existence of very strong intermetallic energy transfers in this family of compounds. It is also noticeable that some coordination polymers based on weakly emissive lanthanide ions exhibit very well defined emission spectra.
The role of High Performance Computing in Bioinformatics (2014)

We are witnessing one of the major revolutions in parallel systems. The consolidation of heterogeneous systems at dierent levels -from desktop computers to large-scale systems such as supercomputers, clusters or grids, through all kinds of low-power devices- is providing a computational power unimaginable just few years ago, trying to follow the wake of Moore's law. This landscape in the high performance com- puting arena opens up great opportunities in the simulation of relevant biological systems and for applications in Bioinformatics, Computational Biology and Computational Chemistry. This introductory article shows the last tendencies of this active research eld and our perspectives for the forthcoming years.
CATIONIC LIPID-MEDIATED TRANSFER OF THE hIL-10 GENE PROLONGS SURVIVAL OF ALLOGENEIC HEPATOCYTES IN NAGASE ANALBUMINEMIC RATS1,2 (1996)

Gene transfer techniques can be used as a drug delivery system to achieve local immunosuppression. We performed a series of experiments to identify the cationic lipid that most efficiently transfects isolated, cultured, rat hepatocytes; to optimize conditions for efficient transfection; to determine the duration of gene expression in vitro; and finally, to determine the survival of allogeneic hepatocytes transplanted into Nagase rats. Our results suggest that DOTAP is the best cationic lipid for transfection of cultured rat hepatocytes. In addition, the following conditions appear to optimize transfection efficiency: a DNA:DOTAP ratio of 1:6; a 24 exposure time of the hepatocytes to the DNA-DOTAP complex; a DNA dose of 4 microg/35 mm culture plate seeded with 2.5x10(5) rat hepatocytes. When transfected as described above, cultured hepatocytes expressed the hIL-10 gene for approximately 14 days. Accordingly, Nagase rats transplanted with 4x10(7) DOTAP-hIL-10 transfected, allogeneic hepatocytes had an abrupt rise in serum albumin levels that peaked within 7 days of the transplant, decreased abruptly after 15 days, and approached baseline by day 40. In contrast, control animals had a smaller albumin peak that returned to baseline within 10 days (P<0.01). In all animals, serum hIL-10 levels were undetectable when tested. We conclude that DOTAP is the best cationic lipid for transfection of cultured rat hepatocytes. Furthermore, hIL-10 transfected hepatocytes have a prolonged survival in an allogeneic host which is probably limited by loss of gene expression. Further studies using other vectors capable of prolonged gene expression will help determine if indefinite hIL-10 gene expression leads to indefinite graft survival.
How to Lengthen the Long-Term Stability of Enzyme Membranes: Trends and Strategies (2017)

In this review, factors that contribute to enhancing the stability of immobilized enzyme membranes have been indicated, and the solutions to each factor, based on examples, are discussed. The factors are divided into two categories: one is dependent on the improvement of enzyme properties, and the other, on the development of supporting materials. Improvement of an enzyme itself would effectively improve its properties. However, some novel materials or novel preparation methods are required for improving the properties of supporting materials. Examples have been provided principally aimed at improvements in membrane stability.
Gamma tocotrienol and tocopherol-mediated cells death occurs through the production of 15-HETE in prostate cancer cells. (2007)

A106 Dietary vitamin E exists as either tocopherols or tocotrienols. Evidence indicates that vitamin Es other than α-tocopherol, may be potent cancer preventive agents. Growth arrest of the PC-3 prostate cancer cell lines was compared in the presence of dietary α-, γ-, and δ-vitamin E by the MTT assay. Physiological concentrations of γ-tocotrienol were tested for apoptotic potential using fluorescent microscopy. QPCR, Western blot, PPAR γ dominant negative and scintillation proximity assays were used to determine the effects of vitamin E on PPAR γ. The effect of vitamin E on 15-S-HETE was determined using ELISA. Tocotrienols induced more growth arrest than tocopherols. The gamma isoforms demonstrated selectivity for growth inhibition toward the cancer cells versus normal prostate epithelia. In PC-3 cells, cell death occurs with 1 µM at 24 hours and apoptosis occurs with 5 µM at 72 hours. PPAR γ was up regulated by dietary γ-vitamin Es. Dietary γ-vitamin E mediated growth arrest was demonstrated to be PPAR γ-dependent using a PPAR γ dominant negative vector. Neither γ-vitamin Es are direct PPAR γ ligands. Concentrations of 15-S-HETE in PC-3 cells were found to be up regulated by treatment with R-γ tocotrienol. These data support that tocotrienols could be more effective as prostate chemopreventive agents than tocopherols. As the γ-vitamin Es are not direct PPAR γ ligands, and 15-S-HETE is up regulated, our data suggest that R-γ-tocotrienol modulates arachidonic acid metabolism by up regulation of 15-S-HETE which induces the PPAR γ pathway, potentiating apoptosis.
Defeating distributed denial of service attacks (2000)

Security experts generally acknowledge that the long-term solution to distributed denial of service attacks is to increase the security level of Internet computers. Attackers would then be unable to find zombie computers to control. Internet users would also have to set up globally coordinated filters to stop attacks early. However, the critical challenge in these solutions lies in identifying the incentives for the Internet's tens of millions of independent companies and individuals to cooperate on security and traffic control issues that do not appear to directly affect them. We give a brief introduction to: network weaknesses that DDoS attacks exploit; the technological futility of addressing the problem solely at the local level; potential global solutions; and why global solutions require an economic incentive framework.
A reduction in the human adenovirus virion size through use of a shortened fibre protein does not enhance muscle transduction following systemic or localised delivery in mice (2014)

We have investigated whether reducing the overall size of adenovirus (Ad), through use of a vector containing a shortened fibre, leads to enhanced distribution and dissemination of the vector. Intravenous or intraperitoneal injection of Ad5SlacZ (12 nm fibre versus the normal Ad5 37 nm fibre) or Ad5SpKlacZ (shortened fibre with polylysine motif in the H-I loop of fibre knob domain) led to similar levels of lacZ expression compared to Ad5LlacZ (native Ad5 fibre) in the liver of treated animals, but did not enhance extravasation into the tibialis anterior muscle. Direct injection of the short-fibre vectors into the tibialis anterior muscle did not result in enhanced spread of the vector through muscle tissue, and led to only sporadic transgene expression in the spinal cord, suggesting that modifying the fibre length or redirecting viral infection to a more common cell surface receptor does not enhance motor neuron uptake or retrograde transport.
Cyanobacteria as agents for the control of pollution by pesticides and chlorinated organic compounds (1998)

Cyanobacteria are phototrophic aquatic micro-organisms that are found in a variety of environments, including polluted ones. Fifteen strains of cyanobacteria that belong to three taxonomic groups are able to degrade lindane (λ-hexachlorocyclohexane, a recalcitrant pesticide). The initial degradation pathway has been studied in two filamentous nitrogen-fixing strains of Anabaena sp. PCC 7120 and Nostoc ellipsosporum. These cyanobacteria dechlorinated loindane first to pentachlorocyclohexene and then to a mixture of trichlorobenzenes, and possibly further. Lindane dechlorination by these organisms occurred only in the presence of nitrate in the medium. Both ammonium and darkness inhibited the process. This combination of observations led us to the hypothesis that the nitrate-reduction system of cyanobacteria may be involved in dechlorination. The hypothesis was proven by the analysis of Anabaena sp. transpositional mutants in four genes of the nir operon. The mutants were unable to dechlorinate lindane. However, there was no correlation between lindane dechlorination and activities of individual proteins encoded by this operon. Genetic engineering of Anabaena sp. and N. ellipsosporum that introduced linA lindane dechlorination operon from Psuedomonas paucimobilis allowed us to uncouple dechlorination from nitrate requirement. Introduction, by genetic engineering, of fcABC (the 4-chlorobenzoate dechlorination system from Arthrobacter globiformis) to Anabaena sp and N. ellipsosporum rendered these strains newly capable of 4-chlorobenzoate dechlorination both constitutively and inducible by an environmental factor.
Effects of tannins and polyphenols of some medicinal plants on bacterial agents of urinary tract infections (2003)

Five medicinal plants, Enantia chloranthia, Kigelia africana, Bridelia ferruginea, Trema nitems and Drypetes gossweilerri were screened for phytochemical components. The plants were found to contain tannins, phlobatannins, alkaloids, cardiac glycosides, anthranoids, anthraquinones, saponins and polyphenols. The crude aqueous and ethanolic extracts as well as tannins and polyphenols of the plants were tested on some bacterial agents of urinary tract infections (UTI). The results revealed that the extracts inhibited Staphylococcus aureus, Pseudomonas aerugosina, Klebsiella sp., Proteus sp. and Escherichia coli to varying degrees. However, the ethanolic extracts showed greater degree of inhibitory activity on the organisms than the aqueous extracts. Similarly, the tannins and polyphenols inhibited S. aureus, Klebsiella sp., Proteus sp. and E. coli but had no inhibitory effect on Pseudomonas aeruginosa. The minimal inhibitory concentration (MIC) values for the test bacteria varied but generally ranged between 3% and 7%. Mixing the ethanolic extracts of all five medicinal plants together resulted in lower MIC values for the organisms. The utilization of these plants for the manufacture of drugs for the treatment of UTI is highlighted. Keywords: Tannins, polyphenols, bacteria, urinary tract infections (Global Journal of Pure and Applied Sciences: 2003 9(2): 193-198)
Thiamazol-induzierte Arthritis (2020)

We report the case of a 42-year-old male patient with acute onset of asymmetrical polyarthritis of the medium and large joints as well as fever and elevated serological inflammation markers. The symptoms began shortly after initiation of thiamazole treatment for newly diagnosed Graves' disease. Antithyroid arthritis syndrome (AAS) is a rare but serious adverse side effect of antithyroid treatment with thioamides such as thiamazole. Clinically, AAS may present with myalgia, arthralgia, fever, exanthema and polyarthritis. In the case of suspected AAS, when possible the thionamide medication should be rapidly discontinued or modified in consultation with the endocrinologist. In some cases anti-inflammatory therapy with NSAID or corticosteroids may be required for symptom control.