Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Antibiotic Treatment against “Candidatus Helicobacter suis” in a Mouse Model

ABSTRACT “Helicobacter heilmannii” (proposed name) type 1 colonizes the human stomach. It has been shown to be identical to“ Candidatus Helicobacter suis,” a Helicobacter species colonizing the stomachs of >60% of slaughter pigs. This bacterium has not been isolated in vitro until now. Antibiotic susceptibility testing of “Candidatus Helicobacter suis” has not been carried out so far. For the present study, a mouse model was adopted to evaluate the antibiotic susceptibility of this organism. Mice infected with“ Candidatus Helicobacter suis” were treated with amoxicillin and omeprazole, a therapy which is used to treat H. heilmannii infections in humans. Two different isolates of“ Candidatus Helicobacter suis” were tested. The excretion of bacterial DNA was assessed during treatment, using PCR on fecal samples. At the end of the experiment, 8 days after the cessation of treatment, the presence of infection was evaluated using a urease test and a PCR test on stomach samples. A marked decrease in the excretion of bacterial DNA was observed a few days after the onset of treatment, and the level remained low until the end of the experiment. A difference in susceptibility between the two“ Candidatus Helicobacter suis” isolates was pointed out. The in vivo mouse model infected with“ Candidatus Helicobacter suis” will be useful for further screening of potential therapeutic regimens.
Relationship between the sensitivity of EBV‐carrying lymphoblastoid lines to superinfection and the inducibility of the resident viral genome

Human, EBV‐carrying lymphoblastoid lines show wide differences in their sensitivity to superinfection with EBV concentrates and also in their sensitivity to the activation of the resident viral genome by BUDR and IUDR. A significant correlation was found between sensitivity to superinfection and activation in 23 virus‐receptor‐positive lines. In 10 receptor‐negative lines, there was no such correlation: they were resistant to superinfection since they could not adsorb the virus, but differed widely in their activatability. The findings suggest that the intracellular restrictive mechanism that limits superinfection in the receptor‐positive, resistant lines, can also restrict the function of the activated genome, derived from within. Since some of the lines that were resistant to both superinfection and activation were spontaneous producers, however, it appears that the same mechanism does not necessarily affect the “spontaneous” function of the resident genome.
Detection of Staphylococcus aureus Enterotoxin Type I using qPCR

Epidemiological surveillance reports revealed that Staphylococcus aureus ranked third among top bacterial pathogens causing food poisoning in Thailand during 2010-2012. Thailand Food and Drug Administration (FDA) abides by the international “zero tolerance” policy for staphylococcal enterotoxins (SEs). Specifically, SEs must be absent in 25 g of food, while the bacteria are tolerated at low level depending on the types of food. Increasing numbers of S. aureus isolates from foods carried the newly described staphylococcal enterotoxin type I (SEI) and type G (SEG) rather than the classic types (e.g., SEA and SEB) previously identified as the common cause of staphylococcal food poisoning. In this study, we developed a quantitative PCR (qPCR) for detection of SEI-encoding gene as SEI is the most prevalent enterotoxin in newly described SE subgroup 3 and is increasingly found in S. aureus isolates from food samples causing food poisoning. The designed sei primer and probe set is specific to S. aureus sei gene and can detect as low as 150 femtogram of the target (approximately 50 bacterial cells/ml of milk). We proposed that our sei primer and probe set can be used in multiplex qPCR assay along with the already developed primer and probe sets targeting classic sea and seb genes for enterotoxin detection in food safety surveillance.
Evolutionary Optimization of Computationally Expensive Problems via Surrogate Modeling

We present a parallel evolutionary optimization algorithm that leverages surrogate models for solving computationally expensive design problems with general constraints, on a limited computational budget. The essential backbone of our framework is an evolutionary algorithm coupled with a feasible sequential quadratic programming solver in the spirit of Lamarckian learning. We employ a trust-region approach for interleaving use of exact modelsfortheobjectiveandconstraintfunctionswithcomputationallycheapsurrogatemodelsduringlocalsearch. In contrastto earlier work, we construct local surrogatemodels using radial basis functionsmotivated by theprinciple of transductive inference. Further, the present approach retains the intrinsic parallelism of evolutionary algorithms and can hence be readily implemented on grid computing infrastructures. Experimental results are presented for some benchmark test functions and an aerodynamic wing design problem to demonstrate that our algorithm converges to good designs on a limited computational budget.
Insights into the nature of uranium target proteins within zebrafish gills after chronic and acute waterborne exposures

New data on the nature of the protein targets of uranium (U) within zebrafish gills were collected after waterborne exposure, with the aim of a better understanding of U toxicity mechanisms. Some common characteristics of the U protein target binding properties were found, such as their role in the regulation of other essential metals and their phosphorus content. In total, 21 potential protein targets, including hemoglobin, are identified and discussed in terms of the literature. Environ Toxicol Chem 2016;35:736–741. © 2015 SETAC
Inhibition of Natural Killer Cell Activity by Antigen‐Antibody Complexes

The natural killer (NK) cell activity of human peripheral blood mononuclear cells was found to be inhibited by precipitated tetanus toxoid anti‐tetanus toxoid complexes (Te/ aTe) as well as soluble Te/aTe, Preincubation of the immune complexes with protein A decreased the inhibition of NK cell activity. When mononuclear cells were preincubated with interferon (IF) or interleukin 2 (II‐2) before incubation with Te/aTe, the immune complex‐induced inhibition was decreased, while IF or II‐2 added after incubation with the immune complexes had no effect. Using NK cell‐enriched suspensions in a single cell agarose assay, the immune complexes were shown to inhibit NK cell activity by inhibiting the formation of effector/target cell conjugates.
Atmospheric Response in Aurora experiment: Observations of E and F region neutral winds in a region of postmidnight diffuse aurora

The goal of the Atmospheric Response in Aurora (ARIA) experiment carried out at Poker Flat, Alaska, on March 3, 1992, was to determine the response of the neutral atmosphere to the long-lived, large-scale forcing that is characteristic of the diffuse aurora in the postmidnight sector. A combination of chemical release rocket wind measurements, intrumented rocket composition measurements, and ground-based optical measurements were used to characterize the response of the neutral atmosphere. The rocket measurements were made at the end of a 90-min period of strong Joule heating. We focus on the neutral wind measurements made with the rocket. The forcing was determined by running the assimilated mapping of ionospheric electrodynamics (AMIE) analysis procedure developed at the National Center for Atmospheric Research. The winds expected at the latitude and longitude of the experiment were calculated using the spectral thermospheric general circulation model developed at the Danish Meteorological Institute. Comparisons of the observations and the model suggest that the neutral winds responded strongly in two height ranges. An eastward wind perturbation of {approximately}100 m s{sup -1} developed between 140 and 200 km altitude with a peak near 160 km. A southwestward wind with peak magnitude of {approximately}150 m s{sup -1} developed nearmore » 115 km altitude. The large amplitude winds at the lower altitude are particularly surprising. They appear to be associated with the upward propagating semidiurnal tide. However, the amplitude is much larger than predicted by any of the tidal models, and the shear found just below the peak in the winds was nomially unstable with a Richardson number of {approximately}0.08. 17 refs., 12 figs.« less
The impact of immigration on the development of adolescent schizophrenia.

PROBLEM Impact of immigration on the development of adolescent schizophrenia. METHODS The review of literature used Academic Search Premier, CINHAL, PsychINFO, PubMed, and MEDLINE databases to examine reasons given to immigration as a risk factor to adolescent schizophrenia. FINDINGS There is not a single factor or a group of related factors that could explain why the incidence of schizophrenia among immigrants is higher compared with natives of the host county. CONCLUSION Further inquiry into this phenomenon is needed to understand factors that increase the risk of schizophrenia among immigrant children and to help plan and implement strategies for prevention.
Student Recruitment Classification using Data Mining Techniques

Data Mining can be used in educational field to enhance our understanding of learning process to focus on identifying, extracting and evaluating variables related to the learning process. This presented work focus on implementing different data mining approaches on student database. This paper works in three phases. First phase, provide profili ng of students according to their grades via clustering t hen, a number of different segments are formed on the basis of type of grades provided to the student by the institution. The students according to their grades are grouped into different clusters according to the company rating. Second phase considers validating the student data using J-48 algorithms. In third ph ase, a comparison is made between different algorithms ( J48, LMT and BayesNet algorithms) to improve prediction accuracy of student recruitment datasets .
In vivo epidermal thickness measurement: ultrasound vs. confocal imaging

Background/purpose: In this study, in vivo skin imaging methods, ultrasound (US) and confocal microscopy (CM) were compared with regards to their accuracy in measuring the epidermal thickness. In addition an attempt was made to clarify the biological significance of the second echo‐rich line observed on US skin images, i.e. whether it represents the dermal–epidermal junction or the papillar–reticular dermis limit.
Strained Silicon Directly on Insulator N- and P-FET nanowire transistors

High-performance strained Silicon-On-Insulator (sSOI) nanowire (NW) transistors with gate length and NW width down to 15 nm are reported. We demonstrate sSOI π-Gate n-FET NWs with I<sub>ON</sub> current of 1410 μA/μm (when I<sub>OFF</sub> = 70 nA/μm) at V<sub>DD</sub>=0.9V and a good electrostatic immunity (DIBL = 140 mV/V, SS<sub>SAT</sub> = 76 mV/dec). Effectiveness of sSOI substrates for n-FETs is shown with an I<sub>ON</sub> improvement up to +40% at short gate lengths. More generally, size- and orientation-dependent strain impact on electron and hole transport in long and short channel π-Gate (s)SOI NW transistors is systematically studied.
Wet chemical etching silicon wafer with low-reflection and super-hydrophobicity

Successful etching silicon wafer for solar cells has been already prepared. In this work, wet chemical etching process at room temperature was introduced to fabricate large-area growth of Si nanowire (SiNW) arrays. The process was carried out on p-type (100) silicon wafer in aqueous HF+AgNO3 etching solution at room temperature. The wafer surface consisting of SiNW arrays shows the characteristics of low-reflection as low as less than 5% in the 450–790 nm wavelength range. The surface also exhibits super hydrophobicity with a high water contact angle up to 150°. Si wafers with large-area SiNW arrays on the surfaces displaying properties of low-reflection and super-hydrophobicity will have potential applications for fabricating high-efficiency and self-cleaning silicon solar cells.
Sexually transmitted infections: impact on male fertility

The impact of sexually transmitted diseases (STD) on male fertility is strongly dependent on the local prevalence of the STDs. In Western countries STD‐infections are of minor relevance. In other regions, i.e. Africa or South East Asia, the situation appears to be different. Acute urethritis could not be associated with male infertility. Chronic infections (gonorrhoea) can cause urethral strictures and epididymo‐orchitis. Chlamydia trachomatis and Neisseria gonorrhoea can be transmitted to the female partner and cause pelvic inflammatory disease with tubal obstruction. Ureaplasma urealyticum may impair spermatozoa (motility, DNA condensation). Trichomonas vaginalis has, if any, only minor influence on male fertility. The relevance of viral infections (HPV, HSV) for male infertility is not resolved. Any STD increases the chances of transmission of the human immunodeficiency virus (HIV). The HIV infection is associated with infectious semen and the risk of virus transmission. Semen quality deteriorates with the progression of immunodeficiency. Special counselling of serodiscordant couples is needed. STDs should be treated early and adequately to prevent late sequelae for both men and women.
Buying or Making, What's it to Be? The Choice between Acquiring or Generating Genetically Modified Animals or Embryos in the Light of the three Rs

This paper discusses whether acquiring genetically modified animals or embryos from an existing strain, as opposed to generating a new founder, is to be preferred, with respect to animal use and animal distress. To address this question, the results of an inventory performed in 17 Dutch research institutes are presented. It is argued that the acquisition of embryos is to be preferred to the acquisition or generation of animals. Furthermore, it is argued that patenting may lead to the generation of already existing strains.
Nanocrystalline cellulose prepared from softwood kraft pulp via ultrasonic-assisted acid hydrolysis

Scanning electron microscopy, transmission electron microscopy, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy were used for determination of morphology, crystal structure, and surface chemical groups. Thermal behavior was analyzed by thermogravimetric analysis. can induce cellulose folding, surface erosion, and , together with the shorter average length of NCC (96 nm) than that prepared without ultrasonication (150 nm). Due to the smaller size and larger number of free ends of chains, the thermal stability of NCC was lower than BSKP. The degradation of BSKP exhibited one significant pyrolysis stage within the range of 300 to 420 °C. In contrast, UH-NCC exhibited three pyrolysis stages within the range of 210 to 450 °C. NCC prepared with ultrasonication decomposed at lower temperature and over a wider temperature range, together with higher char yield of 43% (compared with 27% for that without ultrasonication). The obtained NCC had similar (74%).
A regression shrinkage method tailored to qualitative regressors and clustered data

We propose a shrinkage method for estimation in linear regression models with qualitative regressors. Due to the nature of the shrinkage constraint, this method tends to give estimates that are exactly zero for some groups of coefficients belonging to the same regressor. The method hence results in concise models, since some of the regressors are entirely eliminated. In conjunction with this estimation method, a model with a fixed cluster effect turns out to be closely related to frailty models. We apply the method for modelling hospital readmissions. Copyright © 2004 John Wiley & Sons, Ltd.
The problem of visual excitation.

This paper attempts to come to grips with the problem, how the action of light on a visual pigment results in a nervous excitation. The only action of light in vision is to isomerize retinene, the chromophore of the visual pigments, from the 11-cis to the all-trans configuration. This change triggers a progressive opening-up of the protein structure, exposing new reactive groups. Since the absorption of one photon by one molecule of visual pigment may stimulate a dark-adapted rod, some large amplification process is needed between the act of absorption and the response. This may be an enzymatic catalysis, or the consequence of puncturing a critical membrane. A microspectrophotometric study of retinas and single rods shows the outer segment to have a quasi-crystalline structure, in which the visual pigments are almost perfectly oriented, and even “free” molecules capable of diffusion maintain a degree of orientation. Examination of mud puppy retinas in the electron microscope has revealed several new aspects of structure: (1) A system of cytoplasmic filaments (“dendrites”) springing from the inner segments of the rods and cones and standing like palisades around the outer segments. These may facilitate exchanges of material between the inner and outer segments. (2) Systems of particles in the membranes of the dendrites and pigment epithelium processes, which may be involved in interchanges of material with the outer segments. (3) A system of particles in crystalline array in the rod lamellae, which may contain the visual pigment. If so, measurements of the visual pigment in situ show that each particle should contain about 50 molecules of pigment. Such typically solid-state processes as exciton migration and photoconduction probably have at most very limited scope in the outer segments of rods and cones. The seat of excitation is probably the plasma membrane which envelops rod outer segments and composes also the lamellae in cones.
Structural and thermal investigation for FBAR reliability in wireless applications

This paper describes work carried out to assess the failure mechanisms of film bulk acoustic resonators (FBARs) developed for wireless applications. Two experimental benches were setup: one X-ray based (including diffraction, radiography and fluorescence analysis) and, for the first time, a high resolution infrared, in-situ thermal mapping apparatus. Finite element modeling was used to draw out the self heating of those components under high RF signal levels. In the paper, we describe each of those setups and highlight the improvements provided by their use when evaluating FBAR failure analysis mechanisms.
INCREASED RATES OF MOLECULAR EVOLUTION IN AN EQUATORIAL PLANT CLADE: AN EFFECT OF ENVIRONMENT OR PHYLOGENETIC NONINDEPENDENCE?

Abstract A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNA sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the phylogenetic nonindependence of the species examined, given that all six equatorial species of Mearnsia form a clade. To distinguish between the effect of latitude and that of phylogenetic nonindependence, we have employed a variety of comparative approaches that use independent contrasts to test for an effect of environment across this entire subgenus. We find very little evidence for an effect of latitude on rate of molecular evolution using these approaches and believe that the shared evolutionary history of the clade is a plausible explanation of the apparent rate difference between equatorial and subequatorial Mearnsia species.
Cbl-3-Deficient Mice Exhibit Normal Epithelial Development

ABSTRACT Cbl family proteins are evolutionarily conserved ubiquitin ligases that negatively regulate signaling from tyrosine kinase-coupled receptors. The mammalian cbl family consists of c-Cbl, Cbl-b, and the recently cloned Cbl-3 (also known as Cbl-c). In this study, we describe the detailed expression pattern of murine Cbl-3 and report the generation and characterization of Cbl-3-deficient mice. Cbl-3 exhibits an expression pattern distinct from those of c-Cbl and Cbl-b, with high levels of Cbl-3 expression in epithelial cells of the gastrointestinal tract and epidermis, as well as the respiratory, urinary, and reproductive systems. Cbl-3 expression was not detected in nonepithelial cells, but within epithelial tissues, the levels of Cbl-3 expression varied from undetectable in the alveoli of the lungs to very strong in the cecum and colon. Despite this restricted expression pattern, Cbl-3-deficient mice were viable, healthy, and fertile and displayed no histological abnormalities up to 18 months of age. Proliferation of epithelial cells in the epidermises and gastrointestinal tracts was unaffected by the loss of Cbl-3. Moreover, Cbl-3 was not required for attenuation of epidermal growth factor-stimulated Erk activation in primary keratinocytes. Thus, Cbl-3 is dispensable for normal epithelial development and function.
Genotypic and phenotypic characterization of Borrelia burgdorferi isolated from ticks and small animals in Illinois

We have characterized 33 isolates of Borrelia burgdorferi from northern Illinois (32 isolates) and Wisconsin (1 isolate) representing the largest series of midwestern isolates investigated to date. The techniques used for molecular analysis of strains included (i) genospecies typing with species-specific PCR primers, (ii) plasmid profiling by pulsed-field gel electrophoresis of total genomic DNA, (iii) large-restriction-fragment pattern (LRFP) analysis by pulsed-field gel electrophoresis of MluI-digested genomic DNA (J. Belfaiza, D. Postic, E. Bellenger, G. Baranton, and I. Saint Girons, J. Clin. Microbiol. 31:2873-2877, 1993), (iv) sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total proteins, (v) microsequencing of high-performance liquid chromatography-purified peptides derived from proteins showing high levels of expression, (vi) amino acid composition analysis of proteins, and (vii) immunological analysis of proteins with a polyclonal antiserum of human origin. Five reference strains as well as two atypical tick isolates from California (DN127) and New York (25015) were included for comparison. All of the Illinois and Wisconsin isolates were typed as B. burgdorferi sensu stricto with genospecies-specific PCR primers. The isolates were found to be heterogeneous with regard to their plasmid and protein profiles. One isolate from Illinois possessed two large-molecular-size plasmids instead of the usual 49-kb plasmid. Fragment patterns resulting from MluI digestion of genomic DNA from the 33 isolates and strains DN127 and 25015 were separable into six distinct LRFPs, five of which have not previously been described. Strain 25015 and an isolate from Illinois (CT39) shared an unusual LRFP that is not typical of other B. burgdorferi sensu stricto strains, suggesting that they may represent a fifth species of B. burgdorferi sensu lato. Five of the 33 isolates and strains DN127 and 25015 showed high-level expression of proteins with molecular masses of approximately 22 kDa. Investigation of these proteins by microsequencing of individual peptides and total amino acid composition analysis indicated that the 22-kDa proteins expressed by the seven strains were polymorphic OspC proteins. By using a polyclonal serum of human origin, expression of OspC could be detected in all 33 Illinois and Wisconsin isolates.