Miracle-dz/UniFAR-FTUs huggingface dataset:
The Choline-Converting Pathway inStaphylococcus xylosus C2A: Genetic and Physiological Characterization

ABSTRACT A Staphylococcus xylosus C2A gene cluster, which encodes enzymes in the pathway for choline uptake and dehydrogenation (cud), to form the osmoprotectant glycine betaine, was identified. The cud locus comprises four genes, three of which encode proteins with significant similarities to those known to be involved in choline transport and conversion in other organisms. The physiological role of the gene products was confirmed by analysis ofcud deletion mutants. The fourth gene possibly codes for a regulator protein. Part of the gene cluster was shown to be transcriptionally regulated by choline and elevated NaCl concentrations as inducers.
A 1.8GHz Digital PLL in 65nm CMOS

A 1.8GHz high-accuracy, ring-oscillator based Digital Phase Lock Loop (DPLL), suitable for Serializer-Deserializer (SERDES) applications like HDMI, eSATA and USB2.0 is presented here. Sigma-Delta (? ) dithering followed by passive filtering, along with Temperature Compensation is used to ensure frequency accuracy and low accumulated jitter, over a large temperature range. A re-circulating delay line based Time to Digital Converter (T2D) is used to handle large phase differences between the reference and feedback clocks. The DPLL is built in 65nm technology, and provides up to 1.8GHz output, with a phase noise of –87dBc/Hz at 1 MHz offset, and a frequency accuracy of +/-100ppm. It supports input frequencies in the range 0.7MHz to 50MHz, occupies a core area of 0.11 sq mm, and does not require external components.
Bovine immunoglobulin M as a major factor contributing to serum-induced head-to-head agglutination in bovine spermatozoa.

One ejaculate from each of 5 bulls was used to characterize the factor from heifer serum which causes head-to-head agglutination in bovine spermatozoa. Serum from 10 virgin heifers was pooled, heat-treated and fractionated by Sepharose 6B chromatography. The fractions causing head-tohead agglutination and those which did not cause head-to-head agglutination were identified, pooled and lyophiized. The agglutinating fraction, nonagglutinating fraction or whole serum were added to 30 X 106 spermatozoa. Agglutinating fractions caused higher (P 90%. This protein precipitated with monospecific goat anti-bovine 1gM and gave only single precipitin bands with goat anti-bovine serum via agarose immunoelectrophoresis and Ouchterlony double immunodiffusion. Semen from a bull producing semen of average quality from Experiment 1 was used to determine the degree of head-to-head agglutination caused by purified bovine 1gM, porcine 1gM, whole serum, agglutinating fraction, nonagglutinating fraction, bovine IgGi and lgG2. Total protein per 30 X 106 sperm required to induce half-maximal head-to-head agglutination was 0.49 mg, 1.14 mg and 2.8 mg for purified bovine 1gM, agglutinating fraction and whole serum, respectively. The total 1gM per 30 X 106 sperm required to induce half-maximal head-to-head agglutination was 0.45 mg, 0.21 mg and 0.11 mg for purified bovine 1gM, agglutinating fraction and whole serum, respectively. Porcine 1gM was as effective as bovine 1gM in causing head-to-head agglutination, but neither IgG1 nor lgG2 caused head-to-head agglutination. There were no differences in acrosomal maintenance among treatments and levels of protein added. These data suggest that 1gM is a major factor in serum responsible for causing head-to-head agglutination in bovine spermatozoa.
New methods for the construction of Voronoi Diagram and the nearest neighbor query

The existing methods for the construction of Voronoi Diagram and the nearest neighbor query have several disadvantages. In view of the disadvantages, the new methods were studied in detail. To construct the Voronoi diagram effectively, the datasets were grouped in advance, and then the divide-and-conquer method combined with the increment method was used to generate Delaunay triangulation. By generating the Voronoi diagram from Delaunay triangulation, the Creat_Vor algorithm was proposed. In order to effectively query and update the nearest neighbors of the given points, the methods based on the spatial grids and the Voronoi diagram were studied. The VGride_NN algorithm and VGride_BNN algorithm were put forward. Theory and experiments show that the new methods have advantages in dealing with the dynamic dataset.
Relation between macular retinal ganglion cell/inner plexiform layer thickness and multifocal electroretinogram measures in experimental glaucoma.

PURPOSE We investigated relations between macular retinal ganglion cell plus inner plexiform layer (RGC+IPL) thickness and macular retinal function revealed by multifocal electroretinonography (mfERG) in a nonhuman primate model of experimental glaucoma. METHODS Retinal ganglion cell (RGC) structure and function were followed with spectral-domain optical coherence tomography (SD-OCT) and ERGs in five macaques with unilateral experimental glaucoma. Linear regression was used to study correlations in control (Con) and experimental (Exp) eyes between peripapillary retinal nerve fiber layer (RNFL) thickness, macular RGC+IPL thickness, multifocal photopic negative response (mfPhNR) and high-frequency multifocal oscillatory potentials (mfOP) in slow-sequence mfERG, and low-frequency component (mfLFC) in global-flash mfERG. We used ANOVA and paired t-tests to compare glaucoma-related mfERG changes between superior and inferior hemifields, foveal hexagon, inner three rings, and four quadrants of macula. RESULTS Average macular RGC+IPL and temporal RNFL thickness were strongly correlated (r(2) = 0.90, P < 0.001). In hexagon-by-hexagon analysis, all three mfERG measures were correlated (P < 0.001) with RGC+IPL thickness for Con (r(2), 0.33-0.51) and Exp eyes (r(2), 0.17-0.35). The RGC structural and functional metrics decreased as eccentricity increased. The reduction in amplitude of mfERG measures in Exp eyes relative to Con eyes was proportionally greater, in general, than the relative thinning of RGC+IPL at the same location for eyes in which structural loss was not evident, or mild to moderate. Although not statistically significant, percent amplitude reduction of mfERG measures was greatest in the inferior temporal quadrant. CONCLUSIONS Macular RGC+IPL thickness and mfERG measures of RGC function can be complementary tools in assessing glaucomatous neuropathy.
The Effect of Digester Retention Time on Microbial Extracellular Polymer Production and its Associated Impact on Sludge Dewaterability

SUMMARY Anaerobic digestion of wastewater sludge has found widespread use as a method of sludge stabilization, but the waste sludge produced can be difficult to dewater. One factor that can influence the sludge dewaterability is microbial extracellular polymer (ECP). To assess the effect of digester retention time on ECP production and its associated impact on sludge dewaterability, 6 laboratory scale anaerobic digesters were constructed and operated, as matched pairs, over a range of retention times: 10, 15 and 30 days. After operating for 4 full retention periods, the digesters were dismantled and the ECP extracted from the sludge. The yield of ECP was related to the sludge dewaterability, as measured using the Capillary Suction Time (CST) test. A strong, positive correlation (0.999) was found between the ECP yield and sludge dewaterability, but no relationship was found between ECP yield and digester retention time. The extracted ECP was further analyzed for protein and carbohydrate content and the ECP ionic composition established. The retention time had no effect on the ECP organic and inorganic composition, but the ECP composition did have an impact on the sludge dewaterability.
A guideline for leaf senescence analyses: from quantification to physiological and molecular investigations

Leaf senescence is not a chaotic breakdown but a dynamic process following a precise timetable. It enables plants to economize with their resources and control their own viability and integrity. The onset as well as the progression of leaf senescence are co-ordinated by a complex genetic network that continuously integrates developmental and environmental signals such as biotic and abiotic stresses. Therefore, studying senescence requires an integrative and multi-scale analysis of the dynamic changes occurring in plant physiology and metabolism. In addition to providing an automated and standardized method to quantify leaf senescence at the macroscopic scale, we also propose an analytic framework to investigate senescence at physiological, biochemical, and molecular levels throughout the plant life cycle. We have developed protocols and suggested methods for studying different key processes involved in senescence, including photosynthetic capacities, membrane degradation, redox status, and genetic regulation. All methods presented in this review were conducted on Arabidopsis thaliana Columbia-0 and results are compared with senescence-related mutants. This guideline includes experimental design, protocols, recommendations, and the automated tools for leaf senescence analyses that could also be applied to other species.
Fast incremental method for smooth nonconvex optimization

We analyze a fast incremental aggregated gradient method for optimizing nonconvex problems of the form minΣifi(x). Specifically, we analyze the SAGA algorithm within an Incremental First-order Oracle framework, and show that it converges to a stationary point provably faster than both gradient descent and stochastic gradient descent. We also discuss a Polyak's special class of nonconvex problems for which SAGA converges at a linear rate to the global optimum. Finally, we analyze the practically valuable regularized and minibatch variants of SAGA. To our knowledge, this paper presents the first analysis of fast convergence for an incremental aggregated gradient method for nonconvex problems.
Nitric-Oxide Mediated Effects of Transdermal Capsaicin Patches on the Ischemic Threshold in Patients with Stable Coronary Disease

Background Capsaicin has been shown to exert direct vasodilating effects through increased calcitonin gene-related peptide (CGRP) release. However, no data exist on its effect following systemic administration in humans. Methods Twelve male patients with stable coronary disease and a persistently positive exercise were selected for study. According to a double blind, placebo-controlled, cross-over study, patients were randomized to placebo or 3 g oleic capsaicin-containing patches, on 2 different days and with a 2-day interval between treatments. Patients performed treadmill exercise testing according to the Bruce protocol. Time to 1 mm ST segment depression and to peak exercise, maximal ST segment depression, and the number of ECG leads showing diagnostic changes were also measured. Blood samples for nitric oxide (NO) and CGRP were drawn at baseline, 2, 6, and 24 hours after exercise. Results On placebo, all patients had a positive ECG during exercise test. Only 1 patient experienced angina, on both treatments. With capsaicin, 1 patient had a negative exercise, while 8 patients significantly increased time to 1 mm ST depression from 328 ± 167 to 401 ± 174 seconds (P = 0.01). Of the remaining patients, 1 did not show any changes and 2 showed a worse ischemic threshold when on capsaicin. CGRP levels were not significantly different between placebo and capsaicin treatment. Conversely, when on capsaicin, NO significantly increased at 6 hours. Conclusions Transdermal capsaicin may improve ischemic threshold in patients with stable coronary disease, probably through arteriolar vasodilation. Increased capsaicin-induced NO availability could represent the principal mechanism of action.
Antibody biodistribution coefficients

Tissue vs. plasma concentration profiles have been generated from a physiologically-based pharmacokinetic model of monoclonal antibody (mAb). Based on the profiles, we hypothesized that a linear relationship between the plasma and tissue concentrations of non-binding mAbs could exist; and that the relationship may be generally constant irrespective of the absolute mAb concentration, time, and animal species being analyzed. The hypothesis was verified for various tissues in mice, rat, monkey, and human using mAb or antibody-drug conjugate tissue distribution data collected from diverse literature. The relationship between the plasma and various tissue concentrations was mathematically characterized using the antibody biodistribution coefficient (ABC). Estimated ABC values suggest that typically the concentration of mAb in lung is 14.9%, heart 10.2%, kidney 13.7%, muscle 3.97%, skin 15.7%, small intestine 5.22%, large intestine 5.03%, spleen 12.8%, liver 12.1%, bone 7.27%, stomach 4.98%, lymph node 8.46%, adipose 4.78%, brain 0.351%, pancreas 6.4%, testes 5.88%, thyroid 67.5% and thymus is 6.62% of the plasma concentration. The validity of using the ABC to predict mAb concentrations in different tissues of mouse, rat, monkey, and human species was evaluated by generating validation data sets, which demonstrated that predicted concentrations were within 2-fold of the observed concentrations. The use of ABC to infer tissue concentrations of mAbs and related molecules provides a valuable tool for investigating preclinical or clinical disposition of these molecules. It can also help eliminate or optimize biodistribution studies, and interpret efficacy or toxicity of the drug in a particular tissue.
User rankings of search engine results

In this study, we investigate the similarities and differences between rankings of search results by users and search engines. Sixty-seven students took part in a 3-week-long experiment, during which they were asked to identify and rank the top 10 documents from the set of URLs that were retrieved by three major search engines (Google, MSN Search, and Yahoo! ) for 12 selected queries. The URLs and accompanying snippets were displayed in random order, without disclosing which search engine(s) retrieved any specific URL for the query. We computed the similarity of the rankings of the users and search engines using four nonparametric correlation measures in [0,1] that complement each other. The findings show that the similarities between the users' choices and the rankings of the search engines are low. We examined the effects of the presentation order of the results, and of the thinking styles of the participants. Presentation order influences the rankings, but overall the results indicate that there is no "average user," and even if the users have the same basic knowledge of a topic, they evaluate information in their own context, which is influenced by cognitive, affective, and physical factors. This is the first large-scale experiment in which users were asked to rank the results of identical queries. The analysis of the experimental results demonstrates the potential for personalized search.
Sur quelques modèles hétérogènes en mécanique des fluides

Cette these est consacree a l'analyse mathematique de quelques modeles heterogenes intervenants en mecanique des fluides. En particulier, elle est consacre a l'etude theorique des systemes d'equations aux derivees partielles decrivants les trois modeles principaux que nous voulons presenter dans la suite. Le premier modele etudie dans cette these est consacre a l'etude de l'ecoulement d'un fluide visqueux newtonien et incompressible dans un bassin avec bathymetrie qui degenere proche du bord. Le modele mathematique etudie provient alors des equations de Navier-Stokes incompressible. On cherche a montrer que le probleme de Cauchy correspondant est bien pose, au sens qu'on peut garantir l'existence globale et l'unicite de solutions faibles. Nous discuterons aussi la regularite de la solution faible. Finalement,nous etablissons la convergence de la solution du modele visqueux vers celle du modele non visqueux quand le coefficient de viscosite tend vers zero.La deuxieme partie est dediee a l'etude d'un modele issu du systeme de Navier-Stokes dispersif ( il contient une correction dispersive) qui est lui meme obtenu a partir de la theorie cinetique des gaz. Notre modele mathematique est derive a partir de ce dernier en supposant que le nombre de Mach est tres faible. Le modele obtenu est nomme effet fantome (ou ghost effect an anglais), puisqu'il ne peut pas etre obtenu a partir du modele de Navier-Stokes compressible classique. L'objectif dans ce cadre sera d'etendre un resultat concernant l'existence locale d'une solution forte vers l'existence globale d'une solution faible. L'ingredient principal dans notre analyse est une nouvelle inegalite fonctionnelle de type Log-Sobolev.La troisieme partie de ce document est une contribution a une thematique de recherche se proposant d'analyser la comprehension des phenomenes rencontres en geophysique qui font intervenir des milieux granulaires. Le modele mathematique choisi est de type Bingham incompressible dont on fait dependre le seuil de plasticite et le coe fficient de viscosite de la pression. On montre un resultat d'existence globale d'une solution faible du probleme de Cauchy associe.
Inhibition of cell wall turnover and autolysis by vancomycin in a highly vancomycin-resistant mutant of Staphylococcus aureus

A highly vancomycin-resistant mutant (MIC = 100 microg/ml) of Staphylococcus aureus, mutant VM, which was isolated in the laboratory by a step-pressure procedure, continued to grow and synthesize peptidoglycan in the presence of vancomycin (50 microg/ml) in the medium, but the antibiotic completely inhibited cell wall turnover and autolysis, resulting in the accumulation of cell wall material at the cell surface and inhibition of daughter cell separation. Cultures of mutant VM removed vancomycin from the growth medium through binding the antibiotic to the cell walls, from which the antibiotic could be quantitatively recovered in biologically active form. Vancomycin blocked the in vitro hydrolysis of cell walls by autolytic enzyme extracts, lysostaphin and mutanolysin. Analysis of UDP-linked peptidoglycan precursors showed no evidence for the presence of D-lactate-terminating muropeptides. While there was no significant difference in the composition of muropeptide units of mutant and parental cell walls, the peptidoglycan of VM had a significantly lower degree of cross-linkage. These observations and the results of vancomycin-binding studies suggest alterations in the structural organization of the mutant cell walls such that access of the vancomycin molecules to the sites of wall biosynthesis is blocked.
A finite-element study of the effects of electrode position on the measured impedance change in impedance cardiography

Traditional impedance cardiography (ICG) technique uses band electrodes both for delivering current to and measuring impedance change in the thorax. The use of spot electrodes increases the ease of electrode placement and comfort level for patients. Research has shown that changes in thoracic impedance can have multiple causes. In this study, we used finite element modeling to investigate the sources of impedance change for both band-electrode and spot-electrode ICG, and focused on how differences in electrode location affect the contribution of different sources to changes in impedance. The ultimate purpose is to identify the optimal electrode type and placement for the sensing of stroke volume (SV). Our models were built on sets of end-diastolic and end-systolic magnetic resonance images of a healthy human subject. The results showed that the effect of ventricular contraction is opposite to that of the other changes in systole: the expansion of major vessels, decrease in blood resistivity due to increased blood flow velocity, and decrease in lung resistivity due to increased blood perfusion. Ventricular contraction, the only factor that tends to increase systolic impedance, has a larger effect than any of the other factors. When spot electrodes are placed on the anterior chest wall near the heart, ventricular contraction is so dominant that the measured impedance increases from end-diastole to end-systole, and the change represents 82% of the contribution from ventricular contraction. When using the common band-electrode configuration, the change in measured impedance is a more balanced combination of the four effects, and ventricular contraction is overcome by the other three factors so that the impedance decreases. These results suggest that the belief that ICG can be used to directly measure SV based on the change in the whole thoracic impedance may be invalid, and that spot electrodes may be more useful for understanding local physiological events such as ventricular volume change. These findings are supported by previously reported experimental observations.
Detection of CoHV‐1 by loop‐mediated amplification (LAMP). Application of LAMP for CoHV‐1 incidence monitoring in domestic pigeons

The occurrence of Columbid herpesvirus‐1 (CoHV‐1) in domestic pigeons presents a potential threat for their husbandry and trade. CoHV‐1 causes Smadel disease among pigeons but may not be manifested by any clinical signs and complicates secondary infections. The material for our study originated from 42 domestic pigeons sent to private veterinary practice in Lublin, Poland, between 2011 and 2013. Some of birds showed clinical signs similar to Smadel disease. The cytological examination also indicated on CoHV‐1 infection. The incidence of CoHV‐1 was tested in DNA extracted from liver of birds by loop‐mediated isothermal amplification (LAMP). LAMP was used for the monitoring of CoHV‐1 presence among pigeons in Poland. Our study showed that LAMP was capable of detecting CoHV‐1 presence in 8 (19%) of 42 examined birds without the use of any advanced laboratory equipment. The results were confirmed by real‐time PCR and virus isolation in chicken embryo fibroblasts. This is the first report on LAMP application for successful detection of CoHV‐1 in domestic pigeons.
Lupus Mastitis in the Male Breast Mimicking Inflammatory Carcinoma

A 42-year-old man presented with a moderate and diffuse enlargement of the left breast. The skin presented as a red and scaly patch, centered in the nipple (Fig. 1). Laboratory parameters, including IgG and IgM, antiBorrelia burgdorferi antibodies, and luetic determinations by rapid plasma reagent (RPR), were normal. Histopathologic study demonstrated the typical characteristics of lupus profundus: a mixed lobular and septal lymphocytic panniculitis (Fig. 2), some lymphoid follicles in the infiltrate, lymphocytic vasculitis (Fig. 3), and vacuolar alteration all along the dermoepidermal junction with a smudged appearance, and a thickened basement membrane (Fig. 4). Immunohistochemical study showed a mixed population of B (CD20+) and T (CD3+, CD4+, CD8–) lymphocytes, as well as hystiocytes (CD68+). Molecular studies by polymerase chain reaction (PCR) demonstrated polyclonal rearrangement of IgH (CDR2, CDR3), as well as of TCR-gamma. Serum IgG antinuclear antibodies, lupic anticlotting factor, double-strained DNA antibodies, and extractable nuclear antigen antibodies were all negative.
Timing synchronization using 1PPS for crosswell electromagnetic logging tools

After analyzing the shortcomings of existing synchronization methods based on GPS and the research status of synchronization for Crosswell Electromagnetic Imaging Logging Tool(CEMIT), a feasible synchronization method combined the actual conditions of CEMIT with the basis of existing research is proposed. First of all, GPS receiver provides a high accurate 1PPS, which received by Surface System, and then it will be broadened and driven to achieve transmission through the 7000m cable. After transmission delay between Surface System and Downhole System has been measured, the synchronization clock in Downhole System will be calibrated according to the delay information. Lastly, the synchronization between receiver and transmitter is achieved. Experiment results show that synchronization clock error is less than 1us between receiver clock and transmitter clock, which corresponds to a phase accuracy of 0.36 degree at 1 KHz. The method can meet the needs of phase difference measurement in CEMIT.