Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Gene Content Evolution in Phytoplasmas and Mycoplasmas

Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in genome sequencing, comparative genome analysis provides a new approach to facilitate our understanding of these bacteria. In this study, our main focus is to investigate the evolution of gene content in phytoplasmas, mycoplasmas, and their common ancestor. By using a phylogenetic framework for comparative analysis of 12 complete genome sequences, we characterized the putative gains and losses of genes in these obligate parasites. Our results demonstrated that the degradation of metabolic capacities in these bacteria has occurred predominantly in the common ancestor of Mollicutes, prior to the evolutionary split of phytoplasmas and mycoplasmas. Furthermore, we identified a list of genes that are acquired by the common ancestor of phytoplasmas and are conserved across all strains with complete genome sequences available. These genes include several putative effectors for the interactions with hosts and may be good candidates for future functional characterization.
Inflation, holography, and the choice of vacuum in de Sitter space

A family of de Sitter vacua introduced in hep-th/0203198 as plausible initial conditions for inflation, are discussed from the point of view of de Sitter holography. The vacua are argued to be physically acceptable and the inflationary picture provides a physical interpretation of a subfamily of de Sitter invariant vacua. Some speculations on the issue of vacuum choice and the connection between the CMBR and holography are also provided.
Simplifying schema mappings

A schema mapping is a formal specification of the relationship holding between the databases conforming to two given schemas, called source and target, respectively. While in the general case a schema mapping is specified in terms of assertions relating two queries in some given language, various simplified forms of mappings, in particular LAV and GAV, have been considered, based on desirable properties that these forms enjoy. Recent works propose methods for transforming schema mappings to logically equivalent ones of a simplified form. In many cases, this transformation is impossible, and one might be interested in finding simplifications based on a weaker notion, namely logical implication, rather than equivalence. More precisely, given a schema mapping M, find a simplified (LAV, or GAV) schema mapping M' such that M' logically implies M. In this paper we formally introduce this problem, and study it in a variety of cases, providing techniques and complexity bounds. The various cases we consider depend on three parameters: the simplified form to achieve (LAV, or GAV), the type of schema mapping considered (sound, or exact), and the query language used in the schema mapping specification (conjunctive queries and variants over relational databases, or regular path queries and variants over graph databases). Notably, this is the first work on comparing schema mappings for graph databases.
Speeded up Gaussian Mixture Model algorithm for background subtraction

Adaptive Gaussian Mixture Models (GMM) have been one of the most popular and successful approaches to perform foreground segmentation on multimodal background scenes. However, the good accuracy of the GMM algorithm comes at a high computational cost. An improved GMM technique was proposed by Zivkovic to reduce computational cost by minimizing the number of modes adaptively. In this paper, we propose a modification to his adaptive GMM algorithm that further reduces execution time by replacing expensive floating point computations with low cost integer operations. To maintain accuracy, we derive a heuristic that computes periodic floating point updates for the GMM weight parameter using the value of an integer counter. Experiments show speedups in the range of 1.33 − 1.44 on standard video datasets where a large fraction of pixels are multimodal
Predicting hydraulic conductivity changes from aggregate mean weight diameter

Rapid wetting of structurally unstable soils results in aggregate disintegration, soil densification, reduced porosity, and changes in the pore‐size distribution and intake hydraulic properties. Knowledge of changes in these properties is critical for use in hydrological, solute transport, or erosion models. Multiple determinations of these parameters as they evolve over time are needed for short time step models. Routine measurement of all these properties is time‐consuming, and it would therefore be practical if some of them could be used to predict others. A model is proposed to predict hydraulic conductivity changes based on aggregate size distribution, stability, and wetting rate information in order to determine the stability of the pore network during wetting. Two independent experiments were conducted in the laboratory on two different soil types to evaluate the proposed model. The decrease in mean weight diameter of aggregates exposed to different rates of wetting was used to predict the mean weight diameter after wetting, which was then used in a model to predict changes in hydraulic conductivity. The results show that the changes in predicted and measured hydraulic conductivities between the potentials of −0.5 and −4 kPa were significantly correlated for both soils, despite an overestimation of the measured changes. The close correlation suggests that this bias could be empirically estimated from measurements of aggregate size and that information on aggregate size and stability would be useful for predicting changes in hydraulic conductivity.
Empirical conversion of the vertical profile of reflectivity from Ku‐band to S‐band frequency

This paper presents an empirical method for converting reflectivity from Ku‐band (13.8 GHz) to S‐band (2.8 GHz) for several hydrometeor species, which facilitates the incorporation of Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) measurements into quantitative precipitation estimation (QPE) products from the U.S. Next‐Generation Radar (NEXRAD). The development of empirical dual‐frequency relations is based on theoretical simulations, which have assumed appropriate scattering and microphysical models for liquid and solid hydrometeors (raindrops, snow, and ice/hail). Particle phase, shape, orientation, and density (especially for snow particles) have been considered in applying the T‐matrix method to compute the scattering amplitudes. Gamma particle size distribution (PSD) is utilized to model the microphysical properties in the ice region, melting layer, and raining region of precipitating clouds. The variability of PSD parameters is considered to study the characteristics of dual‐frequency reflectivity, especially the variations in radar dual‐frequency ratio (DFR). The empirical relations between DFR and Ku‐band reflectivity have been derived for particles in different regions within the vertical structure of precipitating clouds. The reflectivity conversion using the proposed empirical relations has been tested using real data collected by TRMM‐PR and a prototype polarimetric WSR‐88D (Weather Surveillance Radar 88 Doppler) radar, KOUN. The processing and analysis of collocated data demonstrate the validity of the proposed empirical relations and substantiate their practical significance for reflectivity conversion, which is essential to the TRMM‐based vertical profile of reflectivity correction approach in improving NEXRAD‐based QPE.
Distribution of Areal Strain on Mercury: Insights Into the Interaction of Volcanism and Global Contraction

Shortening tectonic structures within Mercury's two largest geological units display a clear contrast in relief, length, and spatial density. The volcanic smooth plains units are deformed by smaller‐scale structures yet host more features per area than the older intercrater plains. Although faulting in the intercrater plains is dominantly attributed to global contraction, it has been unclear whether the smooth plains faults result from volcanic loading, global contraction, or both. We use estimates of fault length and displacement to calculate spatial variations of areal strain for each unit. We find that high strain concentrations within the smooth plains suggest that global contraction has contributed to deformation in these units. The observed contrast in morphology and spatial density of structures between units may primarily reflect differences in mechanical and/or structural characteristics of the lithosphere when faulting was initiated.
Novel Orally Available Salvinorin A Analog PR-38 Inhibits Gastrointestinal Motility and Reduces Abdominal Pain in Mouse Models Mimicking Irritable Bowel Syndrome

The opioid and cannabinoid systems play a crucial role in multiple physiological processes in the central nervous system and in the periphery. Selective opioid as well as cannabinoid (CB) receptor agonists exert a potent inhibitory action on gastrointestinal (GI) motility and pain. In this study, we examined (in vitro and in vivo) whether PR-38 (2-O-cinnamoylsalvinorin B), a novel analog of salvinorin A, can interact with both systems and demonstrate therapeutic effects. We used mouse models of hypermotility, diarrhea, and abdominal pain. We also assessed the influence of PR-38 on the central nervous system by measurement of motoric parameters and exploratory behaviors in mice. Subsequently, we investigated the pharmacokinetics of PR-38 in mouse blood samples after intraperitoneal and oral administration. PR-38 significantly inhibited mouse colonic motility in vitro and in vivo. Administration of PR-38 significantly prolonged the whole GI transit time, and this effect was mediated by µ- and κ-opioid receptors and the CB1 receptor. PR-38 reversed hypermotility and reduced pain in mouse models mimicking functional GI disorders. These data expand our understanding of the interactions between opioid and cannabinoid systems and their functions in the GI tract. We also provide a novel framework for the development of future potential treatments of functional GI disorders.
The value of DALY life: problems with ethics and validity of disability adjusted life years.

Disability adjusted life years (DAL Ys) have been launched by the World Bank and backed by the World Health Organisation as a measure of the global burden of disease. 1.2 The aim is ambitious: 'The burden of disease has yet to entirely replace traditional approaches to the assessment of health needs as an influence on political decision making. ' 3 Just like quality adjusted life years (QALYs), DALYs combine information about morbidity and mortality in numbers of health years lost. In the DALY approach, each state of health is assigned a disability weighting on a scale from zero (perfect health) to one (death) by an expert panel. 2 To calculate the burden of a certain disease, the disability weighting is multiplied by the number of years lived in that health state and is added to the number of years lost due to that disease (Figure 1 ) . Future burdens are discounted at a rate of 3% per year, and the value of the lifetime is weighted so that years of life in childhood and old age are counted less .
Group C meningococcus vaccination in the southwest region of France

Between 1995 and 2000, the incidence of confirmed serogroup C invasive meningococcal infection (IMIC) in France, adjusted for undernotification, increased from 0.14 to 0.24 cases per 100 000 inhabitants. In 2001, the rate reached 0.40/100 000, which was attributable to an increase in the incidence of all invasive meningococcal infections (IMI), and also to the fact that the proportion of IMIC increased from 23% to 35% of all IMI(1).
Focused Impedance Measurement (FIM): A New Technique with Improved Zone Localization

Abstract: Conventional four‐electrode impedance measurements (FEIM) cannot localize a zone of interest in a volume conductor. On the other hand, the recently developed electrical impedance tomography (EIT) system offers an image with reasonable resolution, but is complex and needs many electrodes. By placing two FEIM systems perpendicular to each other over a common zone at the center and combining the two results, it is possible to obtain enhanced sensitivity over this central zone. This is the basis of the proposed new method of focused impedance measurement (FIM). Sensitivity maps in both 2D and 3D show the desired improvement. A comparison of stomach‐emptying studies also indicates the improvement achieved. This new method may be useful for impedance measurements of large organs like stomach, heart, and lungs. Being much simpler in comparison to EIT, multifrequency systems can be simply built for FIM. Besides, FIM may have utility in other fields like geology where impedance measurements are performed.
Attending to global versus local stimulus features modulates neural processing of low versus high spatial frequencies: an analysis with event-related brain potentials

Spatial frequency (SF) selection has long been recognized to play a role in global and local processing, though the nature of the relationship between SF processing and global/local perception is debated. Previous studies have shown that attention to relatively lower SFs facilitates global perception, and that attention to relatively higher SFs facilitates local perception. Here we recorded event-related brain potentials (ERPs) to investigate whether processing of low versus high SFs is modulated automatically during global and local perception, and to examine the time course of any such effects. Participants compared bilaterally presented hierarchical letter stimuli and attended to either the global or local levels. Irrelevant SF grating probes flashed at the center of the display 200 ms after the onset of the hierarchical letter stimuli could either be low or high in SF. It was found that ERPs elicited by the SF grating probes differed as a function of attended level (global versus local). ERPs elicited by low SF grating probes were more positive in the interval 196–236 ms during global than local attention, and this difference was greater over the right occipital scalp. In contrast, ERPs elicited by the high SF gratings were more positive in the interval 250–290 ms during local than global attention, and this difference was bilaterally distributed over the occipital scalp. These results indicate that directing attention to global versus local levels of a hierarchical display facilitates automatic perceptual processing of low versus high SFs, respectively, and this facilitation is not limited to the locations occupied by the hierarchical display. The relatively long latency of these attention-related ERP modulations suggests that initial (early) SF processing is not affected by attention to hierarchical level, lending support to theories positing a higher level mechanism to underlie the relationship between SF processing and global versus local perception.
Unexpected resilience to experimental gingivitis of subepithelial connective tissue grafts in gingival recession defects: a clinical-molecular evaluation.

BACKGROUND AND OBJECTIVE The subepithelial connective tissue graft (SCTG) is the most widely used procedure for the treatment of gingival recession defects. Little is known, however, as to whether the apposed gingival flaps are more predisposed to develop plaque-related inflammation compared to healthy sites. This has salient clinical implications, as the long-term results of root coverage will depend largely on the level of inflammation of the grafted tissue. METHODS In the present split-mouth case-control study, clinical and biomolecular parameters were used to assess the level of inflammation of periodontal sites 12 mo after treatment with SCTG (test) and healthy non-treated gingivae (control) following the induction of plaque-related gingivitis in 19 patients. RESULTS The data showed that test sites had a significantly (P < 0.05) lower gingival index and angulated bleeding score compared to control sites (gingival index = 1.05 ± 0.23 vs. 1.34 ± 0.47; angulated bleeding score = 0.34 ± 0.37 vs. 0.61 ± 0.39) after induction of experimental gingivitis, whereas the plaque index did not differ in the two groups (P > 0.05). With regard to the biomolecular parameters, baseline levels of the proinflammatory cytokine interleukin-1β were higher in the gingival crevicular fluid of test sites. However, control sites exhibited more pronounced increase in the levels of interleukin-1β compared to test sites, upon plaque accumulation, so that the final concentration was similar in both groups. No changes were recorded in the gingival crevicular fluid volume. CONCLUSION Analysis of the data demonstrates that the sites of gingival recession treated with SCTG develop a lower degree of plaque-induced inflammation compared to healthy gingivae. This strongly suggests that SCTG does not predispose to inflammation and to further gingival recession and makes it a safe technique in the treatment of gingival defects.
An Accelerated Approach to Tissue Expansion for Breast Reconstruction: Experience with Intraoperative and Rapid Postoperative Expansion in 370 Reconstructions

&NA; Breast reconstruction with tissue expansion is a wellestablished technique that offers satisfactory aesthetic results with minimal patient morbidity. The traditional period of expansion, however, continues to be a significant source of patient inconvenience and dissatisfaction. The objective of this study was to develop and evaluate a protocol for rapid tissue expansion. A total of 370 breast reconstructions in 314 patients who underwent rapid tissue expansion were retrospectively reviewed. Contraindications to rapid expansion were considered to be previous radiation, mastectomy skin flaps of questionable viability, and an excessively tight skin envelope. All expanders were placed submuscularly and filled to 40 to 50 percent of tissue expander volume. Office expansion was undertaken within 10 to 14 days after the operation and continued on a weekly basis. Each expansion was limited by patient tolerance up to a maximal pressure of 40 mm of water or a volume of 120 cm3. Expansion was considered complete once the expanded breast was 30 to 50 percent larger than the contralateral breast. If required, postoperative chemotherapy was given during the expansion period. Mean patient age was 48 years (range, 23 to 73 years). Two hundred fifty‐eight patients had unilateral reconstructions. Three hundred two patients had immediate reconstruction. Mean tissue expander size was 583 cm3 (SD, 108 cm3). Mean intraoperative expansion was 271 cm3, or 46 percent (SD, 9 percent) of the tissue expander size. The first expansion was started 12 days (SD, 3 days) after the operation. The mean volume of each expansion was 88 cm3 (SD, 23 cm3). Expansion was completed in 4.7 office visits (SD, one visit). Mean final expander volume was 672 cm3 (SD, 144 cm3). The expanders were overexpanded by 15.3 percent (SD, 8.4 percent). The mean time between expander placement and the final expansion was 6.6 weeks (SD, 3 weeks). The overall complication rate was 4 percent. Ten patients developed cellulitis, five patients had hematomas requiring drainage, and one expander became exposed. A total of eight expanders were removed: four for cellulitis, one for a hematoma, one because of locally recurrent disease, one because of expander exposure, and one at the patient's request for no medical reason. Intraoperative and rapid postoperative tissue expansion is a safe and reliable technique that offers a significant improvement over conventional techniques. In this accelerated protocol, expansion may be completed in less than 7 weeks. The result is decreased patient morbidity and delays in adjuvant therapy at no detriment to the final surgical outcome. (Plast. Reconstr. Surg. 111: 1871, 2003.)
Visual Localization of Wireless Capsule Endoscopes Aided by Artificial Neural Networks

Various modalities are used for the examination of the gastrointestinal (GI) tract. One such modality is Wireless Capsule Endoscopy (WCE), a non-invasive technique which consists of a swallowable color camera that enables the detection of GI pathology with only minimal patient discomfort. Currently, tracking of the capsule position is estimated in the 3D abdominal space, using radio-frequency (RF) triangulation. The RF triangulation technique, however, does not provide sufficient information about the location of the capsule along the GI lumen, and consequently, the localization of any possible abnormality. Recently, we proposed a geometric visual odometry (VO) method for the localization of the capsule in the GI lumen. In this paper, we extend this state-of-art method by exploiting an artificial neural network (ANN) to augment the geometric method and achieve higher localization accuracy. The results of this novel approach are validated with an in-vitro experiment that provides ground truth information about the location of the capsule. The mean absolute error obtained, for a distance of 19.6cm, is 0.79&#xb1;0.51cm.
Ferrimagnetic Iron Sulfide Formation and Methane Venting Across the Paleocene‐Eocene Thermal Maximum in Shallow Marine Sediments, Ancient West Siberian Sea

Authigenesis of ferrimagnetic iron sulfide minerals (greigite and monoclinic pyrrhotite) occurred across the Paleocene‐Eocene Thermal Maximum (PETM) within the Bakchar oolitic ironstone in southeastern Western Siberia. Co‐occurrence of these minerals is associated with diagenetic environments that support anaerobic oxidation of methane, which has been validated by methane fluid inclusion analysis in the studied sediments. In modern settings, such ferrimagnetic iron sulfide formation is linked to upward methane diffusion in the presence of minor dissolved sulfide ions. The PETM was the most extreme Cenozoic global warming event and massive methane mobilization has been proposed as a major contributor to the globally observed warming and carbon isotope excursion associated with the PETM. The studied sediments provide rare direct evidence for methane mobilization during the PETM. Magnetic iron sulfide formation associated with methanogenesis in the studied sediments can be explained by enhanced local carbon burial across the PETM. While there is no strong evidence to link local methane venting with more widespread methane mobilization and global warming, the magnetic, petrographic, and geochemical approach used here is applicable to identifying authigenic minerals that provide telltale signatures of methane mobility that can be used to assess methane formation and mobilization through the PETM and other hyperthermal climatic events.