Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and Identification of Mycobacterium tuberculosis Directly from Sputum Sediments by Ligase Chain Reaction

ABSTRACT Sputum specimens received for the diagnosis of tuberculosis or other mycobacterial infections were tested by a ligase chain reaction (LCR)-based assay and acid-fast stain and culture techniques. Results from the LCR assay (Abbott LCx Mycobacterium tuberculosis[MTB] Assay) were compared to results from standard culture techniques held for 6 weeks. Four hundred ninety-three specimens from 205 patients suspected of pulmonary tuberculosis were included in the prospective study. Thirty-four (6.9%) of the specimens were culture positive for M. tuberculosis, and 13 (38%) of these were also fluorochrome stain positive. LCR sensitivities and specificities compared to culture were 74 and 98%, respectively. LCR sensitivity was 100% for fluorochrome stain-positive specimens and 57% for fluorochrome stain-negative specimens. Nine LCR-negative, culture-positive specimens were the result of low concentrations ofM. tuberculosis. No inhibitors were detected in any of these specimens. Of the eight LCR-positive, culture-negative specimens, five were from patients with active tuberculosis. With these considered culture misses, final LCR sensitivity, specificity, positive predictive value, and negative predictive value were 77, 99, 91, and 98%, respectively. The same performance values for the fluorochrome acid-fast bacillus smear were 33, 98, 62, and 94%, respectively. After normal laboratory sputum processing, the Abbott LCx MTB Assay can be completed in 6 h. Thus, it is possible to have results available within 8 h of specimen submission.
The Relationship between Basin Hypsometric Integral Scale Dependence and Rock Uplift Rate in a Range Front Area: A Case Study from the Coastal Range, Taiwan

The hypsometric curve and hypsometric integral (HI) of drainage basins are common tectonic geomorphologic indices. Generally, the hypsometric curve is convex and the HI is high in areas of strong rock uplift. However, previous research indicates that an inverse correlation exists between the HI and rock uplift in the mountain-piedmont junction in California. It has also been proposed that the basin HI in the range front area has scale dependence, which increases the difficulty of inferring tectonic uplift. We therefore examined the effects of tectonic uplift and basin scale on basin HI in the southern Coastal Range of eastern Taiwan. The results showed that basin size could affect the HI. First-order Strahler basins are smaller and have higher HIs, whereas second- and third-order basins are larger and have lower HIs, indicating some form of scale dependence. The coefficient of logarithmic regression between mean area and mean HI of every subbasin was calculated to determine the scale dependence index (SDI). The lower the SDI, the higher the scale dependence. The SDI was utilized to distinguish basins’ topographic tendencies between range interior and range front. We also applied the igneous-area ratio to define spatial tendencies of basins’ lithology distributions. The lower the igneous-area ratio, the greater the spatial tendency toward range front will be. Basins in the middle of the south Coastal Range tended to approach a range interior steady state, with higher SDIs and a positive correlation between HI and rock uplift rate. Basins in the north and south of the south Coastal Range tended to be at a range front nonsteady state, with lower SDIs and a negative correlation between HI and rock uplift rate. The correlations may be applicable to estimate the rock uplift rate.
Some Fundamental Chemical Aspects on Paper Forming

The fundamental physico-chemical aspects of retention chemistry are reviewed in the light of basic concepts in colloid chemistry. Special emphasis has been paid to the surface chemistry of cellulose and cellulosic materials, their origin of charge, dispersion force interactions as well as the implication of certain aspects of peculiar cellulosic surfaces, e.g. the influence of their porosity on polymer adsorption. Charge neutralization, patch flocculation, heterocoagulation, bridging and complex flocculation phenomena are discussed as well as polymer adsorption phenomena at the cellulose/water interface
Dissociable Cortical Pathways for Qualitative and Quantitative Mechanisms in the Face Inversion Effect

Humans' ability to recognize objects is remarkably robust across a variety of views unless faces are presented upside-down. Whether this face inversion effect (FIE) results from qualitative (distinct mechanisms) or quantitative processing differences (a matter of degree within common mechanisms) between upright and inverted faces has been intensely debated. Studies have focused on preferential responses to faces in face-specific brain areas, although face recognition also involves nonpreferential responses in non–face-specific brain areas. By using dynamic causal modeling with Bayesian model selection, here we show that dissociable cortical pathways are responsible for qualitative and quantitative mechanisms in the FIE in the distributed network for face recognition. When faces were upright, the early visual cortex (VC) and occipital and fusiform face areas (OFA, FFA) suppressed couplings to the lateral occipital cortex (LO), a primary locus of object processing. In contrast, they did not inhibit the LO when faces were inverted but increased couplings to the intraparietal sulcus, which has been associated with visual working memory. Furthermore, we found that upright and inverted face processing together involved the face network consisting of the VC, OFA, FFA, and inferior frontal gyrus. Specifically, modulatory connectivity within the common pathways (VC-OFA), implicated in the parts-based processing of faces, strongly correlated with behavioral FIE performance. The orientation-dependent dynamic reorganization of effective connectivity indicates that the FIE is mediated by both qualitative and quantitative differences in upright and inverted face processing, helping to resolve a central debate over the mechanisms of the FIE.
Cytotoxic and Antibacterial Compounds from the Coral-Derived Fungus Aspergillus tritici SP2-8-1

Three novel compounds, 4-methyl-candidusin A (1), aspetritone A (2) and aspetritone B (3), were obtained from the culture of a coral-derived fungus Aspergillus tritici SP2-8-1, together with fifteen known compounds (4–18). Their structures, including absolute configurations, were assigned based on NMR, MS, and time-dependent density functional theory (TD-DFT) ECD calculations. Compounds 2 and 5 exhibited better activities against methicillin-resistant strains of S. aureus (MRSA) ATCC 43300 and MRSA CGMCC 1.12409 than the positive control chloramphenicol. Compound 5 displayed stronger anti-MRSA and lower cytotoxic activities than 2, and showed stronger antibacterial activities against strains of Vibrio vulnificus, Vibrio rotiferianus, and Vibrio campbellii than the other compounds. Compounds 2 and 10 exhibited significantly stronger cytotoxic activities against human cancer cell lines HeLa, A549, and Hep G2 than the other compounds. Preliminary structure–activity relationship studies indicated that prenylation of terphenyllin or candidusin and the tetrahydrobenzene moiety in anthraquinone derivatives may influence their bioactivity.
Salvia Fruticosa, Salvia Officinalis, and Rosmarinic Acid Induce Apoptosis and Inhibit Proliferation of Human Colorectal Cell Lines: The Role in MAPK/ERK Pathway

Epidemiological studies have shown that nutrition is a key factor in modulating sporadic colorectal carcinoma (CRC) risk. Aromatic plants of the genus Salvia (sage) have been attributed many medicinal properties, which include anticancer activity. In the present study, the antiproliferative and proapoptotic effects of water extracts of Salvia fruticosa (SF) and Salvia officinalis (SO) and of their main phenolic compound rosmarinic acid (RA) were evaluated in two human colon carcinoma-derived cell lines, HCT15 and CO115, which have different mutations in the MAPK/ERK and PI3K/Akt signalling pathways. These pathways are commonly altered in CRC, leading to increased proliferation and inhibition of apoptosis. Our results show that SF, SO, and RA induce apoptosis in both cell lines, whereas cell proliferation was inhibited by the two sage extracts only in HCT15. SO, SF, and RA inhibited ERK phosphorylation in HCT15 and had no effects on Akt phosphorylation in CO115 cells. The activity of sage extracts seems to be due, at least in part, to the inhibition of MAPK/ERK pathway.
Contribution to the interpretation of evolving communities in complex networks : Application to the study of social interactions. (Contribution à l'interprétation des communautés en évolution dans des réseaux complexes : Application à l'étude des interactions sociales)

Complex Networks constitute a convenient tool to model real-world complex systems. For this reason, they have become very popular in the last decade. Many tools exist to study complex networks. Among them, community detection is one of the most important. A community is roughly defined as a group of nodes more connected internally than to the rest of the network. In the literature, this intuitive definition has been formalized in many ways, leading to countless different methods and variants to detect communities. In the large majority of cases, the result of these methods is set of node groups in which each node group corresponds to a community. From the applicative point of view, the meaning of these groups is as important as their detection. However, although the task of detecting communities in itself took a lot of attraction, the problem of interpreting them has not been properly tackled until now. In this thesis, we see the interpretation of communities as a problem independent from the community detection process, consisting in identifying the most characteristic features of communities. We break it down into two sub-problems: 1) finding an appropriate way to represent a community and 2) objectively selecting the most characteristic parts of this representation. To solve them, we take advantage of the information encoded in dynamic attributed networks. We propose a new representation of communities under the form of temporal sequences of topological measures and attribute values associated to individual nodes. We then look for emergent sequential patterns in this dataset, in order to identify the most characteristic community features. We perform a validation of our framework on artificially generated dynamic attributed networks. At this occasion, we study its behavior relatively to changes in the temporal evolution of the communities, and to the distribution and evolution of nodal features. We also apply our framework to real-world systems: a DBLP network of scientific collaborations, and a LastFM network of social and musical interactions. Our results show that the detected communities are not completely homogeneous, in the sense several node topic or interests can be identified for a given community. Some communities are composed of smaller groups of nodes which tend to evolve together as time goes by, be it in terms of individual (attributes, topological measures) or relational (community migration) features. The detected anomalies generally fit some generic profiles: nodes misplaced by the community detection tool, nodes relatively similar to their communities, but also significantly different on certain features and/or not synchronized with their community evolution, and finally nodes with completely different interests.
Functional and Mutational Analysis of P19, a DNA Transfer Protein with Muramidase Activity

ABSTRACT Protein P19 encoded by the conjugative resistance plasmid R1 has been identified as being one member of a large family of muramidases encoded by bacteriophages and by type III and type IV secretion systems. We carried out a mutational analysis to investigate the function of protein P19 and used in vivo complementation assays to test those of several P19 mutants. The results indicated that conserved residues present in the presumed catalytic center of P19 are absolutely essential for its function in conjugation of plasmid R1 and infection by the RNA phage R17. Overexpression of protein P19 in an early growth phase resulted in a massive lysis of Escherichia coli cells in liquid culture, as indicated by a rapid and distinct decrease in cell culture densities after induction. Change of the proposed catalytic glutamate at position 44 to glutamine completely abolished this effect. P19-induced cell lysis was directly shown by transmission and scanning electron microscopy. Typically, P19-overexpressing cells showed bulges protruding from the cell surfaces. Our interpretation is that these protrusions arose from a localized and spatially confined disruption of the bacterial cell wall. To our knowledge such an effect has not previously been documented for any member of the lytic transglycosylase family. From the data presented here, we conclude that protein P19 possesses the proposed localized peptidoglycan-hydrolyzing activity. This activity would be a prerequisite for efficient penetration of the cell envelope by the DNA translocation complex encoded by the conjugative plasmid.
The Viral Mimetic Polyinosinic:Polycytidylic Acid Alters the Growth Characteristics of Small Intestinal and Colonic Crypt Cultures

Background & Aims The intestinal epithelium is the first line of defense against enteric pathogens. We investigated the response of small intestinal and colonic crypt cultures to a panel of toll-like receptor ligands to assess the impact of microbial pattern recognition on epithelial growth. Methods Primary murine jejunal enteroids and colonoids were cultured with lipopeptide Pam3CSK4, lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (Poly I:C) for 4 to 6 days. Surface area, budding and survival were assessed. Proliferation and numbers of lysozyme positive cells were quantified by flow cytometry. Gene expression was assessed by Nanostring and qRT-PCR. Results Exposure to Pam3CSK4 and LPS had minimal impact on either enteroids or colonoids. In contrast, Poly I:C increased the surface area of enteroids, while colonoids demonstrated decreased budding. Survival was decreased by Poly I:C in enteroids but not in colonoids. Both enteroids and colonoids exhibited upregulated gene expression of chemokines, but these were increased in magnitude in enteroids. Decreases in gene expression associated with epithelial differentiation and lysozyme positive cells were more apparent in enteroids than in colonoids. Baseline gene expression between enteroids and colonoids differed markedly in levels of stem cell and inflammatory markers. The changes in morphology induced by Poly I:C were mediated by the toll-like receptor adaptor molecule 1 (Ticam1) in enteroids but not in colonoids. Conclusions Poly I:C alters the molecular program of epithelial cells and shifts from absorption and digestion towards defense and inflammation. Diversity of responses to microbial patterns in enteroids and colonoids may underlie differences in susceptibility to infection along the intestinal tract.
Alternative Methods for Analysis of Cyanobacterial Populations in Drinking Water Supplies: Fluorometric and Toxicological Applications Using Phycocyanin

The management of cyanobacteria and potential exposure to associated biotoxins requires the allocation of scarce resources across a range of freshwater resources within various jurisdictions. Cost effective and reliable methods for sample processing and analysis form the foundation of the protocol yielding reliable data from which to derive important decisions. In this study the utilization of new methods to collect, process and analyze samples enhanced our ability to evaluate cyanobacterial populations. Extraction of phycocyanin using the single freeze thaw method provided more accurate and precise measurements (CV 4.7% and 6.4%), offering a simple and cost-effective means to overcome the influence of morphological variability. In-vacuo concentration of samples prior to ELISA analysis provided a detection limit of 0.001 μg·L−1 MC. Fractionation of samples (−1) = −0.279 + (1.368 ∗ Log PC (μg·L−1) while in an Aphanizomemon spp. dominant system Log MC (ng·L−1) = 0.385 + (0.449 ∗ Log PC (μg·L−1). These methods and sampling protocol could be used in other aquatic systems across a broader regional landscape to estimate the levels of microcystins.
New Trends in Neutrosophic Theory and Applications

Neutrosophic theory and applications have been expanding in all directions at an astonishing rate especially after the introduction the journal entitled “Neutrosophic Sets and Systems”. New theories, techniques, algorithms have been rapidly developed. One of the most striking trends in the neutrosophic theory is the hybridization of neutrosophic set with other potential sets such as rough set, bipolar set, soft set, hesitant fuzzy set, etc. The different hybrid structure such as rough neutrosophic set, single valued neutrosophic rough set, bipolar neutrosophic set, single valued neutrosophic hesitant fuzzy set, etc. are proposed in the literature in a short period of time. Neutrosophic set has been a very important tool in all various areas of data mining, decision making, e-learning, engineering, medicine, social science, and some more. The book “New Trends in Neutrosophic Theories and Applications” focuses on theories, methods, algorithms for decision making and also applications involving neutrosophic information. Some topics deal with data mining, decision making, e-learning, graph theory, medical diagnosis, probability theory, topology, and some more. 30 papers by 39 authors and coauthors.
Sediment mass movement of a particle-laden turbidity current based on ultrasound velocity profiling and the distribution of sediment concentration

Abstract Particle-laden flows or turbidity currents along the seafloor are important to the formation and erosion of submarine topography. To understand the mass-transport process, flume tests were carried out with a continuous supply of quartz-laden suspension. The vertical and horizontal velocities were extracted by two pairs of ultrasound Doppler velocity profilers installed at different angles with respect to the bed-normal direction. Due to the head intrusion into the ambient water, the sediment in the suspension was continuously lifted up and mixed, leaving lobes and clefts. The velocity-maximum layer acted as the main sediment conveyor and divided the body into wall and jet regions. The concentration distribution was also quantified based on the relationship between the fluid density and the intensity of light attenuation obtained using a video recording. An area of high sediment concentration was observed just behind the head frontal area. Analysis of the velocity and concentration distribution demonstrated that sediment in the turbidity current was transported mainly by head movement and that continuous sedimentation took place in the wall region. The results indicate that a turbidity current proceeds while maintaining an ordered inner dynamic structure.
Improving pan-European speed-limit signs recognition with a new “global number segmentation” before digit recognition

In this paper, we present an improved European speed-limit sign recognition system based on an original ldquoglobal number segmentationrdquo (inside detected circles) before digit segmentation and recognition. The global speed-limit sign detection and correct recognition rate, currently evaluated on videos recorded on a mix of French and German roads, is around 94%, with a misclassification rate below 1%, and not a single validated false alarm in several hours of recorded videos. Our greyscale-based system is intrinsically insensitive to colour variability and quite robust to illumination variations, as shown by an on-road evaluation under bad weather conditions (cloudy and rainy) which yielded 84% good detection and recognition rate, and by a first night-time on-road evaluation with 75% correct detection rate. Due to recognition occurring at digit level, our system has the potential to be very easily extended to handle properly all variants of speed-limit signs from various European countries. Regarding computation load, videos with images of 640 times 480 pixels can be processed in real-time at ~20 frames/s on a standard 2.13 GHz dual-core laptop.
“Head-to-Side-Chain” Cyclodepsipeptides of Marine Origin

Since the late 1980s, a large number of depsipeptides that contain a new topography, referred to as “head-to-side-chain” cyclodepsipeptides, have been isolated and characterized. These peptides present a unique structural arrangement that comprises a macrocyclic region closed through an ester bond between the C-terminus and a β-hydroxyl group, and terminated with a polyketide moiety or a more simple branched aliphatic acid. This structural pattern, the presence of unique and complex residues, and relevant bioactivity are the main features shared by all the members of this new class of depsipeptides, which are reviewed herein.
Existence and Uniqueness of Equilibrium in Distorted Dynamic Economies with Capital and Labor

In this paper, we provide a set of sufficient conditions under which recursive competitive equilibrium exist and are unique for a large class of distorted dynamic equilibrium models with capital and elastic labor supply. We develop a monotone map approach to the problem. The class of economies for which we are able to obtain our existence result is apparently considerably larger than those considered in previous work. Additionally unlike previous work, we are able to also prove that this equilibrium is unique. We conclude by applying the new results to some important examples of monetary economies often used in applied work.
The Informational Value of Job Search Data and the Dynamics of Search Behaviour: Evidence from Hungary

Labour market analysis places much emphasis on the concept of search. But there is insufficient empirical information on (a) the relationship between reported search and job-finding and (b) how search behaviour changes over a spell without work. We investigate these issues using a sample constructed from Hungarian labour force survey panel data of the flow from jobs to the state of "joblessness". The results on job exits call into question aspects of the standard international classification of "unemployment" and "out of the labour force". Transitions during joblessness in and out of search and the various categories of non-search are found to be only modest.
Effect of quality of colostrum on health, growth and immunoglobulin G concentration in Holstein calves in a hot environment

Abstract The aim of this study was to determine the effect of ingestion of pasteurized and subsequently frozen–thawed pooled colostrum (≥50 mg Ig/mL) with different bacterial counts and immunoglobulin concentration (IgC) on the occurrence of diarrhea and pneumonia in 306 neonatal Holstein calves in a hot environment. Calves were assigned to be fed colostrum with total bacterial counts (TBC) lower or greater than 100 000 colony‐forming units (cfu)/mL, total coliform counts (TCC) greater or lower than 10 000 cfu/mL, and IgC lower or higher than 85 mg Ig/mL. Calves fed colostrum with TBC ≥100 000 cfu/mL were more likely (risk ratio 1.34, confidence interval 1.05–1.71; P < 0.05) to present pneumonia than calves receiving colostrum with lower TBC (incidence 53.2 vs. 39.8%). Calves fed colostrum with high TCC had increased chances of suffering pneumonia (51.4 vs. 42.1%; P < 0.05) than calves fed colostrum with lower TCC. Calves fed colostrum with ≥85 mg Ig/mL tended to present higher daily weight gain (505 ± 113 vs. 484 ± 126 g; P = 0.09). TBC and TCC in colostrum did not influence the incidence rate of diarrhea. It was concluded that under the conditions of the present study, heavy contamination of on‐farm pasteurized frozen–thawed colostrum is seemingly unavoidable and this contamination poses a threat for pneumonia, but not for diarrhea.