Miracle-dz/UniFAR-FTUs huggingface dataset:
Antivirulence Activity of the Human Gut Metabolome

ABSTRACT The mammalian gut contains a complex assembly of commensal microbes termed microbiota. Although much has been learned about the role of these microbes in health, the mechanisms underlying these functions are ill defined. We have recently shown that the mammalian gut contains thousands of small molecules, most of which are currently unidentified. Therefore, we hypothesized that these molecules function as chemical cues used by hosts and microbes during their interactions in health and disease. Thus, a search was initiated to identify molecules produced by the microbiota that are sensed by pathogens. We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion. It has been known for decades that the microbiota protects its hosts from invading pathogens, and these data suggest that chemical sensing may be involved in this phenomenon. Further investigations should reveal the exact biological role of this molecule as well as its therapeutic potential. IMPORTANCE Microbes can communicate through the production and sensing of small molecules. Within the complex ecosystem formed by commensal microbes living in and on the human body, it is likely that these molecular messages are used extensively during the interactions between different microbial species as well as with host cells. Deciphering such a molecular dialect will be fundamental to our understanding of host-microbe interactions in health and disease and may prove useful for the design of new therapeutic strategies that target these mechanisms of communication. Microbes can communicate through the production and sensing of small molecules. Within the complex ecosystem formed by commensal microbes living in and on the human body, it is likely that these molecular messages are used extensively during the interactions between different microbial species as well as with host cells. Deciphering such a molecular dialect will be fundamental to our understanding of host-microbe interactions in health and disease and may prove useful for the design of new therapeutic strategies that target these mechanisms of communication.
The effects of coronavirus on human nasal ciliated respiratory epithelium

Human coronavirus (HCoV) accounts for 15–30% of common colds, but only one case report has described the effect of a coronavirus infection, that was asymptomatic, on human respiratory epithelium. The authors examined the effects of infection with HCoV on ciliary structure and function in healthy volunteers infected by intranasal inoculation with HCoV 229E. A further four volunteers were sham infected with ultraviolet-inactivated virus. Immediately before inoculation (day 0) and 3 days later (day 3), ciliated epithelium was obtained by brushing the inferior nasal turbinate. Ciliary beat frequency was determined and beat pattern analysed for evidence of dyskinesia (0=normal, 3=severely dyskinetic) using digital high-speed video photography. Ciliary ultrastructure was examined by transmission electron microscopy. Symptom diaries were kept for the duration of the study. All subjects inoculated with HCoV, including the three who did not develop symptoms of an upper respiratory tract infection, had disruption of their respiratory epithelium on day 3. Although there was no difference in the mean ciliary beat frequency between day 0 (11.3 Hz (95% confidence interval (CI): 8.6–14.0) and day 3 (9.4 Hz (95% CI 7.2–11.6)), there was a significant increase (p<0.05) in the ciliary dyskinesia score between day 0 (0.2 (95% CI 0–0.5)) and day 3 (1.1 (95% CI 0.5–1.7). In sham-infected subjects, no differences in epithelial integrity, or ciliary structure and function were found between day 0 and day 3. Inoculation of healthy volunteers with human coronavirus caused disruption of the ciliated epithelium and ciliary dyskinesia. This is likely to impair mucociliary clearance. Damage to the respiratory epithelium, due to human coronavirus infection, may occur without overt clinical symptoms.
A Novel Septin-Associated Protein, Syp1p, Is Required for Normal Cell Cycle-Dependent Septin Cytoskeleton Dynamics in Yeast

Septins are a family of GTP-binding proteins whose heterooligomeric complex is the basic structural element of the septin filaments found in many eukaryotic organisms. In budding yeast, septins are mainly confined at the mother–daughter junction and are required for cell morphogenesis and division. Septins undergo assembly and disassembly in accordance with the progression of the cell cycle. In this report, we identified the yeast protein Syp1p as a new regulator of septin dynamics. Syp1p colocalizes with septins throughout most of the cell cycle. Syp1p interacts with the septin subunit Cdc10p and can be precipitated by Cdc10p and Cdc12p. In the syp1Δ mutant, both formation of a complete septin ring at the incipient bud site and disassembly of the septin ring in later stages of cell division are significantly delayed. In addition, overexpression of Syp1p causes marked acceleration of septin disassembly. The fluorescence recovery after photobleaching (FRAP) assay further showed that Syp1p promotes septin turnover in different cell cycle stages. These results suggest that Syp1p is involved in the regulation of cell cycle-dependent dynamics of the septin cytoskeleton in yeast.
Effect of Mindfulness-Based Stress Reduction on Anxiety, Depression and Stress in Women With Multiple Sclerosis

Background: Studies suggest that mindfulness-based interventions can improve anxiety, depression and stress in patients with multiple sclerosis (MS). However, no study investigated the effectiveness of this method in patients with a combination of problems such as depression, anxiety and stress simultaneously. However, comorbidities of depression and anxiety in MS are prevalent. Objectives: This study aimed to assess the effects of mindfulness-based stress reduction (MBRS) on anxiety, depression and stress in women with multiple sclerosis. Patients and Methods: This randomized controlled clinical trial was performed in 2013 in Ahvaz MS Society. Forty eight patients were selected by convenient sampling and randomly assigned in experimental and control groups. The patients in the two groups filled out depression, anxiety and stress scale (DASS-21) at initiation of study, 8 weeks later and 1 month after the end of intervention. The experimental group received 8 sessions of MBRS, while the control group treated as usual. Finally, data of 40 patients analyzed using t-test, chi square and repeated measures analysis of variance. Results: In the MBSR group, the mean depression, anxiety and stress were reduced significantly (P < 0.001). The mean depression score was 8.35 ± 1.78 before the intervention and reduced to 4.80 ± 0.83 and 4.45 ± 0.60 after the intervention and follow-up (P < 0.001). Also the mean anxiety score was 8.90 ± 1.97 before the intervention, which was significantly reduced to 4.70 ± 1.38 and 4.55 ± 0.99 after the intervention and follow-up (P < 0.001). The mean stress score was also 8.80 ± 2.35 before treatment and 4.80 ± 1.67 and 4.70 ± 1.34 after the intervention and follow-up (P < 0.001). Conclusions: This study showed that MBSR training can reduce mean depression, anxiety and stress scores in patients with MS. These findings suggest that MBSR is useful for psychological problems such as depression, anxiety and stress in patients with MS.
OntoGen Semi-automatic Ontology

1. Ontology editors The rapid growth of documents, web pages and other types of textual content pose a great challenge to modern content management systems. Ontologies offer an efficient way to reduce the amount of information overload by encoding the structure of a specific domain and offering easier access to the information for the users. However, all major ontology editors (such as Protégé[2], OntoStudio[3], . ) are fully manual and offer little support to the users for structuring domains.
Implicitly strengthened task‐irrelevant stimulus‐response associations modulate cognitive control: Evidence from an fMRI study

The dynamics of cognitive control have been investigated by the proportion congruency effect. However, the theory that this effect is due to attentional modulation has been challenged by contingency learning accounts. This raises the question of how the cognitive control system operates during and after increasing the strength of task‐irrelevant stimulus‐response (S‐R) associations. We employed a novel paradigm that elicits positive and reversed Simon effects via task rule manipulations, and combined it with a between subjects proportion congruency manipulation. The pattern of enhancement and reversal of the positive and reversed Simon effects across conditions suggested that participants used strengthened task‐irrelevant S‐R associations to predict responses. Functional neuroimaging identified proportion congruency effects that interacted with task S‐R associations, showing greater activity when strengthened task‐irrelevant S‐R associations conflicted with task‐defined S‐R associations in frontoparietal regions, including bilateral superior parietal lobule (SPL) and dorsal premotor cortex (dPMC), presupplementary motor area/anterior midcingulate cortex (Pre‐SMA/aMCC), and left dorsolateral prefrontal cortex (DLPFC). These results suggest that the aMCC and DLPFC shifted to responding mainly to the conflict induced by the strengthened irrelevant S‐R associations. The SPL and dPMC might represent the strengthened irrelevant S‐R associations. Hum Brain Mapp 37:756–772, 2016. © 2015 Wiley Periodicals, Inc.
HUNTING AGREEMENTS AS A STRATEGY FOR THE CONSERVATION OF SPECIES: THE CASE OF THE CAZUMBÁ-IRACEMA EXTRACTIVE RESERVE, STATE OF ACRE, BRAZIL

One of the greatest challenges for the conservation of hunting species is not to prevent exploitation in a definitive way, but to avoid that overhunting leads to depletion of the species. As a wildlife management tool for hunting, we can highlight the Hunting Agreement, which consists of prohibiting or restricting the hunting of certain species most vulnerable. Thus, the goal of this study was to determine if the adoption of the Hunting Agreement caused a change in the habits of hunters at the Cazumba-Iracema Extractive Reserve, located in the State of Acre, North Brazil. The Hunting Agreement imposes a ban on the slaughter of species and the use of certain hunting strategies. This study used the methodology of interview to verify the hunting preference and hunting calendar for quantification. We recorded the slaughter of 15 banned individuals namely Ara spp. , Amazona spp, Psittacara leucophthalmus and Tapirus terrestris . The comparison of the absolute abundance of species with a prohibition of hunting or not presented a significant difference, showing that there is a greater slaughter of species without prohibition on hunting. The comparison of prohibited and non-prohibited hunting strategies had a significant difference, demonstrating the greater predominance of the use of permitted strategies. There is a greater slaughter of species without prohibition on hunting. Prohibited hunting strategies represent a punctual behavior within the community. The implementation of the Hunting Agreement pervades not only the population awareness of the population lag of the target species, but mainly cultural, behavioral, economic and legislative changes.
Evaluation of Phytochemicals and Antimicrobial Activity of White and Blue Capitulum and Whole Plant of Silybum Marianum

3 Abstract: Phytochemicals are nonessential nutrients derived from plants, most of them are physiologically active. Majority of the phytochemicals have been known to beer therapeutic activities like antibacterial, antioxidant, antifungal, antispasmodic, anticancer, hepatoprotective etc. Chemical compounds with antimicrobial activity isolated from plants have enormous therapeutic potential and are effective in the treatment of infectious diseases while magitating many of the side effects that are often caused by synynthati c antimicrobial agents. The aqueous extracts of blue and white flowering Silybum marianum were subjected for qualitative and quantitative phytochemical evaluation and the crud ethanolic extract for antimicrobial activity. Data shows that flavonoids, phenols and tannins are present in both blue and white flowering (whole) plant of S.marianum while saponin and alkaloid were not detected. It has been found that, flavonoids are in high quantity (21%) in blue flowering and less (19%) in the white flowering plant. Contents of phenol and tannins are noted very less as compared to flavonoid i.e. 0.430 % phenol is recorded in blue flowering and 0.4321% in the white flowering plant. Contents of tannin is noted high in the white flowering (0.8455%) and less (0.6930%) in the blue flowering (whole) plant of S. marianum. Silymarin has been found very active against all gram positive bacteria and demonstrated moderate to significant antibacterial activity against tested pathogens, while inactive against gram negative bacteria and fungi.
C-terminal elongation of NS1 of H9N2 influenza virus induces a high level of inflammatory cytokines and increases transmission.

H9N2 avian influenza viruses are enzootic around the world and can infect many different avian and mammalian hosts, including humans. Unlike the H9N2 viruses, which mainly originated in other countries and possess a non-structural protein 1 (NS1) of 230 aa, 98 % of the H9N2 viruses isolated in China lack the 13 aa at the C terminus of NS1 (217 aa in total). The biological significance of NS1 elongation remains elusive. To examine the effect of NS1 C-terminal elongation in the influenza virus, we used reverse genetics to generate a wt avian influenza H9N2 virus containing a 217 aa NS1 (H9N2NS1217) and two mutant viruses with elongated NS1s of 230 and 237 aa (H9N2NS1230 and H9N2NS1237). C-terminal elongation of NS1 did not have a significant impact on virus replication in Madin-Darby canine kidney cells or DF-1 cells. The three variants exhibited similar replicability in mice; however, the H9N2NS1230 and H9N2NS1237 variants exhibited an upregulation in the level of inflammatory cytokines. In addition, both the H9N2NS1230 and H9N2NS1237 viruses increased replication and induced a high level of inflammatory cytokines and transmission in chickens, compared with the wt virus. These findings suggest that the NS1 extension conferred a gain of fitness to some extent.
Shock tunnel operation and correlation of boundary

Form Approved OMB No. 0704-0188 Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM-YYYY) May 2013 2. REPORT TYPE Technical Paper 3. DATES COVERED (From To) May 2013-July 2013 4. TITLE AND SUBTITLE Shock tunnel operation and correlation of boundary layer transition on a cone in hypervelocity flow 5a. CONTRACT NUMBER In-House
IMMUNOLOGY OF SPONTANEOUS MAMMARY CARCINOMAS IN MICE. II. RESISTANCE TO A RAPIDLY AND A SLOWLY DEVELOPING TUMOR.

Summary Mice of the C3H/f/Crgl and C3H/Crgl/2 sublines acquired a considerable degree of heightened resistance to the growth of implants of 2 recently arisen spontaneous C3H/Crgl mammary carcinomas as a result of previous exposure to living and killed tumor cells. Pretreatment with normal C3H/2 tissues did not induce tumor resistance, and tumor-resistant mice accepted C3H/2 skin isografts. The mutual isogenicity of the C3H, C3H/f, and C3H/2 sublines was further shown by the permanent acceptance of first and second set reciprocal skin grafts exchanged between randomly chosen pairs of young adult females. The tumor resistance evoked by the previous tumor experience could not be ascribed, therefore, to a residual heterozygosis of normal isoantigenic characteristics among or between the 3 C3H sublines employed, but appears to have evoked by immunogenic properties related to the tumors. The immunologic nature of the tumor resistance was indicated by a significant enlargement of the lymph nodes of the resistant animals, and by the ability of lymph node and peritoneal washing cells, but not of serum, to passively transfer the resistance to normal isogenic animals. Both tumors developed more rapidly in neonatal than in adult hosts. The more rapidly developing tumor of the 2 appeared to the more immunogenic. The possible reasons for this are discussed.
RASL: Robust alignment by sparse and low-rank decomposition for linearly correlated images

This paper studies the problem of simultaneously aligning a batch of linearly correlated images despite gross corruption (such as occlusion). Our method seeks an optimal set of image domain transformations such that the matrix of transformed images can be decomposed as the sum of a sparse matrix of errors and a low-rank matrix of recovered aligned images. We reduce this extremely challenging optimization problem to a sequence of convex programs that minimize the sum of ℓ1-norm and nuclear norm of the two component matrices, which can be efficiently solved by scalable convex optimization techniques with guaranteed fast convergence. We verify the efficacy of the proposed robust alignment algorithm with extensive experiments with both controlled and uncontrolled real data, demonstrating higher accuracy and efficiency than existing methods over a wide range of realistic misalignments and corruptions.
A comparison of the chromosome complement of inner cell mass and trophoblast cells in day-10 pig embryos.

Cytogenetic examination was made of 31 entire, Day-10 pig embryos, 39 separated inner cell masses and 38 of the related trophoblast samples. The incidence of mixoploidy was 64\m=. \5,5\m=. \1and 47\m=. \4%respectively. The incidence of triploidy was 2\m=. \9%. It was concluded that polyploid cells in entire Day-10 pig embryos were primarily located in the trophoblast and that the incidence of true mixoploidy in porcine embryos is very low.
Mining schema matching between heterogeneous databases

Schema matching plays a key role in heterogeneous data sources integration which can find out semantic correspondences between elements of two schemas. In this paper, a schema matching algorithm named HDSM is proposed. It can discover both 1:1 and complex matches, and find mappings between opaque columns. Experiments prove that HDSM can not only discover matches between heterogeneous databases roundly, but also enhance the efficiency and precision of schema matching.
Prevalence and risk factors associated with geographic tongue among US adults.

OBJECTIVE To characterize the prevalence of geographic tongue (GT) among US adults. DESIGN Population-based case-control study. MAIN OUTCOME MEASURES The presence or absence of GT. SUBJECTS AND METHODS Data from 16 833 adults examined during The Third National Health and Nutrition Examination Survey, 1988-1994 (NHANES III), a study based on multistage probability sampling were analyzed using SAS-callable SUDAAN 9.0. 1. RESULTS Geographic tongue point prevalence was 1.8% (95% CI: 1.4, 2.3). Multivariate logistic regression showed significant effects of race-ethnicity, with Whites (AOR = 1.8; 1.3, 2.5) and Blacks (AOR = 1.6; 1.2, 2.1) having greater odds of GT than Mexican-Americans; current corticosteroid therapy (AOR = 3.7; 1.54, 8.6). Cigarette smokers had lower GT prevalence (AOR = 0.4; 0.3, 0.6). Fissured tongue (FT) was strongly associated with GT among non-smokers: AOR = 17.5 (7.8, 39.5). We did not find significant associations with age, gender, oral contraceptive use, diabetes mellitus, allergy or atopy, psychological or dermatological conditions as previous research has suggested. CONCLUSIONS Geographic tongue was more prevalent among Whites and Blacks compared with Mexican-Americans, positively associated with FT, and inversely associated with cigarette smoking.
Supervised Filter Learning for Representation Based Face Recognition

Representation based classification methods, such as Sparse Representation Classification (SRC) and Linear Regression Classification (LRC) have been developed for face recognition problem successfully. However, most of these methods use the original face images without any preprocessing for recognition. Thus, their performances may be affected by some problematic factors (such as illumination and expression variances) in the face images. In order to overcome this limitation, a novel supervised filter learning algorithm is proposed for representation based face recognition in this paper. The underlying idea of our algorithm is to learn a filter so that the within-class representation residuals of the faces' Local Binary Pattern (LBP) features are minimized and the between-class representation residuals of the faces' LBP features are maximized. Therefore, the LBP features of filtered face images are more discriminative for representation based classifiers. Furthermore, we also extend our algorithm for heterogeneous face recognition problem. Extensive experiments are carried out on five databases and the experimental results verify the efficacy of the proposed algorithm.
Collimated Jet or Expanding Outflow: Possible Origins of Gamma-Ray Bursts and X-Ray Flashes

We investigate the dynamics of an outflow propagating in a progenitor in the context of the collapsar model for GRBs through two-dimensional axisymmetric relativistic hydrodynamic simulations. Initially, we locally inject an outflow near the center of a progenitor. We calculate 25 models, in total, by fixing its total input energy (1051 ergs s-1) and radius of the injected outflow (7 × 107 cm) while varying its bulk Lorentz factor, Γ0 = 1.05-5, and its specific internal energy, ϵ0/c2 = 0.1-30 (with c being speed of light). We find a smooth but dramatic transition from a collimated jet to an expanding outflow among calculated models. The half opening angle of the outflow (θsim) is sensitive to Γ0; we find θsim < 2° for Γ0 ≳ 3. The maximum Lorentz factor is, on the other hand, sensitive to both Γ0 and ϵ0: roughly Γmax ~ Γ0(1 + ϵ0/c2). In particular, a very high Lorentz factor of Γmax ≳ 100 is achieved in one model. A variety of opening angles can arise by changing ϵ0, even when the maximum Lorentz factor is fixed. The jet structure totally depends on Γ0. When Γ0 is high, high-pressure progenitor gas heated by the bow shock collimates the outflow to form a narrow, relativistic jet. When Γ0 is low, on the contrary, the outflow expands soon after the injection, since the bow shock is weak and thus the pressure of the progenitor gas is not high enough to confine the flow. Our finding will explain a smooth transition between the GRBs, X-ray-rich GRBs (XRRs), and X-ray flashes (XRFs) by the same model but with different ϵ0 values.