Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
DEMOCRACY ON THE WEB

This paper addresses a fundamental empirical question using data collected in a northeastern US city: does deliberation occur in online forums? While face-to-face deliberation is well documented, there are few empirical studies that address its online counterpart. Deliberation is supposed to foster an educative, rational, open and inclusive dialogue that leads to legitimate policy outcomes. In this paper, the authors develop and operationalize a measure of deliberation in order to investigate the extent to which it is manifested online. In particular, the authors study five regionally defined web forums hosted by the primary newspaper of a mid-sized northeastern US city. Drawing a two-week sample of posts from these forums, the authors then examine them for indicators of deliberation. Firstly, this paper addresses research about if and how the internet affects social life, including traditional notions of deliberation. Next, the authors argue that sociological studies of democratic participation require conceptualization of lived deliberation, and outline a Symbolic Interactionist approach to studying online, deliberative interaction in order to do so. The paper concludes by discussing the implications of this work for future theory and empirical investigation.
The evaluation of the effect of carbon dioxide laser radiation on dentine tissue.

of this study was to analyze the effects of carbon dioxide (CO2) laser light on the structure and elemental composition of dentine. METHODS The evaluation was conducted on samples from extracted teeth. The surface of the dentine was exposed to the radiation from a CTL 1401 CO2 laser (Centre of Laser Technology, Poland). The radiation and frequency parameters were as follows: group I with 5 W and 1 Hz, group II with 10 W and 1 Hz, group III with 5 W and 5 Hz, and group IV with 10 W and 5 Hz. The altered dentine structure was macroscopically and microscopically evaluated using a Nova NanoSEM 200 Scanning Electron Microscope (FEI Europe) with integrated microanalysis X-ray system for elemental analysis in points. RESULTS There were significant differences between groups in the macro- and microstructure of laser defects. CONCLUSIONS CO2 laser radiation causes irreversible, destructive changes in dentine. The structural dentine lesions developed under the influence of the CO2 laser radiation may hinder proper adhesion of bonding systems with the damaged tissue. Laser defects in the structure should be treated like defects of noncarious origin requiring preparation and filling with composite materials in accordance with the procedures.
Low-Cost 3D Scanning by Exploiting Virtual Image Symmetries

We present a low-cost, hybrid active/passive 3D scanning system based on an off-the-shelf camera, a laser stripe illuminator and a turntable. The system combines the good accuracy of active triangulation approaches with the flexibility of self-calibration based approaches. System operation is based on the construction of a single view of a virtual surface of revolution, from which camera calibration (both intrinsic and extrinsic parameters) is performed by exploiting the same object being scanned. Shape acquisition is finally obtained by laser profile reconstruction and collation. Experiments with both synthetic and real data are shown, providing an insight into both camera calibration and shape reconstruction performance.
Long-Term Sympathoinhibitory Effects of Surgically Induced Weight Loss in Severe Obese Patients

Weight loss improves insulin sensitivity and exerts sympathomodulatory effects. No data, however, are available on the effects of the weight loss induced by vertical sleeve gastrectomy on sympathetic neural drive, insulin sensitivity, and their reciprocal cross talks. In 10 severe obese hypertensives (age, 54.0±2.3 years [mean±SEM]), we measured sphygmomanometric blood pressure, heart rate, body mass index, homeostatic model assessment index, plasma leptin, muscle sympathetic nerve traffic (microneurography), and baroreflex sensitivity (vasoactive drug technique). Measurements were performed 2 to 3 days before surgery and repeated 6 and 12 months after the procedure. Ten matched hypertensive obeses not undergoing gastrectomy served as controls. Six months after bariatric surgery, a significant (P<0.05) reduction in body mass index (−9.1±1.4 kg/m2), sphygmomanometric systolic blood pressure (−10.2±4.5 mm Hg), heart rate (−11.0±2.4 bpm), homeostatic model assessment index (−3–3±1.3 AU), plasma leptin (−53.6±8.8 &mgr;g/L), and muscle sympathetic nerve traffic (−15.0±3.4 bursts/100 heart beats) was observed. The weight loss, the plasma leptin reduction, and the sympathetic inhibition were maintained after 12 months, whereas homeostatic model assessment index showed a tendency to return toward presurgery values. A significant improvement in baroreflex control of sympathetic nerve traffic was observed both 6 (+32.1%; P<0.05) and 12 months (+60.7%; P<0.01) after gastrectomy. No significant changes in the above-mentioned variables were detected in the control group. These data provide evidence that massive weight loss induced by sleeve gastrectomy triggers profound sympathoinhibitory effects, associated with a stable and significant reduction in plasma leptin levels, whereas the improvement in insulin sensitivity was attenuated with time and unrelated to the sympathoinhibition.
Estimation and Accuracy After Model Selection

Classical statistical theory ignores model selection in assessing estimation accuracy. Here we consider bootstrap methods for computing standard errors and confidence intervals that take model selection into account. The methodology involves bagging, also known as bootstrap smoothing, to tame the erratic discontinuities of selection-based estimators. A useful new formula for the accuracy of bagging then provides standard errors for the smoothed estimators. Two examples, nonparametric and parametric, are carried through in detail: a regression model where the choice of degree (linear, quadratic, cubic, …) is determined by the Cp criterion and a Lasso-based estimation problem.
Buffer and controller minimisation for time-constrained testing of system-on-chip

Test scheduling and test access mechanism (TAM) design are two important tasks in the development of a system-on-chip (SOC) test solution. Previous test scheduling techniques assume a dedicated designed TAM which has the advantage of high flexibility in the scheduling process. However hardware overhead is incurred for implementing the TAM and additional routing is required. In this paper, we propose a technique that makes use of the existing functional buses for the test data transportation inside the SOC. We have dealt with the test scheduling problem with this new assumption and developed a technique to minimise the test-controller and buffer size for a bus-based multi-core SOC. We have solved the problem by using a constraint logic programming (CLP) technique and demonstrated the efficiency of our approach by running experiments on benchmark designs.
Estrogen Receptor in Human Breast Cancer Cell Lines Comparison of Histochemical and Biochemical Assays for Updated

Two human breast cancer lines, MCF-7 and T47D cells, were investigated for the presence of estrogen receptor (ER) by biochemical and histochemical techniques. Using the dextrancoated charcoal technique and isoelectric focusing, MCF-7 cells were ER positive, and T47D cells were ER negative. Fluorescein conjugates to 17/i-estradiol by the sixth carbon (17/i-estradiol6-carboxymethyloxime:bovine serum albumin: fluorescein isothiocyanate and ^/S-estradiol-G-iminooxyacetylfluoresceinamine) and by the 17th carbon |A/-fluoresceino-A/ '-[17/3-(estradiol hemisuccinamide)ethyl]thiourea, 17-FEj were prepared for cytochemical evaluation of the ER status of the two cell lines. The binding affinity of the estradici conjugates for ER varied, the 17FE conjugate having the highest affinity of 0.08 relative to 17/3estradiol. Following incubation with 10 nM 17-FE, both MCF-7 and T47D cells displayed cytoplasmic and nuclear fluorescent staining. Isoelectric focusing of MCF-7 cytosol incubated in the presence of 10 nM 17-FE revealed binding of the fluorescein conjugate to a protein species which did not bind 170-[3H]estradiol. Isoelectric focusing of T47D cytosol revealed binding of 17-FE to two protein components, neither one of which showed specific binding of 17/Ã®-[3H]estradiol. The results suggest different protein binding species for fluoresceinated estradici conjugates and [3H]estradiol and help to explain reported differ ences in histochemical and biochemical ER analyses.
Older people are at risk of sexually transmitted infections

The highest age of participants in the current National Surveys of Sexual Attitudes and Lifestyles (NATSAL III) is 74 years; the rise from 44 year in NATSAL II is both timely and apposite. Analysis of UK surveillance data shows that while younger people still account for the majority of sexually transmitted infections (STIs), the fastest growing increases are in people over 45 years.1 For example, between 1999 and 2008, there was a 102% increase in reported cases of Chlamydia among 16–19 year old women …
Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site

Flavivirus proteins are produced by co- and posttranslational proteolytic processing of a large polyprotein by both host- and virus-encoded proteinases. The viral serine proteinase, which consists of NS2B and NS3, is responsible for cleavage of at least four dibasic sites (2A/2B, 2B/3, 3/4A, and 4B/5) in the nonstructural region. Since the amino acid sequence preceding NS4B shares characteristics with signal peptides used for translocation of nascent polypeptides into the lumen of the endoplasmic reticulum, it has been proposed that cleavage at the 4A/4B site is mediated by a cellular signal peptidase. In this report, cell-free translation and in vivo transient expression assays were used to study processing in the NS4 region of the yellow fever virus polyprotein. With a construct which contained NS4B preceded by 17 residues constituting the putative signal peptide (sig4B), membrane-dependent cleavage at the 4A/4B site was demonstrated in vitro. Surprisingly, processing of NS4A-4B was not observed in cell-free translation studies, and in vivo expression of several yellow fever virus polyproteins revealed that the 4A/4B cleavage occurred only during coexpression of NS2B and the proteinase domain of NS3. Examination of mutant derivatives of the NS3 proteinase domain demonstrated that cleavage at the 4A/4B site correlated with expression of an active NS2B-3 proteinase. From these results, we propose a model in which the signalase cleavage generating the N terminus of NS4B requires a prior NS2B-3 proteinase-mediated cleavage at a novel site (called the 4A/2K site) which is conserved among flaviviruses and located 23 residues upstream of the signalase site. In support of this model, mutations at the 4A/4B signalase site did not eliminate processing in the NS4 region. In contrast, substitutions at the 4A/2K site, which were engineered to block NS2B-3 proteinase-mediated cleavage, eliminated signalase cleavage at the 4A/4B site. In addition, the size of the 3(502)-4A product generated by trans processing of a truncated polyprotein, 3(502)-5(356), was consistent with cleavage at the 4A/2K site rather than at the downstream 4A/4B signalase site.
CrowdLang - First Steps Towards Programmable Human Computers for General Computation

Crowdsourcing markets such as Amazon’s Mechanical Turk provide an enormous potential for accomplishing work by combining human and machine computation. Today crowdsourcing is mostly used for massive parallel information processing for a variety of tasks such as image labeling. However, as we move to more sophisticated problem-solving there is little knowledge about managing dependencies between steps and a lack of tools for doing so. As the contribution of this paper, we present a concept of an executable, model-based programming language and a general purpose framework for accomplishing more sophisticated problems. Our approach is inspired by coordination theory and an analysis of emergent collective intelligence. We illustrate the applicability of our proposed language by combining machine and human computation based on existing interaction patterns for several general computation
Intradimer/Intermolecular Interactions Suggest Autoinhibition Mechanism in Endophilin A1

Endophilin A1 is a homodimeric membrane-binding endocytic accessory protein with a high dimerization affinity. Its function has been hypothesized to involve autoinhibition. However, the autoinhibition mechanism, as well as the physicochemical basis for the high dimerization affinity of endophilin in solution, have remained unclear. In this contribution, we use a Förster resonance energy transfer (FRET) method to investigate the homodimerization mechanism and intradimer molecular interactions in endophilin. For the endophilin N-BAR domain (which lacks the SH3 domain including a linker region of the full length protein), we observe a large temperature dependence of the dimerization affinity and dimer dissociation kinetics, implying large dimerization enthalpy and dissociation activation enthalpy, respectively. Our evaluation of the protein concentration dependence of dimer dissociation kinetics implies that endophilin reversibly forms monomers via a dissociation/reassociation mechanism. Furthermore, we use a kinetic method that allows us to compare the dissociation kinetics of full-length endophilin to that of truncated mutants. We find that mutants that lack either H0 helix or SH3 domain show significantly faster dissociation kinetics relative to full-length endophilin. This observation supports the presence of an intradimer, intermonomer cross-interaction between H0 helix and SH3 domain from different subunits within a homodimer. Because the H0 helix is known to play a significant role in endophilin’s membrane interactions, our measurements support a syngergistic model where these interactions are inhibited in the absence of SH3 domain binding ligands such as dynamin’s prolin rich domains, and where the binding of these ligands may be suppressed for non-membrane-bound endophilin.
Serum apolipoprotein A1 and haptoglobin, in patients with suspected drug-induced liver injury (DILI) as biomarkers of recovery

Background There is a clear need for better biomarkers of drug-induced-liver-injury (DILI). Aims We aimed to evaluate the possible prognostic value of ActiTest and FibroTest proteins apoliprotein-A1, haptoglobin and alpha-2-macroglobulin, in patients with DILI. Methods We analyzed cases and controls included in the IMI-SAFE-T-DILI European project, from which serum samples had been stored in a dedicated biobank. The analyses of ActiTest and FibroTest had been prospectively scheduled. The primary objective was to analyze the performance (AUROC) of ActiTest components as predictors of recovery outcome defined as an ALT <2x the upper limit of normal (ULN), and BILI <2x ULN. Results After adjudication, 154 patients were considered to have DILI and 22 were considered to have acute liver injury without DILI. A multivariate regression analysis (ActiTest-DILI patent pending) combining the ActiTest components without BILI and ALT (used as references), apolipoprotein-A1, haptoglobin, alpha-2-macroglobulin and GGT, age and gender, resulted in a significant prediction of recovery with 67.0% accuracy (77/115) and an AUROC of 0.724 (P<0.001 vs. no prediction 0.500). Repeated apolipoprotein-A1 and haptoglobin remained significantly higher in the DILI cases that recovered (n = 65) versus those that did not (n = 16), at inclusion, at 4–8 weeks and at 8–12 weeks. The same results were observed after stratification on APAP cases and non-APAP cases. Conclusions We identified that apolipoprotein-A1 and haptoglobin had significant predictive values for the prediction of recovery at 12 weeks in DILI, enabling the construction of a new prognostic panel, the DILI-ActiTest, which needs to be independently validated.
Representations of Two-Variable Elementary Functions Using EVMDDs and their Applications to Function Generators

This paper proposes a method to represent two-variable elementary functions using edge-valued multi-valued decision diagrams (EVMDDs), and presents a design method and an architecture for function generators using EVMDDs. To show the compactness of EVMDDs, this paper introduces a new class of integer-valued functions, l-restricted Mp-monotone increasing functions, and derives an upper bound on the number of nodes in an edge-valued binary decision diagram (EVBDD) for the l-restricted Mp-monotone increasing function. EVBDDs represent l-restricted Mp- monotone increasing functions more compactly than MTB- DDs and BMDs when p is small. Experimental results show that all the two-variable elementary functions considered in this paper can be converted into l-restricted Mp- monotone increasing functions with p = 1 or p = 3, and can be compactly represented by EVBDDs. Since EVMDDs have shorter paths and smaller memory size than EVBDDs, EVMDDs can produce fast and compact elementary function generators.
TIBIAL SPUR FEEDING IN GROUND CRICKETS: LARGER MALES CONTRIBUTE LARGER GIFTS (ORTHOPTERA: GRYLLIDAE)

Abstract Many male insects provide somatic nuptial gifts that may strongly influence reproductive fitness by insuring an effective copulation or by increasing paternal investment. In the striped ground cricket, Allonemobius socius (Scudder), females receive a nuptial gift by chewing on a specialized spur on the male’s hind tibia during copulation. Using a series of no-choice trials, we attempted to quantify gift magnitude and to determine the relationships between male size, gift contribution, and male mating success. Tibial spur chewing duration was a significant predictor of gift contribution (F1,17 = 17.02, P < 0.001) and the magnitude of the gift ranged between 0.2% and 8% of the male’s body mass, implying that females receive mostly hemolymph. Large males produced bigger gifts than small males (2.52 ± 0.59 mg vs. 1.33 ± 0.28 mg, t17 = 1.88, P < 0.05, respectively) and females were more likely to mate with larger males (F1,39 = 4.76, P < 0.05). If gift size is shown to influence female reproductive fitness, then nuptial gifts may play a large role in the evolution of male body size.
Lysosomal impairment in Parkinson's disease

Impairment of autophagy‐lysosomal pathways (ALPs) is increasingly regarded as a major pathogenic event in neurodegenerative diseases, including Parkinson's disease (PD). ALP alterations are observed in sporadic PD brains and in toxic and genetic rodent models of PD‐related neurodegeneration. In addition, PD‐linked mutations and post‐translational modifications of α‐synuclein impair its own lysosomal‐mediated degradation, thereby contributing to its accumulation and aggregation. Furthermore, other PD‐related genes, such as leucine‐rich repeat kinase‐2 (LRRK2), parkin, and phosphatase and tensin homolog (PTEN)‐induced putative kinase 1 (PINK1), have been mechanistically linked to alterations in ALPs. Conversely, mutations in lysosomal‐related genes, such as glucocerebrosidase (GBA) and lysosomal type 5 P‐type ATPase (ATP13A2), have been linked to PD. New data offer mechanistic molecular evidence for such a connection, unraveling a causal link between lysosomal impairment, α‐synuclein accumulation, and neurotoxicity. First, PD‐related GBA deficiency/mutations initiate a positive feedback loop in which reduced lysosomal function leads to α‐synuclein accumulation, which, in turn, further decreases lysosomal GBA activity by impairing the trafficking of GBA from the endoplasmic reticulum‐Golgi to lysosomes, leading to neurodegeneration. Second, PD‐related mutations/deficiency in the ATP13A2 gene lead to a general lysosomal impairment characterized by lysosomal membrane instability, impaired lysosomal acidification, decreased processing of lysosomal enzymes, reduced degradation of lysosomal substrates, and diminished clearance of autophagosomes, collectively contributing to α‐synuclein accumulation and cell death. According to these new findings, primary lysosomal defects could potentially account for Lewy body formation and neurodegeneration in PD, laying the groundwork for the prospective development of new neuroprotective/disease‐modifying therapeutic strategies aimed at restoring lysosomal levels and function. © 2013 Movement Disorder Society
Screening for depression in primary care Development and validation of the Depression Scale, a screening instrument for depression

Depression is a common mental disorder; effective methods for treating it are also available. Its recognition and diagnosis are prerequisite to effective treatment. A majority of depressed patients are generally managed in the primary care setting; only a half of the cases, however, are identified at their first visit. Screening instruments to improve recognition of depression have therefore been developed. The Depression Scale (DEPS), consisting of 10 items, was developed and tested in primary care patients aged 18 to 64 years. Clinical assessments were made on the basis of Present State Examination interviews with 436 patients. The DEPS proved to be satisfactory. Increasing age and poor education had an adverse effect on the screening process, however. The sensitivity of the DEPS for clinical depression was 74% and the specificity for non‐depression 85%. The sensitivity for severe depression was 84% and the specificity for symptom‐free patients 93%. The DEPS seems to improve the recognition of depression in primary care and may also be suitable for screening depression in the general population and for identifying high‐risk groups.
Measurement Considerations for Assessing Unidirectional Latencies �

This paper presents a study of single direction latencies to selected destinations of the Internet utilizing a variety of paths The objective is to demonstrate that round trip latencies are an insu cient and sometimes misleading method to determine unidirectional delays This claim has signi cant implications for high speed multi application wide area tra c aggregating network ing environments which often require predictability of precise delay