Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation

Transmembrane β-barrels (TMBs) are one important class of membrane proteins that play crucial functions in the cell. Membrane proteins are difficult wet-lab targets of structural biology, which call for accurate computational prediction approaches. Here, we developed a novel method named MemBrain-TMB to predict the spanning segments of transmembrane β-barrel from amino acid sequence. MemBrain-TMB is a statistical machine learning-based model, which is constructed using a new chain learning algorithm with input features encoded by the image sparse representation approach. We considered the relative status information between neighboring residues for enhancing the performance, and the matrix of features was translated into feature image by sparse coding algorithm for noise and dimension reduction. To deal with the diverse loop length problem, we applied a dynamic threshold method, which is particularly useful for enhancing the recognition of short loops and tight turns. Our experiments demonstrate that the new protocol designed in MemBrain-TMB effectively helps improve prediction performance.
Rethinking macroeconomic theory before the next crisis

Misguided economics policies relying on an unrealistic macroeconomic theory that denied the possibility of a crisis are at the origins of the Global Financial Crisis. The goal of the present paper is to recall how the end of the Great Moderation has been interpreted by the advocates of mainstream economics, and how they have questioned their own macroeconomic theories as a consequence of what happened during and after the financial crisis. There is thus a need to reconsider most aspects of mainstream theory. In particular, the crisis has once more demonstrated that potential output is influenced by aggregate demand – a phenomenon associated with hysteresis which also questions concepts such as the natural rate of interest and crowding-out effects.
Influence of morphogenesis and connecting with a river on a rate of oxbow lake evolution in young glacial river valleys

The oxbow lakes are water reservoirs being a sub-type of river lakes that are morphogenetically associated with the main river channel (CHOIŃSKI 1988). They are usually distinguished by semi-circle shape resulting from complex hydrodynamic processes (erosion-accumulation) in a river bed, that lead to bends and meanders formation. Against common opinion on boring semi-circle shapes and similarity of morphometric and biocenotic features, these reservoirs are characterized by extremely abundant diversity of shapes, dimensions, and hence reactions towards hydrological processes (CONSTANTINE, DUNNE 2008; HEIN et al. 2004; WEIHAUPT 1989). The oxbow lakes, spreading on both sides of river beds, enrich the hydrographic and biocenotic structure of a valley (OBOLEWSKI et al. 2009; PENCZAK et al. 2005; VAN DEN BRINK et al. 1993) by accompanying numerous natural or anthropogenically transformed water ecosystems. Their value results from a wide spectrum of ecological benefits, including the help in water purification processes, flood control, habitat features for freshwater biocenoses, and landscape virtues (CABEZAS et al. 2009; MITSCH, GOSSELINK 2000). The specificity of the origin, morphometry, and hydrodynamics of oxbow lakes indicate that they should be considered as a type of aqueous ecosystems differing from postglacial lakes that are common in young-glacial landscape. At comparisons of oxbow lakes with postglacial ones, following attributes resulting from below features should be taken into account: • genesis. The oxbow lake's genesis is associated with a slow meander migration down the river valley and enhancing of its curvature till both arms connection and cutting off the river. Davis (1903) and Tower (1904) were the first who documented and described in details the oxbow lake genesis. The effect of a screw-type water flow due to the presence of any obstacle (e.g. a rock resistant to washing out) is the main reason for river bed bending and free meanders formation. Then, one of the river-side (concave) gets eroded, and materials accumulate on the other side (convex) that is situated down the river course. An oblong sandbar is formed at convex embankment that makes the waters are directed to opposite (concave) one
Biologically Mediated Anaerobic Methane Oxidation — The Missing Sink in an Active Martian Methane Cycle?

ACTIVE MARTIAN METHANE CYCLE? R. L. Harris, B. L. Ehlmann, R. Bhartia, and T. C. Onstott; Dept. of Geosciences, Princeton University, Princeton, NJ 08544 (rlh6@princeton.edu, tullis@princeton.edu). Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91126 (ehlmann@caltech.edu). Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (rohit.bhartia@jpl.nasa.gov).
Parameters Estimation and Stability Analysis of Nonlinear Fractional-Order Economic System Based on Empirical Data

and Applied Analysis 3 for all roots λ of the following equation ([18]): det (diag ([λmq1λmq2 . . . λmq1]) − J) = 0. (5) For fractional-order system (2), the necessary stability condition for it to remain chaotic is keeping at least one eigenvalue λ in the unstable region (see [19]). Suppose that the unstable eigenvalues of scroll saddle points are λ 1,2 = a 1,2 ± ib 1,2 . The necessary condition to exhibit double-scroll attractor of the system remaining in the unstable region is exhibited in [19]. The condition for commensurate derivatives order is
Salmonella—how a metabolic generalist adopts an intracellular lifestyle during infection

The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, “-omics” data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.
Bone Related Health Status in Adolescent Cyclists

Purpose To describe bone status and analyse bone mass in adolescent cyclists. Methods Male road cyclists (n = 22) who had been training for a minimum of 2 years and a maximum of 7 years with a volume of 10 h/w, were compared to age-matched controls (n = 22) involved in recreational sports activities. Subjects were divided in 2 groups based on age: adolescents under 17 yrs (cyclists, n = 11; controls, n = 13) and over 17 yrs (cyclists, n = 11; controls, n = 9). Peak oxygen uptake (VO2max) was measured on a cycloergometer. Whole body, lumbar spine, and hip bone mineral content (BMC), density (BMD) and bone area were assessed using dual x-ray absorptiometry (DXA). Volumetric BMD (vBMD) and bone mineral apparent density (BMAD) were also estimated. Results The BMC of cyclists was lower for the whole body, pelvis, femoral neck and legs; BMD for the pelvis, hip, legs and whole body and legs bone area was lower but higher in the hip area (all, P≤0.05) after adjusting by lean mass and height. The BMC of young cyclists was 10% lower in the leg and 8% higher in the hip area than young controls (P≤0.05). The BMC of cyclists over 17 yrs was 26.5%, 15.8% and 14.4% lower BMC at the pelvis, femoral neck and legs respectively while the BMD was 8.9% to 24.5% lower for the whole body, pelvis, total hip, trochanter, intertrochanter, femoral neck and legs and 17.1% lower the vBMD at the femoral neck (all P≤0.05). Grouped by age interaction was found in both pelvis and hip BMC and BMD and in femoral neck vBMD (all P≤0.05). Conclusion Cycling performed throughout adolescence may negatively affect bone health, then compromising the acquisition of peak bone mass.
Biotechnological Innovations in the Forestry Sector and their Economic Impacts on Other Sectors via Embodied Technology Transfer: An Investigation within Dynamic GTAP Framework

Abstract In this paper, we consider technology transfers embodied in trade flows within a seven-region, seven-traded-commodity version of the dynamic GTAP model. 0.63% Hicks-Neutral technical progress in forestry sector (logging) in source regions has differential impacts on productivity of the logging-user sectors. This is ascribed to the differential rates of induced technology transmission via traded intermediates. Destination regions’ ability to utilize new technology depends on their absorptive capacity (AC) and structural similarity (SS). Together with trade flows, these two factors determine the recipient’s success in assimilating foreign technology. Sectors intensive in logging like wood products, paper products, publishing register higher productivity growth. Differences in productivity improvements depend on the differentials in the magnitude of technology capture.
Role of medical history and medication use in the aetiology of upper aerodigestive tract cancers in Europe: the ARCAGE study.

BACKGROUND The study aimed to investigate the role of medical history (skin warts, Candida albicans, herpetic lesions, heartburn, regurgitation) and medication use (for heartburn; for regurgitation; aspirin) in the aetiology of upper aerodigestive tract (UADT) cancer. METHODS A multicentre (10 European countries) case-control study [Alcohol-Related CAncers and GEnetic susceptibility (ARCAGE) project]. RESULTS There were 1779 cases of UADT cancer and 1993 controls. History of warts or C. albicans infection was associated with a reduced risk [odds ratio (OR) 0.80, 95% confidence interval (CI) 0.68-0.94 and OR 0.73, 95% CI 0.60-0.89, respectively] but there was no association with herpetic lesions, heartburn, regurgitation or medication for related symptoms. Regurgitation was associated with an increased risk for cancer of the oesophagus (OR 1.47, 95% CI 0.98-2.21). Regular aspirin use was not associated with risk of UADT cancer overall but was associated with a reduced risk for cancer of oesophagus (OR 0.51, 95% CI 0.28-0.96), hypopharynx (OR 0.53, 95% CI 0.28-1.02) and larynx (OR 0.74, 95% CI 0.54-1.01). CONCLUSIONS A history of some infections appears to be a marker for decreased risk of UADT cancer. The role of medical history and medication use varied by UADT subsites with aspirin use associated with a decreased risk of oesophageal cancer and suggestive of a decreased risk of hypopharyngeal and laryngeal cancers.
Neoadjuvant, surgery and adjuvant chemotherapy without radiation for esophageal cancer.

BACKGROUND A phase II trial to evaluate neoadjuvant (NAD), surgery and adjuvant (AD) combination chemotherapy without radiation therapy (RT) for patients with esophageal adenocarcinoma staged with endoscopic ultrasound and CT as T3N1 was carried out. METHODS Thirty-three eligible patients were enrolled. NAD therapy was administered in two 49-day cycles and included cisplatin, floxuridine, paclitaxel and leucovorin. Esophageal resection was performed followed by AD therapy. RESULTS Thirty-three patients initiated NAD therapy; 10 experienced grade 3 and 4 toxicities, which included leucopenia, fatigue, nausea, diarrhea and stomatitis. Additionally, 16 patients experienced grade 1 and 2 hematologic and non-hematologic toxicities. Fifteen patients were down-staged, of whom five were T2, seven were T1, and three had nodal disease with no evidence of residual cancer in the esophageal bed. Fifteen patients remained T3, and two showed progressive disease. Thirty-two patients proceeded to surgery and 30 were resected. Although all resected patients were eligible for AD therapy, 15 did not receive it either because of patient refusal or surgeon recommendation. Fifteen patients received AD therapy: nine who had remained T3 and six who had down-staged. Three patients experienced grade 3 and 4 toxicities similar to those in NAD therapy. Six patients had grade 1 and 2 toxicities. Kaplan-Meier estimates of overall survival at 1, 3 and 5 years were 73% (95% CI: 58-88%), 52% (95% CI: 34-69%) and 29% (95% CI: 13-45%), respectively. Median survival was 42 months. CONCLUSION Deletion of RT may safely allow for more aggressive chemotherapy and increase chances of survival. The results need to be confirmed in a randomized phase II or larger phase III trial.
Inhibition Shapes Sex Selectivity in the Mouse Accessory Olfactory Bulb

Laterally connected inhibitory circuitry is found throughout the nervous system, including many early sensory processing systems. The extent to which it plays a role in shaping neuronal stimulus selectivity in systems like olfaction, however, which lack a simple two-dimensional representation of their stimulus space, has remained controversial. We examined this issue using an experimental preparation that allowed electrophysiological recording from the accessory olfactory bulb of an anesthetized mouse during the controlled delivery of pheromonal stimuli, in this case derived from the urine of male and female mice. We found that individual neurons were often highly selective for the sex of the urine donor. Examination of both explicitly inhibitory responses, as well as responses to mixtures of male and female urine, revealed that laterally connected inhibition was both prevalent and of large magnitude, particularly for male-selective neurons. Pharmacological manipulation of this inhibition resulted in a shift in many neurons' stimulus selectivities. Finally, we found that a behavioral response (pregnancy block) evoked by the presence of unfamiliar male urine could be suppressed by the addition of female urine to the stimulus, demonstrating that this system displays a behavioral opponency consistent with neural inhibition. Together, these results indicate that laterally connected inhibitory circuitry in the accessory olfactory bulb plays an important role in shaping neural selectivity for natural stimuli.
3 What Has Personality Got to Do With Relationships ?

G what I have proposed as a new way to look at relationships—as connected to social order, as based in language and performance, as connected with identity and the persuasion of others, as about the presentation of preferred ways of looking at the world as a whole in the hope of having other people accept those views, as a form of action based on symbols—then several key issues arise. First, what happens to the view that relationships are based on similarity of personality? What is personality, and how does personality influence choice of friends or romantic partner? Second, given that a lot of the research reviewed briefly so far considers the influence of self, attitudes, personality, and disclosure of one’s inner being andprivate thoughts,howdoes the newway connect to such a concept as personality? Third, given that many of us believe that our personality is formed to a large extent in childhood, how do our early experiences influence later—apparently free—choices in relationships?
Research on reactive power compensation for distribution network based on biogeography-based optimization algorithm

Distribution network reactive power optimization, which can effectively reduce distribution network wastage, can not only improve voltage distribution network quality, but also realize the distribution network security control. Stable operation provides solid foundation for the electric power enterprise economy. Unlike genetic algorithm that shares the feature information between the chromosomes, the unique migration pattern of BBO algorithm makes the good feature in the habitats broadcast widely among habitats, thus, the optimization process would be accelerated and the reactive power compensation location could be confirmed quickly. And by using BBO algorithm in the example analysis and conducting simulation through PSASP, it proves that biogeography optimization algorithm is quite effective when applied in distribution network reactive power optimization.
Braga-Portugal THERMOELECTRIC THIN-FILMS FOR MICROCOOLERS AND ENERGY SCAVENGING MICROSYSTEMS

The cold area of the device (4 mm) is cooled using four pair of thermoelectric elements, connected in series with aluminum/nickel contacts (Fig. 3). Flexible substrates add uncommon mechanical properties to the composite film-substrate and enable their integration with many novel types of electronic devices. Kapton was chosen as substrate because of its low thermal conductivity (0.16 W.m.K), thus allowing for higher performance of cooler devices. The value of thermal expansion coefficient of Kapton (12×10 K), which closely matches the thermal expansion coefficient of the telluride films, reduces residual stress and increases adhesion of thermoelectric films. Films were deposited by co-evaporation of Bismuth and Tellurium or Antimony and Tellurium to obtain Bi2Te3 or Sb2Te3 compounds (Fig. 2), respectively. The performance of thermoelectric devices depends on figure of merit (ZT) of the film, given by ZT = αT/(κρ), where α, T, κ and ρ are the Seebeck coefficient, absolute temperature, thermal conductivity and electrical resistivity, respectively. Optimal growing deposition parameters allow the fabrication of films with ZT = 0.9 and ZT = 0.5 for Bi2Te3 and Sb2Te3, respectively. These values are comparable with the best published results for the same material, under various fabrication methods (thermal co-evaporation [1], sputtering, MO-CVD, flash-evaporation or electrochemical deposition). A layered structure (superlattice) can increase films performance and a figure of merit of 2.4 can be achieved [2] in a layered Bi2Te3/Sb2Te3. Seebeck coefficient is increased and thermal conductivity reduced, by controlling the transport of phonons and electrons in the superlattice structure.
User identification design by fusion of face recognition and speaker recognition

Intelligent human-robot interface helps a mobile robot to extract external information and interact with a user. User identification information allows a robot to generate appropriate behaviors and make personalized human-robot interaction (PHRI) more natural and safe. Most of service robots move around in various application settings, and biometric features always change during relative movements. In this work, a fusion recognition system based on face and speaker classifiers is designed to achieve the user recognition in various environments. We propose a method to fuse face and speech recognition results based on the concept of confidence indices. Through the derived confidence indices, the system combines the two classifiers and gives improved recognition results. Experiments on a laboratory home service robot show that person recognition rates in 15 environmental situations all outperform those of using single modality.
M. paratuberculosis Heat Shock Protein 65 and Human Diseases: Bridging Infection and Autoimmunity

Mycobacterium avium subspecies paratuberculosis (MAP) is the known infectious cause of Johne's disease, an enteric inflammatory disease mostly studied in ruminant animals. MAP has also been implicated in the very similar Crohn's disease of humans as well as sarcoidosis. Recently, MAP has been associated with juvenile sarcoidosis (Blau syndrome), autoimmune diabetes, autoimmune thyroiditis, and multiple sclerosis. While it is intuitive to implicate MAP in granulomatous diseases where the microbe participates in the granuloma, it is more difficult to assign a role for MAP in diseases where autoantibodies are a primary feature. MAP may trigger autoimmune antibodies via its heat shock proteins. Mycobacterial heat shock protein 65 (HSP65) is an immunodominant protein that shares sequential and conformational elements with several human host proteins. This molecular mimicry is the proposed etiopathology by which MAP stimulates autoantibodies associated with autoimmune (type 1) diabetes, autoimmune (Hashimoto's) thyroiditis, and multiple sclerosis. This paper proposes that MAP is a source of mycobacterial HSP65 and acts as a trigger of autoimmune disease.
Penalized least-square CT reconstruction without and with statistical weights : effect on lesion detection performance with human observers

Iterative CT reconstruction with the penalized leastsquare model may offer significant gains in terms of image quality at equal dose, and may thereby allow either dose reduction or improved diagnostic. In this work, we are interested in evaluating image quality improvements that result from using statistical weights in this model. Image quality is assessed in terms of lesion detection with unknown location, using the principles of LROC analysis with human observers. Reconstruction without and with statistical weights are compared for two penalties: a quadratic penalty, and an edge-preserving penalty. Interestingly, our study failed showing any major improvements due to the use of weights. Furthermore, it was even observed that performance with weights could be even worse, possibly due to the utilization of weights leading to disturbing discretization errors. Because there are a lot of degrees of freedom in our experimental set-up, it should not be concluded that statistical weights are not useful. However, we can state that improvements are not straightforward and may depend on many aspects including the task and anatomical location. This observation is valuable from a computational viewpoint since using statistical weights generally leads to long reconstruction times; if weights can be ignored in some settings, reconstruction times can be largely improved for these settings.
ON USING AN EMULATIVE MIDDLEWARE TO MODEL WIRELESS NETWORKS : SIMULATION RESULTS AND VALIDATION

Setting up and using realistic wide area testbeds for developing and testing large-scaled distributed applications and communication mechanisms may be very expensive. Therefore, designers use simulative technologies to obtain elastic and reproducible frameworks where those experiments may be safely carried out in local lab-based environments. Conventional simulators are based on the idea that the model of the real system must be completely simulated. In contrast with this idea, most recent simulation technologies say that not all entities should be simulated, but some should be real. That is, the simulation experiments must not be confined to isolated simulation worlds but have to embrace also emulation scenarios with real operational network devices. By exploiting this idea, we have designed and developed a simulative platform for networked applications (called Interceptor), where an emulation interface has been developed both to integrate into the simulation real network communication traffic, coming from different networked end-systems, and to incorporate into the simulation environment entire communication protocol layers, without the need of specifying them into the simulation model. In this paper we present the architecture of Interceptor and discuss some relevant examples of wireless simulation modeling using our emulation-based approach.