Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Prediction of Conformational B-Cell Epitopes from Antigen Primary Structures by Ensemble Learning

Motivation The conformational B-cell epitopes are the specific sites on the antigens that have immune functions. The identification of conformational B-cell epitopes is of great importance to immunologists for facilitating the design of peptide-based vaccines. As an attempt to narrow the search for experimental validation, various computational models have been developed for the epitope prediction by using antigen structures. However, the application of these models is undermined by the limited number of available antigen structures. In contrast to the most of available structure-based methods, we here attempt to accurately predict conformational B-cell epitopes from antigen sequences. Methods In this paper, we explore various sequence-derived features, which have been observed to be associated with the location of epitopes or ever used in the similar tasks. These features are evaluated and ranked by their discriminative performance on the benchmark datasets. From the perspective of information science, the combination of various features can usually lead to better results than the individual features. In order to build the robust model, we adopt the ensemble learning approach to incorporate various features, and develop the ensemble model to predict conformational epitopes from antigen sequences. Results Evaluated by the leave-one-out cross validation, the proposed method gives out the mean AUC scores of 0.687 and 0.651 on two datasets respectively compiled from the bound structures and unbound structures. When compared with publicly available servers by using the independent dataset, our method yields better or comparable performance. The results demonstrate the proposed method is useful for the sequence-based conformational epitope prediction. Availability The web server and datasets are freely available at http://bcell.whu. edu.cn.
FP-LMTO Investigation of the Structural and Electronic Properties of CuxAg1–xI Alloys

The structural and electronic properties of the ternary CuxAg1–xI, alloy have been calculated, using the full-potential linear muffin-tin-orbital (FP-LMTO) method based on density functional theory, within both the local density approximation and the generalized gradient approximation (GGA). The equilibrium lattice constants and the bulk modulus are compared with previous theoretical calculations. The concentration dependence of the electronic band structure and the direct-indirect band gaps is also investigated. Using the approach of Zunger and co-workers the microscopic origins of the gap bowing were also explained.
Integration of metabolomics data into metabolic networks

Metabolite levels together with their corresponding metabolic fluxes are integrative outcomes of biochemical transformations and regulatory processes and they can be used to characterize the response of biological systems to genetic and/or environmental changes. However, while changes in transcript or to some extent protein levels can usually be traced back to one or several responsible genes, changes in fluxes and particularly changes in metabolite levels do not follow such rationale and are often the outcome of complex interactions of several components. The increasing quality and coverage of metabolomics technologies have fostered the development of computational approaches for integrating metabolic read-outs with large-scale models to predict the physiological state of a system. Constraint-based approaches, relying on the stoichiometry of the considered reactions, provide a modeling framework amenable to analyses of large-scale systems and to the integration of high-throughput data. Here we review the existing approaches that integrate metabolomics data in variants of constrained-based approaches to refine model reconstructions, to constrain flux predictions in metabolic models, and to relate network structural properties to metabolite levels. Finally, we discuss the challenges and perspectives in the developments of constraint-based modeling approaches driven by metabolomics data.
Fabrication and Properties of Cu/MgB2 Composites by Vacuum Sintering

Cu/MgB2 composites with different content of MgB2 (10, 20, 30 vol.%) were fabricated by vacuum sintering of copper and MgB2 powders. The effects of MgB2 content and sintering process on the properties of Cu/MgB2 composites including the microstructures, relative density, electrical conductivity and hardness were then investigated. The results showed that the distribution uniformity of MgB2 on copper matrix decreased obviously with the increase of MgB2 content, the hardness of Cu/MgB2 composites increased and the relative density decreased slightly though the electrical conductivity decreased greatly. The relative density and hardness of Cu/MgB2 composites increased after the repressing-resintering process, the electrical conductivity was also improved slightly.
Pulsed-laser machining and polishing of silica micro-optical components using a CO2 laser and an acousto-optic modulator

Laser ablation and laser smoothing of silica is investigated as a method of manufacturing custom micro-optics for use with high-power, diode laser arrays. A highly flexible machining regime has been identified that uses 30 to 60 microseconds square pulses, generated from a stabilized CO2 laser by an acousto-optical modulator (AOM). Refractive optical surfaces with apertures of 1 mm x 1 mm have been generated by the multi-pulse, raster scanning method with cut depths in the range of 10 to 30 μm controlled to an accuracy of better than 150 nm. A subsequent laser "fire polishing" step to smooth out the surface, using the same laser system as for machining, but in a long pulse mode at an energy fluence that just avoids further ablation of the surface. The objective of the research is to produce rapid prototyping of arrays of refractive elements, to avoid the tooling or mask-writing steps of alternative methods. A particular interest is in the generation of corrective optical elements to improve the beam quality of arrays of diode laser bars.
Distribution of aroma volatile compounds in tangerine hybrids and proposed inheritance.

BACKGROUND With the desirable combination of sugars and acids, volatile compounds contribute to the essential organoleptic attributes of citrus. This study evaluated the aroma volatiles of 20 tangerine hybrids of the University of Florida breeding program. Volatiles were sampled from hand-squeezed juice by headspace solid-phase microextraction (SPME), and analyzed by gas chromatography-mass spectrometry. Principal component analysis (PCA) and cluster analysis (CA) were used to find similarities among samples due to volatile composition with effect of genetic background. RESULTS In total, 203 volatiles were detected in all samples. Volatiles in lower amounts were widely distributed among samples and were classified mainly as terpene hydrocarbons and oxygenated compounds, such as aldehydes, esters, alcohols and ketones. PCA, based on relative peak areas (content) clearly separated the samples higher in volatile content, mainly those with sweet orange genetic contributions in their background. CA, based on volatile presence/absence, grouped samples into five clusters, each showing distinctive volatile profiles. CONCLUSION The genetic background of tangerine hybrids affected volatile composition and content of samples. In general, tangerines were characterized by fewer volatiles (in both quality and quantity) and more aldehydes, and hybrids with sweet orange in their background had more sesquiterpenes and esters, which would likely affect their aroma.
A systematic review of the effectiveness of treadmill training for children with cerebral palsy

Purpose. The development of efficient and independent walking is an important therapeutic goal for many children with cerebral palsy (CP). Consequently, there has been growing interest in determining the effects of treadmill training programs for these children. Method. A systematic review of the literature was conducted to evaluate the effectiveness of treadmill training for children with CP. Relevant trials were identified by searching electronic databases and by citation tracking. Results. Of 125 papers initially identified, five met the criteria for review. Results showed that treadmill training is safe and feasible for children with CP across a wide range of ages and functional abilities. Children with more severely affected walking ability significantly increased their walking speed (d = 1.48, 95% CI: 0.49–2.40) and gross motor performance (d = 1.5, 95% CI: 0.50–2.50) after training. However, the results also suggested that treadmill speed and length of training sessions might need to be set to specifically match desired intervention goals such as increasing walking speed or endurance. Conclusions. The review suggests that treadmill training is safe and feasible for children with CP and indicates that there may be some positive benefits in walking speed over short distances and in general gross motor skills. The provision of PBWS may be particularly beneficial for children with more severe walking disability (GMFCS III and IV). Further research is necessary before it can be concluded that treadmill training is beneficial for children with CP.
Agents Behavior and Preferences Characterization in Civilization IV

Player Modeling is becoming an important feature in Digital Games. It basically consists in understanding and modeling the player characteristics and behaviors during the game and has been mainly used to improve the games artificial intelligence, making games more adaptable to different players. In this paper, we try to characterize the preference of the players using a novel approach in games: we use mathematical regressions to characterize players behavior, looking for functions that best fit these behaviors. Using AI controlled players in Civilization IV as a testbed, this characterization is performed by extracting game data (score and resources, for example) at the end of each turn and generating functions that characterize the data evolution during the game. We were able to obtain models that distinguish the agents preferences showing the effectiveness of this approach.
Renoprotective Effect and Cost-Effectiveness of Using Benidipine, a Calcium Channel Blocker, to Lower the Dose of Angiotensin Receptor Blocker in Hypertensive Patients with Albumiuria

In hypertensive patients with chronic renal disease, angiotensin receptor blockers (ARBs) are among the first-line drugs, and calcium channel blockers (CCBs) are recommended as a second line. We examined the effects of two therapeutic strategies using ARBs and benidipine, a CCB, on blood pressure (BP), urinary albumin excretion (UAE), and cost-effectiveness in hypertensive patients with albuminuria. Patients whose BP was 140/90 mmHg or higher despite treatment with low- or medium-dose ARBs were assigned randomly to two groups. In Group A (n=14), the ARB dose was maximized and then benidipine was added until BP targets were reached (<130/85 mmHg). In Group B (n=18), benidipine was administered first and then the ARB dose was increased until BP targets were reached. The BP targets were achieved by ARB alone in 36% of Group A patients and by the addition of benidipine in 83% of Group B patients. Finally, BP decreased in each group, reaching the targets in 93% of Group A patients and 94% of Group B patients after a 4-month therapeutic period. UAE was decreased in both groups after a 4-month therapeutic period compared to the allocation period (−33±6% in Group A, −31±6% in Group B; p<0.001, respectively). The monthly drug cost was higher (11,426±880 vs. 8,955±410 yen, p=0.012) and the cost-effectiveness of antihypertensive treatment was lower (p=0.003) in Group A than in Group B. We conclude that the addition of benidipine to low- or medium-dose ARB is, in light of the renal protection and the cost-effectiveness of this approach, a useful therapeutic strategy for controlling BP in hypertensive patients with albuminuria.
Yet Another Flawed “Placebo Controlled” Study in Crohn's Disease?

Accumulating data suggest that some variants of Crohn’s disease (CD) may be consequent to a Mycobacterium avium subspecies paratuberculosis (MAP) infection. Opportunely, a prospective study (Kalfus, 2013) is addressing the therapeutic role of appropriate antimycobacterial antimicrobials in CD. Potential inflammatory bowel disease (IBD) benefits may include identification of a mycobacterial etiology, improvement on current therapies, and possibly prevention. MAP is inhibited by agents that the scientific community categorizes as anti-inflammatory (Greenstein et al., 2007) and immune-modulators. (Krishnan et al., 2009) A muchcited 2007 ‘‘placebo controlled’’ trial of anti-MAP antibiotics concluded that there was ‘‘no significant role for MAP in the pathogenesis of CD’’ (Selby et al., 2007). Subsequent correspondence dismissed the possible corrupting influence of unanticipated ‘‘immune-modulator’’ anti-MAP inhibition as being ‘‘not consistent’’ with prevailing dogma. This was despite the editorial accompanying the 2007 study emphasizing significant improvement associated with concomitant use of ‘‘immune-modulators’’ (Selby et al., 2007). Disconcertingly, the inclusion criteria in the ongoing study (Kalfus, 2013) are essentially identical to the prior ‘‘placebo’’-controlled study (Selby et al., 2007). Both ignore MAP inhibition by ‘‘anti-inflammatory’’ (Greenstein et al., 2007) and ‘‘immune-modulators. ’’ (Krishnan et al., 2009) The 2007 study (Selby et al., 2007) was designed before relevant MAP inhibition data (Greenstein et al., 2007; Krishnan et al., 2009) were published. The designers of the study now recruiting (Kalfus, 2013) should explain why they ignore unrefuted published data that render their ‘‘placebo-controlled’’ study as flawed as previously (Selby et al., 2007). We suggest that calling the study now recruiting (Kalfus, 2013) ‘‘placebo-controlled’’ is unscientific (Greenstein et al., 2014). Multiple medications that inhibit infectious agents (Greenstein et al., 2014) are permitted in both the ‘‘placebo’’ as well as treated groups. (Greenstein et al., 2014). Previously, we have suggested that ‘‘add-on studies’’ is scientifically more accurate than ‘‘placebo-controlled’’ (Greenstein et al., 2014). A consistently flawed study design may yet again be misinterpreted as showing no added efficacy of anti-MAP agents in CD. Consequently, the potential identification of the etiology of IBD as being due to the zoonosis of MAP may irrevocably be lost.
Sentence extraction and rhetorical classification for flexible abstracts

Knowledge about the discourse-level structure of a scientific article is useful for flexible and sub-domain independent automatic abstraction. We are interested in the automatic identification of content units ("argumentative entities") in the source text, such as GOAL OR PROBLEM STATEMENT, CONCLUSIONS and RESULTS. In this paper, we present an extension of Kupiec et al.’s methodology for trainable statistical sentence extraction (1995). Our extension additionally classifies the extracted sentenccs according to their argumentative status; because only low-level properties of the sentence are taken into account and no external knowledge sources other than meta-level linguistic ones are used, it achieves robustness and partial domain-independence.
Effects of zinc oxide nanoparticles on the physical properties of polyacrylonitrile

Polyacrylonitrile (PAN)/zinc oxide (ZnO) nanocomposites were prepared by solution mixing in dimethylacetamide, followed by film casting, and their physical properties were investigated. The heating scan of differential scanning calorimetry displayed only a single crystallization peak (Tc) without a melting peak, regardless of the presence of ZnO. The incorporation of ZnO nanoparticles decreased Tc by 13°C, and increased the heat of crystallization by 18%. Further, it greatly improved the thermal stability of PAN, even at the ZnO content as low as 0.1 wt %. The nanocomposites showed the UV transmittance peak at 365 nm, whose intensity was increased as ZnO content was increased. The presence of ZnO did not produce new peak nor shift the peaks with respect to PAN in wide angle X-ray diffraction pattern. Introduction of a small amount of ZnO nanoparticles did not have notable effect on the tensile properties. However, 5 wt % loading of the nanoparticles increased the tensile modulus of PAN by 14.5% and decreased elongation at break dramatically. PAN nanocomposites with 5 wt % ZnO did not show any plateau region in stress–strain curve. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1854–1858, 2006
Integrins Regulate Mouse Embryonic Stem Cell Self‐Renewal

Extracellular matrix (ECM) components regulate stem‐cell behavior, although the exact effects elicited in embryonic stem (ES) cells are poorly understood. We previously developed a simple, defined, serum‐free culture medium that contains leukemia inhibitory factor (LIF) for propagating pluripotent mouse embryonic stem (mES) cells in the absence of feeder cells. In this study, we determined the effects of ECM components as culture substrata on mES cell self‐renewal in this culture medium, comparing conventional culture conditions that contain serum and LIF with gelatin as a culture substratum. mES cells remained undifferentiated when cultured on type I and type IV collagen or poly‐d‐lysine. However, they differentiated when cultured on laminin or fibronectin as indicated by altered morphologies, the activity of alkaline phosphatase decreased, Fgf5 expression increased, and Nanog and stage‐specific embryonic antigen 1 expression decreased. Under these conditions, the activity of signal transducer and activator of transcription (STAT)3 and Akt/protein kinase B (PKB), which maintain cell self‐renewal, decreased. In contrast, the extracellular signal‐regulated kinase (ERK)1/2 activity, which negatively controls cell self‐renewal, increased. In the defined conditions, mES cells did not express collagen‐binding integrin subunits, but they expressed laminin‐ and fibronectin‐binding integrin subunits. The expression of some collagen‐binding integrin subunits was downregulated in an LIF concentration‐dependent manner. Blocking the interactions between ECM and integrins inhibited this differentiation. Conversely, the stimulation of ECM‐integrin interactions by overexpressing collagen‐binding integrin subunits induced differentiation of mES cells cultured on type I collagen. The results of the study indicated that inactivation of the integrin signaling is crucial in promoting mouse embryonic stem cell self‐renewal.
Diabetes as a risk factor for dementia and mild cognitive impairment: a meta‐analysis of longitudinal studies

This study examined the association of diabetes with the onset of dementia (including Alzheimer's disease (AD), vascular dementia (VD) and any dementia) and mild cognitive impairment (MCI) by using a quantitative meta‐analysis of longitudinal studies. EMBASE and MEDLINE were searched for articles published up to December 2010. All studies that examined the relationship between diabetes and the onset of dementia or MCI were included. Pooled relative risks were calculated using fixed and random effects models. Nineteen studies met our inclusion criteria for this meta‐analysis, and 6184 subjects with diabetes and 38 530 subjects without diabetes were included respectively. All subjects were without dementia or MCI at baseline. The quantitative meta‐analysis showed that subjects with diabetes had higher risk for AD (relative risk (RR):1.46, 95% confidence interval (CI): 1.20–1.77), VD (RR: 2.48, 95% CI: 2.08–2.96), any dementia (RR: 1.51, 95% CI: 1.31–1.74) and MCI (RR: 1.21, 95% CI: 1.02–1.45) than those without. The quantitative meta‐analysis showed that diabetes was a risk factor for incident dementia (including AD, VD and any dementia) and MCI.
E‐health in Australia: time to plunge into the 21st century

E‐health is the health care buzzword of the moment, with a person‐controlled electronic health record funded in the 2010 federal Budget and legislation to introduce health identifiers recently passed by Parliament. E‐health can ease the patient journey, improve quality of care and reduce costs. Australia's health care system lags behind all other sectors of our economy in the use of computerised systems. While general practice and community pharmacy are highly computerised, the hospital sector is not. Adopting e‐health is likely to result in higher quality practice, but general practice and hospitals need a mechanism for securely sharing patient data. Uncoordinated implementation of differing, incompatible systems within and between hospitals compounds a dire lack of national coordination of effort. Multiple funding streams and jurisdictions and the lack of an implementation strategy have slowed e‐health development. Government programs underestimate the costs of change management and the need for training and technology. Confusion reigns about responsibilities, but governments must ensure connectivity between health care providers and recognise that the benefits will accrue into the future. The National E‐Health Transition Authority has developed national open‐access standards, and its foundation projects and the National Broadband Network are now coming into place. To ensure the clinical relevance, utility, safety and acceptability of e‐health systems, health professionals urgently need technical capacity and expert guidance.
Human taeniasis: current insights into prevention and management strategies in endemic countries

Human taeniasis is a zoonotic condition resulting from infection with the adult stages of Taenia saginata (“beef tapeworm”), Taenia solium (“pork tapeworm”) or Taenia asiatica (“Asian tapeworm”). Although these parasites have a worldwide distribution, the overwhelming burden is felt by communities in low- and middle-income countries. This is particularly true for T. solium, whereby infection of the central nervous system with the larval stage of the parasite (neurocysticercosis) is a major cause of acquired epilepsy in low-resource settings. With a focus on endemic countries, this review provides an insight into the prevention and management of human taeniasis, concluding with some recent case studies describing their implementation. Discussion of the opportunities and challenges regarding current fecal and serological diagnostic assays for detecting Taenia spp. highlights the importance of accurate and accessible diagnostic options for the field situation. The lack of long-term impact on the parasites’ lifecycle from human anthelmintic treatment, coupled with the propensity for adverse reactions, highlights the importance of a “two-pronged” approach that considers the relevant animal hosts, particularly in the case of T. solium. Aside from the therapeutic options, this review reiterates the importance of adequate assessment and consideration of the associated behavioral and policy aspects around sanitation, hygiene and meat inspection that have been shown to support parasite control, and potential elimination, in endemic regions.
A scalable and efficient content-based multimedia retrieval system

In this work the problem of content-based information retrieval is approached from a new perspective. We look at a probabilistic approach in CBIR from the angle of Bayesian networks. Our data structure serves to break two bottlenecks of retrieval performance: (1) high dimensionality of feature vectors and (2) poor mapping of raw features into highlevel content that a human understands (the semantic gap). We use the network structure instead of the feature space, and propose updating the higherlevel content description by utilising the relevance feedback obtained from the user. Strategies for display update for the next iteration are studied. A new approach for selecting the next display set is tied to our data structure.