Miracle-dz/UniFAR-FTUs huggingface dataset:
A KS-type dehydrin and its related domains reduce Cu-promoted radical generation and the histidine residues contribute to the radical-reducing activities

Dehydrin is a plant disordered protein whose functions are not yet totally understood. Here it is reported that a KS-type dehydrin can reduce the formation of reactive oxygen species (ROS) from Cu. AtHIRD11, which is the Arabidopsis KS-type dehydrin, inhibited generation of hydrogen peroxide and hydroxyl radicals in the Cu–ascorbate system. The radical-reducing activity of AtHIRD11 was stronger than those of radical-silencing peptides such as glutathione and serum albumin. The addition of Cu2+ reduced the disordered state, decreased the trypsin susceptibility, and promoted the self-association of AtHIRD11. Domain analyses indicated that the five domains containing histidine showed ROS-reducing activities. Histidine/alanine substitutions indicated that histidine is a crucial residue for reducing ROS generation. Using the 27 peptides which are related to the KnS-type dehydrins of 14 plant species, it was found that the strengths of ROS-reducing activities can be determined by two factors, namely the histidine contents and the length of the peptides. The degree of ROS-reducing activities of a dehydrin can be predicted using these indices.
A Software Tool for Estimation of Burden of Infectious Diseases in Europe Using Incidence-Based Disability Adjusted Life Years

The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS). To meet this goal, a user-friendly software tool (BCoDE toolkit), was developed. This stand-alone application, written in C++, is open-access and freely available for download from the website of the European Centre for Disease Prevention and Control (ECDC). With the BCoDE toolkit, one can calculate DALYs by simply entering the age group- and sex-specific number of cases for one or more of selected sets of 32 communicable diseases (CDs) and 6 healthcare associated infections (HAIs). Disease progression models (i.e., outcome trees) for these communicable diseases were created following a thorough literature review of their disease progression pathway. The BCoDE toolkit runs Monte Carlo simulations of the input parameters and provides disease-specific results, including 95% uncertainty intervals, and permits comparisons between the different disease models entered. Results can be displayed as mean and median overall DALYs, DALYs per 100,000 population, and DALYs related to mortality vs. disability. Visualization options summarize complex epidemiological data, with the goal of improving communication and knowledge transfer for decision-making.
Major Carbohydrate Antigen of Echinococcus multilocularis Induces an Immunoglobulin G Response Independent of αβ+ CD4+ T Cells

ABSTRACT Echinococcus multilocularis causes alveolar echinococcosis, one of the most lethal helminthic (accidental) infections in humans, as the life cycle predominantly includes wildlife rodents as intermediate hosts. The physical barrier between the proliferating parasitic metacestode and the host tissue is the acellular laminated layer (LL), which is characterized by its rich high-molecular-weight polysaccharide composition. Conversely to a crude protein-rich vesicular fluid antigen, a major carbohydrate antigen of the LL—the Em2(G11) antigen—did not stimulate murine T-cell proliferation in vitro. In fact, the persistent metacestode growth and antigenic stimulation induced a Th2 shift in vivo following conventional infection by intraperitoneal inoculation of 100 metacestode vesicles into C57/BL6 mice. Concurrently, the expression of Th1 cytokines (interleukin-2 and gamma interferon) remained persistently low until the late stage of chronic infection. In comparison to a recombinant proteinic II/3 antigen, the specific immunoglobulin G (IgG) response against the Em2(G11) antigen (including all IgG isotypes) maintained persistently low avidity. Furthermore, the Em2(G11) antigen induced a specific IgM and IgG response in T-cell-deficient athymic nude, TCRβ−/−, major histocompatibility complex class II (MHCII)−/−(CD4-deficient), and CD40−/−mice. The Em2(G11)-specific IgG synthesized in nude TCRβ−/− and MHCII−/− mice was predominantly of the IgG3 and IgG2a isotypes and of the IgG3 and IgG2b isotypes in CD40−/− mice. This finding suggested that in vivo, the IgG response to major carbohydrate antigen Em2(G11) ofE. multilocularis could take place independently of αβ+ CD4+ T cells and in the absence of CD40-CD40 ligand interactions; thus, the Em2(G11) antigen of the acellular LL represents a T-cell-independent antigen. Functionally, the encapsulating LL, and especially its major carbohydrate antigen, Em2(G11), seems to be one of the key factors in the parasite's survival strategy and acts by modulating the host immune response by virtue of its T-cell-independent nature.
PID control of laser surface hardening of steel

We discuss control strategies for the laser surface hardening of steel. The goal is to achieve a prescribed hardening depth avoiding surface melting. Our mathematical model consists of a system of ordinary differential equations (ODEs) for the phase volume fractions coupled with the heat equation. The system is solved semi-implicitely using the finite element method. To obtain a uniform hardening depth the first attempt is to use proportional integral differential (PID) control to achieve a constant temperature in the hot spot of the laser beam on the surface. However, the numerical results prove that this is not sufficient. We show that the best strategy is to control the temperature close to the lower boundary of the hardening zone. Then one can compute the optimal temperature in the hot spot of the beam and use it as the setpoint for the pyrometer control of the real process
World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia Part 3: Update 2015 Management of special circumstances: Depression, Suicidality, substance use disorders and pregnancy and lactation

Abstract These updated guidelines are based on the first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in the years 2005 and 2006. For this 2015 revision, all available publications pertaining to the biological treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations which are clinically and scientifically relevant. They are intended to be used by all physicians diagnosing and treating patients with schizophrenia. Based on the first version of these guidelines a systematic review, as well as a data extraction from national guidelines have been performed for this update. The identified literature was evaluated with respect to the strength of evidence for its efficacy and subsequently categorised into six levels of evidence (A–F) and five levels of recommendation (1–5). This third part of the updated guidelines covers the management of the following specific treatment circumstances: comorbid depression, suicidality, various comorbid substance use disorders (legal and illegal drugs), and pregnancy and lactation. These guidelines are primarily concerned with the biological treatment (including antipsychotic medication and other pharmacological treatment options) of patients with schizophrenia.
L2P2: Location-aware location privacy protection for location-based services

Location privacy has been a serious concern for mobile users who use location-based services provided by the third-party provider via mobile networks. Recently, there have been tremendous efforts on developing new anonymity or obfuscation techniques to protect location privacy of mobile users. Though effective in certain scenarios, these existing techniques usually assume that a user has a constant privacy requirement along spatial and/or temporal dimensions, which may not be true in real-life scenarios. In this paper, we introduce a new location privacy problem: Location-aware Location Privacy Protection (L2P2) problem, where users can define dynamic and diverse privacy requirements for different locations. The goal of the L2P2 problem is to find the smallest cloaking area for each location request so that diverse privacy requirements over spatial and/or temporal dimensions are satisfied for each user. In this paper, we formalize two versions of the L2P2 problem, and propose several efficient heuristics to provide such location-aware location privacy protection for mobile users. Through multiple simulations on a large data set of trajectories for one thousand mobile users, we confirm the effectiveness and efficiency of the proposed L2P2 algorithms.
Kinematics and Singularity Analysis of a Novel Type of 3-CRR 3-DOF Translational Parallel Manipulator

A new three-degrees-of-freedom (3-DOF) translational parallel manipulator (TPM) with linear actuators, i.e., 3-CRR TPM, is first proposed. The rotation singularity analysis, the inverse kinematics, the forward kinematics, and the kinematic singularity analysis of the 3-CRR TPM are then performed. The analysis shows that the proposed TPM has the following kinematic merits over previous TPMs. (1) The forward displacement analysis can be performed by solving a set of linear equations. (2) The Jacobian matrix of the TPM is constant. The inverse of the Jacobian matrix can be pre-calculated, and there is no need to calculate repeatedly the inverse of the Jacobian matrix in performing the forward displacement analysis and forward velocity analysis. (3) There is no rotation singularity. (4) There is no uncertainty singularity. (5) The TPM has a fewer number of links or joints. The geometric condition for a 3-CRR TPM to be isotropic is also revealed. Two additional kinematic merits exist for the isotropic 3-CRR TPM. The first is that an isotropic 3-CRR TPM is isotropic in its whole workspace. The second is that no calculation is needed in order to pre-determine the inverse of the Jacobian matrix. Finally, preliminary design considerations are presented.
Visualisation of interaction footprints for engagement and motivation in online communities – results of first interviews

Glahn, C. , Specht, M. , & Koper, R. (2008). Visualisation of interaction footprints for engagement and motivation in online communities – results of first interviews. In M. Kalz, R. Koper, V. Hornung-Prahauser & M. Luckmann (Eds.), Proceedings of the 1st Workshop on Technology Support for Self-Organized Learners (TSSOL08) (pp. 29-43). June, 2-3, 2008, Salzburg, Austria. Available at http://sunsite.informatik. rwth-aachen.de/Publications/CEUR-WS/Vol-349/glahn.pdf
Low rank metric learning for social image retrieval

With the popularity of social media applications, large amounts of social images associated with rich context are available, which is helpful for many applications. In this paper, we propose a Low Rank distance Metric Learning (LRML) algorithm by discovering knowledge from these rich contextual data, to boost the performance of CBIR. Different from traditional approaches that often use the must-links and cannot-links between images, the proposed method exploits information from the visual and textual domains. We assume that the visual similarity estimated by the learned metric is expected to be consistent with the semantic similarity in the textual domain. Since tags are usually noisy, misspelling or meaningless, we also leverage the preservation of visual structure to prevent overfitting those noisy tags. On the other hand, the metric is straightforward constrained to be low rank. We formulate it as a convex optimization problem with nuclear norm minimization and propose an effective optimization algorithm based on proximal gradient method. With the learned metric for image retrieval, some experimental evaluations on a real-world dataset demonstrate the outperformance of our approach over other related work.
Earthquake Early Warning with GPS Data

The combined use of seismic and geodetic observations is now a common practice for finite-fault modeling and seismic source parametrization. With the advent of highrate 1Hz GPS stations the seismological community has recently begun looking at GPS data as a valid complement to the seismic-based methodologies for Earthquake Early Warning (EEW). In the standard approaches to early warning, the initial portion of the P-wave signal is used to rapidly characterize the earthquake magnitude and to predict the expected ground shaking at a target site, before the arrival of the most damaging waves. Whether the final magnitude of an earthquake can be predicted while the rupture process is underway, still represents a controversial issue; the point is that the limitations of the standard approaches when applied to giant earthquakes have become evident after the experience of the Mw 9.0, 2011 Tohoku-Oki earthquake. Here we explore the application of GPS data to EEW and investigate whether they can be used to provide reliable and independent magnitude estimations. The large size and the complex rupture process, together with the huge number of high-quality GPS records available, make the 2011 Tohoku-Oki earthquake a unique and ideal casestudy for our purposes.
Normalized Fuzzy Control of High Density Aquiculture’s Dissolved Oxygen

The viscosity of DO(dissolved oxygen) in high density aquiculture is affected by many factors, and its characters have nonlinearity, hysteresis and big-inertial. Normal PID control is difficult to achieve perfect purpose. According to the variety of DO’s viscosity, a fuzzy algorithm was advanced to make system output relevant voltage/frequency to be master of transducer. It can control the electric machine’s rev to ensure the steady DO’s viscosity, at the same time it can also save energy and prolong equipment’s useful time
Examination of the Roles of Sgs1 and Srs2 Helicases in the Enforcement of Recombination Fidelity in Saccharomyces cerevisiae

Mutation in SGS1, which encodes the yeast homolog of the human Bloom helicase, or in mismatch repair (MMR) genes confers defects in the suppression of mitotic recombination between similar but nonidentical (homeologous) sequences. Mutational analysis of SGS1 suggests that the helicase activity is required for the suppression of both homologous and homeologous recombination and that the C-terminal 200 amino acids may be required specifically for the suppression of homeologous recombination. To clarify the mechanism by which the Sgs1 helicase enforces the fidelity of recombination, we examined the phenotypes associated with SGS1 deletion in MMR-defective and recombination-defective backgrounds. Deletion of SGS1 caused no additional loss of recombination fidelity above that associated with MMR defects, indicating that the suppression of homeologous recombination by Sgs1 may be dependent on MMR. However, the phenotype of the sgs1 rad51 mutant suggests a MMR-independent role of Sgs1 in the suppression of RAD51-independent recombination. While homologous recombination levels increase in sgs1Δ and in srs2Δ strains, the suppression of homeologous recombination was not relaxed in the srs2 mutant. Thus, although both Sgs1 and Srs2 limit the overall level of mitotic recombination, there are distinct differences in the roles of these helicases with respect to enforcement of recombination fidelity.
Polymorphisms in the Calcium-Sensing Receptor Gene Are Associated with Clinical Outcome of Neuroblastoma

Background Neuroblastic tumors include the neuroblastomas, ganglioneuroblastomas, and ganglioneuromas. Clinical behavior of these developmental malignancies varies from regression to aggressive growth with metastatic dissemination. Several clinical, histological, genetic, and biological features are associated with this diversity of clinical presentations. The calcium-sensing receptor (CaSR) is a G-protein coupled receptor with a key role in calcium homeostasis. We have previously reported that it is expressed in benign, differentiated neuroblastic tumors, but silenced by genetic and epigenetic events in unfavorable neuroblastomas. We have now analyzed three functionally relevant polymorphisms clustered at the signal transduction region of the CaSR (rs1801725, rs1042636 and rs1801726) to assess if genetic variants producing a less active receptor are associated with more aggressive disease course. Methods Polymorphisms were analyzed in DNA samples from 65 patients using specific Taqman Genotyping Assays. Results Mildly inactivating variant rs1801725 was associated with clinical stage 4 (P = 0.002) and the histological subgroup of undifferentiated neuroblastomas (P = 0.046). Patients harboring this polymorphism had significantly lower overall (P = 0.022) and event-free survival (P = 0.01) rates than those who were homozygous for the most common allele among Caucasians. However, this single locus genotype was not independently associated with outcome in multivariate analyses. Conversely, the tri-locus haplotype TAC was independently associated with an increased risk of death in the entire cohort (Hazard Ratio = 2.45; 95% Confidence Interval [1.14–5.29]; P = 0.022) and also in patients diagnosed with neuroblastomas (Hazard Ratio = 2.74; 95% Confidence Interval [1.20–6.25]; P = 0.016). Conclusions The TAC haplotype includes the moderately inactivating variant rs1801725 and absence of the gain-of-function rs1042636 polymorphism. Thus, its association with metastatic disease and poor outcome would add to our previous data and further support that inactivation of the CaSR gene is a mechanism associated with neuroblastoma malignant behavior.
Treatment of patients with advanced neurofibromatosis type 2 with novel molecularly targeted therapies: from bench to bedside.

Minimal treatment options exist for advanced, inoperable neurofibromatosis type 2 (NF2), which is a rare tumor-prone disorder. NF2 results from a mutation in the NF2 tumor-suppressor gene on chromosome 22q12. NF2 is genetically and phenotypically distinguished from neurofibromatosis type 1, which results from a mutation in the NF1 tumor-suppressor gene located on chromosome 17q11.1,2 Clinically, NF2 is inherited in an autosomal dominant fashion and manifests through the appearance of bilateral acoustic neuromas (vestibular schwannomas), which lead to progressive hearing loss.3 Vestibular schwannomas and other lesions seen in patients with NF2 that arise progressively from other sites, such as meningiomas, spinal schwannomas, astrocytomas, ependymomas, rarely neurofibromas, and peripheral neuropathies, lead to profound morbidity in this debilitating disease.1,4 Few options are available to these patients outside of surgery, which is the mainstay of treatment for NF2-associated lesions, and, in some instances, radiation therapy.1,2 Despite our understanding of the underlying genetics and molecular pathophysiology of this disorder, patients become debilitated from tumor-related comorbidities. Recently, the anti–vascular endothelial growth factor (VEGF) antibody bevacizumab and erlotinib exhibited promising activity in pilot trials.5–8 Other than these two agents, no medical options are available for patients with NF2 with surgically unresectable disease. Because patients with NF2 harbor an aberration in a single gene, merlin, the protein product of which impacts multiple signals, including PI3-kinase/Akt, Raf/mitogen-activated protein/extracellular signal-regulated kinase, and mammalian target of rapamycin (mTOR), it is conceivable that one of the many agents that target these pathways that have already shown antitumor activity in malignancies will also cause the regression of NF2-related tumors.9–11 Because of its extreme rarity, conducting large clinical trials in NF2 is generally unfeasible.9 Therefore, we enrolled patients with NF2 onto various rationally targeted trials and sought response signals. We reviewed the records of consecutive patients with NF2 who were referred to the Clinical Center for Targeted Therapy (phase I Clinical Trials Program clinic) who were treated in more than one trial starting in January 2007 to December 2010. All trials were approved by the MD Anderson institutional review board, which also granted a waiver of informed consent and a waiver of authorization for this retrospective study. Patients were evaluated every 6 to 8 weeks for response by using RECIST with computed tomography and magnetic resonance imaging.
Effect of nano structuration on molecular response

The concept of nanostructuration of polymer composites is now recognized as having produced an important class of nanocomposites. The dielectric and insulation properties arising from nanostructuration can be dramatically affected, and significantly enhanced, by controlling the structure at the nanometer level. In this paper, some particular traits, rules and drawbacks related to nanometric size fillers are explored in reference to the molecular scale and response.
Semi-supervised Speech Act Recognition in Emails and Forums

In this paper, we present a semi-supervised method for automatic speech act recognition in email and forums. The major challenge of this task is due to lack of labeled data in these two genres. Our method leverages labeled data in the Switchboard-DAMSL and the Meeting Recorder Dialog Act database and applies simple domain adaptation techniques over a large amount of unlabeled email and forum data to address this problem. Our method uses automatically extracted features such as phrases and dependency trees, called subtree features, for semi-supervised learning. Empirical results demonstrate that our model is effective in email and forum speech act recognition.
Hepatitis C virus (HCV) genotypes and the influence of HCV subtype 1b on the progression of chronic hepatitis C in Korea: a single center experience

Background/Aims There is some controversy regarding whether or not hepatitis C virus (HCV) subtype 1b is more influential than non-1b subtypes on the progression of chronic hepatitis (CH) C to liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Methods We retrospectively analyzed 823 patients with chronic HCV infection, including 443 CH patients, 264 LC patients, and 116 HCC patients, who were HCV RNA positive and HBsAg negative. These patients had not received any prior treatment with either interferon alone or a combination of interferon and ribavirin. Results HCV subtypes 1b (51.6%) and 2a/2c (39.5%) were the two most common genotypes. The proportions of genotypes 2 (2a/2c, 2b, and 2) and 3 were 45.8% and 1.1%, respectively. One case of genotype 4 was found. HCV subtype 1b (47.3%) was less common than the non-1b subtypes (52.7%) in non-LC patients, but its proportion (56.9%) was higher than that of non-1b subtypes (43.1%) in LC patients (P=0.006). The proportions of patients with HCV subtype 1b did not differ significantly between the LC (55.3%) and HCC (60.3%) groups. Older age, male gender, and the relative progression of liver damage (non-LC vs. compensated LC vs. decompensated LC) were significant risk factors for HCC, with odds ratios of 1.081 (95% confidence interval [CI], 1.056-1.106), 5.749 (95% CI, 3.329-9.930), and 2.895 (95% CI, 2.183-3.840), respectively. HCV subtype 1b was not a significant risk factor for HCC (odds ratio, 1.423; 95% CI, 0.895-2.262). Conclusions HCV subtypes 1b and 2a/2c were the two most common HCV genotypes. HCV subtype 1b seemed to be more influential than non-1b subtypes on the progression of CH to LC, but not on the development of HCC from LC.