Miracle-dz/UniFAR-FTUs huggingface dataset:
Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition

The principles of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) are reviewed together with the basic thermodynamic formalism on which the two techniques are based. Although ITC is particularly suitable to follow the energetics of an association reaction between biomolecules, the combination of ITC and DSC provides a more comprehensive description of the thermodynamics of an associating system. The reason is that the parameters ΔG, ΔH, ΔS, and ΔCp obtained from ITC are global properties of the system under study. They may be composed to varying degrees of contributions from the binding reaction proper, from conformational changes of the component molecules during association, and from changes in molecule/solvent interactions and in the state of protonation. Copyright © 1999 John Wiley & Sons, Ltd.
Spectrum analysis of speech signal based on SPTool

This paper utilizes the powerful capability of Matlab and its graphical user guide to design rational digital filters, realizes spectral analysis of the speech signal with noise. First of all, a speech was recorded, and some noises were added to the original speech signal; then several common digital filters were used to filter the speech signal, playing the sound before and after filtering; then we compared and analyzed the results. Eventully, this paper realized spectrum analysis of the speech signal with noise, and realized the purpose of filtering noise.
JASIST special issue on biomedical information retrieval

Correction to Moskovitch R. , Wang F. , Pei J., and Friedman C. , “JASIST Special Issue on Biomedical Information Retrieval. ” Journal of the Association for Information Science and Technology 68(11) 2017, 2525–2528. DOI: 10.1002/ asi.23972 In the above mentioned article, one of the references was published incorrectly. The corrected reference is below: Koopman, B. , Zuccon, G. , & Bruza, P. (2017). What makes an effective clinical query and querier? Journal of the Association for Information Science and Technology, 68, 2557–2571. The authors regret any confusion caused by this error.
SeED: secure non-interactive attestation for embedded devices

Remote attestation is a security service that is typically realized by an interactive challenge-response protocol that allows a trusted verifier to capture the state of a potentially untrusted remote device. However, existing attestation schemes are vulnerable to Denial of Service (DoS) attacks, which can be carried out by swamping the targeted device with fake attestation requests. In this paper, we propose SeED, the first non-interactive attestation protocol that mitigates DoS attacks and is highly efficient. Designing such a protocol is not straightforward, since it relies on a potentially malicious prover to trigger the attestation process. We investigate the related challenges and subtleties and describe how to address them with minimal assumptions. As evaluation results show, our non-interactive attestation protocol is particularly suitable for resource-constrained embedded devices, since it is highly efficient in terms of power consumption and communication.
Immunohistochemical and Biogenetic Features of Diffuse-Type Tenosynovial Giant Cell Tumors: The Potential Roles of Cyclin A, P53, and Deletion of 15q in Sarcomatous Transformation

Purpose: Diffuse-type tenosynovial giant cell tumor (D-TSGCT) is an aggressive proliferation of synovial-like mononuclear cells with inflammatory infiltrates. Despite the COL6A3-CSF1 gene fusion discovered in benign lesions, molecular aberrations of malignant D-TSGCTs remain unidentified. Experimental Design: We used fluorescent in situ hybridization and in situ hybridization to evaluate CSF1 translocation and mRNA expression in six malignant D-TSGCTs, which were further immunohistochemically compared with 24 benign cases for cell cycle regulators involving G1 phase and G1-S transition. Comparative genomic hybridization, real-time reverse transcription-PCR, and a combination of laser microdissection and sequencing were adopted to assess chromosomal imbalances, cyclin A expression, and TP53 gene, respectively. Results: Five of six malignant D-TSGCTs displayed CSF1 mRNA expression by in situ hybridization, despite only one having CSF1 translocation. Cyclin A (P = 0.008) and P53 (P < 0.001) could distinguish malignant from benign lesions without overlaps in labeling indices. Cyclin A transcripts were more abundant in malignant D-TSGCTs (P < 0.001). All malignant cases revealed a wild-type TP53 gene, which was validated by an antibody specifically against wild-type P53 protein. Chromosomal imbalances were only detected in malignant D-TSGCTs, with DNA losses predominating over gains. Notably, −15q was recurrently identified in five malignant D-TSGCTs, four of which showed a minimal overlapping deletion at 15q22-24. Conclusions: Deregulated CFS1 overexpression is frequent in malignant D-TSGCTs. The sarcomatous transformation involves aberrations of cyclin A, P53, and chromosome arm 15q. Cyclin A mRNA is up-regulated in malignant D-TSGCTs. Non–random losses at 15q22-24 suggest candidate tumor suppressor gene(s) in this region. However, P53 overexpression is likely caused by alternative mechanisms rather than mutations in hotspot exons.
Complement Activation Is Required for Induction of a Protective Antibody Response against West Nile Virus Infection

ABSTRACT Infection with West Nile virus (WNV) causes a severe infection of the central nervous system (CNS) with higher levels of morbidity and mortality in the elderly and the immunocompromised. Experiments with mice have begun to define how the innate and adaptive immune responses function to limit infection. Here, we demonstrate that the complement system, a major component of innate immunity, controls WNV infection in vitro primarily in an antibody-dependent manner by neutralizing virus particles in solution and lysing WNV-infected cells. More decisively, mice that genetically lack the third component of complement or complement receptor 1 (CR1) and CR2 developed increased CNS virus burdens and were vulnerable to lethal infection at a low dose of WNV. Both C3-deficient and CR1- and CR2-deficient mice also had significant deficits in their humoral responses after infection with markedly reduced levels of specific anti-WNV immunoglobulin M (IgM) and IgG. Overall, these results suggest that complement controls WNV infection, in part through its ability to induce a protective antibody response.
Tales of tuning - prototyping for automatic classification of emotional user states

Classification performance for emotional user states found in the few realistic, spontaneous databases available is as yet not very high. We present a database with emotional children’s speech in a human-robot scenario. Baseline classification performance for seven classes is 44.5%, for four classes 59.2%. We discuss possible strategies for tuning, e.g., using only prototypes (based on annotation correspondence or classification scores), or taking into account requirements and feasibility in possible applications (weighting of false alarms or speakerspecific overall frequencies).
Von Willebrand Factor in Cardiovascular Disease: Focus on Acute Coronary Syndromes

von Willebrand factor (VWF) plays a pivotal role in platelet adhesion and aggregation at sites of high shear rates (eg, in coronary arteries that have stenotic or ruptured atherosclerotic plaque lesions). Numerous studies have investigated the relationship between VWF plasma levels and thromboembolic cardiovascular events. In contrast to the rather weak association in the general population, in patients with preexisting vascular disease, VWF is significantly predictive for adverse cardiac events, including death. Likewise, VWF typically rises during the course of acute coronary syndrome, and the extent of this VWF release is an independent predictor of adverse clinical outcome in these patients. Various lines of evidence indicate that VWF is not only a marker but also actually an important effector in the pathogenesis of myocardial infarction. This central role of VWF in thrombogenesis has made it a promising target for research into new antiplatelet therapies that specifically inhibit VWF. This review focuses on the role of VWF in acute coronary syndrome and further outlines the relevance of therapeutic interventions targeting VWF for acute coronary syndrome patients.
Identification of a titratable lysine residue that determines sensitivity of kidney potassium channels (ROMK) to intracellular pH.

Potassium (K+) homeostasis is controlled by the secretion of K+ ions across the apical membrane of renal collecting duct cells through a low‐conductance inwardly rectifying K+ channel. The sensitivity of this channel to intracellular pH is particularly high and assumed to play a key role in K+ homeostasis. Recently, the apical K+ channel has been cloned (ROMK1,2,3 = Kir1.1a, Kir1.1b and Kir1.1c) and the pH dependence of ROMK1 was shown to resemble closely that of the native apical K+ channel. It is reported here that the steep pH dependence of ROMK channels is determined by a single amino acid residue located in the N‐terminus close to the first hydrophobic segment M1. Changing lysine (K) at position 80 to methionine (M) removed the sensitivity of ROMK1 channels to intracellular pH. In pH‐insensitive IRK1 channels, the reverse mutation (M84K) introduced dependence on intracellular pH similar to that of ROMK1 wild‐type. A detailed mutation analysis suggests that a shift in the apparent pKalpha of K80 underlies the pH regulation of ROMK1 channels in the physiological pH range.
Alkohol & Coping – Ett webbaserat självhjälpsprogram för ungdomar vars föräldrar har alkoholproblem

Det finns ett behov av att kunna erbjuda stodjande insatser till barn och ungdomar som vaxer upp i familjer med alkoholproblem. Eftersom det ar svart att na ut med traditionellt stod behovs nya effektiva strategier och stod via internet kan vara en mojlighet. Syftet med denna studie ar att undersoka om ett webbaserat informations- och stodprogram, Alkohol & Coping, kan vara ett satt att na fram till den berorda gruppen. Resultatet visar att Alkohol & Coping nadde ett stort antal ungdomar och att de som tog del av programmet minskade sin alkoholkonsumtion. En stor andel ungdomar uppvisade ocksa symptom pa depression och en slutsats ar att denna grupp av ungdomar ar i behov av ett mer omfattande internetbaserat stod.
Human glioma immunobiology in vitro: implications for immunogene therapy.

OBJECTIVE Human gliomas are known to be immunosuppressive. Recent reports have suggested novel strategies to overcome this immunosuppression, including immunogene therapy. We examined expression of 10 immunologically important molecules by human gliomas in vitro, and we discuss the implications for immunogene therapy. METHODS Early passage human glioma cultures and established human glioma cell lines were analyzed by flow cytometry for expression of Class I and II major histocompatibility complex (MHC), B7-2 (CD86), and Fas (CD95). Culture supernatants were assayed by enzyme-linked immunosorbent assay for interleukin (IL)-6, IL-10, IL-12, transforming growth factor beta2, prostaglandin E2, and granulocyte-macrophage colony-stimulating factor levels. RESULTS All cultures (16 of 16 samples) expressed Class I MHC and Fas, but few expressed Class II MHC (1 of 16 samples) or B7-2 (0 of 16 samples). Nearly all expressed high levels of IL-6 (19 of 21 samples; mean, 36.5 +/- 10.8 ng/10(6) cells/d) and prostaglandin E2 (21 of 21 samples; mean, 15.6 +/- 4.5 ng/10(6) cells/d) levels, and many expressed transforming growth factor beta2 (13 of 21 samples; mean, 8.6 +/- 3.7 ng/10(6) cells/d). Although several cultures (6 of 14 samples) expressed granulocyte-macrophage colony-stimulating factor, expression levels were very low (mean, 0.2 +/- 0.1 ng/10(6) cells/d). Few cultures (4 of 21 samples) expressed measurable IL-10, and none (0 of 22 samples) expressed IL-12. CONCLUSION Class I MHC and Fas expression suggests that human glioma cells may be susceptible to Class I MHC-dependent cytotoxic T cell recognition and Fas-mediated killing. Unfortunately, transforming growth factor beta2 and prostaglandin E2 probably impair T cell activation, and IL-6 may shift immunity to less effective humoral (T helper 2) responses. Proinflammatory gene expression (B7-2, granulocyte-macrophage colony-stimulating factor, and/or IL-12) is lacking. Together, these results suggest that modifying glioma cells via proinflammatory gene transfer or immunoinhibitory gene suppression might stimulate immune responses that are effective against unmodified tumors.
Black-hole attractors in N = 1 supergravity

We study the attractor mechanism for N = 1 supergravity coupled to vector and chiral multiplets and compute the attractor equations of these theories. These equations may have solutions depending on the choice of the holomorphic symmetric matrix f? which appears in the kinetic lagrangian of the vector sector. Models with non trivial electric-magnetic duality group which have or have not attractor behavior are exhibited. For a particular class of models, based on an N = 1 reduction of homogeneous special geometries, the attractor equations are related to the theory of pure spinors.
Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping.

The crystal structure of cyanovirin-N (CV-N), a protein with potent antiviral activity, was solved at 1.5 A resolution by molecular replacement using as the search model the solution structure previously determined by NMR. The crystals belong to the space group P3221 with one monomer of CV-N in each asymmetric unit. The primary structure of CV-N contains 101 residues organized in two domains, A (residues 1 to 50) and B (residues 51 to 101), with a high degree of internal sequence and structural similarity. We found that under the conditions of the crystallographic experiments (low pH and 26 % isopropanol), two symmetrically related monomers form a dimer by domain swapping, such that domain A of one monomer interacts with domain B' of its crystallographic symmetry mate and vice versa. Because the two swapped domains are distant from each other, domain swapping does not result in additional intramolecular interactions. Even though one of the protein sample solutions that was used for crystallization clearly contained 100 % monomeric CV-N molecules, as judged by various methods, we were only able to obtain crystals containing domain-swapped dimers. With the exception of the unexpected phenomenon of domain swapping, the crystal structure of CV-N is very similar to the NMR structure, with a root-mean-square deviation of 0.55 A for the main-chain atoms, the best agreement reported to date for structures solved using both techniques.
Human-Robot Co-Transportation with Human Uncertainty-Aware MPC and Pose Optimization

—This paper proposes a new control algorithm for human-robot co-transportation based on a robot manipulator equipped with a mobile base and a robotic arm. The primary focus is to adapt to human uncertainties through the robot’s whole-body dynamics and pose optimization. We introduce an augmented Model Predictive Control (MPC) formulation that explicitly models human uncertainties and contains extra variables than regular MPC to optimize the pose of the robotic arm. The core of our methodology involves a two-step iterative design: At each planning horizon, we select the best pose of the robotic arm (joint angle combination) from a candidate set, aiming to achieve the lowest estimated control cost. This selection is based on solving an uncertainty-aware Discrete Algebraic Ricatti Equation (DARE), which also informs the optimal control inputs for both the mobile base and the robotic arm. To validate the effectiveness of the proposed approach, we provide theoretical derivation for the uncertainty-aware DARE and perform simulated and proof-of-concept hardware experiments using a Fetch robot under varying conditions, including different nominal trajectories and noise levels. The results reveal that our proposed approach outperforms baseline algorithms, maintaining similar execution time with that do not consider human uncertainty or do not perform pose optimization.
Broad-spectrum antiviral agents

Development of highly effective, broad-spectrum antiviral agents is the major objective shared by the fields of virology and pharmaceutics. Antiviral drug development has focused on targeting viral entry and replication, as well as modulating cellular defense system. High throughput screening of molecules, genetic engineering of peptides, and functional screening of agents have identified promising candidates for development of optimal broad-spectrum antiviral agents to intervene in viral infection and control viral epidemics. This review discusses current knowledge, prospective applications, opportunities, and challenges in the development of broad-spectrum antiviral agents.
Lightweight weapon system for robot soldier

With the development of science and technology and the coming information age, robot soldier will gradually become indispensable to the armed forces on the battlefield. Due to the use of different objects, lightweight weapon which is equipped for robot soldiers awaits to further develop. Some preliminary research and analysis on the lightweight weapon for the robot soldiers is carried out, and the requirement of the lightweight weapon for the robot soldiers is analyzed. The characteristics of the operating and using, and some problems need to solve are discussed, which will promote the research of light weapons for robot soldier.
JACS South Asia. Sustainable development in marginal regions of South Asia

The population of the South Asian subcontinent includes 500 million people who subsist on less than one dollar a day and together make up 40 % of the world’s poor. In a workshop, participants from Bangladesh, India, Pakistan and Nepal, among them scientists as well as NGO representatives, joined together to determine the focus of NCCR North-South research activities in South Asia. The consensus was that core problems associated with syndromes of global change are most acute in marginal regions and among marginalised people. As many of South Asia’s marginal areas are mountainous, problem clusters were considered to be specific to the “highland-low-land” syndrome context. It was concluded that within the JACS South Asia there is a need for research on the impact of global change upon marginal areas and within both the “highland-lowland” and the “urban-peri-urban” syndrome contexts as defined by the NCCR. Research will therefore be focused upon marginal or fragile mountain areas (i.e. those at risk due to climatic or environmental conditions in addition to their economic situation). In selected case study localities, rural livelihood strategies will be analysed to identify key factors impacting upon sustainable development. Institutions and policies that shape important processes like natural resource use, migration and rural development will form the focus of analyses.
Preserving breastfeeding practice through the HIV pandemic

Breastfeeding, particularly for the first 6 months of life, is unquestionably the ideal way to feed most infants. However, the human immunodeficiency virus (HIV) pandemic has caused debate and confusion about the best way for HIV‐positive mothers to feed their children. This review provides recent key findings and opinions around making breastfeeding safer for HIV‐positive women, and argues for preservation of breastfeeding, as opposed to complete avoidance of breastfeeding for all HIV‐positive women.
Investigation on a Multimode Switched Reluctance Motor: Design, Optimization, Electromagnetic Analysis, and Experiment

A switched reluctance motor (SRM) with 12/10 poles is investigated in this paper. Compared with the conventional SRMs with single mode, the machine is not only able to be worked as a six-phase motor but also could be used as a three-phase motor, which is thus named multimode SRM (MMSRM). The primary dimensions of the stator and rotor cores are calculated by considering it as a six-phase SRM with long magnetic paths, and the performances of three-phase mode with short magnetic paths are used to test the parameters. The arcs of stator and rotor pole are treated as the optimization objects to minimize torque ripple and copper loss per torque and maximize torque per ampere of the MMSRM. A function is selected to solve the multiobjective problem and the final values of arcs of stator and rotor pole are determined based on the results of finite-element method. The effects of arcs of stator and rotor pole on electromagnetic performances of MMSRM are discussed independently, and a prototype is manufactured to test the simulations. A good agreement between the simulated and measured results verifies the validity of the analytical method and results.
A Lytic Bacteriophage with Potential for Inactivation of a Fish Pathogenic Streptococcus agalactiae

Bacteriophage S14 specific to Streptococcus agalactiae PS01, a fish pathogenic strain, was isolated from fish pond water. It was a lytic bacteriophage that could lyse all four strains of S. agalactiae used in this study. It was tolerant to high temperature (up to 70°C), to a wide range of pH (3-11), and to antimicrobial chemicals commonly used in aquaculture. One-step growth curve showed that the bacteriophage had latent and burst periods of 40 and 160, respectively and burst size of 145 PFU/infected cell. Transmission electron microscopy reveals that the bacteriophage had an icosahedral head of 52 ± 4.6 nm in diameter and a noncontractile tail of 12 ± 0.4 nm in width and 210 ± 11.8 nm in length. Its nucleic acid was double stranded DNA because it was digested by Eco RI, but not by RnaA and nuclease S 1 . Based on its morphology and genome, the bacteriophage S14 was likely to be a member of the family Siphoviridae . This study showed that bacteriophage S14 had specificity, host range and stability favoring its use as a therapeutic agent against S. agalactiae infection in aquaculture.