Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Protein Domains Contribute to the Action of the Copper Chaperone for Superoxide Dismutase*

The copper chaperone for superoxide dismutase (SOD1) inserts the catalytic metal cofactor into SOD1 by an unknown mechanism. We demonstrate here that this process involves the cooperation of three distinct regions of the copper chaperone for SOD1 (CCS): an amino-terminal Domain I homologous to the Atx1p metallochaperone, a central portion (Domain II) homologous to SOD1, and a short carboxyl-terminal peptide unique to CCS molecules (Domain III). These regions fold into distinct polypeptide domains as revealed through proteolysis protection studies. The biological roles of the yeast CCS domains were examined in yeast cells. Surprisingly, Domain I was found to be necessary only under conditions of strict copper limitation. Domain I and Atx1p were not interchangeable in vivo, underscoring the specificity of the corresponding metallochaperones. A putative copper site in Domain II was found to be irrelevant to yeast CCS activity, but SOD1 activation invariably required a CXC in Domain III that binds copper. Copper binding to purified yeast CCS induced allosteric conformational changes in Domain III and also enhanced homodimer formation of the polypeptide. Our results are consistent with a model whereby Domain I recruits cellular copper, Domain II facilitates target recognition, and Domain III, perhaps in concert with Domain I, mediates copper insertion into apo-SOD1.
Correlation between non-Debye behavior and Q behavior of the alpha relaxation in glass-forming polymeric systems.

By means of quasielastic neutron scattering we have shown that the dynamics of the α relaxation on three different polymeric glasses shows a clear non-Debye behavior on a mesoscopic time scale. The spectral shape is found to be independent of temperature and momentum transfer (Q). The characteristic relaxation time follows a power-law Q dependence, τ(Q)∞Q -n (n>2), n being dependent on the system. We found that the Q behavior and the non-Debye behavior are directly correlated. These results have important implications concerning the physical mechanisms behind the dynamics of the α relaxation
Super Junction MOSFETs above 600V with Parallel Gate Structure Fabricated by Deep Trench Etching and Epitaxial Growth

600 V class superjunction (SJ) MOSFETs fabricated by deep-trench etching and epitaxial growth method are experimentally investigated. Planar SJ MOSFETs with both parallel and orthogonal gate structures are fabricated. The SJ MOSFET with parallel gate structure exhibits an improved specific on-resistance of 17 mOmegaldrcm2, which is about 30% lower than that of orthogonal gate structures with the same breakdown voltage of 650 V.
A local obstacle avoidance control law for mobile robot navigation based on Beam Curvature Method

This paper focuses on the based Beam Curvature Method for two wheeled mobile robot navigation in partially known environments. Local obstacle avoidance problem by indoor mobile robots has been a well-researched subject by several robotics researchers. There are various reactive strategies which operate in the velocity space such as the Dynamic Windows Approach (DWA), the Curvature Velocity Method (CVM), the Lane Curvature Method (LCM) and the Beam Curvature Method (BCM). These approaches formulate the local obstacle avoidance problem and take into account the robot dynamics and environment physical constraints. In this paper we present a comparison between two methods based on the Beam Curvature Method and the Dynamic Window Approach.
Mistyping of two Slovenian hepatitis C virus subtype 2c isolates as subtype 2b by two 5' noncoding region genotyping methods

During our recent comparison of the reliabilities of four different hepatitis C virus (HCV) genotyping methods (4, 5), two Slovenian HCV subtype 2c isolates which were misclassified as subtype 2b by the two most widely used genotyping methods, second-generation line probe assay (Inno LiPA; Innogenetics, Ghent, Belgium) (7) and restriction fragment length polymorphism (RFLP) (1) analysis, were identified. Namely, although these two 59 noncoding region (59NCR)based genotyping methods clearly identified both isolates as HCV subtype 2b, this subtype could not be confirmed by two core-based genotyping methods and by sequence analysis of the 270-bp fragment of the NS-5 region. Thus, a commercial core-based nested PCR coupled with DNA enzyme immunoassay (GEN-ETI-K-DEIA; Sorin Biomedica, Saluggia, Italy) (8) assigned genotype 2 and excluded subtypes 2a and 2b for both Slovenian isolates, since the genotype 2-specific probe included in the assay hybridized with PCR products and both subtype 2a- and 2b-specific probes did not. By the second core-based genotyping method, Okamoto’s genotype-specific PCR (3), HCV subtype could not be exactly determined in either isolate due to multiple PCR products obtained. Finally, sequence and phylogenetic analysis of the 270-bp fragment of the NS-5 regions, performed as described previously (6), clearly classified both Slovenian isolates as subtype 2c.
Harmonisation of global land-use scenarios for the period 1500–2100 for IPCC-AR5

In preparation for the fifth Intergovernmental Panel on Climate Change climate change assessment (IPCC-AR5), the international community is developing new advanced computer models (CMs) to address the combined effects of human activities (e.g. land-use and fossil fuel emissions) on the carbon-climate system. In addition, four Representative Concentration Pathway (RCP) scenarios of the future (2005-2100) are being developed by four Integrated Assessment Modeling teams (IAMs) to be used as input to the CMs for future climate projections. The diversity of requirements and approaches among CMs and IAMs for tracking land-use changes (past, present, and future), presents major challenges for treating land-use comprehensively and consistently between these communities. As part of an international working group, we have been working to meet these challenges by developing a "harmonized" set of land-use change scenarios that smoothly connects gridded historical reconstructions of land-use with future projections, in a format required by CMs. This approach to harmonizing the treatment of land-use between two key modeling communities, CMs and IAMs, represents a major advance that will facilitate more consistent and fuller treatments of land-use/land-use change effects including both CO2 emissions and corresponding land-surface changes.
Practical Nonorthogonal Decoy State Quantum Key Distribution with a Heralded Single Photon Source

For the Bennett-Brassard 1984 (BB84) quantum key distribution, longer distance and higher key generation rate is shown with a heralded single photon source (HSPS). In this paper, the nonorthogonal encoding protocol SARG04 based on one vacuum and two weak decoy states with HSPS is presented. According to the public announcement of Alice's detection events, the overall gain of Bob's detector and quantum bit error rate (QBER) can be divided into two groups, triggered components and nontriggered components. We present a new protocol that use both triggered and nontriggered components to estimate the fraction and QBER of single-photon and two-photon pulses, and then deduce the final secure key generation rate. The final key generation rate over transmission distance is simulated, which shows that we can obtain a higher key rate than that of the existing methods.
Differential cortical processing of location and pitch changes in dichotic pitch

The objective of this study was to determine whether the auditory mismatch negativity can be elicited by changes in spatial and nonspatial cues within dichotic pitches. Participants were presented with blocks of standard dichotic pitch stimuli in which location or pitch was occasionally varied. A mismatch negativity was reliably elicited by deviant locations; in contrast, no measurable mismatch negativity response was found for deviant pitches. A separate psychophysical screening procedure ruled out the possibility that participants could not hear the pitch deviations. The results indicate that spatial and nonspatial features of dichotic pitch receive differential processing at a preattentive level of analysis within the auditory system and are supportive of recent notions of dual processing streams in audition.
Design and Analysis of A 5.3-pJ 64-kb Gated Ground SRAM With Multiword ECC

This paper presents an SRAM architecture employing a multiword-based ECC (MECC) scheme for soft error mitigation and a row virtual ground technique for array leakage reduction. The MECC combines four data words to form a 128 bit composite ECC word, two of which are interleaved in a row to mitigate cosmic neutron-induced multi-bit errors. The use of a composite word reduces the number of check-bits by 68%, however, requires a unique write operation that updates the check-bits by writing one data word while reading the other three data words. The ground potential of the composite word is raised to a nonzero value during retention in order to limit the leakage power consumption. A critical charge-based soft error rate (SER) model is proposed to estimate the resulting increase in the SER. Both the MECC scheme and the SER model are verified by implementing a 64-kb SRAM macro in 90 nm CMOS technology. The SRAM consumes 5.34 pJ energy with a data latency of 3.3 ns, thus showing up to 82% per-bit energy saving and 8x speed improvement over previously reported multiword ECC schemes. Accelerated neutron radiation test of the SRAM confirms 85% soft error correction by the MECC and 90% accuracy of the SER model.
Oral administration of metal chelator ameliorates motor dysfunction after a small hemorrhage near the internal capsule in rat

Cerebral hemorrhage leads to local production of free iron, radicals, cytokines, etc. To investigate whether a decrease of iron‐mediated radical production influences functional recovery after intracerebral hemorrhage (ICH), a modified ICH rat model with a small hemorrhage near the internal capsule (IC) accompanied with relatively severe motor dysfunction was first developed. Then clioquinol (CQ), an iron chelator that reduces hydroxyl radical production, was orally administrated. Injection of different doses of Type IV collagenase (1.4 μl 1–200 U/ml) into the left striatum near the IC in Wistar rats showed that injection of 7.5 U/ml collagenase resulted in a small hemorrhoidal lesion near the IC with relatively severe motor dysfunction (IC model). Retrograde labeling of neurons in the sensory‐motor cortex and axons in the corticospinal tract using Fluoro‐gold (FG) injection into the spinal cord (C3–C4) showed that few labeled neurons in the sensory‐motor cortex were detected in the IC model, FG‐labeled axons disappeared, and FG‐including ED‐1‐positive cells appeared within 24 hr in the IC. Assessments of behavior and histologic analysis after oral administration of CQ in the IC model indicated that oral administration of CQ prevented a decrease of FG‐labeled neurons, and resulted in better motor‐function recovery. CQ inhibited hydrogen peroxide‐induced cell toxicity in oligodendrocytes in vitro, but not in neurons. Our data suggests that CQ ameliorated motor dysfunction after a small hemorrhage near the IC by a mechanism that is related to reduction of chain‐reactive hydroxyl radical production in oligodendrocytes. © 2006 Wiley‐Liss, Inc.
Synthesis, crystal structure, and catalytic properties of 2,2'-bipyridyl-dicyano-palladium(II)

In the solvothermal condition, a Pd(II) complex with a in situ synthesis ligand, [Pd(2,2’-bipy)2(CN)2] (1) was obtained and characterized by elemental analysis, IR, UV, TG, and powder X-ray analysis. The single crystal X-ray analysis showed that the title complex is different from the reported 2,2’-bipyridyl-dicyanopalladium(II) (2) in crystal system and structural parameters. The catalytic investigation for the reactions of the disproportionation of hydrogen peroxide and oxidation of sulfide showed that the complex 1 is an active homogeneous catalyst in the presence of imidazole and 2-sulfobenzoic acid, respectively.
ORACLE CHARACTERIZATION FOR ACTIVE LEARNING FOR PROTEIN-PROTEIN INTERACTION PREDICTION

Discovery of human interactome is crucial for the understanding of complex biological processes and pathways, and for drug discovery. Bench-work experiments to determine protein-protein interactions (PPIs) are costly in terms of time, materials, equipment, and technical and scientific expertise. Thus, in recent years computational machine learning methods have been proposed to predict PPIs. These methods require training data to learn the classification models; but, currently known interactions are not sufficient to create an accurate model to predict the whole interactome or even a significant fraction thereof. If it is poss ible to seek additional training data experimentally, which are the protein-pairs that should be chosen to yield maximally-informative instances so as to maximize prediction accuracy for a given cost/effort level? Active machine learning (AL) methods are designed to select instances (protein-pairs) to create optimal training data and thus maximize their value in terms of prediction accuracy. Improving the relative accuracy is the pursuit of research in AL. However AL assumes the existence of an omniscient oracle (an experiment or an expert), which would give the correct label for every instance that it is asked, and it would do so for both pos itive and negative labels. In reality in the context of PPIs, an “oracle” can provide labels for only some interacting pairs (reluctance), and cannot give labels for noninteracting pairs (one-class nature). We develop algorithms for AL appropriate to this scenario of PPI prediction. Our results are superior compared to both a random baseline and also generic state-of-the-art AL.
Reliability of a commercially available and algorithm-based kinetic analysis software compared to manual-based software

Abstract There is a need for reliable analysis techniques for kinetic data for coaches and sport scientists who employ athlete monitoring practices. The purpose of the study was: (1) to determine intra- and inter-rater reliability within a manual-based kinetic analysis program; and (2) to determine test-retest reliability of an algorithm-based kinetic analysis program. Five independent raters used a manual analysis program to analyse 100 isometric mid-thigh pull (IMTP) trials obtained from previously collected data. Each trial was analysed three times. The same IMTP trials were analysed using an algorithm-based analysis software. Variables measured were peak force, rate of force development from 0 to 50 ms (RFD50) and RFD from 0 to 200 ms (RFD200). Intraclass correlation coefficients (ICC) and coefficient of variation (CV) were used to assess intra- and inter-rater reliability. Nearly perfect reliability was observed for the manual-based (ICC > 0.92). However, poor intra- and inter-rater CV was observed for RFD (CV > 16.25% and CV > 32.27%, respectively). The algorithm-based method resulted in perfect reliability in all measurements (ICC = 1.0, CV = 0%). While manual methods of kinetic analysis may provide sufficient reliability, the perfect reliability observed within the algorithm-based method in the current study suggest it is a superior method for use in athlete monitoring programs.
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes

ABSTRACT A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of thedsrAB gene homologs of the sulfite reducerDesulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genusThermodesulfobacterium (a separate bacterial division) were monophyletic with δ-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is thatdsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the δ-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for adsrAB lateral gene transfer event also was found within the δ-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes inArchaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.
Method for the estimation of a double hinge kinematic model for the trapeziometacarpal joint using MR imaging

In this paper, we propose a method to estimate the parameters of a double hinge model of the trapeziometacarpal joint (TMC) by MRI-based motion analysis. The model includes two non-orthogonal and non-intersecting rotation axes accounting for flexion–extension (F–E) and adduction–abduction (A–A). We evaluated the quality of the estimated model parameters in the prediction of the relative motion of the first metacarpal bone with respect to the trapezium. As a result, we obtained that: (a) the estimated location and orientation of the F–E and A–A axes were in agreement with previous in vitro studies, (b) the motion of the first metacarpal predicted by the 2 degrees of freedom (2DoF) model exhibits a maximum surface distance error in the range of about 2 mm and (c) four thumb postures at the boundary of the TMC range of motion are sufficient to provide a good estimation of the 2DoF TMC kinematic model and good reproducibility (∼1.7 mm) of the real thumb motion at TMC level.
Carnivorous syndrome in Asian pitcher plants of the genus Nepenthes.

BACKGROUND AND AIMS Pitcher plants Nepenthes alata and N. mirabilis are carnivorous species with leaves composed of a photosynthetic part (lamina) and a pitcher trap. This characteristic permitted direct physiological and anatomical comparison between these two distinct parts of the leaves to determine those features involved in the 'carnivorous syndrome', which include low net photosynthetic assimilation rate (A(N)) and low photosynthetic nitrogen use efficiency (PNUE). METHODS Photosynthetic rate (A(N)) and respiration rate (R(d)) were measured gasometrically, chlorophyll concentration was determined spectrophotometrically and nitrogen concentration was determined using a CHN elemental analyser in lamina and trap separately. Anatomy of N. alata was observed using light, fluorescence and transmission electron microscopy. A(N), foliar nitrogen and chlorophyll concentration were also compared with values for other carnivorous plant species (genera Sarracenia, Drosera) that combine both autotrophic and carnivorous functions into the same physical organ. KEY RESULTS It was found that the A(N) in Nepenthes lamina was low and PNUE was only slightly higher or similar in comparison with other carnivorous plants. It was not observed that the pitcher had a higher R(d) than the lamina, but A(N) in the pitcher was significantly lower than in the lamina. Nepenthes possesses a cluster of characters that could result in reduced photosynthesis in the pitcher and be responsible for carnivorous function of the leaf: replacement of chlorophyll-containing cells with digestive glands, low chlorophyll and nitrogen concentration, compact mesophyll with a small portion of intercellular spaces, absence of palisade parenchyma and low stomatal density. CONCLUSION Low photosynthetic capacity, nitrogen efficiency, chlorophyll and nitrogen concentration of Nepenthes pitchers was found, together with a set of features that characterized the carnivorous syndrome. Dual use of leaves for photosynthesis and nutrient gain can decrease photosynthetic efficiency in carnivorous plants in general.
Route-Based Online Energy Management of a PHEV and Sensitivity to Trip Prediction

In this paper, we present a method of optimizing the energy management of a plug-in hybrid electric vehicle (PHEV) using GIS-assisted stochastic trip prediction. A process was developed to synthesize speed profiles through a combination of Markov chains and information from a geographical information system (GIS) about the future route. In a potential real-world scenario, the future trip (speed, grade, stops, etc.) can be estimated, but not deterministically known. The stochastic trip prediction process models such uncertainty. The route-based energy management presented in this paper uses the Pontryagin Minimum Principle (PMP). A PMP strategy was implemented in a Simulink controller for a model of Prius-like PHEV and compared to a baseline strategy using Autonomie, an automotive modeling environment. An itinerary was defined, and several speed profiles were synthesized. It was then possible to evaluate the sensitivity of PMP tuning to the speed profile, providing insights about the applicability of PMP control in real-world situations.
Visualization Tools Integrated in Multivariate Calculus Instruction and Their Impact on the Quality of Students’ Knowledge

This paper presents a comprehensive pedagogical research related to mathematics instruction at the tertiary, university-level. Developed educational materials in electronic format, using the Matlab software package are integrated into instruction. The impact of using ICT on the essential knowledge related to the multivariate calculus, intensive use of 3D static and dynamic visualization tools has been statistically investigated. Some of students (experimental group) involved in the research study have individually created Matlab programs. Part of the research study is focused on the potential impacts of programming skills on learning mathematical concepts.
Zika virus-a review for clinicians.

Zika virus—a review for clinicians Yin Mo*, Brenda Mae Alferez Salada, and Paul Anantharajah Tambyah Ministry of Health Holdings, University Medicine Cluster, National University Health System, 1 Maritime Square, Singapore 099253, Singapore, Division of Infectious Diseases, University Medicine Cluster, National University Health System, 1E Kent Ridge Road, Level 10, 119228, Singapore, and Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Rd 119228, NUHS Tower Block, Level 11, Singapore 117597, Singapore