Miracle-dz/UniFAR-FTUs huggingface dataset:
A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences

Abstract The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbcL, matK and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q. baolamensis sp. nov., Q. bidoupensis sp. nov. and Q. honbaensis sp. nov. These new species are all phenotypically similar to Q. langbianensis s. str. in having lanceolate to oblanceolate leaf shape, upper 4–5/6–serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5–9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, Q. bidoupensis is not close to any other species. In the Bayesian tree, Q. honbaensis is sister to both Q. blaoensis and Q. camusiae that are found in the same locality but morphologically distinct and those three species are sister to Q. langbianensis s. str. , while Quercus baolamensis is not sister to Q. langbianensis s. str. in both the Bayesian tree and MIG-seq tree. In addition, Q. cambodiensis and Q. baniensis previously reduced to Q. langbianensis s. lat. have been recognised as distinct species. Six species were in need of lectotypification and that is undertaken herein.
To Fidget or Not to Fidget, That Is the Question: A Systematic Classroom Evaluation of Fidget Spinners Among Young Children With ADHD

Objective: To examine how fidget spinners affect children with ADHD’s gross motor activity and attentional functioning in class, both during the initial and final phase of an intensive evidence-based behavioral treatment. Method: Using an A-B-A-B design, 60 children (Mage = 4.86 years, 83% Hispanic) diagnosed with ADHD participated in the study. Following a baseline period, four random children from each classroom were given fidget spinners across three separate days (n = 48). Children wore accelerometers and were videotaped for 5-min during class in which attentional data were coded. Results: During the initial phase of treatment (but not during the final phase), the use of fidget spinners was associated with a decrease in activity levels. Children’s use of fidget spinners was associated with poorer attention across both phases of treatment. Conclusion: Fidget spinners negatively influence young children with ADHD’s attentional functioning, even in the context of an evidence-based classroom intervention.
The development of multi-channel action-potential generator for testing neurophysiologic data acquisition/analysis system

In our research, the multi-channel action-potentials (APs) generator based on high-speed USB interface is designed to test neurophysiologic data acquisition/analysis system. This multi-channel APs generator is composed of a personal computer and an external hardware unit. This generator is not only capable of generating a simulated APs waveform, and also generating random occurred APs with a specified rate ranging form 1 to 200 events per second. The waveform of each channel can be easily changed by using 2 parameters. Additionally, the programmable system on a Chip (PSoC/sup /spl trade//) component is adopted to simplify circuit units. Specifically, 16 channels, the maximum of the functions in this generator, can be spontaneously reached. Moreover, an application software is developed to generate APs waveform and a digital oscilloscope is used to verify the waveform as well. The voltage waveform produced by APs generator can be used to test neurophysiologic data acquisition systems for recording a spike trains and testing multispike-train analysis.
Noise reduction for binaural hearing aids using unsupervised diffuse noise estimator

In this paper a new noise reduction algorithm for binaural hearing aids is proposed. This algorithm is capable of suppressing both nonstationary diffuse noise and unknown directional interferences without distorting the directional cues. For the estimation of the diffuse noise power spectral density (PSD), we utilize the eigenstructure of the 2×2 input covariance matrix, together with a compensation process for preventing the underestimation at low frequencies. The interference PSD is estimated from the target cancelled input signals through the signal prediction. Effectiveness of the proposed algorithm was confirmed according to the computer simulations in terms of noise reduction and binaural cue preservation.
Nano-bio-imaging with Radiopharmaceuticals and its Application to Health Sciences

“Nano-bio-imaging” is the entirety of various kinds of imaging technology supported by “nanotechnology”, and it enables further progress of research in nanomedicine and nanotechnology. Although there are various available methods, our team is in charge of nano-bio-imaging using a nuclear medicine technique. In the methodology of nuclear medicine, we administer various kinds of radiopharmaceuticals to investigate events taking place in a living body from the outside. The foundation of this technique could date back to the early 20th century when it was originally developed as a "tracer method". This method was first explored by Dr. George von Hevesy, a Nobel laureate in chemistry in 1943. This method continued to make progress, and it came to be applied to human studies and was then called "nuclear medicine" in the latter half of the 20th century. The initial system was called scintigraphy, and later it was combined with computed tomography at the end of the 20th century. The technique was later fused with technology of computed tomography, and has been established as the "single photon ejection dislocation method" (SPECT), and "positron emission dislocation method" (PET), both of which seemed to be the most suitable tools for “nano-bio-imaging” since they can be used to visualize pharmacodynamic/pharmacokinetic information in the body of living subjects by injecting only a small amount of radiopharmaceuticals (1 to 2 nano-moles). Here, the term “a tracer” means injected radiopharmaceuticals used for obtaining information (signals) on phenomena in the body, and sometimes can also be called "a probe", meaning that we can probe the presence of extremely small amounts of biological substances. Thus, in the nuclear medicine technique, radiolabelling with high specific activity is very important to visualize the presence of very small amounts of materials in a “nano-” to “pico-” mole order. Therefore, it can be said that this technique is the right tool optimized for nano-bio-imaging. Our group has been seeking further potential and new applications of this radionuclide technique to clinical evaluation/diagnosis and health promotion science. We are aiming at promoting the medical use of the radionuclide technique and its further applications to health promotion science; mainly in terms of image analysis and medical engineering research and development as follows: [1] modeling in neural transmission function nano-bio-imaging and temporary establishment of an assay, [2] application of nano-bio-imaging technology to preventive medicine/health generation science, [3] development of research software hardware related to cancer examination of 3 focus, and promotion of related studies. In 2007, we mainly promoted the following study themes, particularly on PET studies.
Precedence tests and confidence bounds for complete data : an overview and some results

SUMMARY An overview of some nonparametric procedures based on precedence (or exceedance) statistics is given. The procedures include both tests and confidence intervals. In particular, the construction of some simple distribution-free confidence bounds for location difference of two distributions with the same shape is considered and some properties are derived. The asymptotic relative efficiency of an asymptotic form of the corresponding test relative to Wilcoxon's two-sample rank sum test and the two-sample Student t-test is given for various cases. Some K-sample problems are discussed where precedence-type tests are useful, along with a review of the literature.
A decoupling technique for efficient timing analysis of VLSI interconnects with dynamic circuit switching

In today's high-speed/high-density very large scale integrated (VLSI) circuit designs with coupled interconnect lines, signal transients are strongly correlated with the input switching patterns. Signal-delay variations due to the input-switching patterns may be more than /spl plusmn/50% of the delay of an isolated single line. Thus, blind static timing-analysis techniques without consideration of the detailed switching effects may not be accurate enough to meet tight timing margins for today's deep submicron (DSM)-based VLSI circuits. In this paper, the signal-transient responses of multicoupled interconnect lines due to various input-switching patterns are analyzed in terms of the effective capacitances and effective inductances. Thereby, the critical delay line of multicoupled interconnect lines is decoupled into an effective single-isolated line. With the proposed novel decoupling technique for multicoupled interconnect lines, the accurate dynamic delay of strongly coupled interconnect lines can be readily determined with physical layout information. For example, in switching patterns, the paper shows that the signal delays calculated by using the effective single-line models have excellent agreement with SPICE simulations using the generic coupled interconnect circuit models. That is, the accuracy for both RC-dominant lines and RLC lines is within 10% error (but often within 5% error). Thus, without any significant modification of existing IC computer-aided design frameworks, the technique can be directly as well as usefully employed for accurate timing verification of DSM-based VLSI designs.
Age-Related Brain Activation Changes during Rule Repetition in Word-Matching

Objective: The purpose of this study was to explore the age-related brain activation changes during a word-matching semantic-category-based task, which required either repeating or changing a semantic rule to be applied. In order to do so, a word-semantic rule-based task was adapted from the Wisconsin Sorting Card Test, involving the repeated feedback-driven selection of given pairs of words based on semantic category-based criteria. Method: Forty healthy adults (20 younger and 20 older) performed a word-matching task while undergoing a fMRI scan in which they were required to pair a target word with another word from a group of three words. The required pairing is based on three word-pair semantic rules which correspond to different levels of semantic control demands: functional relatedness, moderately typical-relatedness (which were considered as low control demands), and atypical-relatedness (high control demands). The sorting period consisted of a continuous execution of the same sorting rule and an inferred trial-by-trial feedback was given. Results: Behavioral performance revealed increases in response times and decreases of correct responses according to the level of semantic control demands (functional vs. typical vs. atypical) for both age groups (younger and older) reflecting graded differences in the repetition of the application of a given semantic rule. Neuroimaging findings of significant brain activation showed two main results: (1) Greater task-related activation changes for the repetition of the application of atypical rules relative to typical and functional rules, and (2) Changes (older > younger) in the inferior prefrontal regions for functional rules and more extensive and bilateral activations for typical and atypical rules. Regarding the inter-semantic rules comparison, only task-related activation differences were observed for functional > typical (e.g., inferior parietal and temporal regions bilaterally) and atypical > typical (e.g., prefrontal, inferior parietal, posterior temporal, and subcortical regions). Conclusion: These results suggest that healthy cognitive aging relies on the adaptive changes of inferior prefrontal resources involved in the repetitive execution of semantic rules, thus reflecting graded differences in support of task demands.
Knowing What You're Doing or Knowing what to do: How Stress Management Apps Support Reflection and Behaviour Change

Feelings of stress can have negative impacts on mental and physical health. In response, a significant number of stress management applications (apps) have been developed but little is known about their functionality. We conducted a feature analysis of 26 stress management and monitoring apps to identify required improvements. We found that the reviewed apps supported users with reflection, but did not include adequate functions to support action taking (i.e. initiating and maintaining behaviour change). This paper contributes a discussion of how to improve the design of stress management apps with examples of good practice and how healthcare providers can use this information to leverage such apps in clinical care.
microRNAs and siRNAs Determinants of targeting by endogenous and exogenous

Vertebrate mRNAs are frequently targeted for post-transcriptional repression by microRNAs (miRNAs) through mechanisms involving pairing of 39 UTR seed matches to bases at the 59 end of miRNAs. Through analysis of expression array data following miRNA or siRNA overexpression or inhibition, we found that mRNA fold change increases multiplicatively (i.e., log-additively) with seed match count and that a single 8 mer seed match mediates down-regulation comparable to two 7 mer seed matches. We identified several targeting determinants that enhance seed match-associated mRNA repression, including the presence of adenosine opposite miRNA base 1 and of adenosine or uridine opposite miRNA base 9, independent of complementarity to the siRNA/miRNA. Increased sequence conservation in the ;50 bases 59 and 39 of the seed match and increased AU content 39 of the seed match were each independently associated with increased mRNA down-regulation. All of these determinants are enriched in the vicinity of conserved miRNA seed matches, supporting their activity in endogenous miRNA targeting. Together, our results enable improved siRNA off-target prediction, allow integrated ranking of conserved and nonconserved miRNA targets, and show that targeting by endogenous and exogenous miRNAs/siRNAs involves similar or identical determinants.
A selective class of inhibitors for the CLC-Ka chloride ion channel

Significance Chloride ion channels and transporters (CLCs) are critical to cardiovascular, neurological, and musculoskeletal function. Small molecules capable of selectively inhibiting CLCs would serve as valuable tools for investigating CLC function and would have potential applications for treating CLC-related disorders. The lack of such agents has impeded efforts to study this family of proteins. This work introduces a class of inhibitors with unprecedented selectivity for a single CLC homolog, CLC-Ka. Insights gained through experiments to validate a predicted ligand binding site and to evaluate structure–activity relationships rationalize inhibitor potency and CLC-Ka selectivity. Our findings provide tools for studies of CLC-Ka function and will assist subsequent efforts to advance specific molecular probes for different CLC homologs. CLC proteins are a ubiquitously expressed family of chloride-selective ion channels and transporters. A dearth of pharmacological tools for modulating CLC gating and ion conduction limits investigations aimed at understanding CLC structure/function and physiology. Herein, we describe the design, synthesis, and evaluation of a collection of N-arylated benzimidazole derivatives (BIMs), one of which (BIM1) shows unparalleled (>20-fold) selectivity for CLC-Ka over CLC-Kb, the two most closely related human CLC homologs. Computational docking to a CLC-Ka homology model has identified a BIM1 binding site on the extracellular face of the protein near the chloride permeation pathway in a region previously identified as a binding site for other less selective inhibitors. Results from site-directed mutagenesis experiments are consistent with predictions of this docking model. The residue at position 68 is 1 of only ∼20 extracellular residues that differ between CLC-Ka and CLC-Kb. Mutation of this residue in CLC-Ka and CLC-Kb (N68D and D68N, respectively) reverses the preference of BIM1 for CLC-Ka over CLC-Kb, thus showing the critical role of residue 68 in establishing BIM1 selectivity. Molecular docking studies together with results from structure–activity relationship studies with 19 BIM derivatives give insight into the increased selectivity of BIM1 compared with other inhibitors and identify strategies for further developing this class of compounds.
Methylmercury inhibits growth and induces membrane changes in Pseudomonas putida

A bacterial model system (Pseudomonas putida DSM 50026) was used in this research to assess toxicity of the environmentally relevant concentrations of mercury species (MeHg and Hg(II)) that represent important pollutants of aquatic ecosystems at sites of industrial or mining activities. In addition to direct monitoring of bacterial growth, we also analyzed fatty acid profiles of exposed and non-exposed cultures to determine possible toxic effects manifested on membrane level. The results showed that exposure of P. putida to Hg(II) in concentrations of 0.2–200 µg/L did not have any significant effects on growth nor fatty acid composition of exposed bacterial culture. On the other hand, when bacteria were exposed to up to 1600-times lower concentrations of MeHg (0.12–12.5 µg/L), growth inhibition as well as significant changes in fatty acid composition were detected. Observed adaptive membrane changes due to MeHg exposure were similar to those associated with responses to organic solvents and some other membrane-disrupting compounds.
The impact of routine data quality assessments on electronic medical record data quality in Kenya

Background Routine Data Quality Assessments (RDQAs) were developed to measure and improve facility-level electronic medical record (EMR) data quality. We assessed if RDQAs were associated with improvements in data quality in KenyaEMR, an HIV care and treatment EMR used at 341 facilities in Kenya. Methods RDQAs assess data quality by comparing information recorded in paper records to KenyaEMR. RDQAs are conducted during a one-day site visit, where approximately 100 records are randomly selected and 24 data elements are reviewed to assess data completeness and concordance. Results are immediately provided to facility staff and action plans are developed for data quality improvement. For facilities that had received more than one RDQA (baseline and follow-up), we used generalized estimating equation models to determine if data completeness or concordance improved from the baseline to the follow-up RDQAs. Results 27 facilities received two RDQAs and were included in the analysis, with 2369 and 2355 records reviewed from baseline and follow-up RDQAs, respectively. The frequency of missing data in KenyaEMR declined from the baseline (31% missing) to the follow-up (13% missing) RDQAs. After adjusting for facility characteristics, records from follow-up RDQAs had 0.43-times the risk (95% CI: 0.32–0.58) of having at least one missing value among nine required data elements compared to records from baseline RDQAs. Using a scale with one point awarded for each of 20 data elements with concordant values in paper records and KenyaEMR, we found that data concordance improved from baseline (11.9/20) to follow-up (13.6/20) RDQAs, with the mean concordance score increasing by 1.79 (95% CI: 0.25–3.33). Conclusions This manuscript demonstrates that RDQAs can be implemented on a large scale and used to identify EMR data quality problems. RDQAs were associated with meaningful improvements in data quality and could be adapted for implementation in other settings.
Microbial production of biosurfactants and their importance

A large variety of microorganisms produce potent surface-active agents, biosurfactants, which vary in their chemical properties and molecular size. While the low molecular weight surfactants are often glycolipids, the high molecular weight surfactants are generally either polyanionic heteropolysaccharides containing covalently-linked hydrophobic side chains or complexes containing both polysaccharides and proteins. The yield of the biosurfactant greatly depends on the nutritional environment of the growing organism, The enormous diversity of biosurfactants makes them an interesting group of materials for application in many areas such as agriculture, public health, food, health care, waste utilization, and environmental pollution control such as in degradation of hydrocarbons present in soil.
Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar.

The electrostatic enhancement of the association rate of barnase and barstar is calculated using a transition-state theory like expression and atomic-detail modeling of the protein molecules. This expression predicts that the rate enhancement is simply the average Boltzmann factor in the region of configurational space where association occurs instantaneously in the diffusion-controlled limit. Based on experimental evidence, this "transition state" is defined by configurations in which, relative to the stereospecifically bound complex, the two proteins are shifted apart by approximately 8 A (so a layer of water can be accommodated in the interface) and the two binding surfaces are rotated away by 0 degrees to 3 degrees. The values of the average Boltzmann factor, calculated by solving the Poisson-Boltzmann equation, for the wild-type complex and 16 complexes with single mutations are found to correlate well with experimental results for the electrostatic rate enhancement. The predicted rate enhancement is found to be somewhat insensitive to the precise definition of the transition state, due to the long-range nature of electrostatic interactions. The experimental ionic strength dependence of the rate enhancement is also reasonably reproduced.
Fast foot prints re-planning and motion generation during walking in physical human-humanoid interaction

In this paper a system allowing real-time interaction between a human and a humanoid robot while walking is presented. The aim of this work is to integrate humanoid robots into collaborative working environment. Co-located realization of a task is one instance of such collaboration. To achieve such task whole-body motion generation while keeping balance is mandatory. This is obtained using a real-time pattern generator allowing on-line foot-print modification integrated in a stack of controllers. Several experiments of direct interaction between a human and a HRP-2 humanoid robot illustrates the results.