Miracle-dz/UniFAR-FTUs huggingface dataset:
Topology preserving approximation of free configuration space

We present a simple algorithm for approximating the free configuration space of robots with low degrees of freedom (DOFs). We represent the free space as an arrangement of contact surfaces. We approximate the free space using an adaptive volumetric grid that is computed by performing simple geometric tests on the contact surfaces. We use an isosurface extraction algorithm to compute a piecewise-linear approximation to the boundary of the free space. We prove that our approximation is topologically equivalent to the exact free space boundary. We also ensure that our approximation is geometrically close to the exact free space boundary by bounding its two-sided Hausdorff error. We have applied our algorithm to compute the free configuration space for the following instances: (1) a 2D polygonal robot with translational and rotational DOFs navigating among polygonal obstacles, and (2) a 3D polyhedral robot translating among polyhedral obstacles. In practice, our algorithm works well on robots with three DOFs
Self-Cross-Linking Hydrogenated Nitrile-Butadiene Rubber Latex/Polyvinyl Chloride Emulsion Composite Film and Its Properties

A new type of self-cross-linking hydrogenated carboxylated nitrile-butadiene rubber (HXNBR)/polyvinyl chloride (PVC) composite film was prepared from their mixed emulsions. HXNBR latex was obtained by diimide hydrogenation. The HXNBR/PVC composite film can be self-cross-linked without any additional cross-linking agent. The properties of composite films, including film-forming property, morphology, physical properties, swelling behavior, and ageing properties were investigated. When PVC content was lower than 30%, the composite film showed no crack in the surface, especially at 20% of PVC content, the composite film showed excellent mechanical properties. The addition of 20% PVC improved thermal stability of HXNBR film.
In vitro and in vivo effects of penicillin and clindamycin on expression of group A beta-hemolytic streptococcal capsule

Encapsulation of group A beta-hemolytic streptococci (GABHS) is an important virulence factor. The changes that occur in the frequency of encapsulation of GABHS during pharyngotonsillitis, in 20 patients treated with penicillin and 20 treated with clindamycin, were investigated. The effects of subinhibitory concentrations of these agents were also evaluated in vitro. At day 4, 8 of 10 (80%) GABHS isolates recovered from children treated with penicillin were encapsulated, compared with 1 of 5 (20%) of those from children treated with clindamycin (P < 0.05). Two days following 10 days of therapy, GABHS was eliminated from 13 of the 20 (65%) children treated with penicillin and from all treated with clindamycin (P < 0.05). At that time, six of the seven GABHS isolates recovered in patients treated with penicillin were encapsulated. GABHS were not detected after 4 days of therapy in those treated with clindamycin. Incubation of GABHS isolates with one-half of the MIC of clindamycin reduced the frequency of encapsulation, compared with that after incubation with one-half of the MIC of penicillin (12.5 versus 67.5%). These data illustrate the superiority of clindamycin over penicillin in reducing the expression of a capsule by GABHS.
Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates

Hydrolysis is an often-encountered obstacle in the crystallization of proteins complexed with their substrates. As the duration of the crystallization process, from nucleation to the growth of the crystal to its final size, commonly requires several weeks, non-enzymatic hydrolysis of an “unstable” ligand occurs frequently. In cases where the crystallization conditions exhibit non neutral pH values this hydrolysis phenomenon may be even more pronounced. ChoX, the substrate binding protein of a choline ABC-importer, produced crystals with its substrate acetylcholine after one month. However, these crystals exhibited only choline, an acetylcholine hydrolysis product, in the binding site. To overcome this obstacle we devised a microseeding protocol leading to crystals of ChoX with bound acetylcholine within 24 hours. One drawback we encountered was the high twinning fraction of the crystals, possibly was due to the rapid crystal growth.
Internet Job Search and Unemployment Durations

After decades of stability, the technologies used by workers to locate new jobs began to change rapidly with the diffusion of internet access in the late 1990’s. Which types of persons incorporated the internet into their job search strategy, and did searching for work on line help these workers find new jobs faster? We address these questions using measures of internet job search derived from the December 1998 and August 2000 CPS Computer and Internet Supplements, matched with job search outcomes from subsequent CPS files. We find that internet searchers are positively selected on observables, but negatively selected on unobservables. A beneficial (unemployment-duration reducing) causal effect of internet job search is consistent with our estimates only if negative selection on unobservables is especially strong, in other words only if the population of on-line resumes is strongly adversely selected.
Design, modeling and control of a novel amphibious robot with dual-swing-legs propulsion mechanism

This paper describes a novel amphibious robot, which adopts a dual-swing-legs propulsion mechanism, proposing a new locomotion mode. The robot is called FroBot, since its structure and locomotion are similar to frogs. Our inspiration comes from the frog scooter and breaststroke. Based on its swing leg mechanism, an unusual universal wheel structure is used to generate propulsion on land, while a pair of flexible caudal fins functions like the foot flippers of a frog to generate similar propulsion underwater. On the basis of the prototype design and the dynamic model of the robot, some locomotion control simulations and experiments were conducted for the purpose of adjusting the parameters that affect the propulsion of the robot. Finally, a series of underwater experiments were performed to verify the design feasibility of FroBot and the rationality of the control algorithm.
Convenient single-step, one tube purification of PCR products for direct sequencing.

Structural alterations of the apolipoprotein E (apo E) are known to influence the lipid metabolism. The three most common isoproteins Arg 158) are encoded by three co-dominant alleles (e2, el, e4). Phenotyping is cumbersome and, therefore, several methods for apo E genotyping have been developed. Of these, PCR-RFLP (restriction fragment length polymorphism) is currently most rapid and cost-effective (1). To detect mutations not affecting restriction sites, direct PCR sequencing of apo E fragments is the method of choice. This, however, requires purification of PCR products, which is routinely accomplished by techniques like gel electrophoresis or chromatography. We have established a new purification method using exonuclease I (exo I) and shrimp alkaline phosphatase (sAP) to degrade excess primers and nucleotides, which are the main factors interfering with dideoxy PCR sequencing. This procedure simply requires the addition of the enzymes to the PCR product, avoiding frequent sample handling and DNA loss through technical manipulation. Human DNA was extracted from 50 iA EDTA blood with Tris-EDTA lysis and proteinase K digestion. The PCR reaction mix (50 ill) was optimized to contain 10 /tl of DNA extract, 30 pmol of the primers F4 and F6 (2), 5 pi of dimethyl sulfoxide (DMSO), 10 pmol of each dNTP, 2 U of Taq polymerase 5 ii\ of 10 X PCR buffer (GeneAMP; Perkin-Elmer). After initial denaturation (95°C 5 min) 35 cycles (95°C 20 sec, 60°C 30 sec, 72 °C 30 sec) of amplification were performed, followed by a final extension (72°C 10 min; DNA Thermal Cycler 480, Perkin-Elmer). 2 jil of PCR product (244 bp) were mixed with 1 U exo I and 1 U sAP (USB, Cleveland, USA) and incubated for 1 h at 37°C. The enzymes were inactivated for 15 min at 72°C. The purified PCR product was diluted to a final volume of 10 /tl for cycle sequencing (3) with 0.5 pmol biotinylated primer F6 (A Taq™ Cycle Sequencing Kit; USB) under the same conditions as for PCR of genomic DNA. For chemiluminescence detection (4) we used the 'Sequenase® Images™ non-isotopic DNA sequence detection kit' (USB). Sequencing data obtained with sAP/exo I purified DNA are at least equal to those after column chromatography and superior to those using unpurified templates (Figure 1). Adjusting the purified DNA solutions for dilution we saw a slightly better efficiency of cycle sequencing in the enzymatically purified DNA.
Informing the Design of Novel Input Methods with Muscle Coactivation Clustering

This article presents a novel summarization of biomechanical and performance data for user interface designers. Previously, there was no simple way for designers to predict how the location, direction, velocity, precision, or amplitude of users’ movement affects performance and fatigue. We cluster muscle coactivation data from a 3D pointing task covering the whole reachable space of the arm. We identify 11 clusters of pointing movements with distinct muscular, spatio-temporal, and performance properties. We discuss their use as heuristics when designing for 3D pointing.
Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45). (ABSTRACT TRUNCATED AT 400 WORDS)
Adolescents and parental perception of family strength: relation to Malay adolescent emotional and behavioural adjustments

Adolescent and parental evaluation of family strength may have different significant impact on adolescent emotional and behavioural adjustment. The aim of this study was to examine adolescents’ and parents’ perception of family strength and the relationship of these perceptions to adolescent adjustment. 180 families participated in the study through a survey and standardized self-administered questionnaires were utilised. Significant differences were found regarding family strength between adolescent and their parent. Result showed adolescent perception of family strength was a significant predictor of their emotional and behavioural adjustment. The results of this study emphasise the importance of adolescent perception of family strength, and provide support to be taken into account when implementing any family programme.
Visualization of Large, Time-Dependent, Abstract Data with Integrated Spherical and Parallel Coordinates

Parallel coordinates is one of the most popular and widely used visualization techniques for large, high dimensional data. Often, data attributes are visualized on individual axes with polylines joining them. However, some data attributes are more naturally represented with a spherical coordinate system. We present a novel coupling of parallel coordinates with spherical coordinates, enabling the visualization of vector and multi-dimensional data. The spherical plot is integrated as if it is an axis in the parallel coordinate visualization. This hybrid visualization benefits from enhanced visual perception, representing vector data in a more natural spatial domain and also reducing the number of parallel axis within the parallel coordinates plot. This raises several challenges which we discuss and provide solutions to, such as, visual clutter caused by over plotting and the computational complexity of visualizing large abstract, time-dependent data. We demonstrate the results of our work-in-progress visualization technique using biological animal tracking data of a large, multi-dimensional, time-dependent nature, consisting of tri-axial accelerometry samples as well as several additional attributes. In order to understand marine wildlife behavior, the acceleration vector is reconstructed in spherical coordinates and visualized alongside with the other data attributes to enable exploration, analysis and presentation of marine wildlife behavior.
Thermophysical Parameters of Organic PCM Coconut Oil from T-History Method and Its Potential as Thermal Energy Storage in Indonesia

The thermophysical parameters of organic phase change material (PCM) of coconut oil (co_oil) have been studied by analyzing the temperature vs time data during liquid-solid phase transition (solidification process) based on T-history method, adopting the original version and its modified form to extract the values of mean specific heats of the solid and liquid co_oil and the heat of fusion related to phase transition of co_oil. We found that the liquid-solid phase transition occurs rather gradually, which might be due to the fact that co_oil consists of many kinds of fatty acids with the largest amount of lauric acid (about 50%), with relatively small supercooling degree. For this reason, the end of phase transition region become smeared out, although the inflection point in the temperature derivative is clearly observed signifying the drastic temperature variation between the phase transition and solid phase periods. The data have led to the values of mean specific heat of the solid and liquid co_oil that are comparable to the pure lauric acid, while the value for heat of fusion is resemble to those of the DSC result, both from references data. The advantage of co_oil as the potential sensible and latent TES for room-temperature conditioning application in Indonesia is discussed in terms of its rather broad working temperature range due to its mixture composition characteristic.
Humanized Chronic Graft-versus-Host Disease in NOD-SCID il2rγ-/- (NSG) Mice with G-CSF-Mobilized Peripheral Blood Mononuclear Cells following Cyclophosphamide and Total Body Irradiation

Chronic graft-versus-host disease (cGvHD) is the major source of late phase morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Humanized acute GvHD (aGvHD) in vivo models using NOD-SCID il2rγ-/- (NSG) mice are well described and are important tools for investigating pathogenicity of human cells in vivo. However, there have been only few reported humanized cGvHD mouse models. We evaluated if prolonged inflammation driven by low dose G-CSF-mobilized human PBMCs (G-hPBMCs) would lead to cGvHD following cyclophosphamide (CTX) administration and total body irradiation (TBI) in NSG mice. Engraftment was assessed in peripheral blood (PB) and in specific target organs by either flow cytometry or immunohistochemistry (IHC). Tissue samples were harvested 56 days post transplantation and were evaluated by a pathologist. Some mice were kept for up to 84 days to evaluate the degree of fibrosis. Mice that received CTX at 20mg/kg did not show aGvHD with stable expansion of human CD45+ CD3+ T-cells in PB (mean; 5.8 to 23.2%). The pathology and fibrosis scores in the lung and the liver were significantly increased with aggregation of T-cells and hCD68+ macrophages. There was a correlation between liver pathology score and the percentage of hCD68+ cells, suggesting the role of macrophage in fibrogenesis in NSG mice. In order to study long-term survival, 6/9 mice who survived more than 56 days showed increased fibrosis in the lung and liver at the endpoint, which suggests the infiltrating hCD68+ macrophages may be pathogenic. It was shown that the combination of CTX and TBI with a low number of G-hPBMCs (1x106) leads to chronic lung and liver inflammation driven by a high infiltration of human macrophage and mature human T cells from the graft, resulting in fibrosis of lung and liver in NSG mice. In conclusion this model may serve as an important pre-clinical model to further current understanding of the roles of human macrophages in cGvHD.
Problem Solving: What are the Important Questions?

Problem solving research is in need for re-thinking main questions. The purpose of this paper is a stock-taking of some of the identified problems, to discuss potential remedies for them, and to look for future perspectives. I see three areas for discussion: (1) What are the phenomena to be explained? (2) What methods should be used? What methodology is appropriate to the subject? (3) What is the progress in theory since the legendary work from Newell and Simon (1972)? What can we expect from new data sources? How can we relate data to theoretical assumptions?
Can Tweets Predict Citations? Metrics of Social Impact Based on Twitter and Correlation with Traditional Metrics of Scientific Impact

Background Citations in peer-reviewed articles and the impact factor are generally accepted measures of scientific impact. Web 2.0 tools such as Twitter, blogs or social bookmarking tools provide the possibility to construct innovative article-level or journal-level metrics to gauge impact and influence. However, the relationship of the these new metrics to traditional metrics such as citations is not known. Objective (1) To explore the feasibility of measuring social impact of and public attention to scholarly articles by analyzing buzz in social media, (2) to explore the dynamics, content, and timing of tweets relative to the publication of a scholarly article, and (3) to explore whether these metrics are sensitive and specific enough to predict highly cited articles. Methods Between July 2008 and November 2011, all tweets containing links to articles in the Journal of Medical Internet Research (JMIR) were mined. For a subset of 1573 tweets about 55 articles published between issues 3/2009 and 2/2010, different metrics of social media impact were calculated and compared against subsequent citation data from Scopus and Google Scholar 17 to 29 months later. A heuristic to predict the top-cited articles in each issue through tweet metrics was validated. Results A total of 4208 tweets cited 286 distinct JMIR articles. The distribution of tweets over the first 30 days after article publication followed a power law (Zipf, Bradford, or Pareto distribution), with most tweets sent on the day when an article was published (1458/3318, 43.94% of all tweets in a 60-day period) or on the following day (528/3318, 15.9%), followed by a rapid decay. The Pearson correlations between tweetations and citations were moderate and statistically significant, with correlation coefficients ranging from . 42 to . 72 for the log-transformed Google Scholar citations, but were less clear for Scopus citations and rank correlations. A linear multivariate model with time and tweets as significant predictors (P < .001) could explain 27% of the variation of citations. Highly tweeted articles were 11 times more likely to be highly cited than less-tweeted articles (9/12 or 75% of highly tweeted article were highly cited, while only 3/43 or 7% of less-tweeted articles were highly cited; rate ratio 0.75/0.07 = 10.75, 95% confidence interval, 3.4–33.6). Top-cited articles can be predicted from top-tweeted articles with 93% specificity and 75% sensitivity. Conclusions Tweets can predict highly cited articles within the first 3 days of article publication. Social media activity either increases citations or reflects the underlying qualities of the article that also predict citations, but the true use of these metrics is to measure the distinct concept of social impact. Social impact measures based on tweets are proposed to complement traditional citation metrics. The proposed twimpact factor may be a useful and timely metric to measure uptake of research findings and to filter research findings resonating with the public in real time.
A wound-healing program is hijacked to promote cancer metastasis

In this issue of JEM, Sundaram et al. report a mechanism by which the normal epithelial wound healing response is “hijacked” to promote invasion and metastasis in head and neck squamous carcinomas (HNSCCs), a finding that unveils new markers of poor outcomes and potential targets for therapeutic intervention.
An Evaluation of Slicing Algorithms for Concurrent Programs

Program slicing is a program-reduction technique for extracting statements that may influence other statements. While there exist efficient algorithms to slice sequential programs precisely, there are only two algorithms for precise slicing of concurrent interprocedural programs with recursive procedures. We implemented both algorithms for Java, applied several new optimizations and examined their precision and runtime behavior. We compared these results with two further algorithms which trade precision for speed. We show that one algorithm may produce incorrect slices and that precise slicing of concurrent programs is very expensive in terms of computation time.
A global transpose-free method with quasi-minimal residual strategy for the Sylvester equations

The Sylvester equation has numerous applications in control and system theory, power system, linear algebra, model reduction and signal processing. In the present paper, a global transpose-free quasi- minimal residual method for the Sylvester equations is proposed. The resulting method, with short- term recurrences, does not involve the multiplication with the transpose of the coefficient matrices, and often exhibits smoother convergence behavior than some other existing global methods. Finally, several numerical examples are reported by comparing the proposed method with some global methods.