Miracle-dz/UniFAR-FTUs huggingface dataset:
Text Categorization using Feature Projections

This paper proposes a new approach for text categorization, based on a feature projection technique. In our approach, training data are represented as the projections of training documents on each feature. The voting for a classification is processed on the basis of individual feature projections. The final classification of test documents is determined by a majority voting from the individual classifications of each feature. Our empirical results show that the proposed approach, Text Categorization using Feature Projections (TCFP), outperforms k-NN, Rocchio, and Naive Bayes. Most of all, TCFP is about one hundred times faster than k-NN. Since TCFP algorithm is very simple, its implementation and training process can be done very easily. For these reasons, TCFP can be a useful classifier in the areas, which need a fast and high-performance text categorization task.
Quenching the quorum sensing system: potential antibacterial drug targets

Emergence of antibiotic and multi-drug resistant pathogenic bacteria has created the need for new drugs and drug targets. During pathogenesis bacteria release signals which regulate virulence and pathogenicity related genes. Such bacteria co-ordinate their virulent behaviour in a cell density dependent phenomenon termed as quorum sensing (QS). In contrast, microbes interfere with QS system by quenching the signals, termed quorum quenching (QQ). As a consequence of disrupted QS, pathogens become susceptible to antibiotics and drugs. In this article, the biodiversity of organisms with potential to quench QS signals and the use of QQ molecules as antibacterial drugs have been reviewed.
Sequential macro-micro modelling with behavioural microsimulations

This paper presents a sequential methodology that combines a macroeconomic CGE model with a behavioural microsimulation, illustrates the approach with applications, and discusses its merits and shortcomings. The microsimulation, based on a household income generation model, allows for incorporating individual fixed effects into macro-micro analysis. We argue that one of the main merits of the sequential approach is its flexibility. However, this flexibility comes at the cost of theoretical inconsistency.
A fuzzy goal programming technique for multi-objective chance constrained programming with normally distributed fuzzy random variables and fuzzy numbers

This paper presents a fuzzy goal programming approach for modelling and solving multi-objective decision making problems having fuzzy random variables and fuzzy numbers associated with the system constraints. In the model formulation process, the problem is converted into an equivalent fuzzy programming problem by using chance constrained programming technique. The problem is then decomposed into sub problems by considering the tolerance limits of fuzzy numbers relating to the system constraints. The individual optimal solution of each objective is found to construct the membership goals. A two-phase fuzzy goal programming model is developed to achieve the highest degree of each of the defined membership goals of the objectives to the extent possible by minimising under deviational variables and thereby obtaining most satisfactory solution in the decision making environment. A numerical example is solved to illustrate the proposed approach and the achieved solutions are compared with other existing methodologies.
Experimental and numerical investigation on the transient vascular thermal response to multi‐pulse Nd:YAG laser

Port wine stains (PWS) are congenital vascular malformations that progressively darken and thicken with age. Laser therapy is currently the most effective way in clinical practice for PWS. A 1,064 nm Nd:YAG laser in the near‐infrared band can achieve a deeper treatment depth compared to the current widely adopted pulsed dye laser. However, because of its relatively weak absorption by blood, single‐pulse Nd:YAG laser requires high energy density to cause effective vessel damage, but may inflict undesirable burning to surrounding collagen. Multi‐pulse laser has great potential in clinical treatment because it needs less energy density for each pulse. This paper presented an experimental and theoretical study of the transient thermal effects of low‐energy multi‐pulse Nd:YAG laser on blood vessels.
The emerging role of NPNT in tissue injury repair and bone homeostasis

Nephronectin (NPNT), a highly conserved extracellular matrix protein, plays an important role in regulating cell adhesion, differentiation, spreading, and survival. NPNT protein belongs to the epidermal growth factor (EGF)‐like superfamily and exhibits several common structural determinants; including EGF‐like repeat domains, MAM domain (Meprin, A5 Protein, and Receptor Protein‐Tyrosine Phosphatase µ), RGD motif (Arg‐Gly‐Asp) and a coiled‐coil domain. It regulates integrins‐mediated signaling pathways via the interaction of its RGD motif with integrin α8β1. Recent studies revealed that NPNT is involved in kidney development, renal injury repair, atrioventricular canal differentiation, pulmonary function, and muscle cell niche maintenance. Moreover, NPNT regulates osteoblast differentiation and mineralization, as well as osteogenic angiogenesis. Altered expression of NPNT has been linked with the progression of certain types of cancers, such as spontaneous breast tumor metastasis and malignant melanoma. Interestingly, NPNT gene expression can be regulated by a range of external factors such as tumor necrosis factor alpha (TNF‐α), transforming growth factor beta (TGF‐β), oncostatin M (OSM), bone morphogenic protein 2 (BMP2), Wnt3a, Vitamin D3, and microRNA‐378 (miR378). Further understanding the cellular and molecular mechanisms by which NPNT regulates tissue homeostasis in an organ‐specific manner is critical in exploring NPNT as a therapeutic target for tissue regeneration and tissue engineering.
Membrane Topology and DNA-Binding Ability of the Streptococcal CpsA Protein

ABSTRACT Many streptococcal pathogens require a polysaccharide capsule for survival in the host during systemic infection. The highly conserved CpsA protein is proposed to be a transcriptional regulator of capsule production in streptococci, although the regulatory mechanism is unknown. Hydropathy plots of CpsA predict an integral membrane protein with 3 transmembrane domains and only 27 cytoplasmic residues, whereas other members of the LytR_cpsA_psr protein family are predicted to have a single transmembrane domain. This unique topology, with the short cytoplasmic domain, membrane localization, and large extracellular domain, suggests a novel mechanism of transcriptional regulation. Therefore, to determine the actual membrane topology of CpsA, specific protein domains were fused to beta-galactosidase or alkaline phosphatase. Enzymatic assays confirmed that the predicted membrane topology for CpsA is correct. To investigate how this integral membrane protein may be functioning in regulation of capsule transcription, purified full-length and truncated forms of CpsA were used in electrophoretic mobility shift assays to characterize the ability to bind the capsule operon promoter. Assays revealed that full-length, purified CpsA protein binds specifically to DNA containing the capsule promoter region. Furthermore, the large extracellular domain is not required for DNA binding, but all cytoplasmic regions of CpsA are necessary and sufficient for specific binding to the capsule operon promoter. This is the first demonstration of a member of this protein family interacting with its target DNA. Taken together, CpsA, as well as other members of the LytR_cpsA_psr protein family, appears to utilize a unique mechanism of transcriptional regulation.
Designed to degrade

Suitably designed degradable polymers can play a role in reducing plastic waste Around 50 years ago, interest arose in making plastics that can degrade in the environment (1). Since then, a stream of research efforts has chased the dream of environmentally friendly materials that disappear without leaving behind fragments or harmful products. Such environmentally degradable plastics are, however, difficult to produce in practice. Durability is one of the requirements for plastic in most technical applications, whereas degradability is necessary for recycling in nature. Although advances are being made in developing degradable materials with suitable properties for particular applications, it is crucial that they are seen as part of a range of approaches and that degradation will always require particular conditions that depend on the specific material and its chemical and physical structure and composition.
Comparison of silhouette shape descriptors for example-based human pose recovery

Automatically recovering human poses from visual input is useful but challenging due to variations in image space and the high dimensionality of the pose space. In this paper, we assume that a human silhouette can be extracted from monocular visual input. We compare three shape descriptors that are used in the encoding of silhouettes: Fourier descriptors, shape contexts and Hu moments. An example-based approach is taken to recover upper body poses from these descriptors. We perform experiments with deformed silhouettes to test each descriptor's robustness against variations in body dimensions, viewpoint and noise. It is shown that Fourier descriptors and shape context histograms outperform Hu moments for all deformations
Shielding of metals from the corrosion induced by water and humidity by using scratch resistant and hydrophobic silica coatings

Abstract The objective of the present paper is to demonstrate the effect of sol-gel derived scratch resistant coatings on different metal surfaces for anticorrosive applications. However, practical applications are limited by problems intrinsic to sol-gel processing or specific of coating/metal systems. Coatings aimed to improve oxidation and wet corrosion resistance have been studied the most. The results published in the literature show that sol-gel coatings may offer good protection against oxidation. More difficult is to achieve a protection against wet corrosion. An important aspect of the application of the sol-gel method for coating metallic objects is also the deposition technique.
Delft University of Technology Numerical Study on Chloride Ingress in Cement-Based Coating Systems and Service Life Assessment

Chloride induced corrosion is a critical issue for reinforced concrete structures. Cement-based coatings can be used to protect the concrete structures with unsatisfactory quality against the chloride ingress. To evaluate the effectiveness of the coatings to extend the service life of the coated concrete structures, evolution of chloride profile in the coated concrete structures should be determined. This paper investigated the mechanism of chloride ingress into coated concrete structures (i.e., coating made of cement paste + concrete substrate). A numerical tool is proposed for calculating the chloride profiles in the coated concrete structures. Parameter study is carried out to investigate the influences of several factors on the chloride ingress, viz. the w/c ratio of the coating, the thickness of the coating, and early or late application of the coating. Preliminary cost analysis of coating materials is carried out. The results show that the effectiveness of the coatings increases with the coating thickness and with a drastic increase of material cost; the effectiveness of the coatings increases with the decrease of the w/c ratio and with a moderate increase of material cost. In order to extend the service life of the substrate, a coating with a low w/c ratio is recommended, while the coating thickness should be designed depending on the requirements. Moreover, the exposure history of the substrate before application of the coating also has an influence on the effectiveness of the coating. In order to protect an existing concrete structure exposed to the chloride environment against rapid chloride ingress, it is preferable to apply a coating as early as possible, since the effectiveness of the coating is reduced by a late application.
A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway

TNF-related weak inducer of apoptosis (TWEAK) is a new member of the TNF superfamily. It signals through TNFRSF12A, commonly known as Fn14. The TWEAK-Fn14 interaction regulates cellular activities including proliferation, migration, differentiation, apoptosis, angiogenesis, tissue remodeling and inflammation. Although TWEAK has been reported to be associated with autoimmune diseases, cancers, stroke, and kidney-related disorders, the downstream molecular events of TWEAK-Fn14 signaling are yet not available in any signaling pathway repository. In this paper, we manually compiled from the literature, in particular those reported in human systems, the downstream reactions stimulated by TWEAK-Fn14 interactions. Our manual amassment of the TWEAK-Fn14 pathway has resulted in cataloging of 46 proteins involved in various biochemical reactions and TWEAK-Fn14 induced expression of 28 genes. We have enabled the availability of data in various standard exchange formats from NetPath, a repository for signaling pathways. We believe that this composite molecular interaction pathway will enable identification of new signaling components in TWEAK signaling pathway. This in turn may lead to the identification of potential therapeutic targets in TWEAK-associated disorders.
Effect of dihydrocapsiate on resting metabolic rate in humans.

BACKGROUND Dihydrocapsiate is a capsinoid found in chili peppers. Dihydrocapsiate is similar to capsaicin, which is known for its thermogenic properties. OBJECTIVE The objective was to determine the acute and chronic effect of dihydrocapsiate on resting metabolic rate (RMR). DESIGN Seventy-eight healthy subjects in a double-blind, parallel-arm trial were randomly assigned to 3 groups receiving 0 (placebo), 3, or 9 mg dihydrocapsiate/d for 28 d. After a 10-h overnight fast, RMR was measured by indirect calorimetry for 30 min before and 120 min after ingestion of dihydrocapsiate. RESULTS RMR was similar in the 3 groups before dosing on day 1 [1714 ± 41 kcal/d (0 mg), 1760 ± 41 kcal/d (3 mg), and 1694 ± 38 kcal/d (9 mg)] and after acute dosing (41 ± 17, 55 ± 17, and 3 ± 24 kcal/d for 3-mg, 9-mg, and placebo groups, respectively). When the chronic effect of dihydrocapsiate on RMR was calculated from the average 2-h RMR on day 28 minus the 30-min preingestion RMR at baseline, a borderline effect in subjects receiving 3 mg dihydrocapsiate/d compared with placebo was observed (61 ± 24 kcal/d compared with -1 ± 12 kcal/d, P = 0.054), whereas no significant increase in RMR in comparison with placebo was noted for the 9-mg/d dose (48 ± 23 kcal/d compared with -1 ± 12 kcal/d, P = 0.12). When data from both groups were combined, the thermic effect of dihydrocapsiate reached significance (53 ± 9 kcal/d compared with -1 ± 12 kcal/d in the placebo group, P = 0.04). Fat oxidation was unaffected by dihydrocapsiate. CONCLUSION After 1 mo of supplementation, dihydrocapsiate had a small thermogenic effect of ≈50 kcal/d, which is in the range of day-to-day RMR variability. This trial was registered at clinicaltrials.gov as NCT00999297.
Resource co-allocation framework based on hybrid gaming model in grid environments

Resource co-allocation is a fundamental infrastructure to aggregate heterogeneous and distributed resources in grid environments. Although it has been widely investigated, co-allocation under multiple QoS constraints still remains an open issue. To address the issue of resource co-allocation with constraints to budget and deadline, a game-based co-allocation framework is proposed. This framework optimises resources deployment and prices scheme by a three-side co-allocation mechanism; meanwhile, it provides quantitative deadline guarantees for applications by applying queuing system to model the working of grid resources. The validity and solutions of the framework are presented theoretically. Experimental results show that the proposed framework can significantly reduce the deadline missing rate and resource costs for those applications with constraints to cost and deadline.
Abstract: A Novel Technique for Duct-Preserving Nipple Eversion

1. Kobayashi, S. ; Takebe, T. ; Inui, M. ; Iwai, S. ; Kan, H. ; Zheng, Y. W. ; Maegawa, J.; Taniguchi, H. Reconstruction of human elastic cartilage by a CD44+ CD90+ stem cell in the ear perichondrium. Proc. Natl. Acad. Sci. USA. 2011;108(35):14479–14484 2. Shintaro,K. ; Takebe,T. ; Kobayashi,S. ; Yabuki,Y. ; Hori,A. ; Hirotomi,K. ; Mikami, T. ; Uemura,T. ; Maegawa,J.; Taniguchi,H. Autotransplantation of monkey ear perichondrium-derived progenitor cells for cartilage reconstruction. Cell Transplant.2016; 25(5):951–62 3. Yanaga, H. ; Imai, K. ; Fujimoto, T. ; Yanaga, K. Generating ears from cultured autologous auricular chondrocytes by using two-stage implantation in treatment of microtia. Plast. Reconstr. Surg. 2009;124(3):817–825 4. Takebe,T. ; Kobayashi,S. ; Kan,H. ; Suzuki,H. ; Yabuki,Y. ; Mizuno,M. ; Adegawa,T. ; Yoshioka,T. ; Tanaka,J.; Maegawa,J.; Taniguchi,H. Human Elastic Cartilage Engineering from Cartilage Progenitor Cells Using Rotating Wall Vessel Bioreactor. Transplant. Proceed. 2012;44(4):1158–1161
Granulocyte function in the Chediak-Higashi syndrome of mice.

Granulocyte function was evaluated using peritoneal exudate granulocytes from a strain of beige mice with the Chediak-Higashi syndrome (CHS). Defective granulocyte chemotaxis of CHS cells (43% normal) was documented. There was no abnormality in the ability of CHS serum to function as a chemotactic stimulus. Phagocytosis of 14C-labeled Staphylococcus aureus by CHS granulocytes was normal. However, there was reduced bactericidal activity of S. aureus and group D streptococcus by CHS cells through 90 min of incubation. The bactericidal defect was most pronounced at early time periods and was related to impaired intracellular killing. These defects of CHS mice granulocytes were analogous to those reported in man and it is concluded that the CHS mouse is a most convenient and representative model of the CHS of man.
Genome-wide association scan in north Indians reveals three novel HLA-independent risk loci for ulcerative colitis

Objective Over 100 ulcerative colitis (UC) loci have been identified by genome-wide association studies (GWASs) primarily in Caucasians (CEUs). Many of them have weak effects on disease susceptibility, and the bulk of the heritability cannot be ascribed to these loci. Very little is known about the genetic background of UC in non-CEU groups. Here we report the first GWAS on UC in a genetically distinct north Indian (NI) population. Design A genome-wide scan was performed on 700 cases and 761 controls. 18 single-nucleotide polymorphisms (SNPs) (p<5×10−5) were genotyped in an independent cohort of 733 cases and 1148 controls. A linear mixed model was used for case–control association tests. Results Seven novel human leucocyte antigen (HLA)-independent SNPs from chromosome 6, located in 3.8-1, BAT2, MSH5, HSPA1L, SLC44A4, CFB and NOTCH4, exceeded p<5×10−8 in the combined analysis. To assess the independent biological contribution of such genes from the extended HLA region, we determined the percentage alternative pathway activity of complement factor B (CFB), the top novel hit. The activity was significantly different (p=0.01) between the different genotypes at rs12614 in UC cases. Transethnic comparisons revealed a shared contribution of a fraction of UC risk genes between NI and CEU populations, in addition to genetic heterogeneity. Conclusions This study shows varying contribution of the HLA region to UC in different populations. Different environmental exposures and the characteristic genetic structure of the HLA locus across ethnic groups collectively make it amenable to the discovery of causative alleles by transethnic resequencing. This may lead to an improved understanding of the molecular mechanisms underlying UC.
Prenatal and postnatal neurological evaluation of a fetus and newborn from pregnancy complicated with IUGR and fetal hypoxemia

In this case report, we present prenatal and postnatal neurological evaluation of a fetus and newborn from pregnancy complicated with intrauterine growth restriction, fetal hypoxemia, and preterm labor. Despite unfavorable intrauterine conditions, this premature infant showed normal early neurological development that was verified not only by postnatal tests but also with a new prenatal neurological screening test.
Integration of optical imaging with a small animal irradiator.

PURPOSE The authors describe the integration of optical imaging with a targeted small animal irradiator device, focusing on design, instrumentation, 2D to 3D image registration, 2D targeting, and the accuracy of recovering and mapping the optical signal to a 3D surface generated from the cone-beam computed tomography (CBCT) imaging. The integration of optical imaging will improve targeting of the radiation treatment and offer longitudinal tracking of tumor response of small animal models treated using the system. METHODS The existing image-guided small animal irradiator consists of a variable kilovolt (peak) x-ray tube mounted opposite an aSi flat panel detector, both mounted on a c-arm gantry. The tube is used for both CBCT imaging and targeted irradiation. The optical component employs a CCD camera perpendicular to the x-ray treatment/imaging axis with a computer controlled filter for spectral decomposition. Multiple optical images can be acquired at any angle as the gantry rotates. The optical to CBCT registration, which uses a standard pinhole camera model, was modeled and tested using phantoms with markers visible in both optical and CBCT images. Optically guided 2D targeting in the anterior/posterior direction was tested on an anthropomorphic mouse phantom with embedded light sources. The accuracy of the mapping of optical signal to the CBCT surface was tested using the same mouse phantom. A surface mesh of the phantom was generated based on the CBCT image and optical intensities projected onto the surface. The measured surface intensity was compared to calculated surface for a point source at the actual source position. The point-source position was also optimized to provide the closest match between measured and calculated intensities, and the distance between the optimized and actual source positions was then calculated. This process was repeated for multiple wavelengths and sources. RESULTS The optical to CBCT registration error was 0.8 mm. Two-dimensional targeting of a light source in the mouse phantom based on optical imaging along the anterior/posterior direction was accurate to 0.55 mm. The mean square residual error in the normalized measured projected surface intensities versus the calculated normalized intensities ranged between 0.0016 and 0.006. Optimizing the position reduced this error from 0.00016 to 0.0004 with distances ranging between 0.7 and 1 mm between the actual and calculated position source positions. CONCLUSIONS The integration of optical imaging on an existing small animal irradiation platform has been accomplished. A targeting accuracy of 1 mm can be achieved in rigid, homogeneous phantoms. The combination of optical imaging with a CBCT image-guided small animal irradiator offers the potential to deliver functionally targeted dose distributions, as well as monitor spatial and temporal functional changes that occur with radiation therapy.