Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal quantile level selection for disease classification and biomarker discovery with application to electrocardiogram data

Classification with a large number of predictors and biomarker discovery become increasingly important in biological and medical research. This paper focuses on performing classification of cardiovascular diseases based on electrocardiogram analysis which deals with many variables and a lot of measurements within variables. We propose an optimal quantile level selection procedure to reduce dimension by characterizing distributions with quantiles and combine with classification tools to produce sensible classification and biomarker discovery results. Simulation and an intensive study of a real data set are performed to illustrate the performance of the proposed method.
A comparative study of the 1918–1920 influenza pandemic in Japan, USA and UK: mortality impact and implications for pandemic planning

SUMMARY Historical studies of influenza pandemics can provide insight into transmission and mortality patterns, and may aid in planning for a future pandemic. Here, we analyse historical vital statistics and quantify the age-specific mortality patterns associated with the 1918–1920 influenza pandemic in Japan, USA, and UK. All three countries showed highly elevated mortality risk in young adults relative to surrounding non-pandemic years. By contrast, the risk of death was low in the very young and very old. In Japan, the overall mortality impact was not limited to winter 1918–1919, and continued during winter 1919–1920. Mortality impact varied as much as threefold across the 47 Japanese prefectures, and differences in baseline mortality, population demographics, and density explained a small fraction of these variations. Our study highlights important geographical variations in timing and mortality impact of historical pandemics, in particular between the Eastern and Western hemispheres. In a future pandemic, vaccination in one region could save lives even months after the emergence of a pandemic virus in another region.
Carotenoid Cleavage Dioxygenase (CmCCD4a) Contributes to White Color Formation in Chrysanthemum Petals1[OA]

The white petals of chrysanthemum (Chrysanthemum morifolium Ramat.) are believed to contain a factor that inhibits the accumulation of carotenoids. To find this factor, we performed polymerase chain reaction-Select subtraction screening and obtained a clone expressed differentially in white and yellow petals. The deduced amino acid sequence of the protein (designated CmCCD4a) encoded by the clone was highly homologous to the sequence of carotenoid cleavage dioxygenase. All the white-flowered chrysanthemum cultivars tested showed high levels of CmCCD4a transcript in their petals, whereas most of the yellow-flowered cultivars showed extremely low levels. Expression of CmCCD4a was strictly limited to flower petals and was not detected in other organs, such as the root, stem, or leaf. White petals turned yellow after the RNAi construct of CmCCD4a was introduced. These results indicate that in white petals of chrysanthemums, carotenoids are synthesized but are subsequently degraded into colorless compounds, which results in the white color.
Fetal lung maturity assessment with MRI fetal lung-to-liver signal-intensity ratio.

OBJECTIVE The purpose of this study was to retrospectively determine whether the ratio of fetal lung-to-liver signal intensities at single-shot fast spin-echo MRI is associated with fetal gestational age. MATERIALS AND METHODS All fetal MRI examinations over a 4-year period were reviewed. All MRI examinations were performed with a 1.5-T magnet for indications other than lung maturity. Only examinations performed with a single-shot fast spin-echo sequence of the fetal chest and abdomen were included in the study. Images from a total of 82 fetal MRI examinations were evaluated. Gestational age ranged from 20 weeks to 39 weeks 3 days. Two board-certified subspecialty-trained radiologists with 11 and 17 years of experience blinded to estimated gestational age (EGA) reviewed the images independently. The regions of interest (ROIs) of the fetal lung and liver were drawn in the same plane and on the same image in each case. Fetal EGA was determined either by first-trimester ultrasound when available or by last menstrual period. Linear regression analysis was used to analyze the relation between the lung-to-liver signal-intensity ratio (LLSIR) in the ROIs and fetal EGA for both readers. The association between the LLSIRs estimated by the two readers was assessed by Bland-Altman plot. RESULTS Summary statistics for LLSIR showed a median value of 2.29 for reader 1 and 2.21 for reader 2. The mean value for reader 1 was 2.4 and for reader 2 was 2.5. The Pearson correlation coefficients between the LLSIR and EGA variables were 0.44 for reader 1 and 0.45 for reader 2. Linear regression analysis showed a statistically significant association between LLSIR and EGA for both readers (p < 0.0004). This ratio increased in a linear manner as EGA progressed. CONCLUSION Fetal LLSIR at single-shot fast spin-echo MRI is associated with fetal gestational age.
Scientific Software Development Environment

This paper presents the Adesso, a computational environment for the development of scientific software. The Adesso environment leverages the reusable software component programming model to support the development and integration of components to several scientific programming platforms. The Adesso system is based on an XML component database and a set of XML document transformation tools for the automatic generation of component code, documentation and packaging. An authoring tool, built with the help of the Adesso transformation system itself, is provided to assist the user in the creation of components. The Adesso system has been used for the development of several image processing toolboxes and applications. Some of them are presented briefly in this paper.
A Hierarchical Categorization Approach for Configuration Management Modules

Configuration management tools, CMTs for short, are a set of indispensable software for DevOps (Development and Operations). CMTs automate system deployment and configuration through CMT modules, which are reusable, shareable units of configuration code. Therefore, thousands of CMT modules have been developed for various systems, and are still growing fast. Although CMT repositories usually provide keyword-and tag-based search, a large number of search results could prevent users from finding desired CMT modules. CMT modules could be managed in a hierarchical categorization, which can limit the search scope in specified categories, and thus help to improve search performance. Unfortunately, there is no hierarchical categorization in all CMT repositories. In this paper, we propose a hierarchical categorization approach for CMT modules. Our approach first extracts frequently-used module tags as categories, and constructs the category hierarchy by mining the hierarchical relations among tags. We leverage online module profiles (names, descriptions and tags) as source information to do categorization. It trains a set of classifiers by taking TF-IDF (term frequency-inverse document frequency) of module profiles as features. Finally, our evaluation on more than 11,000 CMT modules shows that our approach could obtain 90 fine-grained and multi-layered categories, and does categorization for CMT modules with high precision (0.81), recall (0.88) and F-Measure (0.85).
Immunogenicity of Simulated PCECV Postexposure Booster Doses 1, 3, and 5 Years after 2-Dose and 3-Dose Primary Rabies Vaccination in Schoolchildren

Objectives. To assess the immunogenicity of intradermal (ID) booster doses of Purified Chick Embryo Cell rabies vaccine (PCECV, Rabipur) administered to Thai schoolchildren one, three and five years after a primary ID pre-exposure (PrEP) vaccination series. Methods. In this follow-up study of a randomized, open-label, phase II clinical trial, two simulated post-exposure booster doses of PCECV were administered on days 0 and 3 intradermally to 703 healthy schoolchildren, one, three or five years after primary vaccination with either two or three ID doses of 0.1 mL PCECV. Blood was drawn immediately before and 7, 14 and 365 days after the first booster dose to determine rabies virus neutralizing antibody (RVNA) concentrations. Results. An anamnestic response of approximately 30-fold increase in RVNA concentrations was demonstrated within 14 days after booster. All children (100%) developed adequate RVNA concentrations above 0.5 IU/mL. No vaccine related serious adverse events were seen in any of the vaccinees. Conclusion. ID rabies PrEP with PCECV is safe and immunogenic in schoolchildren and the anamnestic response to a two booster dose vaccination series was found to be adequate one, three, and five years after a two- or three-dose primary PrEP vaccination series.
Comparison of mesenchymal stem cells isolated from pulp and periodontal ligament.

BACKGROUND Cell-based therapy using mesenchymal stem cells (MSCs) seems promising to obtain regeneration of dental tissues. A comparison of tissue sources, including periodontal ligament (PDL) versus pulp (P), could provide critical information to select an appropriate MSC population for designing predictable regenerative therapies. The purpose of this study is to compare the proliferation and stemness and the MSC-specific and mineralized tissue-specific gene expression of P-MSCs and PDL-MSCs. METHODS MSCs were obtained from PDL and P tissue of premolars (n = 3) extracted for orthodontic reasons. MSC proliferation was evaluated using a real-time cell analyzer for 160 hours. Telomerase activity was evaluated by a telomeric repeat amplification protocol assay based on enzyme-linked immunosorbent assay. Total RNA was isolated from the MSCs on day 3. A polymerase chain reaction (PCR) array was used to compare the expression of MSC-specific genes. The expression of mineralized tissue-associated genes, including Type I collagen (COL I), runt-related transcription factor 2 (RunX2), bone sialoprotein (BSP), and osteocalcin (OCN) messenger RNA (mRNA), was evaluated using quantitative real-time PCR. RESULTS Higher proliferation potential and telomerase activity were observed in the P-MSCs compared to PDL-MSCs of premolar teeth. Fourteen of 84 genes related to MSCs were expressed differently in the PDL-MSCs versus the P-MSCs. The expressions of bone morphogenetic protein 2 (BMP2) and BMP6; sex-determining region Y-box 9 (SOX9); integrin, alpha 6 (ITGA6); melanoma cell adhesion molecule (MCAM); phosphatidylinositol glycan anchor biosynthesis, class S (PIGS); prominin 1 (PROM1); ribosomal protein L13A (RPL13A); and microphthalmia-associated transcription factor (MITF) were higher in the P-MSCs compared to the PDL-MSCs, and higher expression of matrix metalloproteinase 2 (MMP2), interleukin (IL)-6, insulin (INS), alanyl (membrane) aminopeptidase (ANPEP), and IL-10 were observed in the PDL-MSCs. However, there was no statistically significant difference in the expression of mineralized tissue-associated genes, including BSP and RunX2, between the P-MSCs and the PDL-MSCs. Higher expression of COL I and lower expression of OCN mRNA transcripts were noted in the PDL-MSCs compared to the P-MSCs. CONCLUSIONS The results of this study suggest that MSCs isolated from P and PDL tissues show different cellular behavior. To increase the predictability of MSC-based regenerative treatment, differences in dental tissue-derived MSCs and favorable aspects of cell sources should be further clarified.
Truthful Auction Mechanisms with Performance Guarantee in Secondary Spectrum Markets

We study a spectrum auction problem where each request from new spectrum users has spatial, temporal, and spectral features. Our goal is to design truthful auction mechanisms that maximize either the overall social efficiency of new users (a.k.a buyers) or the revenue of the spectrum owner (a.k.a seller). Given that the optimal conflict-free spectrum allocation problem is NP-hard, this paper proposes a series of near-optimal auction mechanisms based on the following approximation techniques: linear programming (LP) relaxation, randomized rounding, derandomized rounding, monotone derandomization, and Lavi-Swamy method. Comparing with the prior art, we make two significant advances: First, our auction mechanisms are not only truthful but also provide theoretically-provable performance guarantee, an important feature that existing work under the same auction model does not have. Second, our auction mechanisms support both spatial and temporal spectral reuse, which makes the problem more challenging than existing work that deals with only spatial or temporal reuse. We perform extensive simulations to study the performance of the proposed mechanisms, and the simulation results corroborate our theoretical analysis.
Preclinical activity of ABT-869, a multitargeted receptor tyrosine kinase inhibitor

ABT-869 is a structurally novel, receptor tyrosine kinase (RTK) inhibitor that is a potent inhibitor of members of the vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) receptor families (e.g., KDR IC50 = 4 nmol/L) but has much less activity (IC50s > 1 μmol/L) against unrelated RTKs, soluble tyrosine kinases, or serine/threonine kinases. The inhibition profile of ABT-869 is evident in cellular assays of RTK phosphorylation (IC50 = 2, 4, and 7 nmol/L for PDGFR-β, KDR, and CSF-1R, respectively) and VEGF-stimulated proliferation (IC50 = 0.2 nmol/L for human endothelial cells). ABT-869 is not a general antiproliferative agent because, in most cancer cells, >1,000-fold higher concentrations of ABT-869 are required for inhibition of proliferation. However, ABT-869 exhibits potent antiproliferative and apoptotic effects on cancer cells whose proliferation is dependent on mutant kinases, such as FLT3. In vivo ABT-869 is effective orally in the mechanism-based murine models of VEGF-induced uterine edema (ED50 = 0.5 mg/kg) and corneal angiogenesis (>50% inhibition, 15 mg/kg). In tumor growth studies, ABT-869 exhibits efficacy in human fibrosarcoma and breast, colon, and small cell lung carcinoma xenograft models (ED50 = 1.5–5 mg/kg, twice daily) and is also effective (>50% inhibition) in orthotopic breast and glioma models. Reduction in tumor size and tumor regression was observed in epidermoid carcinoma and leukemia xenograft models, respectively. In combination, ABT-869 produced at least additive effects when given with cytotoxic therapies. Based on pharmacokinetic analysis from tumor growth studies, efficacy correlated more strongly with time over a threshold value (cellular KDR IC50 corrected for plasma protein binding = 0.08 μg/mL, ≥7 hours) than with plasma area under the curve or Cmax. These results support clinical assessment of ABT-869 as a therapeutic agent for cancer. [Mol Cancer Ther 2006;5(4):995–1006]
Pole-shape optimization of flux-switching permanent magnet machine

Flux-switching permanent magnet (FSPM) machine is a novel double salient structure PM machine with both concentrated armature windings and magnets in the stator, which attracts much attentions due to its high torque density and fault tolerance. However, the back-EMF of traditional FSPM is not perfectly sinusoidal, due to the influence of harmonics, which causes the torque ripple. Hence, in this paper, two shapes of stator teeth will be proposed, and the results of the two-dimensional finite-element analysis (2-D FEA) will be compared. Finally, the optimal stator tooth scheme will be obtained.
Rabin8 regulates neurite outgrowth in both GEF activity–dependent and –independent manners

Several Rab GTPases have been implicated in neurite outgrowth, but their regulatory mechanisms are poorly understood. Rab10 is a novel substrate of a Rab8-GEF, Rabin8, and Rabin8 regulates neurite outgrowth of PC12 cells by coordinating with Rab8, Rab10, and Rab11 and by a GEF activity–independent mechanism.
Detecting Concept-level Emotion Cause in Microblogging

In this paper, we propose a Concept-level Emotion Cause Model (CECM), instead of the mere word-level models, to discover causes of microblogging users' diversified emotions on specific hot event. A modified topic-supervised biterm topic model is utilized in CECM to detect "emotion topics" in event-related tweets, and then context-sensitive topical PageRank is utilized to detect meaningful multiword expressions as emotion causes. Experimental results on a dataset from Sina Weibo, one of the largest microblogging websites in China, show CECM can better detect emotion causes than baseline methods.
CENTELLA ASIATICA (L.): A PLANT WITH IMMENSE MEDICINAL POTENTIAL BUT THREATENED

Centella asiatica (L.) is a perennial, creeper, faintly aromatic and a valuable medicinal herb of both Old World and the New World. It is distributed throughout tropical and subtropical regions of World such as India, China, Nepal, Madagascar, Srilanka and Indonesia etc. The requirement of Centella asiatica is now met from natural population, leading to their gradual depletion and thus followed by its placement in the list of threatened species as mentioned by IUCN. Much of the ancient and contemporary lore surrounding this plant with its chemistry and pharmacology related to efficacy of both herbal preparations and chemical isolates are justified on the basis of experimental evidences. This paper provides its immense importance as economic plant with medicinal value as well as brief information of its products in the market launched, showing its dependability.
Morphology and anatomy of the fruit and seed in development of Chorisia speciosa A

(Morphology and anatomy of the fruit and seed in development of Chorisia speciosa A. St.-Hil. Bombacaceae). The structure of the fruit and seed in development of Chorisia speciosa are described with the main purpose of clarifying the origin and nature of the hairs that cover the seeds and aiding future taxonomical and ecological studies of the group. The fruit is an ellipsoid loculicide capsule and presents the exocarp formed by 7-10 cells layers, with very thick walls and evident simple pits. A great number of mucilage secretory cavities and ramified vascular bundles, accompanied by fibers, occur in the parenchymatic mesocarp. The endocarp derives from the ventral epidermis of the ovary wall, whose cells undergo a gradual elongation, become lignified, and constitute the trichomes which cover the mature seeds. The fruit aperture occurs by means of a suture evident in the ovarian wall in the middle region of the carpel leaf. Anatropous and bitegmic ovules, provided by a hypostase, give rise to campilotropous and bitegmic seeds. The testa is uniseriate, the exotegmen is completely formed by macrosclereids, and mucilage secretory cavities occur in the mesotegmen. The endotegmen, which is differentiated in the endothelium, is crushed in the mature seed. The plicate embryo, which occupies practically the entire seminal cavity, is found between endosperm layers, both being rich in lipids.
Characterization of a blood-meal-responsive proton-dependent amino acid transporter in the disease vector, Aedes aegypti

SUMMARY After anautogenous mosquitoes ingest the required blood meal, proteins in it are rapidly cleaved, yielding a large pool of amino acids. Transport of these amino acids into gut epithelial cells and their subsequent translocation into other tissues is critical for oogenesis and other physiological processes. We have identified a proton amino acid transporter (PAT) in Aedes aegypti (AaePAT1, AAEL007191) which facilitates this transport and is expressed in epithelial cell membranes of larval caecae and the adult midgut. AaePAT1 encodes a 475 amino acid protein showing high similarity to Anopheles gambiae AGAP009896, Culex pipiens CPIJ011438 and Drosophila melanogaster CG7888. When expressed in Xenopus oocytes the transport kinetics showed AaePAT1 is a low affinity transporter with low substrate specificity, having Km and Vmax values of about 7.2 mmol l–1 and 69 pmol oocyte–1 min–1, respectively, for glutamine. A number of other amino acids are also transported by this PAT. In female adult midgut, AaePAT1 transcript levels were induced after ingestion of a blood meal.
Six major steps in animal evolution: are we derived sponge larvae?

SUMMARY A review of the old and new literature on animal morphology/embryology and molecular studies has led me to the following scenario for the early evolution of the metazoans. The metazoan ancestor, “choanoblastaea,” was a pelagic sphere consisting of choanocytes. The evolution of multicellularity enabled division of labor between cells, and an “advanced choanoblastaea” consisted of choanocytes and nonfeeding cells. Polarity became established, and an adult, sessile stage developed. Choanocytes of the upper side became arranged in a groove with the cilia pumping water along the groove. Cells overarched the groove so that a choanocyte chamber was formed, establishing the body plan of an adult sponge; the pelagic larval stage was retained but became lecithotrophic. The sponges radiated into monophyletic Silicea, Calcarea, and Homoscleromorpha. Homoscleromorph larvae show cell layers resembling true, sealed epithelia. A homoscleromorph‐like larva developed an archenteron, and the sealed epithelium made extracellular digestion possible in this isolated space. This larva became sexually mature, and the adult sponge‐stage was abandoned in an extreme progenesis. This eumetazoan ancestor, “gastraea,” corresponds to Haeckel's gastraea. Trichoplax represents this stage, but with the blastopore spread out so that the endoderm has become the underside of the creeping animal. Another lineage developed a nervous system; this “neurogastraea” is the ancestor of the Neuralia. Cnidarians have retained this organization, whereas the Triploblastica (Ctenophora+Bilateria), have developed the mesoderm. The bilaterians developed bilaterality in a primitive form in the Acoelomorpha and in an advanced form with tubular gut and long Hox cluster in the Eubilateria (Protostomia+Deuterostomia).
Economia della cultura: la prospettiva italiana

Despite a slow start, in the last twenty years cultural economics has recorded a growing success in the Italian experience, with the birth and development of various research groups based in different areas of the Country. Often associated with training programmes, and always oriented towards an intensive flow of exchanges and joint projects with economists from other Countries, the research groups have respectively focused upon a variety of subjects and topics, ranging from cultural districts to public policy for the arts, from the features of cultural demand to the relationships between the public and the private sectors. Such an intensive and varied interest for cultural economics appears to be generated on one hand by a strong inclination towards the humanities and the favour for a multidisciplinary approach in carrying out research projects on the arts and culture; on the other hand, by the complexity of the Italian bureaucratic machine, requiring innovation and change and therefore «inviting» economists and political scientists to elaborate new interpretations and proposals. After twenty years, we can also emphasize the relevance of some shared interests, such as contemporary art and the design of cultural policy, whose twofold outcome is the high number of published works and the ability to support the elaboration of policy strategies and tools. If an «Italian» approach for cultural economics exists, it can be tracked in the non-prejudicial way in which the Italian economists have analysed a sector too often influenced by ethical arguments, being able at the same time to avoid the weaknesses of a merely mechanical and quantitative view of the cultural phenomena.