Miracle-dz/UniFAR-FTUs huggingface dataset:
On the problem of boundaries and scaling for urban street networks

Urban morphology has presented significant intellectual challenges to mathematicians and physicists ever since the eighteenth century, when Euler first explored the famous Königsberg bridges problem. Many important regularities and scaling laws have been observed in urban studies, including Zipf's law and Gibrat's law, rendering cities attractive systems for analysis within statistical physics. Nevertheless, a broad consensus on how cities and their boundaries are defined is still lacking. Applying an elementary clustering technique to the street intersection space, we show that growth curves for the maximum cluster size of the largest cities in the UK and in California collapse to a single curve, namely the logistic. Subsequently, by introducing the concept of the condensation threshold, we show that natural boundaries of cities can be well defined in a universal way. This allows us to study and discuss systematically some of the regularities that are present in cities. We show that some scaling laws present consistent behaviour in space and time, thus suggesting the presence of common principles at the basis of the evolution of urban systems.
Development of a Cavity Disinfectant Containing Antibacterial Monomer MDPB

An experimental cavity disinfectant (ACC) that is intended to be used for various direct and indirect restorations was prepared by adding an antibacterial monomer 12-methacryloyloxydodecylpyridinum bromide (MDPB) at 5% into 80% ethanol. The antibacterial effectiveness of ACC and its influences on the bonding abilities of resin cements were investigated. To examine the antibacterial activity of unpolymerized MDPB, the minimum inhibitory and bactericidal concentrations (MIC and MBC) were determined for Streptococcus mutans, Lactobacillus casei, Actinomyces naeslundii, Parvimonas micra, Enterococcus faecalis, Fusobacterium nucleatum, and Porphyromonas gingivalis. Antibacterial activities of ACC and the commercial cavity disinfectant containing 2% chlorhexidine and ethanol (CPS) were evaluated by agar disk diffusion tests through 7 bacterial species and by MIC and MBC measurement for S. mutans. The effects of ACC and CPS to kill bacteria in dentinal tubules were compared with an S. mutans–infected dentin model. Shear bond strength tests were used to examine the influences of ACC on the dentin-bonding abilities of a self-adhesive resin cement and a dual-cure resin cement used with a primer. Unpolymerized MDPB showed strong antibacterial activity against 7 oral bacteria. ACC produced inhibition zones against all bacterial species similar to CPS. For ACC and CPS, the MIC value for S. mutans was identical, and the MBC was similar with only a 1-step dilution difference (1:2). Treatment of infected dentin with ACC resulted in significantly greater bactericidal effects than CPS (P < 0.05, analysis of variance and Tukey’s honest significant difference test). ACC showed no negative influences on the bonding abilities to dentin for both resin cements, while CPS reduced the bond strength of the self-adhesive resin cement (P < 0.05). This study clarified that the experimental cavity disinfectant containing 5% MDPB is more effective in vitro than the commercially available chlorhexidine solution to eradicate bacteria in dentin, without causing any adverse influences on the bonding abilities of resinous luting cements.
Retrospective survival analysis of 261 lithium disilicate crowns in a private general practice.

OBJECTIVES This retrospective study evaluated the clinical performance and long-term survival of glass-ceramic lithium disilicate all-ceramic restorations in anterior and posterior areas over a 10-year period. METHOD AND MATERIALS Following a consistent protocol over 10 years, 261 lithium disilicate crowns (IPS Empress 2, Ivoclar Vivadent), including 101 anterior (38.7%) and 160 posterior (61.3%), were cemented using an adhesive technique and observed by the clinician who prepared and luted them. The data were analyzed using the Kaplan-Meier test. The clinical evaluation adopted the California Dental Association (CDA) modified criteria after recalling all patients between January and May 2008. RESULTS Six crowns failed and were replaced, 4 due to chipping and 2 due to core fracture. The overall survival rate was 95.5%. CONCLUSION In this retrospective evaluation, lithium disilicate ceramic restorations had a low clinical failure rate after up to 120 months.
Durability of Wet Bond of Hybrid Laminates to Cast-in-Place Concrete

Wet bond is a chemical bond developed to connect fiber-reinforced polymer (FRP) stay-in-place formwork to cast-in-place concrete for a composite action. Curing of chemical adhesive and fresh concrete occurs simultaneously in wet bond. Since FRP-concrete composite structure so designed is strongly dependent on the bond between FRP and concrete, a durable bond is of paramount importance. This paper presents a study on durability performance of wet bond exposed to sustained low temperature, freeze-thaw cycles, and wet-dry cycles. Single lap pull-off tests were conducted to evaluate the effect of exposure on bond. It was found that both first crack load and ultimate load of wet bond were reduced in comparison to dry bond. This reduction was more severe in first crack load than in ultimate capacity and was associated with voids, thickness, and surface of adhesive layer. The epoxy in wet bond had reached comparable degree of cure to dry bond and even gained a higher Tg . Environmental exposures did not show mor.
HGTree: database of horizontally transferred genes determined by tree reconciliation

The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.
Subjective Visual Vertical and Postural Performance in Healthy Children

Introduction Verticality is essential in our life, especially for postural stability. Subjective vertical as well as postural stability depends on different sensorial information: visual, vestibular and somesthesic. They help to build the spatial referentials and create a central representation of verticality. Children are more visuo-dependant than adults; however, we did not find any study focusing on how children develop their sense of verticality. Methods We studied two groups of subjects: 10 children (from 6 to 8 years) and 12 young adults. We recorded postural stability with a Techno Concept plateform and perception of subjective visual vertical in the following conditions: while adjusting the vertical in the dark or with visual perturbation, while fixating the vertical bar, and with eyes closed. Results Children are more instable than adults in terms of postural parameters, and also while performing a double task, especially when no visual references are present. They also present a higher variability and lower accuracy than adults in reporting their perception of true vertical reference. Discussion Children might have limited attentional resources, and focus their attention on the more demanding task, corresponding to the U-shaped non-linear model.
RalA and the exocyst complex influence neuronal polarity through PAR-3 and aPKC

Neuronal polarization requires localized cytoskeletal changes and polarized membrane traffic. Here, I report that the small GTPase RalA, previously shown to control neurite branching, also regulates neuronal polarity. RalA depletion, or ectopic expression of constitutively active RalA in cultured neurons inhibit axon formation. However, expression of a constitutively active RalA mutant that is unable to interact with the exocyst complex has no effect on neuronal polarization. Furthermore, depletion of the Sec6, Sec8 or Exo84 subunits of the exocyst complex also leads to unpolarized neurons. Early stages of neuronal polarization are accompanied by increasing levels of interaction of the exocyst complex with PAR-3 and atypical protein kinase C (aPKC), and by the RalA-dependent association of the exocyst complex with PAR-3. Thus, neuronal polarization involves a RalA-regulated association between mediators of vesicle trafficking (exocyst complex) and cell polarity (PAR-3).
Identification of targets of Prox1 during in vitro vascular differentiation from embryonic stem cells: functional roles of HoxD8 in lymphangiogenesis

During lymphatic development, Prox1 plays central roles in the differentiation of blood vascular endothelial cells (BECs) into lymphatic endothelial cells (LECs), and subsequently in the maturation and maintenance of lymphatic vessels. However, the molecular mechanisms by which Prox1 elicits these functions remain to be elucidated. Here, we identified FoxC2 and angiopoietin-2 (Ang2), which play important roles in the maturation of lymphatic vessels, as novel targets of Prox1 in mouse embryonic-stem-cell-derived endothelial cells (MESECs). Furthermore, we found that expression of HoxD8 was significantly induced by Prox1 in MESECs, a finding confirmed in human umbilical vein endothelial cells (HUVECs) and human dermal LECs (HDLECs). In mouse embryos, HoxD8 expression was significantly higher in LECs than in BECs. In a model of inflammatory lymphangiogenesis, diameters of lymphatic vessels of the diaphragm were increased by adenovirally transduced HoxD8. We also found that HoxD8 induces Ang2 expression in HDLECs and HUVECs. Moreover, we found that HoxD8 induces Prox1 expression in HUVECs and that knockdown of HoxD8 reduces this expression in HDLECs, suggesting that Prox1 expression in LECs is maintained by HoxD8. These findings indicate that transcriptional networks of Prox1 and HoxD8 play important roles in the maturation and maintenance of lymphatic vessels.
Mechanisms Driving Galling Success in a Fragmented Landscape: Synergy of Habitat and Top-Down Factors along Temperate Forest Edges

Edge effects play key roles in the anthropogenic transformation of forested ecosystems and their biota, and are therefore a prime field of contemporary fragmentation research. We present the first empirical study to address edge effects on the population level of a widespread galling herbivore in a temperate deciduous forest. By analyzing edge effects on abundance and trophic interactions of beech gall midge (Mikiola fagi Htg.), we found 30% higher gall abundance in the edge habitat as well as lower mortality rates due to decreased top-down control, especially by parasitoids. Two GLM models with similar explanatory power (58%) identified habitat specific traits (such as canopy closure and altitude) and parasitism as the best predictors of gall abundance. Further analyses revealed a crucial influence of light exposure (46%) on top-down control by the parasitoid complex. Guided by a conceptual framework synthesizing the key factors driving gall density, we conclude that forest edge proliferation of M. fagi is due to a complex interplay of abiotic changes and trophic control mechanisms. Most prominently, it is caused by the microclimatic regime in forest edges, acting alone or in synergistic concert with top-down pressure by parasitoids. Contrary to the prevailing notion that specialists are edge-sensitive, this turns M. fagi into a winner species in fragmented temperate beech forests. In view of the increasing proportion of edge habitats and the documented benefits from edge microclimate, we call for investigations exploring the pest status of this galling insect and the modulators of its biological control.
Dominance and immune function in the F1 generation of wild caught field crickets

Summary Female Gryllus bimaculatus have been found to prefer dominant males as mates, and dominant males have shown to have a higher encapsulation rates and higher lytic activities. However, previous studies were conducted with crickets from the laboratory stock culture population that has been in the laboratory for years. Under laboratory conditions, low rates of natural parasites and pathogens may cause unexpected correlations with immune function and life history traits. As a continuation of our previous work, we tested whether the male fighting ability, predicting dominance status, is associated with immune function in the F1 offspring from field collected individuals. To define male dominance we arranged fights between males. Interestingly, the dominance was related to one measure of immune response, but not another. Similarly to previous studies, dominant males had higher encapsulation rates than their subordinates. However, in contrast to earlier studies, dominant males had lower lysozyme-enzyme activities than subordinate males. Furthermore, encapsulation rates and lytic activities correlated negatively with each other. Lytic activities correlated positively with male body mass and encapsulation rates correlated negatively with the male’s body mass. Thus, the current results do not support the hypothesis that dominant males would always have better overall immunocompetence, but rather, suggests that varying environmental conditions may reflect the importance of the immune defence with respect to the success in male-male contests.
Variation in Fitness of the Longhorned Beetle, Dectes texanus, as a Function of Host Plant

Abstract Dectes texanus LeConte (Coleoptera: Cerambycidae) has become a serious pest of two different crops in the American Midwest, sunflower, Helianthus annuus L. and soybean, Glycines max (L.). Laboratory and field studies were used to compare the effects of these two host plants on D. texanus life history and behavior. Insects from soybean were 40–60% smaller than those from sunflower and larval weight at collection was strongly correlated with survival to adulthood, whereas it was not in sunflower, suggesting that body size was more limiting to immature survival in soybean. Pupal weights increased more rapidly with increasing stem diameter in soybean than in sunflower and the correlation was stronger, indicating that body size was more limited by plant size in soybean. Adults collected as larvae from soybean had shorter longevities when starved, fed soybean, or fed an alternating diet of soybean and cultivated sunflower, than did those collected from sunflower, suggesting a negative larval legacy of soybean on adult fitness. Adult beetles that developed in soybean lived longer when fed soybean than when starved, but an adult diet of sunflower doubled longevity compared to soybean for beetles that developed in sunflower, and tripled it for those that developed in soybean. An adult diet of wild H. annuus yielded survivorship equivalent to cultivated H. annuus in one trial, and slightly lower in another. Larval host plant did not influence the numbers of ovipunctures or eggs laid by females in field trials, but adult diet did. Sunflower-fed females punctured more, and laid more eggs, on sunflowers than on soybeans in field cages and the reverse trend was evident, but not significant, in soybean-fed females. It can be concluded that H. annuus is a superior food source to G. max for both larval and adult D. texanus, and that wild sunflowers may represent a valuable food for adults during the pre-reproductive period, prior to invasion of soybean fields, even though they rarely host larvae. We also showed that stable isotope ratios of N can be used to distinguish the larval host plant of beetles regardless of their adult diet.
Mutational analysis of the autoimmune regulator (AIRE) gene in sporadic autoimmune Addison's disease can reveal patients with unidentified autoimmune polyendocrine syndrome type I.

OBJECTIVE To investigate whether patients with Addison's disease and polyendocrine syndromes have undiagnosed autoimmune polyendocrine syndrome type I (APS I). MATERIALS AND METHODS Forty patients with clinical manifestations resembling APS I and with autoantibodies typical of this condition were screened for Norwegian autoimmune regulator (AIRE) gene mutations. RESULTS A 30-year old man who had developed Addison' s disease at the age of 12, but had no other components of APS I, was homozygous for the 1094-1106 deletion mutation in exon 8 of the AIRE gene, the most common mutation found in Norway. CONCLUSIONS APS I patients with milder and atypical phenotypes are difficult to diagnose on clinical grounds. Autoantibody analysis and mutational analysis of AIRE may therefore be helpful modalities for identifying these individuals.
A questionnaire-based cross-sectional study of clinical Johne's disease on dairy farms in New Zealand

Abstract AIM: To investigate associations between both farm management factors and breed of dairy cow, and the incidence of farmer-observed clinical Johne's disease (JD) on dairy farms in four major dairying regions in the North Island of New Zealand. METHODS: A questionnaire-based cross-sectional study was conducted to identify associations between both farm management practices and breed of dairy cow, and the incidence of clinical cases of JD suspected by farmers, on dairy farms in the Waikato, Taranaki, Wellington-Manawatu-Wanganui, and Wairarapa regions of New Zealand. Using multinomial logistic regression, the frequency of management practices was compared between farms on which no clinical cases of JD were observed, farms on which the observed incidence was low, and farms on which the observed incidence was high. RESULTS: Of the 427 responding farmers, 201 (47%) had suspected clinical cases of JD in their herd in the preceding 5 years. Only 56/427 (13%) farmers observed an average annual incidence of >0.5 cases/100 cows during this period. Ninety percent (203/225) of farmers that had not observed clinical cases and 21% (42/201) of farmers that had observed clinical cases did not consider the disease a serious problem. Farmers and veterinarians had a moderate level of agreement regarding the JD status of a farm. Their perceptions were in agreement for 86% (38/44) of the high-incidence herds for which both a farmer's and a veterinarian's perception were available. The presence of Jersey cows in the herd and the purchase of bulls were most strongly associated with the incidence of clinical JD. Grazing calves in the hospital paddock, purchase of a large percentage of heifers, larger-than-average herds within our sample, and the use of induction were also positively associated with JD. Farmers who ensured heifers were at least 2 years old, rather than younger, when mixed with adult stock were likely to observe fewer cases of clinical JD. CONCLUSIONS AND CLINICAL RELEVANCE: The annual incidence of farmer-observed clinical cases of JD was low, and the disease was generally regarded as of little importance by farmers. Farmers that had a high proportion of Jersey cows or that purchased bulls from either one or more than four sources were most likely to report clinical cases of JD. Management practices that could aid in the control of JD are the purchase of bulls free of JD, ensuring that calves do not graze in the hospital paddock, and ensuring that young stock are at least 2 years old prior to contact with adult stock.
Stromal Compartment as a Survival Prognostic Factor in Advanced Ovarian Carcinoma

Objective: We investigated the prognostic significance of stromal compartment on the overall survival of patients with advanced epithelial ovarian cancer. Methods: We evaluated retrospectively the stroma proportion of the tumor surgical specimens of 194 patients with stages III and IV disease, using histochemical staining and fully automatic virtual slide processing. The prognostic significance of stroma proportion and clinical parameters were evaluated using log-rank test and Cox regression. Results: Stroma proportion was found to be an independent prognostic factor by both univariate (P = 0.016) and multivariate analyses (hazards ratio = 1.45, P = 0.011). Conclusion: The present data indicate that a high stroma proportion is related to a poor prognosis of stage III and IV ovarian carcinomas.
TransType2 : The Last Word

This paper presents the results of the usability evaluations that were conducted within TransType2, an international R&D project the goal of which was to develop a novel approach to interactive machine translation. We briefly sketch the TransType system and then describe the methodology that we elaborated for the five rounds of user trials that were held on the premises of two translation agencies over the last eighteen months of the project. We provide the productivity results posted by the six translators who tested the system and we also discuss some of the non-quantitative factors which influenced the users reaction to TransType.
Using Knowledge Driven Matrix Factorization to Reconstruct Modular Gene Regulatory Network

Reconstructing gene networks from micro-array data can provide information on the mechanisms that govern cellular processes. Numerous studies have been devoted to addressing this problem. A popular method is to view the gene network as a Bayesian inference network, and to apply structure learning methods to determine the topology of the gene network. There are, however, several shortcomings with the Bayesian structure learning approach for reconstructing gene networks. They include high computational cost associated with analyzing a large number of genes and inefficiency in exploiting prior knowledge of co-regulation that could be derived from Gene Ontology (GO) information. In this paper, we present a knowledge driven matrix factorization (KMF) framework for reconstructing modular gene networks that addresses these shortcomings. In KMF, gene expression data is initially used to estimate the correlation matrix. The gene modules and the interactions among the modules are derived by factorizing the correlation matrix. The prior knowledge in GO is integrated into matrix factorization to help identify the gene modules. An alternating optimization algorithm is presented to efficiently find the solution. Experiments show that our algorithm performs significantly better in identifying gene modules than several state-of-the-art algorithms, and the interactions among the modules uncovered by our algorithm are proved to be biologically meaningful.
Therapeutic benefit of bisphosphonates in the management of prostate cancer-related bone disease

A diversity of bone pathology is present in men with prostate cancer. Androgen deprivation therapy (ADT) can cause significant and progressive osteopoenia and osteoporosis. Bone is also the primary site for metastases leading to associated pain, skeletal fractures and hypercalcaemia. Bisphosphonate therapy decreases bone resorption, which may prevent or reverse loss of bone mineral density. Both pamidronate and zoledronic acid have proven efficacy in preventing ADT-induced bone loss. In a randomised, placebo-controlled trial, in men with hormone-refractory prostate cancer, there was a decreased incidence of skeletal-related adverse events in men receiving zoledronic acid. So far, randomised trials have failed to show improved pain control. Formalised guidelines are needed to help clinicians decide which patients should be treated with bisphosphonates, when to initiate therapy and for what duration.