Miracle-dz/UniFAR-FTUs huggingface dataset:
Usability and Potential of Geostatistics for Spatial Discrimination of Multiple Sclerosis Lesion Patterns

In multiple sclerosis (MS) the individual disease courses are very heterogeneous among patients and biomarkers for setting the diagnosis and the estimation of the prognosis for individual patients would be very helpful. For this purpose, we are developing a multidisciplinary method and workflow for the quantitative, spatial, and spatiotemporal analysis and characterization of MS lesion patterns from MRI with geostatistics.
Nonlinear regression modeling of nutrient loads in streams: A Bayesian approach

A Bayesian nonlinear regression modeling method is introduced and compared with the least squares method for modeling nutrient loads in stream networks. The objective of the study is to better model spatial correlation in river basin hydrology and land use for improving the model as a forecasting tool. The Bayesian modeling approach is introduced in three steps, each with a more complicated model and data error structure. The approach is illustrated using a data set from three large river basins in eastern North Carolina. Results indicate that the Bayesian model better accounts for model and data uncertainties than does the conventional least squares approach. Applications of the Bayesian models for ambient water quality standards compliance and TMDL assessment are discussed.
Constrained agglomerative hierarchical clustering algorithms with penalties

Semi-supervised clustering with constraints has widely been studied, but there are few studies on constrained agglomerative hierarchical algorithms. We have shown modified kernel algorithms of agglomerative hierarchical clustering, but there is a drawback that the modified kernels are not positive-definite in general. In this paper we consider another idea of agglomerative hierarchical algorithms with pairwise constraints. That is, merging of clusters is with penalties. The centroid method and the Ward method with and without a kernel are considered. Typical numerical examples show effectiveness of the proposed algorithms in generating clusters with nonlinear cluster boundaries. We also compare the results with those by COP K-means, showing that the proposed algorithms outperform the COP K-means.
Glucocorticoids and prostaglandins inhibit the induction of macrophage DNA synthesis by macrophage growth factor and phorbol ester

The tumor‐promoting phorbol ester, 12‐0‐tetradecanoyl‐phorbol‐13‐acetate (TPA), stimulates starch‐elicited mouse peritoneal macrophages to undergo DNA synthesis in vitro, apparently without the generation of an endogenous macrophage growth factor (MGF). No evidence was found for any synergistic interaction between TPA and exogenous colony stimulating factors (CSFs) for macrophage DNA synthesis. Low concentrations of glucocorticoids and also prostaglandins E1 and E2 suppress both the CSF‐1‐stimulated and the TPA‐stimulated macrophage DNA synthesis; these same drugs inhibit the CSF‐1‐mediated and TPA‐mediated enhancement of macrophage plasminogen activator (PA) activity. Thus glucocorticoids and prostaglandins E1 and E2 oppose the action of growth factors and the tumor promoter on macrophage and precursor cell function.
Occurrence of adenovirus and other enteric viruses in limited‐contact freshwater recreational areas and bathing waters

Aims: The goal of this study was to characterize enteric virus concentrations and their infectivity in a variety of limited‐contact recreation and bathing waters, including Great Lakes beaches, inland lakes, rivers, and an effluent‐dominated urban waterway. Additionally, we evaluated associations between point sources of human faecal pollution and enterovirus and adenovirus presence and concentrations.
Separating cause from effect: how does insulin/IGF signalling control lifespan in worms, flies and mice?

Ageing research has been revolutionized by the use of model organisms to discover genetic alterations that can extend lifespan. In the last 5 years alone, it has become apparent that single gene mutations in the insulin and insulin‐like growth‐factor signalling pathways can lengthen lifespan in worms, flies and mice, implying evolutionary conservation of mechanisms. Importantly, this research has also shown that these mutations can keep the animals healthy and disease‐free for longer and can alleviate specific ageing‐related pathologies. These findings are striking in view of the negative effects that disruption of these signalling pathways can also produce. Here, we summarize the body of work that has lead to these discoveries and point out areas of interest for future work in characterizing the genetic, molecular and biochemical details of the mechanisms to achieving a longer and healthier life.
Warming and response to contractile agents in calf cardiac vein: role of the nitric oxide

The effects of warming on the response to various contractile agents of calf cardiac vein were studied using 2.5‐mm long cylindrical segments. Concentration–response curves for carbachol (10−9–3 × 10−4 m), 5‐hydroxytryptamine (5‐HT; 10−8–3 × 10−3), potassium chloride (KCl; 10−4–5 × 10−2 m) and calcium chloride (CaCl2; 10−4–10−2) were isometrically recorded at 37 and 41 °C (warming). During warming the sensitivity, but not the maximal response, of carbachol 5‐HT, KCl, and CaCl2 was significantly higher than at 37 °C. Warming to 41 °C after treatment with NG‐nitro‐L arginine methyl esther (10−5 m) did not modify the effect of warming. These results suggest that nitric oxide seems to have no role in the warming‐induced responses in calf cardiac vein.
Vertex-Weighted Hypergraph Learning for Multi-View Object Classification

3D object classification with multi-view representation has become very popular, thanks to the progress on computer techniques and graphic hardware, and attracted much research attention in recent years. Regarding this task, there are mainly two challenging issues, i.e., the complex correlation among multiple views and the possible imbalance data issue. In this work, we propose to employ the hypergraph structure to formulate the relationship among 3D objects, taking the advantage of hypergraph on high-order correlation modelling. However, traditional hypergraph learning method may suffer from the imbalance data issue. To this end, we propose a vertex-weighted hypergraph learning algorithm for multi-view 3D object classification, introducing an updated hypergraph structure. In our method, the correlation among different objects is formulated in a hypergraph structure and each object (vertex) is associated with a corresponding weight, weighting the importance of each sample in the learning process. The learning process is conducted on the vertex-weighted hypergraph and the estimated object relevance is employed for object classification. The proposed method has been evaluated on two public benchmarks, i.e., the NTU and the PSB datasets. Experimental results and comparison with the state-of-the-art methods and recent deep learning method demonstrate the effectiveness of our proposed method.
Predictors of nurses' perceptions of barriers to research utilization.

AIM To identify predictors of nurses' self-reported barriers to using research findings in clinical practice. BACKGROUND Several studies have shown that nurses perceive barriers to research utilization but to our knowledge predictors of nurses perceptions of barriers to research utilization have not been identified before. METHODS Three questionnaires were answered by 833 nurses: the Barriers Scale, the Quality Work Competence questionnaire and a questionnaire including questions on professional issues. RESULTS Dissatisfaction with support from immediate superiors for participating in research and/or development projects, having no academic degree and unclear and unrealistic workplace goals were identified as factors increasing the risk of perceiving barriers to the use of research findings in clinical practice. CONCLUSIONS The results imply that head nurses, nursing managers and other health care leaders should create strategies for supporting nurses' professional development and possibilities to implement research findings in clinical practice. IMPLICATIONS FOR NURSING MANAGEMENT To support research utilization and evidence-based care health care leaders, head nurses and nurse managers should create clear and realistic goals for the work place including demands on evidence-based care. It is also important for head nurses and nurse managers to create strategies for supporting nurses' professional development and possibilities to implement research findings in clinical practice.
Clinical and genetic heterogeneity in familial focal segmental glomerulosclerosis. International Collaborative Group for the Study of Familial Focal Segmental Glomerulosclerosis.

BACKGROUND Familial forms of focal segmental glomerulosclerosis (FFSGS) that exhibit autosomal dominant or recessive patterns of inheritance have been described. The genetic basis of these hereditary forms of FSGS is unknown. One recent study of a kindred from Oklahoma with an autosomal dominant form of FSGS linked this disease to a region of chromosome 19q. In addition, polymorphisms in a gene in this region on chromosome 19q13 have been linked to congenital nephrotic syndrome of the Finnish type. We have ascertained and characterized a large family with autosomal dominant FFSGS (Duke 6530). METHODS Families were compared for clinical and genetic heterogeneity. To test for linkage of our family to this portion of chromosome 19, genomic DNA was isolated from 102 family members, and polymerase chain reaction was performed using eight microsatellite markers that spanned the area of interest on chromosome 19. Data were evaluated using two-point linkage analysis, multipoint analysis, and an admixture test. RESULTS Linkage was excluded at a distance of +/- 5 to 10 CM for all markers tested with two-point log10 of the odds of linkage (LOD) scores and from an approximate 60 CM interval in this area of chromosome 19q via multipoint analysis. CONCLUSIONS FSGS has been called the "final common pathway" of glomerular injury, as it is a frequent pathological manifestation with diverse etiologies. This diversity likely correlates with the genetic heterogeneity that we have established. Thus, our data demonstrate that there are at least two genes responsible for this disease, and there is genetic as well as clinical heterogeneity in autosomal dominant FSGS.
Social Interaction in Mixed-Income Developments: Relational Expectations and Emerging Reality

ABSTRACT: In many cities, public housing has come to exemplify concentrated urban poverty and the social problems associated with it. One major policy response to addressing these problems is the demolition and redevelopment of public housing complexes as mixed-income communities. Several theoretical propositions that lie behind this policy are based on assumptions about the ways in which living among higher-income residents can lead to relationships and interactions that may benefit poor people. Based on in-depth qualitative research in two mixed-income developments in Chicago, this paper explores the dynamics of social interaction in an effort to better understand the processes and factors that influence such interaction on the ground, the differential experience of residents from different backgrounds, and the factors that contribute to their decision-making about and interpretation of social relations with their neighbors. This analysis helps to better interpret the findings of earlier studies and craft more informed expectations about such interactions and their likely effects.
Implications and management of feral mammals in California

Author(s): Howard, Walter E. ; Marsh, Rex E. | Abstract: "Feral" is defined. For each of the principal species of feral mammals in California, we note the broad ecological implications they have on the environment and the potential or actual management approaches being followed. The main emphasis of this paper, and all of the slides shown, was on how wild horses and burros, two controversial feral species, are managed in California and in other western states. The feral pig is about to become the number one big game animal in California, and muskrats (Ondatra zibethica (L.)), which were introduced or escaped into the Sacramento Valley--hence locally feral--are the state's number one furbearer. Except for these species, the other feral mammals are, for the most part, much less desirable.
Identification and characterization of a novel Nogo‐interacting mitochondrial protein (NIMP)

Nogo is a potent inhibitor of regeneration following spinal cord injury. To develop a better understanding of the mechanisms responsible for regenerative failure we used a yeast two‐ hybrid approach to try and identify proteins that interact with Nogo. We identified a novel mitochondrial protein designated Nogo‐interacting mitochondrial protein (NIMP) in a screen of an adult human brain cDNA library. This interaction was confirmed by co‐immunoprecipitation in both brain tissue (endogenous) and transfected HEK293T cells (overexpressed). In support of these studies we demonstrate that Nogo interacts with the UQCRC1 and UQCRC2 components of complex III, within the mitochondrial respiratory chain. The mitochondrial localization of NIMP was evidenced by confocal image analysis and western blot analysis of isolated mitochondria. NIMP is highly conserved and ubiquitously expressed in mitochondria‐enriched tissues. Within the CNS, NIMP‐like immunoreactivity is present in neurons and astrocytes. These data suggest that NIMP is a novel mitochondrial protein that interacts with Nogo. The interaction of Nogo with mitochondrial proteins may provide insight into the mechanisms for Nogo‐induced inhibition of neurite growth.
Ets‐1 and hypoxia inducible factor‐1α inhibition by angiotensin II type‐1 receptor blockade in hormone‐refractory prostate cancer

Accumulating evidences have suggested that the renin‐angiotensin system (RAS) participates in the regulation of tumor angiogenesis. We previously demonstrated that hormone‐refractory prostate cancer (HRPC) showed significantly higher angiotensin II (Ang II) type‐1 receptor (AT1R) expression, and that the AT1R blocker (ARB) exerted protective effects by inhibiting angiogenesis. However, the downstream transcriptional factors induced by Ang II in prostate cancer cells have not been fully elucidated yet.
Taxonomic revision and molecular phylogeny of Gymnocorymbus Eigenmann, 1908 (Teleostei, Characiformes, Characidae).

Characidae, one of the most diverse families of Characiformes and one of the largest clades of fishes in the world, has a complex taxonomic background, with one issue being the placement of various genera, including Gymnocorymbus. Herein, we generate the first molecular phylogeny for the genus using three nuclear and two mitochondrial loci and review the systematics of Gymnocorymbus. This genus includes the black tetra, a well-known and popular species among aquarists. Molecular phylogeny strongly supports the monophyly of Gymnocorymbus, with this hypothesis corroborated by the presence of three morphological synapomorphies. Of the six previously known nominal species of Gymnocorymbus, three are considered valid herein: Gymnocorymbus bondi from the Río Orinoco basin, Gymnocorymbus ternetzi from the Rio Paraguay basin, and Gymnocorymbus thayeri from the Corantijn and Amazon basin and rivers of northeastern Brazil. A fourth species, Gymnocorymbus flaviolimai sp. n. , is described from the Rio Madeira, Amazon basin. Lectotypes are designated for G. ternetzi and G. thayeri. Our results support previous hypotheses of the alignment of Gymnocorymbus close to the subfamily Stethaprioninae and also support the sister relationship between G. ternetzi and G. thayeri, and of that clade as sister to G. bondi.
The tyrosine-sorting motif of the vacuolar sorting receptor VSR4 from Arabidopsis thaliana, which is involved in the interaction between VSR4 and AP1M2, μ1-adaptin type 2 of clathrin adaptor complex 1 subunits, participates in the post-Golgi sorting of VSR4

μ1-Adaptin of adaptor protein (AP) 1 complex, AP1M, is generally accepted to load cargo proteins into clathrin-coated vesicles (CCVs) at the trans-Golgi network through its binding to cargo-recognition sequences (CRSs). Plant vacuolar-sorting receptors (VSRs) function in sorting vacuolar proteins, which are reportedly mediated by CCV. We herein investigated the involvement of CRSs of Arabidopsis thaliana VSR4 in the sorting of VSR4. The results obtained showed the increased localization of VSR4 at the plasma membrane or vacuoles by mutations in CRSs including the tyrosine-sorting motif YMPL or acidic dileucine-like motif EIRAIM, respectively. Interaction analysis using the bimolecular fluorescence complementation (BiFC) system, V10-BiFC, which we developed, indicated an interaction between VSR4 and AP1M2, AP1M type 2, which was attenuated by a YMPL mutation, but not influenced by an EIRAIM mutation. These results demonstrated the significance of the recognition of YMPL in VSR4 by AP1M2 for the post-Golgi sorting of VSR4. Graphical abstract Clathrin AP1M2-recognizable tyrosine motif for plant VSR4 sorting.
Skill Translation Models in Expert Finding

Finding talented users on Stackoverflow can be a challenging task due to term mismatch between queries and content published on it. In this paper, we propose two translation models to augment a given query with relevant words. The first model is based on a statistical approach and the second one is a word embedding model. Interestingly, the translations provided by these methods are not the same. Although the first model in most cases selects pieces of program codes as translations, the second model provides more semantically related words. Our experiments on a large dataset indicate the efficiency of proposed models.
Characterization of the Spanning Tree Protocol

The simplicity, cost-effectiveness and economies of scale make Ethernet a popular choice for local area networks (LANs) solution. These features together with the fact that more than 90% of IP traffic is generated in Ethernet LANs makes this technology a good candidate for an end-to-end solution across larger networks. However, this new application of Ethernet demands for a set of new requirements. For example, in a service provider network a mandatory aspect is to perform with the maximum efficiency and providing high availability. Since initial protocols were designed to be used in small networks, in this new environment they do not meet these requirements. The Spanning Tree Protocol (STP) is the responsible of building the active tree-shaped topology running on top of the physical network. It takes the order of tens of seconds to create the tree, and this is totally impossible to be imagined for provider networks, which specify a maximum bound of 50msec. Some improvements have been proposed and implemented, but a global solution that achieves all requirements has not been designed yet. This Master Thesis aims at deeply study and characterize the operation of the STP. Since this protocol is the basis of all the versions and enhancements published so far, it is important to start studying the foundations.
Culture temperature modulates aggregation of recombinant antibody in cho cells

During production of therapeutic monoclonal antibodies (mAb), it is highly desirable to remove and control antibody aggregates in the manufacturing process to minimize the potential risk of immunogenicity to patients. During process development for the production of a recombinant IgG in a CHO cell line, we observed atypical high variability from 1 to 20% mAb aggregates formed during cell culture that negatively impacted antibody purification. Analytical characterization revealed the IgG aggregates were mediated by hydrophobic interactions likely caused by misfolded antibody during intracellular processing. Strikingly, data analysis showed an inverse correlation of lower cell culture temperature producing higher aggregate levels. All cultures at 37°C exhibited ≤5% aggregates at harvest. Aggregate levels increased 4–12‐fold in 33°C cultures when compared to 37°C, with a corresponding 2–4‐fold increase in heavy chain (HC) and light chain (LC) mRNA. Additionally, 37°C cases showed a greater excess of LC to HC mRNA levels. Endoplasmic reticulum (ER) chaperone expression and ER size also increased 25–75% at 33°C versus 37°C but to a lesser extent than LC and HC mRNA, consistent with a potential limiting ER folding capacity at 33°C for this cell line. Finally, we identified a 2–5‐fold increase in mAb aggregate formation at 33°C compared to 37°C cultures for three additional CHO cell lines. Taken together, our observations indicate that low culture temperature can increase antibody aggregate formation in CHO cells by increasing LC and HC transcripts coupled with limited ER machinery. Biotechnol. Bioeng. 2012;109: 125–136. © 2011 Wiley Periodicals, Inc.
Building Map Using Peak Amplitude of Sonar Echoes

This paper modified previous models of sonar sensors applied on building the map of environment for mobile robot to improve the map accuracy. Although sonar sensors are fairly accurate in measuring distance, they commonly have significant uncertainty in angular position. The uncertainty with Gaussian distribution or uniform distribution is assigned along an arc in previous researches, base on which the mathematics models of sonar sensor are modified, not only the time of flight (TOF) but also the parameter of incidence angle is considered according to the peak amplitude. Compared with the original one, the new model is effective and the map is more accurate, which is shown by the simulation results
Topological bias and inconsistency of maximum likelihood using wrong models.

Yang (1997) presented interesting and surprising results suggesting that maximum likelihood (ML) using a simple model could do a better job of phylogenetic reconstruction than ML using the correct model. We believe that Yang’s results and others we present here can best be understood in terms of bias in the choice of topology resulting from using ML with an incorrect model. Yang (1997) simulated sequences related by various four-taxon trees using the Jukes-Cantor (JC) model with gamma-distributed site-to-site rate variation (JC 1 G) and a shape parameter a of 0.2. He then used ML to reconstruct the phylogeny, assuming either the true JC 1 G model with a 5 0.2 or the simpler but false JC model. In repeated simulations, the false model reconstructed the correct topology more often than the true model did for three of the five trees Yang tested (namely, trees B, D, and E). With a fourth tree (Yang’s tree A), the two models performed equally well. On the fifth tree (C), the true model performed dramatically better. Trees generated randomly by a coalescent process were also reconstructed correctly more often using the false model. Yang’s results held over a wide range of sequence lengths, suggesting ML with the true model to be less efficient than ML with the false model. This brought into question the theorem that ML, using the correct model, is asymptotically most efficient. Yang suggested one possible explanation for his results: that the proof of asymptotic efficiency of ML might not apply to the discrimination of nonnested models (e.g., different topologies). We put forward here an alternative explanation: that Yang’s (1997) results do not reflect an overall increase in efficiency when using the simpler model of sequence evolution, but rather reflect comparison of a biased, sometimes inconsistent method (ML with false model) with a nearly unbiased, consistent method (ML with true model). As we will show, it appears that most of the trees Yang simulated happen to have topologies favored by the bias of the false model. Others have previously pointed out that false, oversimplified models cause the number of substitutions to be underestimated. The undercounting of substitution events occurs at all distances but becomes more severe for more divergent sequences. This will lead to under-