Miracle-dz/UniFAR-FTUs huggingface dataset:
100% Classification Accuracy Considered Harmful: The Normalized Information Transfer Factor Explains the Accuracy Paradox

The most widely spread measure of performance, accuracy, suffers from a paradox: predictive models with a given level of accuracy may have greater predictive power than models with higher accuracy. Despite optimizing classification error rate, high accuracy models may fail to capture crucial information transfer in the classification task. We present evidence of this behavior by means of a combinatorial analysis where every possible contingency matrix of 2, 3 and 4 classes classifiers are depicted on the entropy triangle, a more reliable information-theoretic tool for classification assessment. Motivated by this, we develop from first principles a measure of classification performance that takes into consideration the information learned by classifiers. We are then able to obtain the entropy-modulated accuracy (EMA), a pessimistic estimate of the expected accuracy with the influence of the input distribution factored out, and the normalized information transfer factor (NIT), a measure of how efficient is the transmission of information from the input to the output set of classes. The EMA is a more natural measure of classification performance than accuracy when the heuristic to maximize is the transfer of information through the classifier instead of classification error count. The NIT factor measures the effectiveness of the learning process in classifiers and also makes it harder for them to “cheat” using techniques like specialization, while also promoting the interpretability of results. Their use is demonstrated in a mind reading task competition that aims at decoding the identity of a video stimulus based on magnetoencephalography recordings. We show how the EMA and the NIT factor reject rankings based in accuracy, choosing more meaningful and interpretable classifiers.
Effective Scale: A Natural Unit for Measuring Scale-Space Lifetime

A manner in which a notion of effective scale can be introduced in a formal way is developed. For continuous signals, a scaling argument directly gives a natural unit for measuring scale-space lifetime in terms of the logarithm of the ordinary scale parameter. That approach is, however, not appropriate for discrete signals since an infinite lifetime would be assigned to structures existing in the original signal. It is shown how such an effective scale parameter can be defined to give consistent results for both discrete and continuous signals. The treatment is based on the assumption that the probability that a local extremum disappears during a short-scale interval should not vary with scale. As a tool for the analysis, estimates are given of how the density of local extrema can be expected to vary with scale in the scale-space representation of different random noise signals both in the continuous and discrete cases. >
One‐level Newton–Krylov–Schwarz algorithm for unsteady non‐linear radiation diffusion problem

In this paper, we present a parallel Newton–Krylov–Schwarz (NKS)‐based non‐linearly implicit algorithm for the numerical solution of the unsteady non‐linear multimaterial radiation diffusion problem in two‐dimensional space. A robust solver technology is required for handling the high non‐linearity and large jumps in material coefficients typically associated with simulations of radiation diffusion phenomena. We show numerically that NKS converges well even with rather large inflow flux boundary conditions. We observe that the approach is non‐linearly scalable, but not linearly scalable in terms of iteration numbers. However, CPU time is more important than the iteration numbers, and our numerical experiments show that the algorithm is CPU‐time‐scalable even without a coarse space given that the mesh is fine enough. This makes the algorithm potentially more attractive than multilevel methods, especially on unstructured grids, where course grids are often not easy to construct. Copyright © 2004 John Wiley & Sons, Ltd.
Astrocytic estrogen receptors and impaired neurotrophic responses in a rat model of perimenopause

In a perimenopausal model of middle-aged rats, the astrocyte estrogen receptor-alpha (ERa): ER-beta (ERb) ratio increased with the onset of acyclicity (constant estrus, CE) in association with impaired neurotrophic responses to estradiol (E2). We report additional data on irregular cycling (IR) from this study of 9 month old perimenopausal subgroups. In particular, irregular cyclers (IR) also show increased ERa:ERb ratio in cerebral cortex astrocytes comparable to acyclic individuals in CE. In mixed glial cultures from these same cycling subgroups, the E2-dependent neurotrophic activity and glial fibrillary acidic protein (GFAP) repression by E2 were impaired in IR to the same degree as in CE-derived glia. The greater importance of cycling status than age during the perimenopause to astrocyte ERs are attributable to individual variations of the residual ovarian follicle pool, which determine the onset of acyclicity. The corresponding loss of E2-dependent GFAP repression and E2-dependent neurotrophic activity add further to the inverse relationship of GFAP expression and astrocyte neurotrophic activity across aging in both sexes. These findings are relevant to impairments of spatial learning and of hippocampal long-term potentiation during the onset of IR in middle-aged rats, and to perimenopausal factors mediating the higher risk of women for Alzheimer disease.
Tissue-engineered bioprosthetic venous valve: a long-term study in sheep.

OBJECTIVE to develop a graft bearing an immunologically tolerated tissue-engineered venous valve (TE graft) that will be incorporated into a native vessel, and restore normal valve function for the treatment of chronic venous insufficiency. METHODS twenty-four TE grafts were grown using decellularised allogeneic ovine veins as donor matrix, which was subsequently repopulated with the future recipient's myofibroblasts (MFB) and endothelial cells (EC). TE grafts were implanted into the external jugular vein. Animals were sacrificed at 1, 6, and 12 weeks (n=4, each). Autografts served as controls (1 week, n=4; 6 weeks, n=4). Specimen for histology and immunohistochemistry were taken. RESULTS the matrix was successfully repopulated with MFB and EC (n=8). Patency on venography in the TE graft-group was44,44, and 34 at 1, 6, and 12 weeks, and44 (44) in autografts at 1 (6) weeks, respectively. Except for 2 TE grafts after 12 weeks, valves were competent (duplex ultrasound). Patent TE grafts were merely distinguishable from autografts with minor inflammatory reactions. Reflux was caused by neo-intima formation related to the basis of the TE graft. CONCLUSION acellularisation and consecutive in vitro autogeneic re-seeding of valved venous conduits can lead to immunologically acceptable, patent, and competent implants in sheep.
Phosphorous magnetic resonance spectroscopy-based skeletal muscle bioenergetic studies in subclinical hypothyroidism

Background: Subclinical hypothyroidism (sHT) is considered to be a milder form of thyroid dysfunction. Few earlier studies have reported neuromuscular symptoms as well as impaired muscle metabolism in sHT patients. Aim/objective: In this study we report our findings on muscle bioenergetics in sHT patients using phosphorous magnetic resonance spectroscopy (31P MRS) and look upon the possibility to use 31P MRS technique as a clinical marker for monitoring muscle function in subclinical thyroid dysfunction. Subjects and methods: Seventeen normal subjects, 15 patients with sHT, and 9 patients with hypothyroidism performed plantar flexion exercise while lying supine in 1.5 T magnetic resonance scanner using custom built exercise device. MR Spectroscopy measurements of inorganic phosphate (Pi), phosphocreatine (PCr), and ATP of the calf muscle were taken during rest, at the end of exercise and in the recovery phase. PCr recovery rate constant (kPCr) and oxidative capacity were calculated by monoexponential fit of PCr vs time (t) at the beginning of recovery. Results: We observed that changes in some of the phosphometabolites (increased phosphodiester levels and Pi concentration) in sHT patients which were similar to those detected in patients with hypothyroidism. However, our results do not demonstrate impaired muscle oxidative metabolism in sHT patients based upon PCr dynamics as observed in hypothyroid patients. Conclusions:31P MRS-based PCr recovery rate could be used as a marker for monitoring muscle oxidative metabolism in sub clinical thyroid dysfunction.
NetFence: preventing internet denial of service from inside out

Denial of Service (DoS) attacks frequently happen on the Internet, paralyzing Internet services and causing millions of dollars of financial loss. This work presents NetFence, a scalable DoS-resistant network architecture. NetFence uses a novel mechanism, secure congestion policing feedback, to enable robust congestion policing inside the network. Bottleneck routers update the feedback in packet headers to signal congestion, and access routers use it to police senders' traffic. Targeted DoS victims can use the secure congestion policing feedback as capability tokens to suppress unwanted traffic. When compromised senders and receivers organize into pairs to congest a network link, NetFence provably guarantees a legitimate sender its fair share of network resources without keeping per-host state at the congested link. We use a Linux implementation, ns-2 simulations, and theoretical analysis to show that NetFence is an effective and scalable DoS solution: it reduces the amount of state maintained by a congested router from per-host to at most per-(Autonomous System).
Guidance on good practice in conducting scientific assessments in animal health using modelling

Abstract The EFSA asked the Panel on Animal Health and Welfare to develop a guidance document on good practice in conducting scientific assessments in animal health using modelling. In previous opinions, the AHAW Panel has responded to two‐thirds of animal health‐related mandates using some kind of modelling. These models range from simple to complex, employing a combination of scientific, economic, socio‐economic or other types of data. Hence, there is strong interest in the development of a guidance document to integrate modelling efforts into the routine process of EFSA working groups. In this document, an ‘operating procedure' (OP) for the use of modelling within an AH working group is presented. The OP provides a detailed flowchart enabling modelling to be transparently and consistently integrated in the assessment. The OP is structured into phases. These phases combine the relevant standard operating procedures and working instructions of EFSA with the modelling process. Each phase includes roles and actions to be taken, expected output and the sequence of agreements that need to be made between all partners in the scientific assessment. In conclusion, it is expected that adherence to the OP will improve transparency of models in EFSA outputs, and it is recommended to adopt it as a standard procedure when responding to AHAW mandates.
Assessment of antibody-dependent respiratory burst activity from mouse neutrophils on Plasmodium yoelii malaria challenge outcome

New tools are required to expedite the development of an effective vaccine against the blood‐stage infection with the human malaria parasite Plasmodium falciparum. This work describes the assessment of the ADRB assay in a mouse model, characterizing the functional interaction between antimalarial serum antibodies and FcRs upon neutrophils. We describe a reproducible, antigen‐specific assay, dependent on functional FcR signaling, and show that ADRB activity is induced equally by IgG1 and IgG2a isotypes and is modulated by blocking FcR function. However, following immunization of mice with the blood‐stage vaccine candidate antigen MSP142, no measurable ADRB activity was induced against PEMS and neither was vaccine efficacy modulated against Plasmodium yoelii blood‐stage challenge in γ−/− mice compared with WT mice. In contrast, following a primary, nonlethal P. yoelii parasite challenge, serum from vaccinated mice and nonimmunized controls showed anti‐PEMS ADRB activity. Upon secondary challenge, nonimmunized γ−/− mice showed a reduced ability to control blood‐stage parasitemia compared with immunized γ−/− mice; however, WT mice, depleted of their neutrophils, did not lose their ability to control infection. Thus, whereas neutrophil‐induced ADRB against PEMS does not appear to play a role in protection against P. yoelii rodent malaria, induction of ADRB activity after challenge suggests that antigen targets of anti‐PEMS ADRB activity remain to be established, as well as further supporting the observation that ADRB activity to P. falciparum arises following repeated natural exposure.
Sirtuins and Proteolytic Systems: Implications for Pathogenesis of Synucleinopathies

Insoluble and fibrillar forms of α-synuclein are the major components of Lewy bodies, a hallmark of several sporadic and inherited neurodegenerative diseases known as synucleinopathies. α-Synuclein is a natural unfolded and aggregation-prone protein that can be degraded by the ubiquitin-proteasomal system and the lysosomal degradation pathways. α-Synuclein is a target of the main cellular proteolytic systems, but it is also able to alter their function further, contributing to the progression of neurodegeneration. Aging, a major risk for synucleinopathies, is associated with a decrease activity of the proteolytic systems, further aggravating this toxic looping cycle. Here, the current literature on the basic aspects of the routes for α-synuclein clearance, as well as the consequences of the proteolytic systems collapse, will be discussed. Finally, particular focus will be given to the sirtuins’s role on proteostasis regulation, since their modulation emerged as a promising therapeutic strategy to rescue cells from α-synuclein toxicity. The controversial reports on the potential role of sirtuins in the degradation of α-synuclein will be discussed. Connection between sirtuins and proteolytic systems is definitely worth of further studies to increase the knowledge that will allow its proper exploration as new avenue to fight synucleinopathies.
Prevalence and Trend of Overweight and Obesity among Schoolchildren in Ahvaz, Southwest of Iran

Introduction: Obesity is an important risk factor for some chronic diseases. Since the effect of obesity is long-standing, monitoring childhood obesity should be the first step in the health policy for interventions regarding early prevention of chronic diseases. In this study we aim to determine the prevalence of overweight and obesity among school children in the city of Ahvaz. Methods: A cross-sectional survey was designed. A sample of 5811 children, 2904 (49.97%) boys and 2907 (50.03%) girls, was selected and their heights and weights were measured in 2012-2013 academic year. Measurements of height and weight were made by using calibrated equipment and according to standardized protocol with the children having light clothes and without wearing shoes. The adjusted odds ratio of obesity and overweight for age and sex were calculated from multiple logistic regression model. Results: A total 685 (23.6%) of boys and 561 (19.3%) of girls were overweight. and 190(6.05%) of boys and 130 (4.5%) of girls were obese. The proportion of overweight and obese boys was significantly higher than that of girls (p<0.001). Logistic regression showed significant increase in the likelihood of being overweight with the increasing age OR=1.50, C.I. 95%: (1.43, 1.57). Conclusion: The prevalence of overweight and obesity increased markedly with age. This shows the importance of early prevention by doing interventions and training since the first year of primary school.
Cross-protection among unrelated leptospira pathogens serovars: an unfinished story.

BACKGROUND The World Health Organization considers leptospirosis the most neglected zoonotic disease in the last decades. One of the major obstacles in the developing of vaccines for the prevention of leptospirosis is the absence of cross-protection among unrelated serovars. It is accepted that cross-protection among related serovars is due to antibodies generated against lipopolysaccharides (LPs), whereas a cross-protection among unrelated serovars is rarely observed. OBJECTIVES The objective of the study was to ascertain the existence of cross-protection among vaccine strains of different serovars. RESULTS The results of this research demonstrated that a cross-protection among unrelated Leptospira serovars strain is possible. The Canicola strain is able to induce protection against homologous, Ballum and Copenhageni strains. The Mozdok strain induced protection only against a homologous challenge. Other strains showed a moderate cross-protection against a heterologous challenge. CONCLUSIONS These findings suggest that the Canicola and Mozdok strains are ideal candidates for developing a new vaccine formulation for use in Cuba.
Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells*

Long noncoding RNAs (lncRNAs), which have emerged in recent years as a new and crucial layer of gene regulators, regulate various biological processes such as carcinogenesis and metastasis. HOTAIR (Hox transcript antisense intergenic RNA), a lncRNA overexpressed in most human cancers, has been shown to be an oncogenic lncRNA. Here, we explored the role of HOTAIR in HeLa cells and searched for proteins regulated by HOTAIR. To understand the mechanism of action of HOTAIR from a systems perspective, we employed a quantitative proteomic strategy to systematically identify potential targets of HOTAIR. The expression of 170 proteins was significantly dys-regulated after inhibition of HOTAIR, implying that they could be potential targets of HOTAIR. Analysis of this data at the systems level revealed major changes in proteins involved in diverse cellular components, including the cytoskeleton and the respiratory chain. Further functional studies on vimentin (VIM), a key protein involved in the cytoskeleton, revealed that HOTAIR exerts its effects on migration and invasion of HeLa cells, at least in part, through the regulation of VIM expression. Inhibition of HOTAIR leads to mitochondrial dysfunction and ultrastructural alterations, suggesting a novel role of HOTAIR in maintaining mitochondrial function in cancer cells. Our results provide novel insights into the mechanisms underlying the function of HOTAIR in cancer cells. We expect that the methods used in this study will become an integral part of functional studies of lncRNAs.
OrthoDisease: A database of human disease orthologs

One of the greatest promises of genome sequencing projects is to further the understanding of human diseases and to develop new therapies. Model organism genomes have been sequenced in parallel to human genomes to provide effective tools for the investigation of human gene function. Many of their genes share a common ancestry and function with human genes, and this is particularly true for orthologous genes. Here we present OrthoDisease, a comprehensive database of model organism genes that are orthologous to human disease genes. OrthoDisease was constructed by applying the Inparanoid ortholog detection algorithm to disease genes derived from the Online Mendelian Inheritance in Man database (OMIM). Pairwise whole genome/proteome comparisons between Homo sapiens and six other organisms were performed to identify ortholog clusters. OMIM numbers were extracted from the OMIM Morbid Map and were converted to gene sequences using the Locuslink mim2loc and loc2acc tables. These were mapped to Inparanoid ortholog clusters using Blast. The number of ortholog clusters in OrthoDisease with each respective species is currently: M. musculus, 1,354; D. melanogaster, 724; C. elegans, 533; A. thaliana, 398; S. cerevisiae, 290; and E. coli, 153. The database is accessible online at http://orthodisease.cgb. ki.se, and can be searched with disease or protein names. The web interface presents all ortholog clusters that include a selected disease gene. A capability to download the entire dataset is also provided. Hum Mutat 24:112–119, 2004. © 2004 Wiley‐Liss, Inc.
Dispersion linéaire de Glossina palpalis gambiensis et de Glossina tachinoides dans une galerie forestière en zone soudano-guinéenne (Burkina-Faso)

Au cours de la saison seche 1980, les auteurs ont etudie la dispersion lineaire de deux glossines riveraines, G. p. gambiensis et G. tachinoides, le long de 35 km d'une galerie forestiere bordant le cours superieur de la Volta Noire, au Burkina-Faso. 35430 glossines ont ete lâchees en tete de galerie apres marquage, par fractions hebdomadaires, au cours de 3 series d'experiences. L'analyse statistique fait appel aux tests non parametriques appliques a 3 indices specialement retenus : un indice de "centralite" (mediane), un indice de longue distance (9e decile) et les distances maximales. Les longueurs parcourues augmentent significativement avec le temps pour les especes et les sexes
Terrestrial Rabies and Human Postexposure Prophylaxis, New York, USA

During 1993–2002, cats accounted for 2.7% of rabid terrestrial animals in New York but for one third of human exposure incidents and treatments. Nonbite exposures and animals of undetermined rabies status accounted for 54% and 56%, respectively, of persons receiving rabies treatments.
The Mos/mitogen-activated protein kinase (MAPK) pathway regulates the size and degradation of the first polar body in maturing mouse oocytes.

Mos is an upstream activator of mitogen-activated protein kinase (MAPK) and, in mouse oocytes, is responsible for metaphase II arrest. This activity has been likened to its function in Xenopus oocytes as a component of cytostatic factor. Thus, Mos-deficient female mice (MOS-/-) are less fertile and oocytes derived from these animals fail to arrest at metaphase II and undergo parthenogenetic activation [Colledge, W. H. , Carlton, M. B. L. , Udy, C. B. & Evans, M. J. (1994) Nature (London) 370, 65-68 and Hashimoto, N. , Watanabe, N. , Furuta. Y. , Tamemoto, B. , Sagata, N. , Yokoyama, M. , Okazaki, K. , Nagayoshi, M. , Takeda, N. , Ikawa, Y. & Aizawa, S. (1994) Nature (London) 370, 68-71]. Here we show that maturing MOS-/- oocytes fail to activate MAPK throughout meiosis, while p34cdc2 kinase activity is normal until late in metaphase II when it decreases prematurely. Phenotypically, the first meiotic division of MOS-/- oocytes frequently resembles mitotic cleavage or produces an abnormally large polar body. In these oocytes, the spindle shape is altered and the spindle fails to translocate to the cortex, leading to the establishment of an altered cleavage plane. Moreover, the first polar body persists instead of degrading and sometimes undergoes an additional cleavage, thereby providing conditions for parthenogenesis. These studies identify meiotic spindle formation and programmed degradation of the first polar body as new and important roles for the Mos/MAPK pathway.
Stochastic multi-type SIR epidemics among a population partitioned into households

We consider a stochastic model for the spread of an SIR (susceptible → infective → removed) epidemic among a closed, finite population that contains several types of individuals and is partitioned into households. The infection rate between two individuals depends on the types of the transmitting and receiving individuals and also on whether the infection is local (i.e., within a household) or global (i.e., between households). The exact distribution of the final outcome of the epidemic is outlined. A branching process approximation for the early stages of the epidemic is described and made fully rigorous, by considering a sequence of epidemics in which the number of households tends to infinity and using a coupling argument. This leads to a threshold theorem for the epidemic model. A central limit theorem for the final outcome of epidemics which take off is derived, by exploiting an embedding representation.