Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

The relationships among the extant five gymnosperm groups—gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads—remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the “gnepines” hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.
Down-regulation of the ALS3 gene as a consequent effect of RNA-mediated silencing of the EFG1 gene in Candida albicans.

BACKGROUND The most important virulence factor which plays a central role in Candida albicans pathogenesis is the ability of this yeast to alternate between unicellular yeast and filamentous hyphal forms. Efg1 protein is thought to be the main positive regulating transcription factor, which is responsible for regulating hyphal-specific gene expression under most conditions. ALS3 is one of the Efg1-associated genes encoding a multi-functional adhesive polypeptide, which mediates adherence to diverse host substrates. In this study, the EFG1 gene was knocked down by using synthetic siRNA in C. albicans and the regulation in ALS3 as one of the Efg1-dependent genes was investigated. METHOD The 19-nucleotide siRNA was designed based on cDNA sequence of EFG1 gene in C. albicans. Transfection was performed using modified- plyethylen glycol/LiAc method. To quantify the level of EFG1 and the hyphal-specific ALS3 gene expression, the cognate EFG1 and ALS3 mRNA were measured in C. albicans by quantitative real-time RT-PCR. RESULTS Fluorescent microscopy pictures indicated that transfection was performed successfully. Also, according to relative expression software tool, expression of EFG1 gene was decreased significantly with 500 nM siRNA as well as 1 µM siRNA (P<0.05). However, more significant down-regulations were observed in the expression of ALS3 in both concentrations of 500 nM and 1 µM siRNA (P<0.05). CONCLUSION In conclusion, we demonstrated the down-regulation of ALS3 gene as a consequent of applying EFG1-specific siRNA in C. albicans. This may lead us to design anti-fungal-specific agents in order to face with C. albicans-associated infections.
Can the Immune System Perform a t-Test?

The self-nonself discrimination hypothesis remains a landmark concept in immunology. It proposes that tolerance breaks down in the presence of nonself antigens. In strike contrast, in statistics, occurrence of nonself elements in a sample (i.e., outliers) is not obligatory to violate the null hypothesis. Very often, what is crucial is the combination of (self) elements in a sample. The two views on how to detect a change seem challengingly different and it could seem difficult to conceive how immunological cellular interactions could trigger responses with a precision comparable to some statistical tests. Here it is shown that frustrated cellular interactions reconcile the two views within a plausible immunological setting. It is proposed that the adaptive immune system can be promptly activated either when nonself ligands are detected or self-ligands occur in abnormal combinations. In particular we show that cellular populations behaving in this way could perform location statistical tests, with performances comparable to t or KS tests, or even more general data mining tests such as support vector machines or random forests. In more general terms, this work claims that plausible immunological models should provide accurate detection mechanisms for host protection and, furthermore, that investigation on mechanisms leading to improved detection in “in silico” models can help unveil how the real immune system works.
Pose recognition using cross correlation for static images of Urdu sign language

Sign language recognition has been an active area of research for around two decades and numerous different sign languages have been extensively studied in order to design reliable sign language recognition systems. Urdu, the national language of Pakistan, and its corresponding sign language, has so far been largely neglected by the academia, which is one of the reasons, it has been chosen for developing an Urdu sign language recognition system. A comprehensive database of static images depicting the signs for different Urdu alphabets is being used as reference and input images are being compared to perform Urdu alphabet recognition. Cross-correlation technique is being used for image registration between input image and images from the database to find the closest match. The tolerance level ensures a trade-off between computational complexity and accuracy of the match between set of images. The algorithm tests on the images have been around 75% successful and attempts are being made for more efficient and robust performance.
Passive protection of mice and sheep against bluetongue virus by a neutralizing monoclonal antibody

A murine hybridoma antibody, 6C2A.4. 2, previously characterized as an immunoglobulin G class 2a that binds in radioimmunoassay to bluetongue virus serotype 17 (BTV-17) but not the other 19 BTV serotypes, neutralizes BTV-17, inhibits hemagglutination with BTV-17, and precipitates viral polypeptides 2 and 3 from BTV-17-infected cells, was produced as an ascites in the peritoneal cavities of hybridoma-inoculated mice. This ascitic fluid, but not those containing other, non-neutralizing anti-BTV-17 antibodies of the same isotype, provided serotype-specific passive protection against BTV-17-induced death of neonatal mice. Antibody 6C2A.4. 2-containing ascitic fluid was injected intravenously into sheep that were later inoculated with BTV-17. These sheep remained free of clinical signs, did not develop viremia or detectable levels of antibodies reactive in the immunodiffusion test used for routine BTV diagnosis in the United States, and developed only low levels of neutralizing antibodies. Control animals became viremic and developed immunodiffusion test reactions and high levels of neutralizing antibodies during recovery, and two of three had lesions and fevers. These results provide evidence that antibodies directed against a single epitope on BTV-17 can prevent bluetongue disease.
QUADS: question answering for decision support

As the scale of available on-line data grows ever larger, individuals and businesses must cope with increasing complexity in decision-making processes which utilize large volumes of unstructured, semi-structured and/or structured data to satisfy multiple, interrelated information needs which contribute to an overall decision. Traditional decision support systems (DSSs) have been developed to address this need, but such systems are typically expensive to build, and are purpose-built for a particular decision-making scenario, making them difficult to extend or adapt to new decision scenarios. In this paper, we propose a novel decision representation which allows decision makers to formulate and organize natural language questions or assertions into an analytic hierarchy, which can be evaluated as part of an ad hoc decision process or as a documented, repeatable analytic process. We then introduce a new decision support framework, QUADS, which takes advantage of automatic question answering (QA) technologies to automatically understand and process a decision representation, producing a final decision by gathering and weighting answers to individual questions using a Bayesian learning and inference process. An open source framework implementation is presented and applied to two real world applications: target validation, a fundamental decision-making task for the pharmaceutical industry, and product recommendation from review texts, an everyday decision-making situation faced by on-line consumers. In both applications, we implemented and compared a number of decision synthesis algorithms, and present experimental results which demonstrate the performance of the QUADS approach versus other baseline approaches.
Antioxidant activity of ethanolic extract of Tinospora cordifolia on N-nitrosodiethylamine (diethylnitrosamine) induced liver cancer in male Wister albino rats

Background: Cancer is a disease that evokes wide spread fear among people and is one of the leading causes of deaths in the world. Diethylnitrosamine (DEN) is a known carcinogen in rodent liver. DENs reported to undergo metabolic activation by cytochrome P450 enzymes to form reactive electrophiles that cause oxidative stress leading to cytotoxicity, mutagenicity and carcinogenicity. Objective: The present study was carried out to evaluate the antioxidant activity of ethanolic extract of Tinospora cordifolia (EETC) in N-nitrosodiethylamine (DEN) induced liver cancer in male Wister albino rats. Materials and Methods: The antioxidant activity was assessed by the levels of lipid peroxidation (LPO), enzymic and nonenzymic antioxidants. Result: A significant levels of LPO was increased as the enzymic and nonenzymic antioxidants values were decreased in liver cancer bearing animals. Conclusions: The administration of EETC to cancer bearing animals reverted the LPO levels, enzymic and nonenzymic antioxidants to near normal
Capsule Expression by Bovine Isolates ofStaphylococcus aureus from Argentina: Genetic and Epidemiologic Analyses

ABSTRACT Staphylococcus aureus is an important cause of bovine mastitis worldwide, and effective preventive or therapeutic modalities are lacking. Although most human S. aureus isolates produce capsular polysaccharides (CPs), few reports have described the prevalence of capsules on bovine isolates. This information is important for the rational design of a vaccine for the prevention of staphylococcal mastitis. We serotyped 195 S. aureus strains isolated between 1989 and 1997 from the milk of mastitic cows in Argentina. Only 14 (7.1%) of the strains were serotype 5, and all were recovered between 1989 and 1992. Thirteen serotype 8 strains were identified, and 12 of these were isolated between 1991 and 1994. The remaining 168 isolates were nonreactive (NR) with CP serotype 5 (CP5)- or CP8-specific antibodies. Hybridization studies performed with genomic DNA from eight NR strains revealed that only three of them carried the capsule genes. Pulsed-field gel electrophoresis (PFGE) performed with 127 of the 195 S. aureus isolates revealed that most (86%) strains belonged to one of four major PFGE groups. Although 8 of 14 CP5 isolates showed a common PFGE pattern (arbitrarily defined as A1), 31 other A1 isolates from the same time period (1989 to 1992) were not CP5 positive. In contrast, only nine PFGE type B3 isolates were recovered between 1990 and 1994, and eight of these were positive for CP8 (P < 0.0003). The results of this study underscore the variability in capsule expression by S. aureus strains isolated from different geographical regions and cast doubt on the roles of CP5 and CP8 in the pathogenesis and immunoprophylaxis of bovine mastitis in Argentina.
Con-text: text detection using background connectivity for fine-grained object classification

This paper focuses on fine-grained classification by detecting photographed text in images. We introduce a text detection method that does not try to detect all possible foreground text regions but instead aims to reconstruct the scene background to eliminate non-text regions. Object cues such as color, contrast, and objectiveness are used in corporation with a random forest classifier to detect background pixels in the scene. Results on two publicly available datasets ICDAR03 and a fine-grained Building subcategories of ImageNet shows the effectiveness of the proposed method.
A Multi-objective Optimization Procedure with Successive Approximate Models

This paper explores the possibility of using approximate model for fitness landscape in multi-objective optimization. A multi-objective genetic algorithm based optimizer, namely, NSGA-II is integrated with artificial neural network (ANN). This presented technique makes use of successive fitness landscape modeling for reducing the precise function evaluation calls while retaining the basic robust search capability of genetic algorithms (GA). The procedure is tried on some of the standard test problems available in literature on multi-objective optimization. The simulation results show a considerable savings in precise function evaluations and a good diversity in the obtained Pareto-front.
A converse bound on Wyner-Ahlswede-Körner Network via Gray-Wyner network

We show a reduction method to construct a code for the Gray-Wyner (GW) network from a given code for the Wyner-Ahlswede-Korner (WAK) network. By combining this reduction with a converse bound on the GW network, we derive a converse bound on the WAK network. The derived bound gives an alternative proof of the strong converse theorem for the WAK network.
Unraveling the neural circuitry of sequence-based navigation using a combined fos imaging and computational approach

Spatial navigation is a complex function requiring the combination of external and self-motion cues to build a coherent representation of the external world and drive optimal behaviour directed towards a goal. This multimodal integration suggests that a large network of cortical and subcortical structures interacts with the hippocampus, a key structure in navigation. I have studied navigation in mice through this global approach and have focused on one particular type of navigation, which consists in remembering a sequence of turns, named sequence-based navigation or sequential egocentric strategy. This navigation specifically relies on the temporal organization of movements at spatially distinct choice points. We first showed that sequence-based navigation learning required the hippocampus and the dorsomedial striatum. Our aim was to identify the functional network underlying sequence-based navigation using Fos imaging and computational approaches. The functional networks dynamically changed across early and late learning stages. The early stage network was dominated by a highly inter-connected cortico-striatal cluster. The hippocampus was activated alongside structures known to be involved in self-motion processing (cerebellar cortices), in mental representation of space manipulations (retrosplenial, parietal, entorhinal cortices) and in goal-directed path planning (prefrontal-basal ganglia loop). The late stage was characterized by the emergence of correlated activity between the hippocampus, the cerebellum and the cortico-striatal structures. Conjointly, we explored whether path integration, model-based or model-free reinforcement learning algorithms could explain mice’s learning dynamics. Only the model-free system, as long as a retrospective memory component was added to it, was able to reproduce both the group learning dynamics and the individual variability observed in the mice. These results suggest that a unique model-free reinforcement learning algorithm was sufficient to learn sequence-based navigation and that the multiple structures this learning required adapted their functional interactions across learning.
A time-dependent Mueller-like formulation for the study of the RF spectrum and time-resolved polarization phenomena in birefringent systems

Using a novel 4/spl times/4 Mueller-like time-dependent matrix to describe the propagation of modulated light in birefringent optical systems, a new method for characterizing the polarization dependence of the RF spectrum in systems having polarization-mode dispersion and polarization-dependent loss is proposed and demonstrated. By measuring the RF spectra for nine different input states of polarization (SOP), the spectrum of any other input SOP is accurately predicted. Another application of the general formulation allows the study of the dependence of the time-resolved characteristics of the SOP of light propagating in a birefringent medium.
The role of neurohumors in early embryogenesis

In a previous paper (Buznikov, Chudakova & Zvezdina, 1964) it has been reported that serotonin (5-hydroxytryptamine, 5-HT) may be involved in early embryogenesis in various groups of animals. This conclusion was confirmed by Baker's recent publication (Baker, 1965) concerning 5-HT synthesis in Xenopus laevis embryos. Some other low molecular weight substances, neurohumors or related compounds, are known to be synthesized in fertilized eggs as well. Acetylcholine (ACh) synthesis in sea-urchin eggs and embryos was demonstrated by Numanoi (1953, 1955, 1959, 1961). It seems possible that ACh can be synthesized in fertilized insect eggs as well (Morley & Schachter, 1963; Schachter, 1964). The synthesis of another neurohumor, dopamine (DA), in early insect embryos seems to be indisputable (Furneaux & McFarlane, 1965). However, in most cases changes in the level of neurohumors with age have not been studied. In the present paper data concerning the change of concentration with age of ACh and catecholamines (adrenaline (A) and noradrenaline (NA)) in early seaurchin embryos will be presented. We thought it would be of interest to investigate the suggestion that serotonin is not the only neurohumor synthesized in embryos of the sea urchin Strongylocentrotus drobachiensis. In addition, we compare the changes in the levels of various neurohumors with age.
Efficacy of Dichloroacetate as a Lactate‐Lowering Drug

Dichloroacetate (DCA) decreases blood, cerebral spinal fluid, and intracellular lactate concentrations by activating the mitochondrial pyruvate dehydrogenase enzyme complex. The authors reviewed the efficacy of this investigational drug in the treatment of acquired or congenital forms of lactic acidosis from data in 40 English‐language publications. The hypolactatemic effect of DCA occurs over a broad range of pretreatment lactate concentrations and is directly related to the baseline lactate level. The maximum lactate‐lowering effect of the drug is dependent on its dose but independent of time following its administration. Recent clinical studies of acquired lactic acidosis suggest that DCA could be rapidly effective in reducing this risk factor of mortality in patients with mild hyperlactatemeia.
The Impact of Inpatient Homicide on Forensic Mental Health Nurses' Distress and Posttraumatic Stress

Violence in mental health units can have a profound impact on staff wellbeing. This cross-sectional study explored the impact of patient-perpetrated double homicide on the psychological wellbeing of forensic mental health nurses. Nurses completed self-report questionnaires assessing the impact of aggression and work stress on posttraumatic stress and distress prior to (N = 97) and after (N = 107) a patient killed two other patients in a forensic psychiatric hospital. Following the homicides, nurses generally demonstrated resilience and there were few differences in posttraumatic stress and distress before and after the incident; however, nurses working on the unit where the homicides occurred appear to have been at increased risk of developing Posttraumatic Stress Disorder. Nurses experiencing increased posttraumatic stress and distress were likely to seek help by accessing psychological support services. Implications for organisations and individual staff members are discussed.
Domain Adaptation for CRF-based Chinese Word Segmentation using Free Annotations

Supervised methods have been the dominant approach for Chinese word segmentation. The performance can drop significantly when the test domain is different from the training domain. In this paper, we study the problem of obtaining partial annotation from freely available data to help Chinese word segmentation on different domains. Different sources of free annotations are transformed into a unified form of partial annotation and a variant CRF model is used to leverage both fully and partially annotated data consistently. Experimental results show that the Chinese word segmentation model benefits from free partially annotated data. On the SIGHAN Bakeoff 2010 data, we achieve results that are competitive to the best reported in the literature.
Predicting the presence and side of extracapsular extension: a nomogram for staging prostate cancer.

PURPOSE We developed a model to predict the side specific probability of extracapsular extension (ECE) in radical prostatectomy (RP) specimens based on the clinical features of the cancer. MATERIALS AND METHODS We studied 763 patients with clinical stage T1c-T3 prostate cancer who were diagnosed by systematic needle biopsy and subsequently treated with RP. Candidate predictor variables associated with ECE were clinical T stage, the highest Gleason sum in any core, percent positive cores, percent cancer in the cores from each side and serum prostate specific antigen (PSA). Receiver operating characteristic (ROC) analyses were performed to assess the predictive value of each variable alone and in combination. We constructed and internally validated nomograms to predict the side specific probability of ECE based on logistic regression analysis. RESULTS Overall 30% of the patients and 17% of 1,526 prostate lobes (left or right) had ECE. The areas under the ROC curves (AUC) of the standard features in predicting side specific probability of ECE were 0.627 for PSA, 0.695 for clinical T stage on each side and 0.727 for Gleason sum on each side. When these features were combined predictive accuracy increased to 0.788. The highest value (0.806) was achieved by adding the percent positive cores and the percent cancer in the biopsy specimen to the standard features. The resulting nomograms were internally validated and had excellent calibration and discrimination accuracy. CONCLUSIONS Standard clinical features of prostate cancer in each lobe-PSA, palpable induration and biopsy Gleason sum-can be used to predict the side specific probability of ECE in RP specimens. The predictive accuracy is increased by adding information from systematic biopsy results. The predictive nomograms are sufficiently accurate for use in clinical practice in decisions such as wide versus close dissection of the cavernous nerves from the prostate.