Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppression Subtractive Hybridization Analysis of Genes Regulated by Application of Exogenous Abscisic Acid in Pepper Plant (Capsicum annuum L.) Leaves under Chilling Stress

Low temperature is one of the major factors limiting pepper (Capsicum annuum L.) production during winter and early spring in non-tropical regions. Application of exogenous abscisic acid (ABA) effectively alleviates the symptoms of chilling injury, such as wilting and formation of necrotic lesions on pepper leaves; however, the underlying molecular mechanism is not understood. The aim of this study was to identify genes that are differentially up- or downregulated in ABA-pretreated hot pepper seedlings incubated at 6°C for 48 h, using a suppression subtractive hybridization (SSH) method. A total of 235 high-quality ESTs were isolated, clustered and assembled into a collection of 73 unigenes including 18 contigs and 55 singletons. A total of 37 unigenes (50.68%) showed similarities to genes with known functions in the non-redundant database; the other 36 unigenes (49.32%) showed low similarities or unknown functions. Gene ontology analysis revealed that the 37 unigenes could be classified into nine functional categories. The expression profiles of 18 selected genes were analyzed using quantitative RT-PCR; the expression levels of 10 of these genes were at least two-fold higher in the ABA-pretreated seedlings under chilling stress than water-pretreated (control) plants under chilling stress. In contrast, the other eight genes were downregulated in ABA-pretreated seedlings under chilling stress, with expression levels that were one-third or less of the levels observed in control seedlings under chilling stress. These results suggest that ABA can positively and negatively regulate genes in pepper plants under chilling stress.
A Review of Human Activity Recognition Methods

Recognizing human activities from video sequences or still images is a challenging task due to problems such as background clutter, partial occlusion, changes in scale, viewpoint, lighting, and appearance. Many applications, including video surveillance systems, human-computer interaction, and robotics for human behavior characterization, require a multiple activity recognition system. In this work, we provide a detailed review of recent and state-of-the-art research advances in the field of human activity classification. We propose a categorization of human activity methodologies and discuss their advantages and limitations. In particular, we divide human activity classification methods into two large categories according to whether they use data from different modalities or not. Then, each of these categories is further analyzed into sub-categories, which reflect how they model human activities and what type of activities they are interested in. Moreover, we provide a comprehensive analysis of the existing, publicly available human activity classification datasets and examine the requirements for an ideal human activity recognition dataset. Finally, we report the characteristics of future research directions and present some open issues on human activity recognition.
A new gene coding for a differentiation antigen recognized by autologous cytolytic T lymphocytes on HLA-A2 melanomas

It has been reported previously that antitumor cytolytic T lymphocyte (CTL) clones can be isolated from blood lymphocytes of HLA-A2 melanoma patients, after stimulation in vitro with autologous tumor cells, and that some of these CTL clones lyse most HLA-A2 melanomas. A first antigen recognized by such CTL clones was previously shown to be encoded by the tyrosinase gene. We report here the identification of another gene that also directs the expression of an antigen recognized on most melanomas by CTL clones that are restricted by HLA-A2. The gene, designated Melan-A, is unrelated to any known gene. It is 18 kb long and comprises five exons. Like the tyrosinase gene, it is expressed in most melanoma tumor samples and, among normal cells, only in melanocytes.
Deferoxamine but Not Dimethyloxalylglycine, L-Mimosine, or Cobalt Dichloride Can Interfere with the MTT Assay

Hypoxia mimetic agents (HMAs) have been shown to have a positive influence on cellular functions in a multitude of tissue regenerative strategies. Novel experimental approaches use biomaterials as carriers for controlled delivery of these HMAs. Here, the cytotoxic aspects of biocompatibility are of key relevance. The MTT assay is widely used to evaluate cytotoxicity and proliferation. Based on the implications from the proceeding research we hypothesized that specific HMAs such as deferoxamine at high concentrations can interfere with the MTT assay. Thus, the aim of this study was to test the repercussions of the HMAs dimethyloxalylglycine, deferoxamine, L-mimosine, and CoCl2 on the validity of the MTT assay. Murine MC3T3-E1 cells were cultured in serum-free alphaMEM and in alphaMEM supplemented with 10 % fetal bovine serum with the HMAs dimethyloxalylglycine, deferoxamine, L-mimosine, and CoCl2, respectively, at 3 mM-0.3 mM for 24 h (experimental groups). Cells without HMAs served as control (control groups). The same experiments were performed with medium and phosphate buffered saline (PBS) without cells. In all settings MTT solution was added to PBS-washed or unwashed culture plates for the last two hours of the incubation period. Then MTT solution was removed and dimethyl sulfoxide was added to dissolve the formazan crystals and absorption was measured. Our data show that the presence of deferoxamine can interfere with the MTT assay if not removed before the addition of MTT. This is particularly important when evaluating cell viability in setups where deferoxamine-loaded biomaterials are used.
Effects of ascorbic acid, phytic acid and tannic acid on iron bioavailability from reconstituted ferritin measured by an in vitro digestion–Caco-2 cell model

The effects of ascorbic acid (AA), phytate and tannic acid (TA) on Fe bioavailability from Fe supplied as reconstituted ferritin were compared with FeSO4 using an in vitro digestion–Caco-2 cell model. Horse spleen apoferritin was chemically reconstituted into an animal-type ferritin (HSF) and a plant-type ferritin (P-HSF) according to the typical ratios of Fe:P found in these molecules. In the presence of AA (Fe:AA molar ratio of 1:20), significantly more Fe was absorbed from FeSO4 (about 303 %), HSF (about 454 %) and P-HSF (about 371 %) when compared with ferrous sulfate or ferritin without AA. Phytic acid (PA; Fe:PA molar ratio of 1:20) significantly reduced Fe bioavailability from FeSO4 (about 86 %), HSF (about 82 %) and P-HSF (about 93 %) relative to FeSO4 and the ferritin controls. Treatment with TA (Fe:TA molar ratio of 1:1) significantly decreased Fe bioavailability (about 97 %) from both FeSO4 and the ferritin samples. AA was able to partially reverse the negative effect of PA (Fe:PA:AA molar ratio of 1:20:20) on Fe bioavailability but did not reverse the inhibiting effect of TA (Fe:TA:AA molar ratio of 1:1:20) on Fe bioavailability from ferritin and FeSO4. Overall, there were no significant differences in bioavailable Fe between P-HSF, HSF or FeSO4. Furthermore, the addition of AA (a known promoter) or the inhibitors, PA and TA, or both, did not result in significant differences in bioavailable Fe from ferritin relative to FeSO4. The results suggest that Fe in the reconstituted ferritin molecule is easily released during in vitro digestion and interacts with known promoters and inhibitors.
Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.
Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains

ABSTRACT Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.
miR-27b Targets KSRP to Coordinate TLR4-Mediated Epithelial Defense against Cryptosporidium parvum Infection

Cryptosporidium is a protozoan parasite that infects the gastrointestinal epithelium and causes a diarrheal disease. Toll-like receptor (TLR)- and NF-κB-mediated immune responses from epithelial cells, such as production of antimicrobial peptides and generation of reactive nitrogen species, are important components of the host's defense against cryptosporidial infection. Here we report data demonstrating a role for miR-27b in the regulation of TLR4/NF-κB-mediated epithelial anti-Cryptosporidium parvum responses. We found that C. parvum infection induced nitric oxide (NO) production in host epithelial cells in a TLR4/NF-κB-dependent manner, with the involvement of the stabilization of inducible NO synthase (iNOS) mRNA. C. parvum infection of epithelial cells activated NF-κB signaling to increase transcription of the miR-27b gene. Meanwhile, downregulation of KH-type splicing regulatory protein (KSRP) was detected in epithelial cells following C. parvum infection. Importantly, miR-27b targeted the 3′-untranslated region of KSRP, resulting in translational suppression. C. parvum infection decreased KSRP expression through upregulating miR-27b. Functional manipulation of KSRP or miR-27b caused reciprocal alterations in iNOS mRNA stability in infected cells. Forced expression of KSRP and inhibition of miR-27b resulted in an increased burden of C. parvum infection. Downregulation of KSRP through upregulating miR-27b was also detected in epithelial cells following LPS stimulation. These data suggest that miR-27b targets KSRP and modulates iNOS mRNA stability following C. parvum infection, a process that may be relevant to the regulation of epithelial anti-microbial defense in general.
The ANML Language

The Action Notation Modeling Language (ANML) provides a high-level, convenient, and succinct alternative to existing planning languages such as PDDL, the IxTeT language, and languages developed at NASA, such as the EUROPA modeling language (NDDL), and the ASPEN modeling language (AML). ANML is based on strong notions of action and state (like PDDL, IxTeT, and AML), uses a variable/value model (like IxTeT, NDDL and AML), supports rich temporal constraints (like IxTeT, NDDL and AML), and provides simple, convenient idioms for expressing the most common forms of action conditions, effects, and resource usage. The language supports both generative and HTN planning models in a uniform framework and has a clear, well-defined semantics. Despite the richness of the language, it is possible to translate it into PDDL, with some increase in the number and complexity of operators and conditions. In this paper, we describe the central and unique features of the ANML language and sketch key parts of the translation to PDDL.
Measuring the effect of nuisance variables on classifiers

In real-world classification problems, nuisance variables can cause wild variability in the data. Nuisance corresponds for example to geometric distortions of the image, occlusions, illumination changes or any other deformations that do not alter the ground truth label of the image. It is therefore crucial that designed classifiers are robust to nuisance variables, especially when these are deployed in real and possibly hostile environments. We propose in this paper a probabilistic framework for efficiently estimating the robustness of state-of-the-art classifiers and sampling problematic samples from the nuisance space. This allows us to visualize and understand the regions of the nuisance space that cause misclassification, in the perspective of improving robustness. Our probabilistic framework is applicable to arbitrary classifiers and potentially high-dimensional and complex nuisance spaces. We illustrate the proposed approach on several classification problems and compare classifiers in terms of their robustness to nuisances. Moreover, using our sampling technique, we visualize problematic regions in the nuisance space and infer insights into the weaknesses of classifiers as well as the features used in classification (e.g., in face recognition). We believe the proposed analysis tools represent an important step towards understanding large modern classification architectures and building architectures with better robustness to nuisance.
Association between Serotonin-Related Polymorphisms in 5HT2A, TPH1, TPH2 Genes and Bipolar Disorder in Korean Population

Objective The aim of the present study was to examine the association between serotonin-related gene polymorphisms and bipolar disorder in the Korean population. In addition, we sought to explore the relationship between the clinical characteristics of bipolar patients and serotonin-related gene polymorphisms. Methods Inpatients with bipolar disorder (n=103) and control subjects (n=86) were genotyped for 5HT2A 1438A/G, tryptophan hydroxylase 1 (TPH1) 218 A/C, and TPH2 703G/T. We divided patients with bipolar disorder into two groups according to the presence of psychotic symptoms. The severity of their symptoms was measured using the Young Mania Rating Scale (YMRS) and the Brief Psychiatric Rating Scale (BPRS). Results There were no significant differences in the genotype distributions or allelic frequencies in the three serotonergic polymorphisms between patients with bipolar disorder and normal controls. There were significant differences in genotype distributions and allele frequencies of the 5-HT2A -1438A/G polymorphism between the psychotic mania group and the non-psychotic mania group (genotype: χ2=7.50, p=0.024; allele: χ2=5.92, p=0.015). However, after Bonferroni correction this signifact difference disappeared. We did not find significant differences in the genotype distributions or allelic frequencies in the TPH1 218 A/C and TPH2 703G/T polymorphisms between the psychotic mania group and non-psychotic mania group. Conclusion We failed to found the statistically significant association between three polymorphisms and bipolar disorder. However, there was a trend towards association between 5-HT2A -1438A/G polymorphism and psychotic symptom in bipolar disorder. Future research should seek to clarify this association.
Critical Success Factors for Effective IT Governance in the Public Sector Organizations in a Developing Country: The Case of Tanzania

Today in many organisations in the public sector, the use of IT has become pervasive in every facet of the organisations' endeavours in supporting and evolving public service delivery. This pervasive use of technology has caused a critical dependency on IT, which in this environment involves a complex mix of political, organisational, technical and cultural concerns that call for a specific focus on effective IT governance. Much research has been done on IT governance effectiveness in these organisations. However adequate focus has not been given to such organisations in a developing country environment like Tanzania, which on one hand is characterised by IT resources, knowledge, and culture constraints and on the other hand by the increase of IT investment and applications. In this paper specifically we address such a gap by identifying the critical success factors (CSFs) for effective IT governance in this environment. The study is based mainly on IT governance focus areas in analysing the relevant CSFs from the literature and five organizations in the Tanzanian public sector. Moreover we have taken into account the fact that the IT value to be achieved due to effective IT governance is related to efficient and cost effective IT delivery, innovation and business impact. As a result of this research we have identified eleven CSFs that should be considered for effective IT governance practice in Tanzanian public sector organizations.
Effects of Tactile Sensations during Finger Painting on Mindfulness, Emotions, and Scope of Attention

Research has shown that creative performance, such as painting, influences affective and cognitive processes. Yet little is known about how tactile sensations experienced during painting determine what individuals feel and how they think while they create. Based on prior research, finger painting (compared to brush painting) was expected to generate more tactile sensations, enhance state mindfulness, and broaden the scope of attention. An effect of painting on emotional processing was also expected. Volunteers (N = 54) were randomly assigned to finger painting or brush painting sessions. The global-local test was used to measure scope of attention. Participants reported state mindfulness with a cued-recall rating dial method. Automated facial expression analysis provided a continuous index of emotions. In support of the hypotheses, finger painting was related to more tactile sensations, more state mindfulness, and a broader attentional focus. These results suggest that assigning finger painting to individuals is a viable method for improving state mindfulness and enhancing scope of attention. The effects for affective processes, however, are mixed.
Absorptive capacity, learning, and performance in international joint ventures

This paper proposes and tests a model of IJV learning and performance that segments absorptive capacity into the three components originally proposed by Cohen and Levinthal (1990). First, trust between an IJV's parents and the IJV's relative absorptive capacity with its foreign parent are suggested to influence its ability to understand new knowledge held by foreign parents. Second, an IJV's learning structures and processes are proposed to influence its ability to assimilate new knowledge from those parents. Third, the IJV's strategy and training competence are suggested to shape its ability to apply the assimilated knowledge. Revisiting the Hungarian IJVs studied by Lyles and Salk (1996) 3 years later, we find support for the knowledge understanding and application predictions, and partial support for the knowledge assimilation prediction. Unexpectedly, our results suggest that trust and management support from foreign parents are associated with IJV performance but not learning. Our model and results offer a new perspective on IJV learning and performance as well as initial insights into how those relationships change over time. Copyright © 2001 John Wiley & Sons, Ltd.
A New Perspective of the Proportional Sampling Strategy

To compare the performance of different testing strategies, P-measure and E-measure are two effectiveness measures used in previous analytical studies. P-measure, which is defined as the probability of detecting at least one failure, is a measure of how likely it is that failure-causing inputs are selected at least once as test cases. E-measure, which is defined as the expected number of failures detected, is a measure of how frequently failure-causing inputs are selected as test cases. However, we have noa priori knowledge of how many failure-causing inputs there are, or where they may lie. In this paper, we study P-measure and E-measure in terms of how much attention an arbitrary input receives. In the context of P-measure, the attention received by an arbitrary input is the probability that the input is selected at least once as a test case, while in the context of E-measure, the attention is the expected number of times that an input is selected as a test case. The attentions received by an input using the proportional sampling strategy and random testing are then compared. The attention received by an input is found to be the same under the two testing strategies for E-measure, whereas for P-measure the attention is always higher for the proportional sampling strategy than for random testing. This new perspective allows us to provide simpler proofs of some known results. Furthermore, we are able to show that the difference in the expected number of distinct test cases considered by the proportional sampling strategy is larger than that of random testing by at most 2k, wherek is the number of partitions and is independent of the number of test cases selected.