Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.)

The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.
Non-preemptive scheduling of optical switches

Many high-speed routers today use input-queued (IQ) architectures with a crossbar switching fabric based on optical technology. Packets in the input queues are divided into cells of unit length and the goal is to find a schedule of minimum makespan that forwards all packets to the output ports. The problem is complicated since in optical switches so called configuration delay, that is the time required to reconfigure the switching fabric, is non-negligible with respect to the cell transmission time. We aim to design a scheduler whose complexity does not depend on the number of packets in the input queues. Thus, we focus on the non-preemptive bipartite scheduling (NPBS) problem, where each input queue is connected to each output port in at most one configuration. We demonstrate that the NPBS problem is NP-hard for any value of the configuration delay and approximation within a ratio smaller than 7/6 is NP-hard as well. For the offline version of the NPBS problem, we show that a simple greedy algorithm achieves an approximation factor of 2 for arbitrary configuration delay. Then we consider the online version of the NPBS problem, where the switch gathers the incoming traffic periodically and then schedules the accumulated batches (batch scheduling). We propose a scheduling algorithm which guarantees strict delay for any admissible traffic provided that the switch has a moderate speedup of two.
Gene Expression Profiling after Radiation-Induced DNA Damage Is Strongly Predictive of BRCA1 Mutation Carrier Status

Purpose: The impact of the presence of a germ-line BRCA1 mutation on gene expression in normal breast fibroblasts after radiation-induced DNA damage has been investigated. Experimental Design: High-density cDNA microarray technology was used to identify differential responses to DNA damage in fibroblasts from nine heterozygous BRCA1 mutation carriers compared with five control samples without personal or family history of any cancer. Fibroblast cultures were irradiated, and their expression profile was compared using intensity ratios of the cDNA microarrays representing 5603 IMAGE clones. Results: Class comparison and class prediction analysis has shown that BRCA1 mutation carriers can be distinguished from controls with high probability (∼85%). Significance analysis of microarrays and the support vector machine classifier identified gene sets that discriminate the samples according to their mutation status. These include genes already known to interact with BRCA1 such as CDKN1B, ATR, and RAD51. Conclusions: The results of this initial study suggest that normal cells from heterozygous BRCA1 mutation carriers display a different gene expression profile from controls in response to DNA damage. Adaptations of this pilot result to other cell types could result in the development of a functional assay for BRCA1 mutation status.
Analysis of Wolbachia Strains Associated with Conotrachelus nenuphar (Coleoptera: Curculionidae) in the Eastern United States

ABSTRACT We studied the distribution patterns of Wolbachia infection associated with plum curculio strains in eight states of the eastern United States. The presence of the Wolbachia-specific gene wsp identified infections of this endosymbiont in 97.8% of the 93 samples tested. Three distinct Wolbachia strains were identified. The strains wCne1 (593 bp) and wCne2 (593 bp) were 97% identical, and their sequences were both 84% identical with wCne3 (590 bp). BLASTN searches through GenBank showed strong similarities between the wsp sequences of the three strains compared with Wolbachia sequenced from other hosts. Degree of similarity with sequences in other Wolbachia strains is discussed. Polymerase chain reaction-restriction fragment length polymorphism was used for superinfection detection. Of 93 samples, 15 (16.1%), 21 (22.6%), 19 (20.4%), and 36 (38.7%) samples were infected by wCne1, wCne2, wCne1 + 2, and wCne3, respectively. Only two (2.2%) samples had no infection. The wCne3 strain was always present as a single infection. Wolbachia strains approximate the distribution of plum curculio strains: northern strain infected with wCne1 and wCne2 strains in supergroup B, and southern strain infected with wCne3 strain in supergroup A, with the mid-Atlantic region as the convergence area. Based on haplotype distribution of plum curculio mitochondrial cytochrome oxidase I, there was a closer relation of the mid-southern plum curculio clade to the far-southern clade than to the northern clade. However, Wolbachia symbionts in mid-southern plum curculio are more closely related to those in northern plum curculio than to those in far-southern plum curculio. The relationship of Wolbachia infection with reproductive incompatibility between plum curculio populations was also discussed.
Octreotide negates the benefit of galantide when used in the treatment of caerulein-induced acute pancreatitis in mice.

BACKGROUND We have previously shown that galantide, a non-specific galanin receptor antagonist, ameliorates acute pancreatitis (AP) induced in mice. Octreotide, a somatostatin analogue, has been used in the treatment of AP with inconsistent outcomes. This study set out to compare the efficacy of a combined treatment of galantide and octreotide with the efficacy of each agent individually in experimental AP. METHODS Acute pancreatitis was induced in mice with 7-hourly caerulein injections. Galantide and/or octreotide were co-administered with each caerulein injection commencing with the first injection. Control animals received galantide, octreotide or saline alone. Pancreata were harvested for histological examination and estimation of myeloperoxidase (MPO) activity. Plasma amylase and lipase activities were measured. RESULTS Galantide significantly reduced AP-induced hyperenzymaemia by 39-45%. Octreotide alone, or in combination with galantide, did not significantly alter AP-induced hyperenzymaemia. Plasma enzyme activity in the control groups was comparable with pre-treatment activity. Galantide and octreotide administered individually reduced MPO activity by 79% and 50%, respectively; however their combination was without effect. Galantide, octreotide and their combination significantly reduced the percentage of abnormal acinar cells by 28-45%. CONCLUSIONS Treatment with galantide alone ameliorated most of the indices of AP studied, whereas treatment with octreotide reduced pancreatic MPO activity and acinar cell damage. Combining the two peptides appears to negate their individual benefits, which suggests an interaction in their mechanism of action.
Efficient feature selection using a self-adjusting harmony search algorithm

Many strategies have been exploited for the task of feature selection, in an effort to identify more compact and better quality subsets. The use of an evaluation metric have been developed recently that can judge the quality of a given subset as a whole, rather than a combination of individual features. Powerful nature-inspired stochastic search techniques have also emerged, allowing multiple good quality features to be discovered without resorting to exhaustive search. Harmony search in particular, is a recently developed technique that mimics musicians' experience, which has been successfully applied to solving feature selection problems. This paper proposes three improvements to the harmony search algorithm that are designed to further enhance its feature selection performance. The resultant technique is more efficient, capable of automatically adjusting the internal components of the algorithm. Systematic experimental evaluation using high dimensional, real-valued data sets has been carried out to verify the benefits of the presented work.
Phenotypic characterization of human decidual macrophages

Pregnancy is a challenge to the immune system, which not only has to protect the mother and the fetus from invading pathogens but to also maintain immunological tolerance against the fetus. However, the mechanisms inhibiting local immune responses in the maternal decidual tissue are poorly understood. We have studied decidual CD14+ macrophages, which may be important in the maintenance of a tolerance against the developing fetus. Decidual macrophages expressed HLA‐DR, but lower levels of costimulatory molecule CD86 than peripheral blood CD14+ monocytes from pregnant and non‐pregnant women. Decidual macrophages produced spontaneously high levels of interleukin‐10. Our findings suggest that decidual macrophages could represent an inhibitory type of APCs. Supporting this conclusion indoleamine 2,3‐dioxygenase (IDO), suggested to have an immunosuppressive role in pregnancy, was expressed in decidual macrophages. Furthermore, decidual macrophages were not able to differentiate into dendritic cells under the influence of IL‐4 + GM‐CSF. These results suggest an immunoinhibitory function of decidual macrophages at the maternal–fetal interface.
Artistic silhouettes: a hybrid approach

We present a new algorithm for rendering silhouette outlines of 3D polygonal meshes with stylized strokes. Rather than use silhouette edges of the model directly as the basis for drawing strokes, we first process the edges in image space to create long, connected paths corresponding to visible portions of silhouettes. The resulting paths have the precision of object-space edges, but avoid the unwanted zig-zagging and inconsistent visibility of raw silhouette edges. Our hybrid screen/object space approach thus allows us to apply stylizations to strokes that follow the visual silhouettes of an object. We describe details of our OpenGL-based stylized strokes that can resemble natural media, but render at interactive rates. We demonstrate our technique with the accompanying still images and animations rendered with our technique. CR Categories and Subject Descriptors: I.3. 3 [Computer Graphics]: Picture/Image Generation - Display algorithms
Does Adiponectin Act as an Antiangiogenic Factor in B-Cell Chronic Lymphocytic Leukemia?

Angiogenesis is involved in the pathogenesis of B-cell chronic lymphocytic leukemia (CLL), and high microvascular density has been found in CLL to be associated with a poor prognosis. In this study, we assessed serum levels of adiponectin in 69 patients with Binet stage A B-CLL, and these values were retrospectively correlated with bone marrow (BM) microvessel area and serum levels of vascular endothelial growth factor (VEGF), fibroblast growth factor-2 (FGF-2), angiogenin, PECAM-1 (CD31), matrix metalloproteinase-9 (MMP-9), interleukin-8 (IL-8), syndecan-1, and the percentage of CD38+ or ZAP-70+ CLL cells. The positive correlation between serum levels of adiponectin and VEGF (P = .03) does not translate into an increase of the extent of BM angiogenesis (P = .404), FGF-2 (P = .348), angiogenin (P = .402), and CD31 (P = .248) serum concentrations. Accordingly, IL-8 (P = .175), syndecan-1 (P = .06), and MMP-9 (P = .144) circulating levels were not likely to reflect adiponectin concentration. Furthermore, patients with higher levels of adiponectin had a more favorable biological profile as defined by a lower number of both CD38− (r = −0.294; P = .02) and ZAP-70+ (r = −0.285; P = .04). Finally, we evaluated the presence of adiponectin in B-CLL cells at gene expression level. RMA intensity values for adiponectin gene transcript denote a homogeneous low expression in B-CLL cells, whereas VEGF transcript was highly expressed with a degree of interpatient variability. Overall, these data seem to indicate that adiponectin could be involved as an antiangiogenic factor in B-CLL.
Response inhibition is modulated by functional cerebral asymmetries for facial expression perception

The efficacy of executive functions is critically modulated by information processing in earlier cognitive stages. For example, initial processing of verbal stimuli in the language-dominant left-hemisphere leads to more efficient response inhibition than initial processing of verbal stimuli in the non-dominant right hemisphere. However, it is unclear whether this organizational principle is specific for the language system, or a general principle that also applies to other types of lateralized cognition. To answer this question, we investigated the neurophysiological correlates of early attentional processes, facial expression perception and response inhibition during tachistoscopic presentation of facial “Go” and “Nogo” stimuli in the left and the right visual field (RVF). Participants committed fewer false alarms after Nogo-stimulus presentation in the left compared to the RVF. This right-hemispheric asymmetry on the behavioral level was also reflected in the neurophysiological correlates of face perception, specifically in a right-sided asymmetry in the N170 amplitude. Moreover, the right-hemispheric dominance for facial expression processing also affected event-related potentials typically related to response inhibition, namely the Nogo-N2 and Nogo-P3. These findings show that an effect of hemispheric asymmetries in early information processing on the efficacy of higher cognitive functions is not limited to left-hemispheric language functions, but can be generalized to predominantly right-hemispheric functions.
Effects of bone marrow mesenchymal stem cells transfected with Ang‐1 gene on hyperoxia‐induced optic nerve injury in neonatal mice

Optic nerve injury triggered retinal ganglion cell (RGC) death and optic nerve atrophy lead to visual loss. Bone marrow mesenchymal stem cells (BMSCs) are stromal cells, capable of proliferating and differentiating into different types of tissues. This aims of this study is to investigate the role of BMSCs transfected with angiopoietin‐1 (Ang‐1) in optic nerve injury induced by hyperoxia in a neonatal mice model. Ang‐1 overexpression vector was constructed and used to transfect BMSCs. Reverse transcription‐quantitative polymerase chain reaction was performed to detect Ang‐1 expression in BMSCs. The hyperoxia‐induced optic nerve injury model was established. The optic nerves at 6–7 mm posterior to the eyeball were extracted, and were treated with luxol fast blue staining, immunohistochemistry, immunofluorescence, and transmission electron microscopy to examine the effects of Ang‐1‐modified BMSCs on optic nerve injury induced by hyperoxia. The mice in the Ang‐1 + BMSCs and BMSCs groups showed remarkably improved myelin sheaths of nerve fibers compared to the hyperoxia saline group. The positive expression and integrated optic density of Ang‐1 in the Ang‐1 + BMSCs group were significantly higher compared to the air control, hyperoxia saline and BMSCs groups. The number and diameter of myelinated nerve fibers, the diameter of axons and the thickness of myelin sheath in the air control and Ang‐1 + BMSCs groups were higher compared to the hyperoxia saline group. Our study provides evidence supporting that Ang‐1‐modified BMSCs may have preventive and therapeutic effects on hyperoxia‐induced optic nerve injury in neonatal mice.
The Effect of Performance Expectancy, Effort Expectancy, Social Influence and Facilitating Conditions on Acceptance of E-Banking Services in Iran: the Moderating Role of Age and Gender

Today people increasingly need banking services. People expect more and faster services with higher quality; so attracting new customers and retaining current ones requires an efficient and effective management at all aspects of banks with emphasis on marketing management. Thus, the purpose of this paper is to investigate the effects of performance expectancy, effort expectancy, social influence and facilitating conditions on acceptance of e-banking services in Iran by considering the role of age and gender. Totally, 350 questionnaires were distributed to customers of Bank Melli, that 310 questionnaires were used for the final analysis, which the results from analysis of them based on simple linear regression show that all four variables i.e. performance expectancy, effort expectancy, social influence and facilitating conditions had a positive and significant effect on users' behavior and intention to use e-banking services and variables of age and gender moderated the relationships between these variables. Therefore in order to achieve effective acceptance of e-banking services, extensive, attractive and insightful activities should be done to raise users' awareness of these advantages and e-banking services should be designed in a way that users face no problems while using them. Also with respect to positive and significant effect of facilitating conditions on using e-banking services, it is recommended that infrastructure e.g. computers and high-speed and affordable internet required in this field is provided to all social classes.
Life is an Adventure! An agent-based reconciliation of narrative and scientific worldviews

The scientific worldview is based on laws, which are supposed to be certain, objective, and independent of time and context. The narrative worldview found in literature, myth and religion, is based on stories, which relate the events experienced by a subject in a particular context with an uncertain outcome. This paper argues that the concept of “agent”, supported by the theories of evolution, cybernetics and complex adaptive systems, allows us to reconcile scientific and narrative perspectives. An agent follows a course of action through its environment with the aim of maximizing its fitness. Navigation along that course combines the strategies of regulation, exploitation and exploration, but needs to cope with often-unforeseen diversions. These can be positive (affordances, opportunities), negative (disturbances, dangers) or neutral (surprises). The resulting sequence of encounters and actions can be conceptualized as an adventure. Thus, the agent appears to play the role of the hero in a tale of challenge and mystery that is very similar to the "monomyth", the basic storyline that underlies all myths and fairy tales according to Campbell [1949]. This narrative dynamics is driven forward in particular by the alternation between prospect (the ability to foresee diversions) and mystery (the possibility of achieving an as yet absent prospect), two aspects of the environment that are particularly attractive to agents. This dynamics generalizes the scientific notion of a deterministic trajectory by introducing a variable “horizon of knowability”: the agent is never fully certain of its further course, but can anticipate depending on its degree of prospect.
Study on the effects of small swing of junction temperature cycles on solder layer in an IGBT module

This paper proposes a method to obtain the effect of junction temperature swing with low amplitudes on the power modules, so that the knowledge about the reliability characteristics of the modules and the lifetime model could be improved. Power cycling tests and finite-element analysis (FEA) models, for non-aged and aged IGBT modules, are designed to illustrate the failure mechanisms of the power modules and the stress distribution. IGBT modules in actual converters such as those in wind turbine systems are usually operated in a junction temperature swing range up to 40°C, therefore small swing junction temperature tests are designed to obtain the effects of small swings of junction temperature on the lifetime of IGBT modules. It is found that such relatively minor stress cycles, which happen frequently during normal operation, may not be able to directly initiate a crack but can contribute to the development of damage in die attach solder layer due to the stress concentration. The experimental results show that the effects of small swing of junction temperature are affected by the ageing state, stress level and load sequence.
sVCAM-1, sICAM-1, TNF-α and IL-6 levels in bipolar disorder type I: Acute, longitudinal and therapeutic implications

Abstract Objectives: To explore the serum levels of soluble vascular cell adhesion molecule-1 (sVCAM-1), soluble intercellular cell adhesion molecule-1 (sICAM-1), tumour necrosis factor-α (TNF-α) and interleukin-6 (IL-6) in patients with bipolar disorder (BD), with regard to acute episode characteristics, course of the disorder and treatment. Methods: The study group consisted of 83 patients diagnosed with BD type I. The control group consisted of 73 healthy individuals, matched with the study group according to age, gender and body mass index. The serum levels of sVCAM-1, sICAM-1, TNF-α and IL-6 were measured by ELISA. Results: Compared with healthy controls, significantly elevated levels of IL-6 and sICAM-1 and significantly lower levels of TNF-α and sVCAM-1 were identified in acute and remission phases of BD. The acute serum levels of sVCAM-1 were associated with the type and severity of acute mood symptoms as well as with course of illness characteristics. TNF-α was associated with duration of untreated disorder and type of treatment. Conclusions: BD is related to both acute and long-term alterations of immune mediators, including adhesion molecules. The potential immunomodulatory role of pharmacotherapeutic treatment is also to be considered in BD.