Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning from Co-expression Networks: Possibilities and Challenges

Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological processes is the discovery of causal genes and regulatory mechanisms controlling these processes. The recent surge of omics data has opened the door to a system-wide understanding of the flow of biological information underlying complex traits. However, dealing with the corresponding large data sets represents a challenging endeavor that calls for the development of powerful bioinformatics methods. A popular approach is the construction and analysis of gene networks. Such networks are often used for genome-wide representation of the complex functional organization of biological systems. Network based on similarity in gene expression are called (gene) co-expression networks. One of the major application of gene co-expression networks is the functional annotation of unknown genes. Constructing co-expression networks is generally straightforward. In contrast, the resulting network of connected genes can become very complex, which limits its biological interpretation. Several strategies can be employed to enhance the interpretation of the networks. A strategy in coherence with the biological question addressed needs to be established to infer reliable networks. Additional benefits can be gained from network-based strategies using prior knowledge and data integration to further enhance the elucidation of gene regulatory relationships. As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes. In this study we review the different approaches for co-expression network inference in plants. We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks. Additionally, we discuss promising bioinformatics approaches that predict networks for specific purposes.
Activation of the lac genes of Tn951 by insertion sequences from Pseudomonas cepacia

We have identified three transposable gene-activating elements from Pseudomonas cepacia on the basis of their abilities to increase expression of the lac genes of the broad-host-range plasmid pGC91.14 (pRP1::Tn951). When introduced into auxotrophic derivatives of P. cepacia 249 (ATCC 17616), this plasmid failed to confer the ability to utilize lactose. The lac genes of Tn951 were poorly expressed in P. cepacia and were not induced by isopropyl-beta-D-thiogalactopyranoside. Lac+ variants of the pGC91.14-containing strains which formed beta-galactosidase at high constitutive levels as a consequence of transposition of insertion sequences from the P. cepacia genome to sites upstream of the lacZ gene of Tn951 were isolated. Certain of the elements also increased gene expression in other bacteria. For example, IS407 strongly activated the lacZ gene of Tn951 in Pseudomonas aeruginosa and Escherichia coli, and IS406 (but not IS407) did so in Zymomonas mobilis. The results indicate that IS elements from P. cepacia have potential for turning on the expression of foreign genes in a variety of gram-negative bacteria.
Antecedents and consequences of sexual harassment in organizations: a test of an integrated model.

Sexual harassment of women in organizational settings has recently become a topic of interest to researchers and the general public alike. Although numerous studies document its frequency, the development of conceptual models identifying antecedents and consequences of harassment has proceeded at a slower pace. In this article, an empirical test of a recently proposed conceptual model is described. According to the model, organizational climate for sexual harassment and job gender context are critical antecedents of sexual harassment; harassment, in turn, influences work-related variables (e.g., job satisfaction); psychological states (e.g., anxiety and depression); and physical health. On the basis of a sample of women employed at a large, regulated utility company, the model's predictions were generally supported.
Commitment Contingencies in the Behavioral Treatment of Obesity.

Commitment is a self-control technique to induce weight lose. Tow targets of commitment contingencies, completion of the study and behavior . change, were examined.among 42 female and 3 male subjects who made a monetary deposit to enroll in the 10-week program. The treatment consisted of self-monitoring of eating and exercise behavior. Subjects were randomly assigned to cne of ttiree treatment groups: (1) no commitment: (2) study.completion coumitment: , and (3) study completion plus behavior change. Attrition, _three measures of study participation, behavior change, and shortand
Inflammation in the Prediabetic State Is Related to Increased Insulin Resistance Rather Than Decreased Insulin Secretion

Background—Elevated levels of proinflammatory proteins are predictive of both cardiovascular (CV) disease and type 2 diabetes. Previously, atherogenic changes in traditional CV risk factors in the prediabetic state were mainly seen in insulin-resistant subjects rather than in those with a predominant defect in insulin secretion. Methods and Results—We studied in prediabetic individuals from the Insulin Resistance Atherosclerosis Study (IRAS) the relation of C-reactive protein (CRP), plasminogen activator inhibitor (PAI)-1, and fibrinogen to defects in insulin sensitivity (SI) and first-phase insulin secretion, respectively, as assessed using a frequently sampled intravenous glucose tolerance test. One hundred forty-eight of 906 (16.3%) nondiabetic individuals developed diabetes after a mean follow-up of 5.2 years. Prediabetic individuals who were insulin resistant had higher levels of PAI-1 (mean [95% CI], 25.83 ng/mL [22.42 to 29.77] versus 16.31 ng/mL [12.56 to 21.18]; P =0.003) and CRP (mean [95% CI], 2.88 mg/L [2.33 to 3.56] versus 1.68 mg/L [1.13 to 2.49]; P =0.018) than insulin-sensitive individuals, but individuals with decreased acute insulin response tended to have lower rather than higher levels of inflammatory proteins compared with those with high insulin secretion. Prediabetic subjects who were predominantly insulin resistant had higher levels of inflammatory proteins compared with both prediabetic subjects with decreased insulin secretion as well as nonconverters. By contrast, prediabetic subjects with a predominant defect in first-phase insulin secretion had levels of inflammatory proteins indistinguishable from those in nonconverters. Conclusions—We have shown an increased proinflammatory state in prediabetic individuals who are predominantly insulin resistant but not in those with a primary defect in &bgr;-cell function. These results provide additional evidence that prediabetic subjects may be at an increased risk of heart disease, and this risk seems to be restricted to subjects with high insulin resistance.
Contextual Analysis of Textured Scene Images

Classifying image regions into one of several pre-defined semantic categories is a typical image understanding problem. Different image regions and object types might have very similar color or texture characteristics making it difficult to categorize them. Without contextual information it is often impossible to find reasonable semantic labeling for outdoor images. In this paper, we combine an efficient SVM-based local classifier with the conditional random field framework to incorporate spatial contex information to the classification. The images are represented with powerful local texture features. Then a discriminative multiclass model for finding good labeling for the image is learned. The performance of the method was evaluated with two different datasets. The approach was also shown to be useful in more general image retrieval and annotation tasks based on classification.
Enhanced Visible Light Photocatalytic Activity of ZnO Nanowires Doped with Mn2+ and Co2+ Ions

In this research, ZnO nanowires doped with Mn2+ and Co2+ ions were synthesized through a facile and inexpensive hydrothermal approach, in which Mn2+ and Co2+ ions successfully substituted Zn2+ in the ZnO crystal lattice without changing the morphology and crystalline structure of ZnO. The atomic percentages of Mn and Co were 6.29% and 1.68%, respectively, in the doped ZnO nanowires. The photocatalytic results showed that Mn-doped and Co-doped ZnO nanowires both exhibited higher photocatalytic activities than undoped ZnO nanowires. Among the doped ZnO nanowires, Co-doped ZnO, which owns a twice active visible-light photocatalytic performance compared to pure ZnO, is considered a more efficient photocatalyst material. The enhancement of its photocatalytic performance originates from the doped metal ions, which enhance the light absorption ability and inhibit the recombination of photo-generated electron-hole pairs as well. The effect of the doped ion types on the morphology, crystal lattice and other properties of ZnO was also investigated.
Differential Involvement of the Suprachiasmatic Nucleus in Lipopolysaccharide-Induced Plasma Glucose and Corticosterone Responses

The hypothalamic suprachiasmatic nucleus (SCN) is an essential component of the circadian timing system, and an important determinant of neuroendocrine and metabolic regulation. Recent data indicate a modulatory role for the immune system on the circadian timing system. The authors investigated how the circadian timing system affects the hypothalamo-pituitary-adrenal (HPA) axis and glucose regulatory responses evoked by an immune challenge induced by lipopolysaccharide (LPS). LPS-induced increases in corticosterone were minimal during the trough of the daily corticosterone rhythm; in contrast, LPS effects on glucose, glucagon, and insulin did not vary across time-of-day. Complete ablation of the SCN resulted in increased corticosterone responses but did not affect LPS-induced hyperglycemia. The paraventricular nucleus (PVN) of the hypothalamus is an important neuroendocrine and autonomic output pathway for hypothalamic information, as well as one of the main target areas of the SCN. Silencing the neuronal activity in the PVN did not affect the LPS-induced corticosterone surge and only slightly delayed the LPS-induced plasma glucose and glucagon responses. Finally, surgical interruption of the neuronal connection between hypothalamus and liver did not affect the corticosterone response but slightly delayed the LPS-induced glucose response. Together, these data support the previously proposed circadian modulation of LPS-induced neuroendocrine responses, but they are at variance with the suggested major role for the hypothalamic pacemaker on the autonomic output of the hypothalamus, as reflected by the effects of LPS on glucose homeostasis. The latter effects are more likely due to direct interactions of LPS with peripheral tissues, such as the liver. (Author correspondence: a.kalsbeek@amc.uva.nl)
Efficient direct search on compressed genomic data

The explosive growth in the amount of data produced by next-generation sequencing poses significant computational challenges on how to store, transmit and query these data, efficiently and accurately. A unique characteristic of the genomic sequence data is that many of them can be highly similar to each other, which has motivated the idea of compressing sequence data by storing only their differences to a reference sequence, thereby drastically cutting the storage cost. However, an unresolved question in this area is whether it is possible to perform search directly on the compressed data, and if so, how. Here we show that directly querying compressed genomic sequence data is possible and can be done efficiently. We describe a set of novel index structures and algorithms for this purpose, and present several optimization techniques to reduce the space requirement and query response time. We demonstrate the advantage of our method and compare it against existing ones through a thorough experimental study on real genomic data.
Constructing dynamic test environments for genetic algorithms based on problem difficulty

In recent years the study of dynamic optimization problems has attracted an increasing interest from the community of genetic algorithms and researchers have developed a variety of approaches into genetic algorithms to solve these problems. In order to compare their performance, an important issue is the construction of standardized dynamic test environments. Based on the concept of problem difficulty, This work proposes a new dynamic environment generator using a decomposable trap function. With this generator, it is possible to systematically construct dynamic environments with changing and bounding difficulty and hence, we can test different genetic algorithms under dynamic environments with changing but controllable difficulty levels.
A review of the peri-operative risk stratification assessment tools used for the prediction of cardiovascular complications in non-cardiac surgery

The development of atherosclerosis is a complex process that involves several inflammatory mechanisms. The evolution of a fatty streak to a mature occlusive atheromatous plaque occurs over several decades. However, during acute plaque rupture, to a varying degree, these same inflammatory systems are involved. Evidence exists that suggests a relationship between the activated inflammatory pathways; in the setting of lower respiratory tract or urinary tract infections and cardiac events such as unstable angina or myocardial infarctions. Peripheral vascular disease patients demonstrate atheromatous disease throughout their arterial tree, with coronary artery involvement in a significant proportion of individuals. The stress that a surgical intervention creates may be the catalyst for an acute coronary syndrome through the activation of these inflammatory pathways. Individual responses to the surgical insult are unpredictable and the extent to which the inflammatory mechanisms are stimulated is variable. The measurements of inflammatory biomarkers, such as C-reactive protein, have been associated with adverse short- and long-term mortality in patients who experience an acute coronary syndrome. This review article looks at the previous assessment tools that have been developed over time to try and predict the peri-operative risk of patients undergoing non-cardiac surgery, based on traditional patient parameters. We also explore the use of bio-markers in addition to these characteristics and how future work is being developed to look at the potential use of these to improve individual risk profiles.
Bootstrapping a Multilingual Part-of-speech Tagger in One Person-day

This paper presents a method for bootstrapping a fine-grained, broad-coverage part-of-speech (POS) tagger in a new language using only one person-day of data acquisition effort. It requires only three resources, which are currently readily available in 60-100 world languages: (1) an online or hard-copy pocket-sized bilingual dictionary, (2) a basic library reference grammar, and (3) access to an existing monolingual text corpus in the language. The algorithm begins by inducing initial lexical POS distributions from English translations in a bilingual dictionary without POS tags. It handles irregular, regular and semi-regular morphology through a robust generative model using weighted Levenshtein alignments. Unsupervised induction of grammatical gender is performed via global modeling of context-window feature agreement. Using a combination of these and other evidence sources, interactive training of context and lexical prior models are accomplished for fine-grained POS tag spaces. Experiments show high accuracy, fine-grained tag resolution with minimal new human effort.
Antibiotics Susceptibility Pattern of Escherichia coli Strains Isolated from Chickens with Colisepticemia in Tabriz Province, Iran

Antimicrobial agents are used extremely in order to reducing the enormous losses caused by Escherichia coli infections (colibacillosis) in Iran poultry industry. In this investigation fifty avian pathogenic Escherichia coli (APEC) strains isolated from broiler chickens with colisepticemia and examined for susceptibility to antimicrobials of veterinary and human significance. In vitro antibiotic activities of 32 antibiotic substances against the isolates were determined by disc diffusion test (Kirby Bauer method). Multiple resistances to antibiotics were observed in all the isolates. The highest rate of resistance was against Nalidixic acid (100%), Lincomycin (100%), Erythromycin (97%), Oxytetracycline (95%), Chlortetracycline (95%), Tetracycline (94%), Flumequine (94%), Tiamulin (91%), Doxycycline (88%), Difloxacin (83%), Neomycin (81%), Streptomycin (81%), Trimethoprim-Sulphamethoxazole (80%), Kanamycin (77%), Enrofloxacin (76%), Norfloxacin (68%), Ciprofloxacin (67%), Chloramphenicol (67%), Furazolidone (66%), Nitrofurantoin (56%), Amoxicillin (53%) and Ampicillin (47%). Resistance to Gentamicin wasn’t observed and to Amikacin, Cefazolin, Colistin, Tobramycin, Ceftizoxime, Cefixime, Lincospectin, Ceftazidime and also Florfenicol were low. This study showed resistance rate against the antibiotics that are commonly used in poultry is very high but against them that are only used in human or less frequently used in poultry is significantly low. These findings confirm significant increase in the incidence of antimicrobial resistance in the E. coli strains is most probably due to increased use of antibiotics as feed additives for growth promotion and prevention of diseases, use of inappropriate antibiotics for treatment of diseases, resistance transfer among different bacteria and possible cross resistance between antibiotics used in poultry. This study also showed that the prevalence of Quinolone-Resistant Escherichia coli (QREC) is very high in broiler farms in Tabriz province. The high presence of QREC from broiler chickens probably is due to overuse of enrofloxacin in these farms for therapeutic purposes. The present study suggests introduction of surveillance programs to monitor antimicrobial resistance in pathogenic bacteria is strongly needed because other than animal health problems, transmission of resistant clones and resistance plasmids of E. coli from food animals (especially poultry) to humans can occur.
Enhancing Intercultural Competence: Begin with the Family.

ABSTRACT To increase intercultural competence, early childhood educators must think globally and act locally, providing their young students with an awareness of different cultures. Teachers can begin and continue the process of teaching intercultural competence by focusing on the family unit. This focus should include four steps: (1) promoting advocacy (examining one's own biases, recognizing different family structures, and undoing biases); (2) maintaining steadfastness (examining and focusing on the various aspects of family diversity on an ongoing basis); (3) utilizing visuals (such as pictures from publications, family photographs, videos, and real objects); and (4) tapping varied resources (including local libraries, bookstores, the Internet, and computer software). (Contains 11 references.)
Process variation aware performance modeling and dynamic power management for multi-core systems

Emerging multi-core platforms are increasingly impacted by the manufacturing process variations that introduce core-to-core and chip-to-chip differences in their power and performance characteristics. This can result in unacceptable yield loss since a large fraction of manufactured parts may not meet the design specifications. In this work, we present some promising, recently proposed solutions to mitigate the impact of process variations on multi-core platforms that deal with variability aware performance modeling, and static and dynamic power reduction. These solutions demonstrate the significant benefits that can be reaped if variability information is considered at the micro-architecture and system level design abstractions.
Signaling and Regulation Breast Cancer Cells Proliferation Is Regulated by Tyrosine Phosphatase SHP 1 through c-jun N-Terminal Kinase and Cooperative Induction of RFX-1 and AP-4 Transcription Factors

In this study, we show that proliferation of breast cancer cells is suppressed by IGF-1–activated JNK MAPK pathway. The molecular mechanism by which c-jun-NH,-kinase (JNK) activation induces antiproliferative signals in IGF-1–stimulated breast cancer cells remains unknown. Tyrosine phosphatase SHP1 is known to negatively regulate signal transduction pathways activated by cell surface receptors including IGF-1. Moreover, SHP1 transcript and protein levels are increased in epithelial tumors. Therefore, we hypothesized that IGF-activated JNK induces expression of SHP1 in breast cancer cells. To further clarify the role of SHP1 in tumor growth, we correlated the proliferation rates of breast adenocarcinoma cells with SHP1 expression and JNK activation. We show that proliferation of serumor IGF-1–stimulated breast adenocarcinoma cells is negatively regulated by SHP1 and show for the first time that IGF-1–activated JNK induces SHP1 expression in MCF-7 cells used as experimental model. In an attempt to understand the mechanism by which serumor IGF-1–activated JNK induces SHP1 expression resulting in suppression of cell proliferation, we reveal for the first time that in serumor IGF-1–stimulated breast cancer MCF-7 cells, JNK induces SHP1 expression through the binding of AP-4 and RFX-1 transcription factors to the epithelial tissue–specific SHP1 promoter. Overall, we show for the first time that IGF-1–stimulated proliferation of breast adenocarcinoma cells is negatively regulated by SHP1 through activation of JNK. Mol Cancer Res; 9(8); 1–14. 2011 AACR.
Expression of L-Selectin, but Not CD44, Is Required for Early Neutrophil Extravasation in Antigen-Induced Arthritis1

L (leukocyte)-selectin (CD62L) and CD44 are major adhesion receptors that support the rolling of leukocytes on endothelium, the first step of leukocyte entry into inflamed tissue. The specific contribution of L-selectin or CD44 to the regulation of cell traffic to joints in arthritis has not been investigated. We used CD44-deficient, L-selectin-deficient, and CD44/L-selectin double knockout mice to determine the requirement for these receptors for inflammatory cell recruitment during Ag-induced arthritis. Intraperitoneal immunization resulted in similar activation status and Ag-specific responses in wild-type and gene-targeted mice. However, extravasation of neutrophil granulocytes, but not the emigration of T cells, into the knee joints after intra-articular Ag injection was significantly delayed in L-selectin-deficient and double knockout mice. Intravital videomicroscopy on the synovial microcirculation revealed enhanced leukocyte rolling and diminished adherence in mice lacking either CD44 or L-selectin, but CD44 deficiency had no significant effect on the recruitment of L-selectin-null cells. Compared with wild-type leukocytes, expression of L-selectin was down-regulated in CD44-deficient cells in the spleen, peripheral blood, and inflamed joints, suggesting that reduced expression of L-selectin, rather than the lack of CD44, could be responsible for the delayed influx of granulocytes into the joints of CD44-deficient mice. In conclusion, there is a greater requirement for L-selectin than for CD44 for neutrophil extravasation during the early phase of Ag-induced arthritis.