Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics analysis of microRNA and putative target genes in bovine mammary tissue infected with Streptococcus uberis.

MicroRNA (miRNA) are small single-stranded noncoding RNA with important roles in regulating innate immunity in nonruminants via transcriptional and posttranscriptional mechanisms. Mastitis causes significant losses in the dairy industry and a wealth of large-scale mRNA expression data from mammary tissue have provided fundamental insights into the tissue adaptations to pathogens. We studied the expression of 14 miRNA (miR-10a, -15b, -16a, -17, -21, -31, -145, -146a, -146b, -155, -181a, -205, -221, and -223) associated with regulation of innate immunity and mammary epithelial cell function in tissue challenged with Streptococcus uberis. Those data, along with microarray expression of 2,102 differentially expressed genes, were used for bioinformatics analysis to uncover putative target genes and the most affected biological pathways and functions. Three miRNA (181a, 16, and 31) were downregulated approximately 3- to 5-fold and miR-223 was upregulated approximately 2.5-fold in infected versus healthy tissue. Among differentially expressed genes due to infection, bioinformatics analysis revealed that the studied miRNA share in the regulation of a large number of metabolic (SCD, CD36, GPAM, and FASN), immune/oxidative stress (TNF, IL6, IL10, SOD2, LYZ, and TLR4), and cellular proliferation/differentiation (FOS and CASP4) target genes. This level of complex regulation was underscored by the coordinate effect revealed by bioinformatics on various cellular pathways within the Kyoto Encyclopedia of Genes and Genomes database. Most pathways associated with "cellular processes," "organismal systems," and "diseases" were activated by putative target genes of miR-31 and miR-16a, with an overlapping activation of "immune system" and "signal transduction. " A pronounced effect and activation of miR-31 target genes was observed within "folding, sorting, and degradation," "cell growth and death," and "cell communication" pathways, whereas a marked inhibition of "lipid metabolism" occurred. Putative targets of miR-181a had a strong effect on FcγR-mediated phagocytosis, toll-like receptor signaling, and antigen processing and presentation, which were activated during intramammary infections. The targets of both miR-31 and miR-223 had an inhibitory effect on "lipid metabolism. " Overall, the combined analyses indicated that changes in mammary tissue immune, metabolic, and cell growth-related signaling pathways during infection might have been mediated in part through effects of miRNA on gene transcription. Differential expression of miRNA supports the view from nonruminant cells/tissues that certain miRNA might be essential for the tissue's adaptive response to infection.
Leptin in cerebrospinal fluid from children: correlation with plasma leptin, sexual dimorphism, and lack of protein binding.

BACKGROUND Previous studies in adults have established that leptin is present at very low concentrations in cerebrospinal fluid (CSF), but few data exist concerning CSF leptin in children. Current evidence suggests that CSF leptin concentrations interact with hypothalamic centers controlling food intake. Serum leptin concentrations manifest a sexual dimorphism that arises during puberty. METHODS Leptin concentrations were determined in CSF from 42 pre- and postpubertal children who had been objectively classified into non-neurological disease or aseptic meningitis groups. Multivariate analysis of the dependence of CSF leptin on gender, pubertal state, body mass index (BMI), presence of aseptic meningitis, and CSF protein concentration was performed. RESULTS CSF leptin concentrations correlated with log-transformed plasma leptin concentrations in concomitantly collected samples (r = 0.582; P = 0.029). BMI and gender were significant determinants of CSF leptin in postpubertal children, but only BMI was significant in prepubertal children. Analysis with HPLC to separate protein-bound and free forms of leptin found only free leptin in CSF. CONCLUSIONS CSF leptin concentrations in children reflect plasma leptin concentrations, including the advent of sexual dimorphism at puberty. Only free leptin is detectable in CSF, suggesting that it is the biologically active form.
Sensitive detection of melamine with silicon nanowire field effect transistor biosensor

Melamine, a widely used industry chemical, has been detected in pet foods and some protein-based food commodities, such as milk as a fraudulent substitute for protein since 2007. Melamine with concentrations higher than the safety limits can cause kidney injury. Therefore there is growing needs for a low cost portable sensor that can detect melamine in food. Here, we demonstrate two assay methods of using functionalized Si nanowire transistors (SiNW FETs) to detect melamine with high sensitivity. The direct detection using antibody coated SiNW FETs shows selective detection of melamine down to 50 ppb level (or 2 μM). Another competitive assay takes advantage of competition reaction between the BSASM2-antibody vs. melamine-antibody to indirectly detect the concentration of melamine selectively down to 20 pM level in buffer solutions. The results show that SiNW has the potential to become a portable low cost sensor for melamine detection.
The kinase, SH3, and SH2 domains of Lck play critical roles in T-cell activation after ZAP-70 membrane localization

Antigenic stimulation of the T-cell antigen receptor initiates signal transduction through the immunoreceptor tyrosine-based activation motifs (ITAMs). When its two tyrosines are phosphorylated, ITAM forms a binding site for ZAP-70, one of the cytoplasmic protein tyrosine kinases essential for T-cell activation. The signaling process that follows ZAP-70 binding to ITAM has been analyzed by the construction of fusion proteins that localize ZAP-70 to the plasma membrane. We found that membrane-localized forms of ZAP-70 induce late signaling events such as activation of nuclear factor of activated T cells without any stimulation. This activity was observed only when Lck was expressed and functional. In addition, each mutation that affects the function of Lck in the kinase, Src homology 2 (SH2), and SH3 domains greatly impaired the signaling ability of the chimeric protein. Therefore, Lck functions in multiple manners in T-cell activation for the steps following ZAP-70 binding to ITAM.
Nuclear and optical dual-labelled imaging agents

Summary Over the last two decades, molecular imaging has been established as a valuable technology, aiming at visualization and characterization of biochemical processes on a molecular level in isolated cells, tissues and higher organisms. Within the wide scope of the various imaging techniques, dual-labelled modalities for nuclear (PET, SPECT) and near-infrared fluorescence (NIRF) imaging show promise owing to their comparable detection sensitivity. Novel materials offer excellent prospects for the development of new non-invasive strategies of early diagnosis and efficient monitoring of therapeutic treatments. In the field of cancer medicine, the combination of different imaging techniques such as PET/SPECT and OI for tracking down tumours and metastases, and subsequent image-guided surgery for tumour resection is particularly attractive. This review focuses on the development of promising dual-labelled agents to be applied in bimodal nuclear/optical imaging, combining radionuclides and fluorescent dyes. The discussion encompasses modular ligands as well as nanoscale systems, including antibodies and their fragments.
Determinant Factors in Maintaining the Exclusive Breastfeeding and Premature Weaning in Postpartum Mothers in the Brazilian Semiarid

This is a cross-sectional, correlational and quantitative study conducted on 210 postpartum women from January to July 2013 at the breastfeeding outpatient clinic of a public maternity. The study was carried out in order to assess the determining factors in maintaining an exclusive breastfeeding in the first month of the newborn’s life, the participation of the nurse in encouraging this process, and the reasons leading to a premature weaning. Prior births proved to be a positive factor for exclusive breastfeeding (Odds Ratio (OR) 0.359; CI 95% 0.137 - 0.941; p = 0.031). The absence of a nurse in the medical appointments resulted in a threefold risk to have no prenatal exclusive breastfeeding guidance whatsoever (OR 3.025; CI 95% 1.567 - 5.840; p = 0.001). The reported reasons for a premature weaning were difficulty latching-on, cracked nipples, poor milk that does not satiate the baby’s hunger, and production of little or no milk at all. The results provide information for the adoption of strategies during pregnancy and the postpartum period aimed to promote an exclusive breastfeeding, checking for the possible influence of the woman’s personal circumstances in her choosing exclusive breastfeeding, as well as the participation of the nurse in the mother’s decision.
Hassle Costs: The Achilles' Heel of Price‐Matching Guarantees*

We show that price-matching guarantees can facilitate monopoly pricing only if firms automatically match prices. If consumers must instead request refunds (thereby incurring hassle costs), we find that any increase in equilibrium prices due to firms' price-matching policies will be small; often, no price increase can be supported. In symmetric markets price-matching guarantees cannot support any rise in prices, even if hassle costs are arbitrarily small In asymmetric markets, higher prices can be supported, but the prices fall well short of maximizing joint profits. Our model can explain why some firms adopt price-matching guarantees while others do not. Copyright (c) 1999 Massachusetts Institute of Technology.
Re-Making Places: HCI, 'Community Building' and Change

We present insights from an extended engagement and design intervention at an urban regeneration site in SE Lon-don. We describe the process of designing a walking trail and system for recording and playing back place-specific stories for those living and working on the housing estate, and show how this is set within a wider context of urban renewal, social/affordable housing and "community building". Like prior work, the research reveals the frictions that arise in participatory engagements with heterogeneous actors. Here we illustrate how material interventions can re-arrange existing spatial configurations, making productive the plurality of accounts intrinsic in community life. Through this, we provide an orientation to HCI and design interventions that are concerned with civic engagement and participation in processes of making places.
Ferrioxamine Siderophores Detected amongst Iron Binding Ligands Produced during the Remineralization of Marine Particles

The microbial degradation of marine particles is an important process in the remineralization of nutrients including iron. As part of the GEOTRACES process study (FeCycle II), we conducted incubation experiments with marine particles obtained from 30 and 100 m depth at two stations during austral spring in the subtropical waters east of the North Island of New Zealand. The particles were collected using in-situ pumps, and comprised mainly of suspended and slow sinking populations along with associated attached heterotrophic bacteria. In treatments with live bacteria, increasing concentrations of Fe binding ligands were observed with an average stability constant of logKFeL,Fe3+ = 21.11±0.37 for station 1 and 20.89±0.25 for station 2. The ligand release rates varied between 2.54 and 11.8 pmol L-1 d-1 (calculated for ambient seawater particle concentration) and were similar to those found in two Southern Ocean subsurface studies from ~110 m depths in subpolar and polar waters. Dissolved iron (DFe) was released at a rate between 0.33 and 2.09 pmol Fe L-1 d-1 with a column integrated (30 -100 m) flux of 107 and 58 nmol Fe m-2 day-1 at station 1 and 2, respectively. Given a mixed layer DFe inventory of ~48 µmol m-2 and ~4 µmol m-2 at the time of sampling for station 1 and 2, this will therefore result in a DFe residence time of 1.2 and 0.18 years, assuming particle remineralization was the only source of iron in the mixed layer. The DFe release rates calculated were comparable to those found in the previously mentioned study of Southern Ocean water masses. Fe-binding ligand producing bacteria (CAS positive) abundance was found to increase throughout the duration of the experiment of 7 to 8 days. For the first time ferrioxamine type siderophores, including the well-known ferrioxamine B and G, have been quantified using chemical assays and LC-ESI-MS. Our subtropical study corroborates prior reports from the Southern Ocean of particle remineralization being an important source of DFe and ligands, and adds unprecedented detail by revealing that siderophores are probably an important component of the ligands released into subsurface waters during particle remineralisation.
Causal attributions, pathway to care and clinical features of first-episode psychosis: A South African perspective

Background: Causal belief systems and help-seeking practices may impact on pathway to care and features of first-episode psychosis (FEP) that have prognostic value. This is particularly relevant in South Africa where many people subscribe to traditional belief systems and consult traditional healers. Aim: To evaluate the relationship between causal attributions and pathway to care and features of FEP that have prognostic value. Method: We tested associations between causal attributions and pathway to care and duration of untreated psychosis (DUP), age of onset, PANSS-rated positive, negative and general symptoms and depressive symptoms (Calgary Depression Scale) in a sample of 54 FEP patients. Results: Spiritual attribution of cause (49% of patients) was associated with long DUP, while consultation with a traditional healer (39% of patients) was associated with long DUP and high negative symptoms. Only 19% had consulted a psychiatrist. Seventy nine per cent (79%) were referred to hospital by family, police were involved in 44% of admissions, and 81% were admitted involuntarily. Conclusions: Spiritual attributions of cause and previous consultation with traditional healers may delay entry to psychiatric care and thereby negatively impact on prognosis of FEP. This highlights the importance of mental health education and developing a positive collaborative relationship with traditional healers, especially in low- and middle-income countries.
Applications, Advantages and Challenges of Ad Hoc Networks

Recent trends in compact computing and wireless technologies are expansion of ad hoc network. Ad hoc network consists of versatile flat forms which are free to move expeditiously. Ad hoc networks are multi-hop network that use wireless communication for transmission without any fixed infrastructure. The networks are form and deform on-the-fly without the need for any system. Ad hoc structure does not require an access point, it is easy to setup, especially in a small or temporary network. Each node in the network forwards the packet without the need of central administration. In ad hoc network, node acts as a router to send and receive the data. An advantage of the system is robustness, flexibility and mobility. Ad hoc network are capable for analyzing radio propagation environment to optimize the performance. This typically requires that the network node have positioning capability as well as memory to recall geographical local condition. An ad hoc network typically refers to any set of network where all devices have equal status on a network and are free to associate with any other ad hoc network device in link range. Ad hoc network often refers to a mode of operation of IEEE802.11 wireless networks. This review is focused on the applications, advantages and challenges of ad hoc networks.
Investigating the Impact of Recommendation Agents on E-commerce Ecosystem

The influence of recommendation agents on e-commerce ecosystem is profound. Technological impact of predictive intelligence could be explained more reasonably by taking a collective perspective. However, the ecosystem perspective has only served as a prologue for discussion regarding technological influence. The lack of research development associated with the technological influence on business in the ecological lens has constrained our understanding of the penetration and the role of technology in business ecosystem evolution. This paper therefore focuses on the impact of recommendation agents for online shopping environment on e-commerce ecosystem. Moreover, this paper observes and explains the phenomena that most participants in the e-commerce ecosystem are taking recommendation agents as one of the strategic technological investments towards further development as a common goal.
[Experimental study on stimulation of guided bone regeneration by acid fibroblast growth factor].

OBJECTIVE To investigate the effect of acid fibroblast growth factor (aFGF) on guided bone regeneration (GBR), to study whether aFGF can promote the repairing ability of GBR in bone defect. METHODS 10 mm long segmental defects were created in the diaphyses of both radii in 16 New Zealand rabbits. The defect was bridged with a silicon tube. Human recombinant aFGF was instilled into the tube on the experimental side, while the contralateral tube was instilled with saline as control group. The radiographic, gross and histologic examination of the samples were analyzed at 2, 4, 6 and 8 weeks after operation. RESULTS On the experimental side, there was new bone formation in the bone medullary cavity, the endosteum and the section surface of the cortex at 2 weeks. At 4 weeks, at the center of the blood clot in the tube there was new bone formation and bone defect was completely healed at 8 weeks. On the control side, new bone formation was less in every period compared with that of the experimental side. At 8 weeks, there was only partial healing of the bone defect. CONCLUSION It can be concluded that aFGF can promote new bone formation and facilitate GBR in bone defect.
Transfer of pRD1 to Pseudomonas syringae and evidence for its integration into the chromosome

Plasmid pRD1 was conjugatively transferred from Escherichia coli to Pseudomonas syringae. Subculturing the transconjugate on a medium that selected for pRD1-determined His+ Kmr resulted in the loss of pRD1 as an extrachromosomal element as detected by agarose gel electrophoresis. DNA hybridization provided evidence for the integration of pRD1 into the P. syringae chromosome.
Neuroprotective effects of candesartan against cerebral ischemia in spontaneously hypertensive rats

The cerebral protective effects of 4-week treatment with candesartan (0.3, 1, 3 mg/kg/day) and ramipril (0.5, 1.5, 5 mg/kg/day) were examined in spontaneous hypertensive rats 24 h after middle cerebral artery occlusion. We found that both candesartan and ramipril could reduce the infarct volume and neurological deficit scores compared with control. Importantly, the neuroprotective effects of candesartan (1 mg/kg/day) were abolished by PD123319 (an AT2 receptor antagonist, 10 mg/kg/day). AT1 receptor gene expression was downregulated while AT2 receptor gene expression was upregulated by candesartan. It is concluded that candesartan appears to provide beneficial effects against stroke in spontaneous hypertensive rats in three ways: AT1 receptor antagonism, downregulation of AT1 receptor expression and upregulation of AT2 receptor expression.
Angiopoietin-1 and its receptor Tie-2 participate in the regulation of capillary-like tubule formation and survival of endothelial cells.

Angiopoietin-1 (Ang-1) and its receptor Tie-2, a trans-membrane tyrosine kinase uniquely expressed by endothelial cells, are shown by null mutation studies to be essential to developmental angiogenesis. The phenotypic abnormalities in these knockout animals suggest that Tie-2 signaling is necessary for the maintenance and expansion of the primitive capillary network. We present in vitro evidence indicating that the Ang-1/Tie-2 system participates in the regulation of capillary tubule formation and is necessary for the survival of confluent endothelial cells. Although recombinant Ang-1, which induces Tie-2 phosphorylation, has no effect on the proliferation of endothelial cells, treatment of confluent adult bovine aortic endothelial cells (ABAE) cells grown on collagen gels with Ang-1 (100 ng/ml) causes the cells to migrate into the collagen gel and form capillary-like tubules. The tubule-forming effect of Ang-1 is similar to the effect caused by FGF-2. A soluble form of the Tie-2 extracellular domain, in fivefold molar excess, blocks Ang-1-induced tubule formation. Specific elimination of Tie-2 protein expression in cultured ABAE cells as a result of transfection with an antisense oligonucleotide causes cell death in a dose-dependent manner (IC(50) = 50 nM). The antisense treatment has no effect on cells that do not express Tie-2. Cells treated with antisense oligonucleotide show a sixfold increase in the rate of apoptosis as assessed by in situ end labeling of fragmented DNA. These findings are consistent with the view that Ang-1/Tie-2 signaling is essential for both angiogenesis and endothelial cell survival.
Hauptseminar : Security-Zwischen formalen Methoden und Praxis Malicious code detection

In any defense mechanism, malicious code detection is a crucial component. To subvert malicious code detectors, e.g anti-virus software, malicious code writers try to subvert these detectors by obfuscating the malicious code. As testing results surprisingly showed, commercial virus scanners were not able to detect infected binaries which were transformed by applying simple obfuscation techniques. This paper presents an architecture called SAFE (a static analyzer for executables) developed at University of Wisconsin which is resilient to common obfuscation transformations by not relying upon signature matching but model-checking techniques.
Combining Top-Down and Bottom-Up Approaches To Energy-Economy Modeling Using Discrete Choice Methods

Recently, hybrid models of the energy-economy have been developed with the objective of combining the strengths of the traditional top-down and bottom-up approaches by simulating consumer and firm behavior at the technological level. We explore here the application of discrete choice research and modeling to the empirical estimation of key behavioral parameters representing technology choice in hybrid models. We estimate a discrete choice model of the industrial steam generation technology decision from a survey of 259 industrial firms in Canada. The results provide behavioral parameters for the CIMS energy-economy model. We then conduct a policy analysis and show the relative effects of an information program, technology subsidy, and carbon dioxide tax on the uptake of alternative industrial steam generation technologies, including boilers and cogeneration systems. We also show how empirically derived estimates of parameter uncertainty can be propagated through the model to provide uncertainty estimates for major model outputs.