Miracle-dz/UniFAR-FTUs huggingface dataset:
Fabrication and characterization of a novel collagen-catechol hydrogel

3,4-Dihydroxybenzaldehyde, a derivative of catechol and an agent with an extensive pharmacological and biological activities, was used to modify collagen and prepared hydrogels. The aldehyde group of 3,4-dihydroxybenzaldehyde interacted with the ɛ-amino group of collagen, and then the catechol group of 3,4-dihydroxybenzaldehyde was oxidized and self-polymerized. The chemical network formed due to the cross-linking bridges of polymerized catechol groups among collagen molecules, resulting in the transformation from solution to hydrogel. The results of the Fourier-transform infrared measurement indicated that the triple helix structure of collagen was integrated after cross-linking. The appearance of hydrogels changed from golden to dark brown with the increasing 3,4-dihydroxybenzaldehyde dose. When the weight ratio of 3,4-dihydroxybenzaldehyde and collagen increased from 0 to 2:1, the thermal denaturation temperature of collagen increased from 40.2 to 77.6℃ while the elastic modulus of collagen increased from 13.6 to 1061.4 Pa. The addition of 3,4-dihydroxybenzaldehyde also caused more compact morphologies and a dramatic enhancement in the enzymatic resistance of hydrogels. Moreover, the results of cell proliferation assay demonstrated the favorable biocompatibility of collagen hydrogels with 3,4-dihydroxybenzaldehyde. These promising data indicate that the novel hydrogels had significant potential for applications.
Activation of the miR-34a/SIRT1/p53 Signaling Pathway Contributes to the Progress of Liver Fibrosis via Inducing Apoptosis in Hepatocytes but Not in HSCs

Liver fibrosis results from a sustained wound healing response to chronic liver injury, and the activation of nonparenchymal hepatic stellate cells (HSCs) is the pivotal process. MicroRNA-34a (miR-34a) is the direct target gene of p53 and activates p53 through sirtuin 1 (SIRT1) simultaneously. The miR-34a/SIRT1/p53 signaling pathway thus forms a positive feedback loop wherein p53 induces miR-34a and miR-34a activates p53 by inhibiting SIRT1, playing an important role in cell proliferation and apoptosis. miR-34a expression has been found to be increased in animal models or in human patients with different liver diseases, including liver fibrosis. However, the exact role of this classical miR-34a/SIRT1/p53 signaling pathway in liver fibrosis remains unclear. In the present study, using a CCl4-induced rat liver fibrosis model, we found that the miR-34a/SIRT1/p53 signaling pathway was activated and could be inhibited by SIRT1 activator SRT1720. Further studies showed that the miR-34a/SIRT1/p53 signaling pathway was activated in hepatocytes but not in HSCs. The activation of this pathway in hepatocytes resulted in the apoptosis of hepatocytes and thus activated HSCs. Our data indicate that the miR-34a/SIRT1/p53 signaling pathway might be a promising therapeutic target for liver fibrosis.
Efficient Subtractive Cloning of Genes Activated by Lipopolysaccharide and Interferon γ in Primary-Cultured Cortical Cells of Newborn Mice

Innate immune responses play a central role in neuroprotection and neurotoxicity during inflammatory processes that are triggered by pathogen-associated molecular pattern-exhibiting agents such as bacterial lipopolysaccharide (LPS) and that are modulated by inflammatory cytokines such as interferon γ (IFNγ). Recent findings describing the unexpected complexity of mammalian genomes and transcriptomes have stimulated further identification of novel transcripts involved in specific physiological and pathological processes, such as the neural innate immune response that alters the expression of many genes. We developed a system for efficient subtractive cloning that employs both sense and antisense cRNA drivers, and coupled it with in-house cDNA microarray analysis. This system enabled effective direct cloning of differentially expressed transcripts, from a small amount (0.5 µg) of total RNA. We applied this system to isolation of genes activated by LPS and IFNγ in primary-cultured cortical cells that were derived from newborn mice, to investigate the mechanisms involved in neuroprotection and neurotoxicity in maternal/perinatal infections that cause various brain injuries including periventricular leukomalacia. A number of genes involved in the immune and inflammatory response were identified, showing that neonatal neuronal/glial cells are highly responsive to LPS and IFNγ. Subsequent RNA blot analysis revealed that the identified genes were activated by LPS and IFNγ in a cooperative or distinctive manner, thereby supporting the notion that these bacterial and cellular inflammatory mediators can affect the brain through direct but complicated pathways. We also identified several novel clones of apparently non-coding RNAs that potentially harbor various regulatory functions. Characterization of the presently identified genes will give insights into mechanisms and interventions not only for perinatal infection-induced brain damage, but also for many other innate immunity-related brain disorders.
Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements[W]

The genome sequence of Ustilago hordei revealed that transposable elements were involved in restructuring of the genome, which affected fungal reproductive biology and evolution of genes encoding effector proteins. Comparison to other smuts indicated loss of genome defense components in Ustilago maydis and control of repetitive sequences by repeat-induced point mutation in U. hordei. Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.
Enhancement of P‐Glycoprotein Expression by Hepatocyte Transplantation in Carbon Tetrachloride‐Induced Rat Liver

The multidrug resistance protein P‐glycoprotein (P‐gp) is physiologically expressed at the bile canalicular membrane of the liver, where it participates in the biliary excretion of various lipophilic drugs. Chronic exposure to carbon tetrachloride (CCI4) is known to induce hepatic fibrosis resulting in hepatotoxicity. This study focuses on the effects of CCI4 and hepatic transplantation (HT) on the P‐gp expressions in rat liver. Male SD rats were treated with CCI4 to induce liver damage for 3, 7, 14, 21, and 28 days, respectively. Immunohistochemistry revealed that P‐gp was widely distributed in the liver and was spread from the cytoplasm to cell membrane of the rat liver. Western blot showed remarkable increase of P‐gp expression in 3 days CCI4‐treated rats, whereas, a continuous decrease in the P‐gp expression was seen in 7, 14, 21, and 28 days CCI4‐treated rats. After HT with cells from the normal rat liver, the level of P‐gp increased comparing with those from the sham operation. Blood biochemistry showed decreased levels of serum alanine transaminase, aspartate transaminase, and alkaline phosphatase and increased serum levels of triglyceride and total protein, which indicated the improved function of the liver damaged by CCI4. These results illustrate the variation of the expression of P‐gp in CCI4‐induced hepatic damage and an increase of P‐gp level after HT in the toxic liver induced by CCI4. We hypothesized that P‐gp may play a protective role in the process of liver injury. HT can be beneficial to ameliorate the rat liver functional damage induced by CCI4. Anat Rec 293:1167–1174, 2010. © 2010 Wiley‐Liss, Inc.
Visualization of the exocyst complex dynamics at the plasma membrane of Arabidopsis thaliana

The exocyst complex localizes to distinct foci at the plasma membrane of Arabidopsis thaliana cells. Their localization at the plasma membrane is insensitive to BFA treatment but is decreased in an exocyst-subunit mutant. In turn, exocyst-subunit mutants show decreased exocytosis.
Family Communication at the End of Life

ABSTRACT This article presents a brief review examining what research has been conducted exploring family communication at the end of life (EOL) and suggestions for future research at the end-of-life context. Future research areas include: 1) the role of culture, 2) family member role and relational climate, 3) ethical considerations in regard to methodological choices, 4) the role of emotional and cognitive development on EOL communication, 5) EOL backstage communication, 6) death circumstances, and 7) the use of interdisciplinary research teams.
Measuring citalopram in blood and central nervous system: revealing a distribution pattern that differs from other antidepressants

The aim of this study was to measure blood and cerebrospinal fluid concentrations of citalopram and its weakly active N-demethylated metabolite desmethylcitalopram to account for the distribution between the two compartments. The findings are discussed in the context with own preceding studies on the distribution pattern of different antidepressants. Concentrations of citalopram were measured in blood serum and cerebrospinal fluid of 18 patients treated with daily doses of 10–40 mg. Daily doses were correlated with serum and cerebrospinal fluid concentrations, and serum concentrations were correlated with concentrations in cerebrospinal fluid. Serum concentrations of citalopram and desmethylcitalopram showed no significant correlation to the daily dose, r=0.164, P=0.515, and r=0.174, P=0.505, respectively, whereas citalopram concentrations in serum and cerebrospinal fluid were highly correlated (r=0.763, P<0.001). The cerebrospinal fluid/serum ratio for citalopram (total=bound+unbound concentration) varied between 0.14 and 0.86 (mean 0.35, SD 0.16). By correcting the mean cerebrospinal fluid/serum ratio for 80% plasma protein binding, cerebrospinal fluid concentrations of citalopram were on average 77% higher than the calculated unbound serum concentration with a ratio of 1.77 (SD 0.81, range 0.68–4.29). Findings indicate a very good ability of citalopram to cross the blood–brain and cerebrospinal fluid barrier. High concentrations of citalopram in the cerebrospinal fluid are indicative of active transport of citalopram into or missing active transport out of the cerebrospinal fluid. The results suggest a high ability of citalopram to enter the brain with sufficiently high drug concentrations at the target sites within the brain, contributing toward clinical efficacy.
Male adaptations to minimize sexual cannibalism during reproduction in the funnel‐web spider Hololena curta

Males of many spider species risk being attacked and cannibalized while searching for, courting, and mating with conspecific females. However, there are exceptions. We show that the funnel‐web spider, Hololena curta, has 3 adaptations that minimize risk to males during courtship and mating, and enhance reproductive success. First, males detected chemical or tactile signals associated with webs of virgin females, and differentiated them from webs of mated females, enabling males to increase encounter rates with virgin females and avoid aggressive mated females. Second, males produced stereotyped vibrational signals during courting which induced female quiescence and suppressed female aggression. Third, when touched by males, sexually receptive females entered a cataleptic state, allowing males to safely approach and copulate. Because males can mate multiple times and the sex ratio in natural populations of H. curta is female biased, overall reproductive output is likely increased by males of this species avoiding sexual cannibalism.
Quantitative Analysis of OX62-Positive Dendritic Cell Distribution in the Rat Laryngeal Complex

Objectives: Dendritic cells (DCs) are key instigators of rejection after transplantation. Their distribution has not been systematically characterized in all locations of the larynx and its surrounding tissues. Methods: Rat larynges were stained with monoclonal antibodies identifying DCs. These cells were then enumerated by a new combination of techniques including immunofluorescence, confocal microscopy, and imaging software. Results: The vast majority of DCs were located in the epithelium and subepithelium of the airway; the mean DC density ranged from 9 cells per square millimeter (0.2% of cells) to 645 cells per square millimeter (10.3% of cells). Their density in the epithelium was 3 to 11 times higher than that in the subepithelium. Non-airway sites (thyroid, parathyroid, muscle, fat) had mean DC densities varying from 3 cells per square millimeter (0.2%) to 57 cells per square millimeter (0.8%). No DCs were detected in cartilage. Conclusions: Dendritic cells are concentrated in the laryngotracheal epithelium and subepithelium and represent a much smaller proportion in the other sites studied. A baseline for laryngeal DC population studies has been established, and a computerized model for consistent quantitation using confocal microscopy has been developed. This unique method will serve as a foundation for investigating DC trafficking after rat laryngeal transplantation.
Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

Elongation by RNA polymerase II (RNAPII) is a finely regulated process in which many elongation factors contribute to gene regulation. Among these factors are the polymerase-associated factor (PAF) complex, which associates with RNAPII, and several cyclin-dependent kinases, including positive transcription elongation factor b (P-TEFb) in humans and BUR kinase (Bur1–Bur2) and C-terminal domain (CTD) kinase 1 (CTDK1) in Saccharomyces cerevisiae. An important target of P-TEFb and CTDK1, but not BUR kinase, is the CTD of the Rpb1 subunit of RNAPII. Although the essential BUR kinase phosphorylates Rad6, which is required for histone H2B ubiquitination on K123, Rad6 is not essential, leaving a critical substrate(s) of BUR kinase unidentified. Here we show that BUR kinase is important for the phosphorylation in vivo of Spt5, a subunit of the essential yeast RNAPII elongation factor Spt4/Spt5, whose human orthologue is DRB sensitivity-inducing factor. BUR kinase can also phosphorylate the C-terminal region (CTR) of Spt5 in vitro. Like BUR kinase, the Spt5 CTR is important for promoting elongation by RNAPII and recruiting the PAF complex to transcribed regions. Also like BUR kinase and the PAF complex, the Spt5 CTR is important for histone H2B K123 monoubiquitination and histone H3 K4 and K36 trimethylation during transcription elongation. Our results suggest that the Spt5 CTR, which contains 15 repeats of a hexapeptide whose consensus sequence is S[T/A]WGG[A/Q], is a substrate of BUR kinase and a platform for the association of proteins that promote both transcription elongation and histone modification in transcribed regions.
Mechanical properties of high strength concrete with recycled steel fibres from waste tyres

Durability of concrete is highly defined by its possibility to resists cracking. Low tensile strength and brittleness are often responsible for micro cracking of concrete surface and accordingly its lower resistance to penetrability of aggressive agents. In highly aggressive environments with presence of dynamic loadings mechanical properties together with permeability of concrete are detrimental for its durability. High strength fibre reinforced concrete can be solution in these environments because it allows control of the crack opening and assures structural continuity. Since use of industrial steel fibres in concrete mixture significantly raises the costs of concrete, nowadays the use of supplement materials is explored. Since 2006, when European Commission prohibited any kind of waste tyres disposal, waste tyres became valuable resource. During mechanical recycling of waste tyres is possible to obtain products which are all reusable in concrete industry ; rubber, steel and textile fibres. In this paper use of recycled steel fibres with and without addition of recycled rubber is explored, all in order to obtain high strength fibre reinforced concrete. Although, steel fibres obtained during mechanical recycling of waste rubber are irregular, with different lengths and diameters previous studies showed that they represent good supplement for industrial fibres. Rubber granulates used during this research have diameter from 0, 5 to 2 mm. Seven concrete mixtures was prepared during this research including different ratios of industrial and recycled steel fibres (100I0R ; 50I50R ; 0I100R) with and without addition of recycled rubber (5% by total volume of aggregate). In order to evaluate the influence of combining industrial and recycled steel fibres, with or without addition of the rubber on mechanical properties of concrete following testing was performed: compressive strength, flexural strength, modulus of elasticity, toughness, abrasion, freezing resistance and shrinkage.
Scale invariant spectrum from variable speed of light metric in a bimetric gravity theory

An approximately scale invariant spectrum generating the seeds of structure formation is derived from a bimetric gravity theory. By requiring that the amplitude of the CMB fluctuations from the model matches the observed value, we determine the fundamental length scale in the model to be a factor of 105 times larger than the Planck length, which results in a scalar mode spectral index: ns≈0.97, and its running: αs≈−5×10−4. This is accomplished in the variable speed of light (VSL) metric frame, in which the dynamics of perturbations of the bimetric scalar field are determined by a minimally-coupled Klein–Gordon equation, and it is assumed that modes are born in a ground state at a scale given by the fundamental length scale appearing in the bimetric structure. We show that while this is taking place for scales of interest, the background (primordial) radiation energy density is strongly suppressed as a result of the bimetric structure of the model. Nevertheless, the enlarged lightcone of matter fields ensures that the horizon and flatness problems are solved.
Intracellular Long-Chain Acyl CoAs Activate TRPV1 Channels

TRPV1 channels are an important class of membrane proteins that play an integral role in the regulation of intracellular cations such as calcium in many different tissue types. The anionic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) is a known positive modulator of TRPV1 channels and the negatively charged phosphate groups interact with several basic amino acid residues in the proximal C-terminal TRP domain of the TRPV1 channel. We and other groups have shown that physiological sub-micromolar levels of long-chain acyl CoAs (LC-CoAs), another ubiquitous anionic lipid, can also act as positive modulators of ion channels and exchangers. Therefore, we investigated whether TRPV1 channel activity is similarly regulated by LC-CoAs. Our results show that LC-CoAs are potent activators of the TRPV1 channel and interact with the same PIP2-binding residues in TRPV1. In contrast to PIP2, LC-CoA modulation of TRPV1 is independent of Ca2+ i, acting in an acyl side-chain saturation and chain-length dependent manner. Elevation of LC-CoAs in intact Jurkat T-cells leads to significant increases in agonist-induced Ca2+ i levels. Our novel findings indicate that LC-CoAs represent a new fundamental mechanism for regulation of TRPV1 channel activity that may play a role in diverse cell types under physiological and pathophysiological conditions that alter fatty acid transport and metabolism such as obesity and diabetes.
Group Elevator Scheduling With Advance Information for Normal and Emergency Modes

Group elevator scheduling has long been recognized as an important problem for building transportation efficiency, since unsatisfactory elevator service is one of the major complaints of building tenants. It now has a new significance driven by homeland security concerns. The problem, however, is difficult because of complicated elevator dynamics, uncertain traffic in various patterns, and the combinatorial nature of discrete optimization. With the advent of technologies, one important trend is to use advance information collected from devices such as destination entry, radio frequency identification, and sensor networks to reduce uncertainties and improve efficiency. How to effectively utilize such information remains an open and challenging issue. This paper presents the optimized scheduling of a group of elevators with destination entry and future traffic information for normal operations and coordinated emergency evacuation. Key problem characteristics are abstracted to establish a two-level separable formulation. A decomposition and coordination approach is then developed, where subproblems are solved by ordinal optimization-based local search, and top ranked nodes are selectively optimized by using dynamic programming. The approach is then extended to handle up-peak with little or no future traffic information, elevator parking for low intensity traffic, and coordinated emergency evacuation. Numerical testing results demonstrate near-optimal solution quality, computational efficiency, the value of future traffic information, and the potential of using elevators for emergency evacuation.