Miracle-dz/UniFAR-FTUs huggingface dataset:
L-3,4-Dihydroxyphenylalanine Recovers Circadian Rhythm Disturbances in the Rat Models of Parkinson's Disease by Regulating the D1R-ERK1/2-mTOR Pathway

Objective: Patients with Parkinson's disease (PD) frequently experience disruptions in the 24-h daily profile of both behavioral and biological markers. However, whether L-3,4-dihydroxyphenylalanine (L-dopa) influences these markers associated with circadian rhythm or not is still an open question. This study aims to explore the L-dopa effects on the rhythmic expression of core clock proteins [brain and muscle Arnt-like protein-1 (BMAL1) and circadian locomotor cycle kaput (CLOCK)], in the striatum of the rat model of PD and its underlying molecular mechanisms. Methods: Unilateral 6-hydroxydopamine (6-OHDA)-lesioned rat models were used in this study. L-dopa administrations were adopted to investigate the changes of circadian rhythm in PD. The behavioral tests and the measurements of the blood pressure (BP) and temperature were evaluated. The striatum was collected at intervals of 4 h. Western blot was used to examine the expressions of clock protein and the molecular protein of the D1R-ERK1/2-mTOR pathway. The rhythmic expressions of symptom parameters and circadian proteins were analyzed using the Cosinor model and/or the coefficient of variability (CV) that was used to describe the variability of the 24-h rhythm. Results: The circadian rhythms of BP and temperature were disrupted in 6-OHDA-lesioned PD rats compared with the sham group, while this process was reversed mildly by L-dopa treatment. The expressions of BMAL1 and CLOCK protein were rhythmic fluctuated without significant phase alterations when 6-OHDA or L-dopa was applied. Furthermore, the expressions of striatal BMAL1 protein in the 6-OHDA-lesioned group were significantly lower than those in the sham group at 04:00, 08:00, and 12:00, and the CLOCK protein was decreased at 04:00, 08:00, 12:00, 16:00, and 20:00 (all p < 0.05). The CV of the expressions of both BMAL1 and CLOCK was decreased in the 6-OHDA group; this process was reversed by L-dopa. Moreover, the CV of BMAL1 and CLOCK was elevated in the L-dopa rats. The phosphorylation levels of ERK1/2, S6K1, and 4E-BP1 in 6-OHDA-lesioned striatum were increased by L-dopa or D1 receptor agonist SKF38393 (p < 0.05, respectively), not by the combination of L-dopa and D1 receptor antagonist SCH23390, which was similar to the expressions of BMAL1 and CLOCK. Conclusion: L-dopa recovers the circadian rhythm disturbances in PD rats by regulating the D1R-ERK1/2-mTOR pathway.
Extremophilic Exopolysaccharides: Biotechnologies and Wastewater Remediation

Various microorganisms thrive under extreme environments, like hot springs, hydrothermal vents, deep marine ecosystems, hyperacid lakes, acid mine drainage, high UV exposure, and more. To survive against the deleterious effect of these extreme circumstances, they form a network of biofilm where exopolysaccharides (EPSs) comprise a substantial part. The EPSs are often polyanionic due to different functional groups in their structural backbone, including uronic acids, sulfated units, and phosphate groups. Altogether, these chemical groups provide EPSs with a negative charge allowing them to (a) act as ligands toward dissolved cations as well as trace, and toxic metals; (b) be tolerant to the presence of salts, surfactants, and alpha-hydroxyl acids; and (c) interface the solubilization of hydrocarbons. Owing to their unique structural and functional characteristics, EPSs are anticipated to be utilized industrially to remediation of metals, crude oil, and hydrocarbons from contaminated wastewaters, mines, and oil spills. The biotechnological advantages of extremophilic EPSs are more diverse than traditional biopolymers. The present review aims at discussing the mechanisms and strategies for using EPSs from extremophiles in industries and environment bioremediation. Additionally, the potential of EPSs as fascinating biomaterials to mediate biogenic nanoparticles synthesis and treat multicomponent water contaminants is discussed.
The SIX Family of Transcription Factors: Common Themes Integrating Developmental and Cancer Biology

The sine oculis (SIX) family of transcription factors are key regulators of developmental processes during embryogenesis. Members of this family control gene expression to promote self-renewal of progenitor cell populations and govern mechanisms of cell differentiation. When the function of SIX genes becomes disrupted, distinct congenital defects develops both in animal models and humans. In addition to the embryonic setting, members of the SIX family have been found to be critical regulators of tumorigenesis, promoting cell proliferation, epithelial-to-mesenchymal transition, and metastasis. Research in both the fields of developmental biology and cancer research have provided an extensive understanding of SIX family transcription factor functions. Here we review recent progress in elucidating the role of SIX family genes in congenital disease as well as in the promotion of cancer. Common themes arise when comparing SIX transcription factor function during embryonic and cancer development. We highlight the complementary nature of these two fields and how knowledge in one area can open new aspects of experimentation in the other.
GC/MS and LC/MS Based Serum Metabolomic Analysis of Dairy Cows With Ovarian Inactivity

Metabolic disorders may lead to the inactive ovaries of dairy cows during early lactation. However, the detailed metabolic profile of dairy cows with inactive ovaries around 55 days postpartum has not been clearly elucidated. The objective of this study was to investigate the metabolic difference in cows with inactive ovaries and estrus from the perspective of serum metabolites. According to clinical manifestations, B-ultrasound scan, rectal examination, 15 cows were assigned to the estrus group (E; follicular diameter 15–20 mm) and 15 to the inactive ovary group (IO; follicular diameter <8 mm and increased <2 mm within 5 days over two examinations). The blood was collected from the tail vein of the cow to separate serum 55–60 days postpartum, and then milked and fasted in the morning. Serum samples were analyzed using gas chromatography time-of-flight mass spectrometry technology (GC-TOF-MS) and ultra-high-pressure liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF-MS). Differences in serum metabolites were identified using multivariate statistical analysis and univariate analysis. Thirty differentially abundant metabolites were identified between the two groups. In cows with inactive ovaries compared with cows in estrus, 20 serum metabolites were significantly higher (beta-cryptoxanthin (p = 0.0012), 9-cis-retinal (p = 0.0030), oxamic acid (p = 0.0321), etc.) while 10 metabolites were significantly lower (monostearin (p = 0.0001), 3-hydroxypropionic acid (p = 0.0005), D-talose (p = 0.0018), etc.). Pathway analysis indicated that the serum differential metabolites of multiparous cows in estrus obtained by the two metabolomics techniques were mainly involved in β-alanine metabolism and steroid biosynthesis metabolism, while other involved metabolic pathways were related to metabolism of glyoxylate; dicarboxylate metabolism; fructose, mannose, glutathione, glycerolipid, glycine, serine, threonine, propanoate, retinol, and pyrimidine metabolism. This indicates that the abnormalities in glucose metabolism, lipid metabolism, amino acid metabolism, and glutathione metabolism of postpartum dairy cows obstructed follicular development.
Evidence of changing sexual behaviours and clinical attendance patterns, alongside increasing diagnoses of STIs in MSM and TPSM

Background Due to rising numbers of STI diagnosis and increasing prevalence of antimicrobial resistance, we explored trends in STI testing frequency and diagnoses, alongside sexual decision making and attitudes concerning condom use and HIV pre-exposure prophylaxis (PrEP) at a large urban UK sexual health clinic. Methods We examined 66 528 electronic patient records covering 40 321 attendees between 2016 and 2019, 3977 of whom were men who have sex with men or trans persons who have sex with men (MSM/TPSM). We also explored responses from MSM/TPSM attendees sent an electronic questionnaire between November 2018 and 2019 (n=1975) examining behaviours/attitudes towards PrEP. We measured trends in STI diagnoses and sexual behaviours including condomless anal intercourse (CAI), using linear and logistic regression analyses. Results Tests resulting in gonorrhoea, chlamydia or syphilis diagnoses increased among MSM/TPSM from 13.5% to 18.5% between 2016 and 2019 (p<0.001). The average MSM/TPSM STI testing frequency increased from 1.5/person/year to 2.1/person/year (p=0.017). Gay MSM/TPSM had the highest proportions of attendances resulting in diagnoses, increasing from 15.1% to 19.6% between 2016 and 2019 (p<0.001) compared with bisexual/other MSM/TPSM increasing from 6.9% to 14.5% (p<0.001), alongside smaller but significant increases in non-MSM/TPSM from 5.9% to 7.7% (p<0.001). The proportion of MSM/TPSM clinic attendees reporting CAI in the previous 3 months prior to at least one appointment in a given year increased significantly from 40.6% to 45.5% between 2016 and 2019 (p<0.0001) and average number of partners from 3.8 to 4.5 (p=0.002). Of 617 eligible questionnaire responses, 339/578 (58.7%) HIV-negative and 29/39 (74.4%) HIV-positive MSM/TPSM indicated they would be more likely to have CAI with someone on PrEP versus not on PrEP. 358/578 (61.9%) HIV-negative respondents said that PrEP use would make them more likely to have CAI with HIV-negative partners. Conclusion Rising numbers of STI diagnoses among MSM/TPSM are not attributable to increased testing alone. Increased CAI and number of partners may be attributable to evolving sexual decision making among PrEP users and their partners. Proportionally, bisexual/other MSM/TPSM have the steepest increase in STI diagnoses.
Optical detection of wound infection in vivo by near infrared diffuse reflectance spectroscopy

ABSTRACT Detection of bacterial infection is important for deciding optimal treatment and management for wound. In the paper, near infrared diffuse reflectance spectroscopy is proposed for detection wound infection in vivo with optical properties. A porcine model is used as experimental subject in the detection of wound infection. The spectrally resolved data of the wounds are analyzed to extract the optical properties including reduced scattering coefficient and absorption coefficient. Based on optical properties, an ensemble model of chain-like agent genetic optimized Support Vector Machine is applied to discriminate wound infection. The experimental results demonstrate the feasibility and effectiveness of the method for rapid and noninvasive detection of wound infection using optical properties.
MicroRNAs regulate gene expression by binding to the 3′-untranslated region (UTR) of target messenger RNAs

MicroRNAs regulate gene expression by binding to the 3′-untranslated region (UTR) of target messenger RNAs (mRNAs). The importance of microRNAs has been shown for several liver diseases, for example, viral hepatitis. MicroRNA-122 is highly abundant in the liver and is involved in the regulation of lipid metabolism. MicroRNA-122 is also an important host factor for the HCV and promotes HCV replication. In contrast to HCV, microRNA-122 inhibits replication of the HBV. MicroRNA-122 acts as a tumour suppressor and reduced levels of microRNA-122 are associated with hepatocellular carcinoma. MicroRNAs other than microRNA-122 have been linked to viral hepatitis, fibrosis and inflammation. In this review, we discuss function and clinical implications of microRNA-122 and other microRNAs in liver diseases, especially viral hepatitis.
Prevalence and endemicity

Although chronic HBV infection is the leading cause of chronic liver disease and death worldwide, there are substantial differences in its clinical courses regarding prevalence, mode of transmission, characteristics of each phase, responses to antiviral therapy, and development of cirrhosis and hepatocellular carcinoma, according to geographical areas (Asia versus Western Europe and North America versus Africa). Furthermore, the clinical course in infected individuals depends on a complex interplay among various factors including viral, host, environmental and other factors. Recently, understanding of molecular characteristics of the prevailing HBV genotypes, frequently accompanied mutations and their clinical implications might explain these geographical differences more pertinently. Hence, in this article, we review the global epidemiology and the natural history of HBV infection, with emphasis on summarizing the different HBV genotypes according to regions.
Background: Achievement of early viral suppression is important in patients with chronic HCV infection treated with telaprevir (TLV) or boceprevir (BOC) to avoid selection

Background: Achievement of early viral suppression is important in patients with chronic HCV infection treated with telaprevir (TLV) or boceprevir (BOC) to avoid selection of drug resistance and attain cure. No head-to-head studies comparing TLV and BOC have been performed so far. Methods: All consecutive individuals who initiated triple HCV therapy with TLV or BOC outside clinical trials at three European clinics were evaluated. Rapid virological response (RVR) was defined as unquantifiable HCV RNA (<25 IU/ml) at week 4 for TLV and at week 8 for BOC (4 weeks after lead-in). Results: A total of 106 patients were evaluated, 33 treated with BOC and 73 with TLV. Median age, gender, body mass index, baseline HCV RNA, HCV subtype 1a (45% versus 42%) and IL28B-CC alleles (29% versus 23%) did not differ significantly in BOC and TLV groups, respectively. HIV coinfection was more prevalent in patients on TLV than BOC (24% versus 44%). Conversely, more patients on BOC than TLV had previously failed pegylated interferon plus ribavirin (82% versus 64%). RVR was achieved by 82% of patients on TLV versus 59% on BOC (P=0.001). Multivariate logistic regression analysis confirmed that TLV use was the strongest predictor of RVR (OR 3.54 [95% CI 1.23, 10.24]; P=0.02), others being HCV subtype 1b versus 1a (OR 3.26 [95% CI 1.17, 9.09]; P=0.02) and low baseline HCV RNA (OR 0.41 [95% CI 0.16, 1.03]; P=0.06). Prior interferon exposure, HIV coinfection or absence of advanced liver fibrosis did not influence the likelihood of RVR. Conclusions: Compared to BOC, triple therapy with TLV produces greater RVR rates. TLV might be a better option in more difficult-to-cure patients, such as those with high baseline HCV RNA and/or HCV 1a subtype. HIV coinfection does not influence early HCV RNA responses.
University of Birmingham Frozen colourings of bounded degree graphs

Let G be a graph with maximum degree ∆ and k be an integer. The k -recolouring graph of G is the graph whose vertices are proper k -colourings of G and where two colourings are adjacent iﬀ they diﬀer on exactly one vertex. Feghali, Johnson and Paulusma showed that the (∆ + 1)-recolouring graph is composed by a unique connected component and (possibly many) isolated vertices, also known as frozen colourings of G . Motivated by its applications to sampling, we study the proportion of frozen colourings of connected graphs. Our main result is that the probability a proper colouring is frozen is exponentially small on the order of the graph. The obtained
Effect of Diet Physical Form on Performance and Diet Digestibility in Finishing Fat-Tailed Lambs

This study was conducted in two experiments to evaluate the dietary physical form on dry matter intake (DMI), performance, carcass traits and nutrient digestibility from Kalkuhy (an Iranian fat–tailed breed) male lambs. Initial lamb body weight (BW) average was, 32 . 81 ± 2 kg, and 110 ± 10 days of age. Three treatments (diet physical form) included T1: total mixture diet (TMR) mixed diet (MD), T2: TMR blocked diet (BD) and T3: TMR pellet diets (PD) that were compared in completely randomized design. Diets had similar composition (80% concentrate to 20% forage). Average DMI of lambs fed by BD was significantly greater than MD diet (P<0.05). Average daily gain of lambs fed by BD was significantly greater than lambs fed MD and PD diets (P<0.05). Hot carcass and fat-tail lamb weights fed the BD treatment were significantly greater than lambs fed MD treatment (P<0.05). Nutrient digestibility was not affected by treatments. Dry matter, organic matter (OM) and crude protein (CP) digestion were not significantly greater for BD. In conclusion, blocking the complete diet for finishing fat-tailed lambs did not change final weight, feed conversion ratio (FCR) and nutrient digestibility, but increased DM intake, which in turn resulted in an increased energy available for fattening. As a result, lambs fed the BD treatment had heavier fat- tails compared to lambs fed either the PD or MD treatments. Hence, TMR block diet (BD) use for fattening Kalkuhy (Iranian fat–tailed breed) male lambs when providing them ad libitum access to feed wasn’t recommended.
Signal exchange in plant-microbe interactions

INTRODUCTION . 193 PLANT DISEASE RESISTANCE . 194 Phytoalexins . 194 Host and pathogen protein factors . 194 Plant cell wall modification . 5 Elicitors of Phytoalexin Synthesis 19 Arachidonic and eicosapentaenoic acid elicitors . 195 j-Glucan elicitors . 196 Plant cell wall fragments that regulate gene expression . 198 Phytoalexins and proteinase inhibitors . 19 Oligosaccharins . 198 Microbial enz;yme elicitors . 1 9 Induction of Gene Expression in the Pathogen . 19 Induction of Gene Expression in Plants by Elicitors . 200 Concluding Remarks . 202 AGROBACTERIUM-CROWN GALL DISEASE . 202 Transfer and Integration of the T-DNA into the Plant Genome . 203 Expression of T-DNA in the Plant Cell . 203 Plant-Induced Expression of the vir Genes Recognition and Attachment . 204 Binding assays . 2 Microfibril synthesis . 05 0-2-Glucan. 205 Specificity of oncogenesis 205 Agrobacterium: a passive or active partner in binding? 6 Concluding Remarks . 20 RHIZOBIUM-LEGUME SYMBIOSIS . 207 Recognition, Attachment, and the Lectin Hypothesis . 20 Location and Regulation of Infectible Host Cells . 9 Induction of Gene Expression by the Presence of the Host . 210 Host-Synthesized Polysaccharide-Degrading Enzymes . 212 Biological Activity Induced by Rhizobium Surface Polysaccharides . 212 Root hair curling . 21 Root hair curling genes . 3 Increased infection and nodulation . 21 Nodule Initiation . 214 Infection threadFormation.214 Bacterial Release from the Infection Thread . 215 Nodule-Specific Host Proteins. 215 Leghemoglobin . N duilins.215 ConcludingRemark 6 CONCLUSION. 217 ACKNOWLEDGMENTS . 218 LITERATURE CITED
Nitrogen control in bacteria

Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn.
Formation of liquid–liquid slug flow in a microfluidic T-junction: Effects of fluid properties and leakage flow

Characteristics of liquid–liquid slug flow are investigated in a microchannel with focus on the leakage flow that bypasses droplets through channel gutters. The results show that the leakage flow rate varies in a range of 10.7–53.5% and 8.3–30.9% of the feed flow rate, during the droplet formation (i.e., at T-junction) and downstream flow (i.e., in the main channel), respectively, which highly depends on Ca number and wetting condition. Empirical correlations are proposed to predict them for perfectly and partially wetting conditions. Leakage flow contribution is further used to improve the Garstecki model for size scaling in order to extend its suitability for both squeezing and shearing regimes. The instantaneous flow rates of the immiscible phases are found to fluctuate periodically with the formation cycles, but in opposite behavior. The effect of the presence of leakage flow on such fluctuation are investigated and compared with gas–liquid systems. © 2017 American Institute of Chemical Engineers AIChE J, 2017
Synthesis and Characterization of Hybrid Particles Obtained in a One-Pot Process through Simultaneous Sol-Gel Reaction of (3-Mercaptopropyl)trimethoxysilane and Emulsion Polymerization of Styrene

Hybrid particles consisting of an organic polymer and silica or polyorganosiloxanes are interesting building blocks for nanocomposites. The synthesis of such particles typically requires multiple reaction steps involving the formation of polymer colloids and the subsequent deposition of silicon-containing material either inside or on the surface of these colloids, or vice versa. In 2014, we reported a facile method for the one-pot synthesis of sub-micron sized hybrid particles based on simultaneous sol-gel conversion of organotrimethoxysilanes and emulsion polymerization of a vinylic monomer, illustrated by the synthesis of polystyrene-polyphenylsiloxane particles from the monomers styrene and phenyltrimethoxysilane (Segers et al (2014). In this process, the required surface active species was formed in situ through hydrolytic conversion of phenyltrimethoxysilane to phenylsilanolate oligomers. Introduction of thiol groups in such hybrid particles should yield particles suited for functionalization with small metal nanoparticles, e.g., Au. Here, we present the synthesis of thiol-containing hybrid particles consisting of poly(3-mercaptopropyl)siloxane and polystyrene using the one-pot synthesis method based on simultaneous conversion of (3-mercaptopropyl)trimethoxysilane and styrene. We prepared particles from different volume ratios of (3-mercaptopropyl)trimethoxysilane and styrene, ranging from 1:99 to 80:20. The resulting spherical hybrid particles displayed different sizes, compositions, and architectures (including core-shell), which were studied in detail using scanning electron microscopy, thermogravimetric analysis, and scanning transmission electron microscopy combined with energy dispersive x-ray spectroscopy. The composition of these particles, and consequently the number of thiol groups available for further functionalization such as metal anchoring, was tunable.
Synthesis of a thin-layer gelatin nanofiber mat for cultivating retinal cell

Thin-layer gelatin nanofiber mats were fabricated as a biodegradable scaffold for proliferating human retinal pigment epithelium. Together with MTT assay, the glucose consumption rate, lactate formation, and lactate dehydrogenase activity of the human retinal pigment epithelium cells—on the gelatin nanofibers—were analyzed as indicators for cell growth and viability. The results showed that gelatin nanofiber did not make any toxic effect on the cells and the growth rate was comparable to the tissue culture plates. Using the fabricated thin-layer nanofibers let the by-product to leave which in turn cause less adverse effect on the cells. The biodegradability and stability of the gelatin nanofibers were optimized as a function of reaction time.