Miracle-dz/UniFAR-FTUs huggingface dataset:
Mobility of Australian flying-foxes, Pteropus spp. (Megachiroptera): evidence from genetic variation

Black (Pteropus alecto) and grey-headed (Pteropus poliocephalus) flying-foxes inhabit large ranges in coastal north and eastern Australia. P. poliocephalus is endemic to the region and is classified as vulnerable. The bats are known to migrate in response to flowering and fruiting of their food plants, but direct observation of movement patterns is difficult. Protein electrophoresis was used to investigate genetic subdivision among populations. High gene flow was inferred for both species with an estimated exchange of 15 (P. alecto) and 28 (P. poliocephalus) individuals between populations per generation. Wright’s FST, an index of among population genetic variation, was low, 0.023 (P. alecto), 0.014 (P. poliocephalus), reflecting the homogenising action of movements across the species’ ranges. An FST value of 0.028 has been reported for a third Australian species, the little red flying-fox, P. scapulatus. The FST values for Australian flying-foxes are closer to those found for birds than the typically higher values for mammals and we conclude that these flying-foxes are essentially panmictic and for management purposes should be treated as migratory species.
Evaluation of Soft-Tissue Balance during Total Knee Arthroplasty

Purpose. To evaluate soft-tissue balance during versus after total knee arthroplasty (TKA). Methods. 18 men and 75 women aged 52 to 85 (mean, 68) years who had moderate-to-severe varus deformity underwent TKAs using the Scorpio non-restrictive geometry posterior-stabilised system (Stryker Howmedica Osteonics; Allendale, [NJ], USA). All surgeries were performed by a single surgeon using the medial parapatellar approach. After the bony and soft-tissue procedures, soft-tissue balance was measured intra-operatively using a tensor/balancer device. The coronal laxity—angles between the cut surfaces of the femur and tibia—were measured at 0° (in extension) and 90° (in flexion). The central gap was also measured. Immediate postoperative soft-tissue balance was measured using an arthrometer, while anteroposterior stress radiographs were being taken. A valgus or varus force was applied just above the knee on the lateral or medial side, with the knee counter-supported and at 15° flexion. Results. Intra-operatively, the mean coronal laxity at 0° (in extension) and 90° (in flexion) was 2.1° and −1.6°, and the mean central gaps were 21.2 and 23.5 mm, respectively. Immediate postoperative mean coronal laxity was 2.9°, indicating that lateral laxity was greater than medial laxity. The postoperative coronal laxity was positively corrected to the intra-operative coronal laxity at 0° (r=0.304, p=0.003), but not to the intra-operative coronal laxity at 90° (r= −0.07, p=0.47). Conclusion. Slightly greater lateral laxity was observed after TKA, although equal medial-lateral balance was achieved intra-operatively.
Activated microglia affect the nigro‐striatal dopamine neurons differently in neonatal and aged mice treated with 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine

Microglia play an important role in the inflammatory process that occurs in Parkinson's disease (PD). Activated microglia produce cytokines and neurotrophins and may have neurotoxic or neurotrophic effects. Because microglia are most proliferative and easily activated during the neonatal period, we examined the effects of neonatal microglia activated with lipopolysaccharide (LPS) on the nigro‐striatal dopamine neurons in mice treated with 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP), in comparison with activated microglia from the aged mice. By MPTP administration to neonatal mice, the number of dopamine neurons in the substantia nigra (SN) was decreased significantly, whereas that in the mice treated with LPS and MPTP was recovered to normal, along with significant microglial activation. Tyrosine hydroxylase (TH) activity, the levels of dopamine and 3,4‐dihydroxyphenylacetic acid (DOPAC), and the levels of pro‐inflammatory cytokines IL‐1β and IL‐6 in the midbrain were elevated in the neonates treated with LPS and MPTP. On the contrary, although the number of dopamine neurons in the 60‐week‐old mice treated with MPTP was also decreased significantly, the microglial activation by LPS treatment caused a further decrease in their number. These results suggest that the activated microglia in neonatal mice are different from those in aged mice, with the former having neurotrophic potential toward the dopamine neurons in the SN, in contrast to the neurotoxic effect of the latter. © 2007 Wiley‐Liss, Inc.
Unusual Heme-Binding PAS Domain from YybT Family Proteins

ABSTRACT YybT family proteins (COG3887) are functionally unknown proteins that are widely distributed among the firmicutes, including the human pathogens Staphylococcus aureus and Listeria monocytogenes. Recent studies suggested that YybT family proteins are crucial for the in vivo survival of bacterial pathogens during host infection. YybT family proteins contain an N-terminal domain that shares minimum sequence homology with Per-ARNT-Sim (PAS) domains. Despite the lack of an apparent residue for heme coordination, the putative PAS domains of BsYybT and GtYybT, two representative members of the YybT family proteins from Bacillus subtilis and Geobacillus thermodenitrificans, respectively, are found to bind b-type heme with 1:1 stoichiometry. Heme binding suppresses the catalytic activity of the DHH/DHHA1 phosphodiesterase domain and the degenerate GGDEF domain. Absorption spectroscopic studies indicate that YybT proteins do not form stable oxyferrous complexes due to the rapid oxidation of the ferrous iron upon O2 binding. The ferrous heme, however, forms a hexacoordinated complex with carbon monoxide (CO) and a pentacoordinated complex with nitric oxide (NO). The coordination of NO, but not CO, to the heme stimulates the phosphodiesterase activity. These results suggest that YybT family proteins function as stress-signaling proteins for monitoring cellular heme or the NO level by using a heme-binding PAS domain that features an unconventional heme coordination environment.
Individual Genetic Variations Related to Satiety and Appetite Control Increase Risk of Obesity in Preschool-Age Children in the STRONG Kids Program

Background/Aims: The burden of the childhood obesity epidemic is well recognized; nevertheless, the genetic markers and gene-environment interactions associated with the development of common obesity are still unknown. In this study, candidate genes associated to satiety and appetite control pathways with obesity-related traits were tested in Caucasian preschoolers from the STRONG Kids project. Methods: Eight genetic variants in genes related to obesity (BDNF, LEPR, FTO, PCSK1, POMC, TUB, LEP, and MC4R) were genotyped in 128 children from the STRONG Kids project (mean age 39.7 months). Data were analyzed for individual associations and to test for genetic predisposition scores (GPSs) with body mass index (BMI) and anthropometric traits (Z-scores, e.g. height-for-age Z-score, HAZ). Covariates included age, sex, and breastfeeding (BF) duration. Results: Obesity and overweight prevalence was 6.3 and 19.5%, respectively, according to age- and sex-specific BMI percentiles. Individual genetic associations of MC4R and LEPR markers with HAZ were strengthened when BF duration was included as a covariate. Our GPSs show that, as the number of risk alleles increased, the risk of higher BMI and HAZ also increased. Overall, the GPSs assembled were able to explain 2-3% of the variability in BMI and HAZ phenotypes. Conclusion: Genetic associations with common obesity-related phenotypes were found in the STRONG Kids project. GPSs assembled for specific candidate genes were associated with BMI and HAZ phenotypes.
Negative group velocity and anomalous transmission in a one-dimensionally periodic waveguide

This study presents a theoretical investigation of the negative group velocity (NGV) and anomalous transmittance of waves in the stop band of a corrugated parallel-plate waveguide (CPPWG). The two different schemes, scattering analysis for a finite CPPWG and the dispersion relation of an infinite CPPWG, were used to investigate the physical insight of the wave process. The NGV zone corresponds to the stopband slanted at an angle on the Brillouin diagram, following the mutual verification of the results obtained by the two different approaches. This class of stopband is caused by the contra-flow interaction between the fundamental mode and the space harmonics of higher-order modes. Additionally, fluctuation was also found in the transmitted coefficient within the conventional stopband, caused by the excitation of the first higher-order mode within the stopband of the fundamental mode.
Multiple Inert Gas Elimination Technique For Determining Ventilation/Perfusion Distributions In Rat During Normoxia, Hypoxia And Hyperoxia

1. The use of the multiple inert gas elimination technique (MIGET) in quantifying ventilation/perfusion distributions (V•A/Q•) in small animals, such as the rat, may cause results to be biased due to haemodilution produced by the large volume of liquid infused intravenously.
Improving functional properties of pea protein isolate for microencapsulation of flaxseed oil

Abstract Unhydrolysed pea protein (UN) forms very viscous emulsions when used at higher concentrations. To overcome this, UN was hydrolysed using enzymes alcalase, flavourzyme, neutrase, alcalase–flavourzyme, and neutrase–flavourzyme at 50 °C for 0 min, 30 min, 60 min, and 120 min to form hydrolysed proteins A, F, N, AF, and NF, respectively. All hydrolysed proteins had lower apparent viscosity and higher solubility than UN. Foaming capacity of A was the highest, followed by NF, N, and AF. Hydrolysed proteins N60, A60, NF60, and AF60 were prepared by hydrolysing UN for 60 min and used further for microencapsulation. At 20% oil loading (on a total solid basis), the encapsulated powder N60 had the highest microencapsulation efficiency (ME = 56.2). A decrease in ME occurred as oil loading increased to 40%. To improve the ME of N60, >90%, UN and maltodextrin were added. Flowability and particle size distribution of microencapsulated powders with >90% microencapsulation efficiency and morphology of all powders were investigated. This study identified a new way to improve pea protein functionality in emulsions, as well as a new application of hydrolysed pea protein as wall material for microencapsulation.
Effects of albuminuria and renal dysfunction on development of dyslipidaemia in type 2 diabetes--the Hong Kong Diabetes Registry.

BACKGROUND It is uncertain whether albuminuria precedes the future development of high total cholesterol (TC > 6.2 mmol/l) and high LDL-C (>4.1 mmol/l) while renal dysfunction precedes the future development of low HDL-C (<0.9 mmol/l) in type 2 diabetes. METHODS A prospective cohort of 2761 type 2 diabetic patients without significant dyslipidaemia and having at least one measurement of TC, LDL-C and HDL-C during 2.8 years of follow-up was analysed. The spline Cox regression model was used to derive hazard ratio (HR) curves of the spot urinary albumin:creatinine ratio (ACR) and the estimated glomerular filtration rate (eGFR) for dyslipidaemia, followed by standard Cox models to confirm the findings from the HR curves. RESULTS Seven percent of the cohort developed high TC, 4.6% developed high LDL-C and 5.7% developed low HDL-C during follow-up. In multivariate analysis, the HR of ACR for high TC and high LDL-C increased rapidly and linearly from zero with no apparent threshold. Patients with macroalbuminuria (ACR >/=25 mg/mmol) were, respectively, 1.6- and 2.4 folds more likely to develop high TC and high LDL-C than those with normoalbuminuria at baseline. The HR of eGFR for low HDL-C increased rapidly with declining eGFR at <110 ml/min/ 1.73 m(2). Subjects with eGFR <60 ml/min/1.73 m(2) and >/=60-<110 ml/min/1.73 m(2), respectively, had 3.0-fold and 1.8-fold risks of low HDL-C compared to those with eGFR >/=110-<140 ml/min/1.73 m(2). CONCLUSIONS In type 2 diabetes, macroalbumninuria predicts high TC and high LDL-C, while reduced renal function, even within normal range, predicts low HDL-C.
Dual Selection Pressure by Drugs and HLA Class I-Restricted Immune Responses on Human Immunodeficiency Virus Type 1 Protease

ABSTRACT To determine the influence of human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells on the development of drug resistance mutations in the HIV-1 protease, we analyzed protease sequences from viruses from a human leukocyte antigen class I (HLA class I)-typed cohort of 94 HIV-1-positive individuals. In univariate statistical analyses (Fisher's exact test), minor and major drug resistance mutations as well as drug-associated polymorphisms showed associations with HLA class I alleles. All correlations with P values of 0.05 or less were considered to be relevant without corrections for multiple tests. A subset of these observed correlations was experimentally validated by enzyme-linked immunospot assays, allowing the definition of 10 new epitopes recognized by CD8+ T cells from patients with the appropriate HLA class I type. Several drug resistance-associated mutations in the protease acted as escape mutations; however, cells from many patients were still able to generate CD8+ T cells targeting the escape mutants. This result presumably indicates the usage of different T-cell receptors by CD8+ T cells targeting these epitopes in these patients. Our results support a fundamental role for HLA class I-restricted immune responses in shaping the sequence of the HIV-1 protease in vivo. This role may have important clinical implications both for the understanding of drug resistance pathways and for the design of therapeutic vaccines targeting drug-resistant HIV-1.
TGFβ3 secretion by three‐dimensional cultures of human dental apical papilla mesenchymal stem cells

Mesenchymal stem cells (MSCs) can be isolated from dental tissues, such as pulp and periodontal ligament; the dental apical papilla (DAP) is a less‐studied MSC source. These dental‐derived MSCs are of great interest because of their potential as an accessible source for cell‐based therapies and tissue‐engineering (TE) approaches. Much of the interest regarding MSCs relies on the trophic‐mediated repair and regenerative effects observed when they are implanted. TGFβ3 is a key growth factor involved in tissue regeneration and scarless tissue repair. We hypothesized that human DAP‐derived MSCs (hSCAPs) can produce and secrete TGFβ3 in response to micro‐environmental cues. For this, we encapsulated hSCAPs in different types of matrix and evaluated TGFβ3 secretion. We found that dynamic changes of cell–matrix interactions and mechanical stress that cells sense during the transition from a monolayer culture (two‐dimensional, 2D) towards a three‐dimensional (3D) culture condition, rather than the different chemical composition of the scaffolds, may trigger the TGFβ3 secretion, while monolayer cultures showed almost 10‐fold less secretion of TGFβ3. The study of these interactions is provided as a cornerstone in designing future strategies in TE and cell therapy that are more efficient and effective for repair/regeneration of damaged tissues. Copyright © 2015 John Wiley & Sons, Ltd.
Development and validation of Iranian children’s participation assessment scale

Background: Participation is mostly cultural and familial based, and there is not any assessment scales for evaluating kids’ participation in Iranian context, therefore the purpose of this study was developing children’s participation assessment scale for Iranian children. Methods: Development of this scale occurred in two phases; phase I: planning: following reviewing the literature and adopting and compiling some items of available evaluation tools in the area (such as CAPE, CPQ, CLASS, Life-H) and receiving advice from two expert panels, the preliminary94- item questionnaire was prepared. Phase II: construct: the survey study was carried out on40 children and 21 of their parents to assess the popularity of the activity in Iran; thus, the items of the questionnaire reduced to 92 and after face and content validity, the final version prepared with 71 items. Results: The final 71-item questionnaire was developed in two parent-report and child-report versions. The 71 items based on the literature and expert panels’ advice were categorized in 8 areas of occupation according to Occupational Therapy Practice Framework (ADL, IADL, Play, leisure, social participation, education, work, and sleep/rest). Conclusion: Iranian children’s participation assessment is a useful and culturally relevant tool to measure participation of Iranian children. It can be used in rigorous clinical and population-based research.
On the Uses and Applications of the Most Commonly Used Measures of Linkage Disequilibrium from the Comparative Analysis of Their Statistical Properties

Background/Objective: The analysis of linkage disequilibrium is relevant for the exploration of the structure and evolution of genomes and for the gene mapping of quantitative characters and human diseases. The strength of linkage disequilibrium between diallelic loci is commonly measured by the coefficients D′ and r. Recent studies suggest that r is more useful than D′ as a general measure of the strength of disequilibrium because it provides much more precise (lower sampling variance) and accurate (lower bias) estimates of disequilibrium. We compared for the first time the statistical properties of D′ and r taking into account their differences in range. Methods: The sampling properties of D′ and r were evaluated by simulation under a variety of realistic population conditions and varying sample sizes using standardised statistics that allow for comparisons of the precision, accuracy and efficiency of estimates with different ranges. Results: Simulations revealed that estimates of r do not tend to be significantly more precise, accurate or efficient than those of D′ when compared by means of standardised statistics. Conclusion: The supposed advantage of r over D′ based on direct comparisons of their sampling distributions is more apparent than real. The obtained results are useful to assess the uses and applications of these widely used disequilibrium measures.
Chemokine receptors in head and neck cancer: Association with metastatic spread and regulation during chemotherapy

Head and neck carcinomas are histologically and clinically heterogeneous. While squamous cell carcinomas (SCC) are characterized by lymphogenous spread, adenoid cystic carcinomas (ACC) disseminate preferentially hematogenously. To study cellular and molecular mechanisms of organ‐specific metastasis, we used SCC and ACC cell lines and tumor tissues, obtained from patients with primary or metastatic disease. Comprehensive analysis at the mRNA and protein level of human chemokine receptors showed that SCC and ACC cells exhibited distinct and nonrandom expression profiles for these receptors. SCC predominantly expressed receptors for chemokines homeostatically expressed in lymph nodes, including CC chemokine receptor (CCR) 7 and CXC chemokine receptor (CXCR)5. No difference in expression of chemokine receptors was seen in primary SCC and corresponding lymph node metastases. In contrast to SCC, ACC cells primarily expressed CXCR4. In chemotaxis assays, ACC cells were responsive to CXCL12, the ligand for CXCR4. Exposure of ACC cells to cisplatin resulted in upregulation of CXCR4 on the cell surface, which was repressed by the transcriptional inhibitor, α‐amanitin. Treatment of ACC cells with CXCL12 resulted in the activation of Akt and ERK1/2 pathways. Furthermore, CXCL12 suppressed the rate of apoptosis induced by cisplatin in ACC cells, suggesting that signaling via CXCR4 may be part of a tumor cell survival program. Discrimination of the chemokine receptor profile in SCC and ACC in vitro and in tissues provided insights into their distinct biologic and clinical characteristics as well as indications that chemokine receptors might serve as future therapeutic targets in these malignancies. © 2005 Wiley‐Liss, Inc.
Transcriptional Regulation of the Human NRIP1/RIP140 Gene by Estrogen Is Modulated by Dioxin Signalling

Receptor interacting protein 140 (RIP140) is a negative transcriptional regulator of nuclear hormone receptors that is required for the maintenance of energy homeostasis and ovulation. In this study, we investigated the mechanisms by which RIP140 expression is controlled by estrogens in breast cancer cells. We first analyzed by real time reverse transcription-polymerase chain reaction the regulation of RIP140 mRNA accumulation by estrogen receptor (ER) ligands in MCF-7 cells. We showed that the induction by estradiol (E2) was rapid and did not affect the apparent stability of the mRNA, suggesting a direct transcriptional regulation. To further study the underlying regulatory mechanisms, we then characterized the human RIP140 gene. We identified several noncoding exons with alternative splicing and localized the promoter region more than 100 kilobases upstream from the coding exon. Although we mapped a perfect consensus estrogen response element able to bind ERα in gel shift and in chromatin immunoprecipitation experiments, the effect of E2 on RIP140 gene transcription was very modest. This might result at least in part from the presence of an overlapping aryl hydrocarbon receptor (AhR) binding site, which interfered with the E2 response on both the transiently transfected reporter construct and the accumulation of the endogenous RIP140 mRNA. Altogether, our data indicate that the RIP140 gene exhibits a complex structure with several noncoding exons and supports transcriptional cross-talk and feedback involving the ERα and AhR nuclear receptors.
Small bowel ischaemia-reperfusion increases plasma concentrations of oxidised proteins in rats.

OBJECTIVES To find out whether plasma concentrations of protein carbonyl (a specific marker of oxidative damage of proteins) are increased during intestinal ischaemia-reperfusion and whether they are correlated with von Willebrand's factor (vWF, a marker of endothelial injury) or myeloperoxidase (a marker of neutrophil activation). DESIGN Randomised experimental study. SETTING University department of surgery, New Zealand. ANIMALS Thirty anaesthetised adult Wistar rats. INTERVENTIONS The sham operated group (n = 10) had laparotomy and isolation of the superior mesenteric artery without clamping. The ischaemia-reperfusion group (IR, n = 10) had the superior mesenteric artery clamped for 1 hour and reperfusion for 15 minutes. The control group (n = 10) had direct puncture of the heart to sample blood. MAIN OUTCOME MEASURES Plasma concentrations of protein carbonyl, vWF, and myeloperoxidase. RESULTS Plasma protein carbonyl concentrations were significantly higher in the IR group than in the sham group (p < 0.02, Mann-Whitney test, median (range) 0.187 (0.141-0.242) compared with 0.144 (0.121-0.185) nmol/mg) and in the control group (p < 0.01, Mann-Whitney test, median (range) 0.187 (0.141-0.242) compared with 0.136 (0.108-0.175) nmol/mg). There was a significant correlation between protein carbonyl and vWF concentrations (r = 0.54, F = 10.9, p < 0.003, linear regression) but not with those of myeloperoxidase. CONCLUSION Intestinal ischaemia-reperfusion caused an increase in the plasma protein carbonyl concentration, which is possibly produced by endothelial cells.