Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the expressed porcine Vβ and Jβ repertoire of thymocytes and peripheral T cells

Transcripts of more than 300 unique T‐cell receptor‐β (TCR‐β) V‐D‐J rearrangements recovered from porcine thymocytes and peripheral T cells were compared. We identified 19 groups (families) of porcine Vβ genes in seven supergroups and provisionally named 17 groups based on their sequence similarity with recognized human Vβ gene families. TRBV4S, 5S, 7S and 12S accounted for > 80% of all Vβ usage, and usage of these groups by thymocytes and peripheral T cells was highly correlated. No TRBV group was uniquely expressed in significant numbers in thymocytes, although small numbers of TRBV groups 2S, 9S and 15S were only recovered from T cells. Usage of Jβ segments from the 5′ D‐J‐C duplicon in thymocytes and peripheral T cells directly correlated with their 5′ position in the locus, and Jβ1·1, 1·2 and 1·3 accounted for ≥ 35% of all Jβ usage in both cell types. This contrasts with the usage of Jβ2 segments in that Jβ2·4, 2·5 and 2·7 accounted for ≈ 30% of Jβ usage by T cells and thymocytes. Jβ2·7 was threefold more frequent among T cells than thymocytes. The Vβ/Jβ combination was not random. Jβ1·1 and 1·2 were used in 29% of rearrangements with high frequency among the major Vβ groups. Combinations of TRBV4 and V12 with Jβ2·7 were only found in T cells and accounted for half of all Jβ2·7 usage. These studies show that unlike porcine heavy chain VH genes, the occurrence and relative usage of porcine TCR‐Vβ groups resembles that of humans. Thus, highly related gene systems can individually diverge within a species.
Risk indicators for mucositis and peri-implantitis: results from a practice-based cross-sectional study

Purpose This practice-based cross-sectional study aimed to investigate whether common risk indicators for peri-implant diseases were associated with peri-implant mucositis and peri-implantitis in patients undergoing supportive implant therapy (SIT) at least 5 years after implant restoration. Methods Patients exclusively restored with a single implant type were included. Probing pocket depth (PPD), bleeding on probing (BOP), suppuration, and radiographic bone loss (RBL) were assessed around implants. The case definitions were as follows: peri-implant mucositis: PPD ≥4 mm, BOP, no RBL; and peri-implantitis: PPD ≥5 mm, BOP, RBL ≥3.5 mm. Possible risk indicators were compared between patients with and without mucositis and peri-implantitis using the Fisher exact test and the Wilcoxon rank-sum test, as well as a multiple logistic regression model for variables showing significance (P<0.05). Results Eighty-four patients with 169 implants (observational period: 5.8±0.86 years) were included. A patient-based prevalence of 52% for peri-implant mucositis and 18% for peri-implantitis was detected. The presence of 3 or more implants (odds ratio [OR], 4.43; 95 confidence interval [CI], 1.36–15.05; P=0.0136) was significantly associated with an increased risk for mucositis. Smoking was significantly associated with an increased risk for peri-implantitis (OR, 5.89; 95% CI, 1.27–24.58; P=0.0231), while the presence of keratinized mucosa around implants was associated with a lower risk for peri-implantitis (OR, 0.05; 95% CI, 0.01–0.25; P<0.001). Conclusions The number of implants should be considered in strategies to prevent mucositis. Furthermore, smoking and the absence of keratinized mucosa were the strongest risk indicators for peri-implantitis in patients undergoing SIT in the present study.
A reversible oxygen redox reaction in bulk-type all-solid-state batteries

A high-capacity positive electrode active material Li2RuO3-Li2SO4 for all-solid-state batteries was developed. An all-solid-state lithium battery using inorganic solid electrolytes requires safety assurance and improved energy density, both of which are issues in large-scale applications of lithium-ion batteries. Utilization of high-capacity lithium-excess electrode materials is effective for the further increase in energy density. However, they have never been applied to all-solid-state batteries. Operational difficulty of all-solid-state batteries using them generally lies in the construction of the electrode-electrolyte interface. By the amorphization of Li2RuO3 as a lithium-excess model material with Li2SO4, here, we have first demonstrated a reversible oxygen redox reaction in all-solid-state batteries. Amorphous nature of the Li2RuO3-Li2SO4 matrix enables inclusion of active material with high conductivity and ductility for achieving favorable interfaces with charge transfer capabilities, leading to the stable operation of all-solid-state batteries.
Vaginal Microbiota Evaluation and Lactobacilli Quantification by qPCR in Pregnant and Non-pregnant Women: A Pilot Study

Pregnancy outcomes and women's health are directly affected by vaginal microbiota. This microbiota consists of a dynamic ecosystem of various microbes in different ratios, which in healthy conditions protect the vaginal epithelium from infections. However, cases of vaginal infection are regularly diagnosed in women of reproductive age, contributing to more severe outcomes. Therefore, our main goal was to determine the prevalence of bacterial vaginosis (BV), aerobic vaginitis (AV), and vulvovaginal candidiasis (VVC) among Ecuadorian pregnant and non-pregnant women. A cross-sectional study was conducted among 217 women between 13 and 40 years old seeking primary healthcare in Carlos Andrade Marin Hospital (HCAM), Gynecological-Obstetric Hospital Isidro Ayora (HGOIA) and Center for Teaching Health Cipriana Dueñas during October 2018 to February 2019. The classical characterization of the vaginal microbiota was performed through microscopy by the Nugent criteria to evaluate the presence of BV, healthy and intermediate microbiota, by the criteria of Donders to determine the presence of AV and by the Marot-Leblond criteria to diagnose VVC. DNA extraction from vaginal samples and Polymerase Chain Reaction (PCR) analysis was performed to characterize the presence of Gardnerella spp. , Mobiluncus mulieris, Escherichia coli, Enterococcus spp. , and Lactobacillus spp. Finally, quantification of the lactobacilli was performed by quantitative real-time PCR (qPCR) for samples from women with normal vaginal microbiota and women with AV. Our results showed 52% of women with healthy microbiota, 7% with intermediate microbiota, and 41% with vaginal dysbiosis, comprising 27% with AV, 8% with BV and 4% with VVC and 2% with co-infections or co-dysbiosis. Additionally, a higher amount of lactobacilli were found in pregnant women when compared to non-pregnant women, while AV cases were characterized by a significant drop of Lactobacillus spp. , more precisely, between 1E3 and 1E5 colony forming units (CFU)/ml. Finally, women with normal vaginal microbiota showed an average load of lactobacilli between 1E6 and 1E7 CFU/ml. This pilot study showed no statistically significant differences between pregnant and non-pregnant women, pointing to the possibility to use lactobacilli quantification for the prevention of future vaginal infections.
Positive Inotropic Effect of Ouabain on Isolated Heart Is Accompanied by Activation of Signal Pathways that Link

Exposure of cultured rat cardiac myocytes to ouabain is known to cause the interaction of Na + /K + -ATPase with adja- cent proteins, leading to activation of multiple signal transduction pathways, regulation of growth-related genes, and hypertrophy. The aim of this work was to determine if the proximal signaling events identified in cultured myocytes also occur in isolated intact hearts of rat and guinea pig in response to positive inotropic doses of ouabain. Langendorff rat heart preparations were exposed to 50 µM ouabain to produce positive inotropy without toxicity, and assayed for Src kinase, protein kinase C, and extracellular signal- regulated kinases 1 and 2 (ERK1/2). These kinases were rapidly activated by ouabain as in cultured cells. In isolated guinea pig hearts, 1 µM ouabain caused ERK1/2 activation comparable to the effect of 50 µM ouabain in rat heart and consistent with the higher ouabain sensitivity of the contractility of guinea pig heart. These data show that the proximal ouabain-induced signal pathways previously noted in cultured cells are not artifacts of dispersion/culturing of myocytes, and are not the peculiar prop- erties of the rat heart with its relatively low ouabain sensitivity. They also suggest that treatment with positive inotropic doses of cardiac glycosides is likely to be associated with changes in the cardiac phenotype.
Senior Associate Editor

no. P12. 10. US Food and Drug Administration. National antimicrobial resistance monitoring system –enteric bacteria (NARMS): 2008 executive report. Rockville (MD); 2010 [cited 2012 Feb 13]. http://www. fda.gov/AnimalVeterinary/SafetyHealth/AntimicrobialResistance/ NationalAntimicrobialResistanceMonitoringSystem/default.htm. 11. Atkinson BA, Lorian V. Antimicrobial agent susceptibility patterns of bacteria in hospitals from 1971 to 1982. J Clin Microbiol.
Food and reproduction of wild house mice. 2. A field experiment to examine the effect of food availability and food quality on breeding in spring

Free-ranging populations of house mice, Mus musculus L. , on contour banks in a rice field in New South Wales were provided with three types of supplementary food of differing nutritional quality for 10 weeks in spring. Four live-trapping sessions were conducted 3-10 weeks after supplementary feeding started. The percentage of females breeding averaged 47% on banks with supplementary food, and 0% on control banks with no supplementary food. The quality of the supplementary food did not affect breeding performance. It is concluded that breeding in rice fields in spring is limited by the food supply, and it is probably the supply of energy, rather than that of specific nutrients, that is limiting.
Measurement of digestibility of cell wall constituents in grass and legume forages by an artificial rumen method

In the present study, to clarify the reason why crude fiber digestibility is generally low in legumes than that in grasses, the digestibility of crude fiber in some grass and legume forages, and the digestibility of neutral detergent fiber(NDF)and acid detergent fiber(ADF)were also determined after refining them from same forages using an artificial rumen method. The following reasons why the digestibility of fiber of legume forages is usually lower than that of grass forages will be shown; a)There is a possibility that the constituents of cell except NDF control(prevent)NDF digestibility in legume for- ages. b)The digestibility of ADF itself is clearly low in legume forages as compared to that in grass forages. It can be also assumed as another reason that the digestion of hemi−cel- lulose proceeds rapidly, and will be degradable condition at early stage of incubation. It can- not be clarified, however that the rapid progress of hemi−cellulose digestion in the early stage during incubation induces a difference in digestibility of crude fiber between legume and grass forages, or not in this study.
Salivary microbiota in periodontal health and disease and their changes following nonsurgical periodontal treatment

Purpose The aims of this study were to examine the salivary microbiota in conditions of periodontal health and disease and to explore microbial changes following nonsurgical periodontal treatment. Methods Non-stimulated saliva samples were collected from 4 periodontally healthy participants at baseline and from 8 patients with chronic periodontitis at baseline and 3 months following nonsurgical periodontal therapy. The V3 and V4 regions of the 16S rRNA gene from the DNA of saliva samples were amplified and sequenced. The salivary microbial compositions of the healthy participants and patients with periodontitis prior to and following nonsurgical treatment of periodontitis were compared based on the relative abundance of various taxa. Results On average, 299 operational taxonomic units were identified in each sample. The phylogenetic diversity in patients with periodontitis was higher than that in healthy participants and decreased following treatment. The abundance of the phylum Spirochaetes and the genus Treponema in patients with periodontitis was 143- and 134-fold higher than in the healthy control group, respectively, but decreased significantly following treatment. The species that were overabundant in the saliva of patients with periodontitis included the Peptostreptococcus stomatis group, Porphyromonas gingivalis, the Fusobacterium nucleatum group, Parvimonas micra, Porphyromonas endodontalis, Filifactor alocis, and Tannerella forsythia. The phylum Actinobacteria, the genus Streptococcaceae_uc, and the species Streptococcus salivarius group were more abundant in healthy participants than in those with periodontitis. There was a trend toward a decrease in disease-associated taxa and an increase in health-associated taxa following treatment. Conclusions Our results revealed differences in the taxa of salivary microbiota between conditions of periodontal health and disease. The taxa found to be associated with health or disease have potential for use as salivary biomarkers for periodontal health or disease.
Neurobiology of Social Behavior

fully solitary lifestyle. Most of the others are characterized by permanent associations between two or more adults and their young. Pair living is relatively rare, being characteristic of only 3% to 4% of primate species. Some of these socially monogamous species (e.g., tamarins and marmosets) have a flexible social organization,inwhich oneadditionaladultmale orfemalemaybetemporarilyassociatedwiththe breeding pair. Stable groups with one adult male and several reproductively active females (i.e., harems) are shown by approximately 35% of primate species. The most common type of social organization in nonhuman primates consists of social groups with multiple adult males and females and their young. These multimale/ multifemale social groups represent the stable form of organization of about 45% primate species, with an additional 15% of species showing fluctuations between such groups and groups with a harem structure. Variation in social organization among primate species has been explained on the basis of variation in ecological variables such as diet, food-related competition and cooperation (e.g., Wrangham, 1980 AQ1 ), and need for protection from predators (e.g., van
Plant protein hydrolysates from soybean and rice grain as a supplement for medium in human skin fibroblast 1184 cell culture.

In cell culture, addition of serum in the medium plays an important role for the growth of the cells. Each medium consists of two main parts which are a basal media and serum. Serum, mainly from animal source is very expensive and possesses higher potential of viral contamination. The alternative for solving this problem is to use a serum-free media with an addition of some supplements. The most important source of supplement is from plants which could reduce the cost. In this study, protein hydrolysates from soybean and rice as a supplement for medium in human skin fibroblast (HSF) 1184 cells to substitute the addition of serum in the medium were investigated. Plant protein hydrolysates from soybean and rice were prepared through enzymatic hydrolysis using two different enzymes; Alcalase and Flavourzyme. These hydrolysates were characterized according to their solubility and peptide size. Different growth behavior was observed when these protein hydrolysates were added in medium with and without Fetal Bovine Serum (FBS). Protein hydrolysates produced using Flavourzyme has no significant effect on cell culture, while hydrolysates from Alcalase were supplementary for HSF 1184 cell culture. Since plant proteins do not contain all the necessary amino acids for HSF 1184 cell culture growth, they cannot be solely substituted with FBS. Depending on the enzyme used, supplementation with hydrolysates corresponding to a high degree of hydrolysis and composition of peptides with small molecular size, led to different maximal cell density. It is whereby degree of hydrolysis for soybean and rice hydrolysed by Alcalaseis slightly higher (31.59% and 36.52% for soybean and rice, respectively) when compared to hydrolysis by Flavourzyme (17.58% and 34.36% for soybean and rice, respectively). Results also demonstrated that preparation procedure for protein isolates were efficient because the protein concentration was about two times greater than primary meal and some undesirable materials for mammalian cell culture were eliminated from meal. From this study, protein hydrolysates from soybean hydrolysed by Alcalase have shown the best performance for supplementation into a medium for HSF 1184 cell growth.
ADVANCING WOMEN IN LEADERSHIP

In this paper, we used a qualitative multiple case study approach. We used the authentic leadership framework (Luthans & Avolio, 2003) to examine how African American women in senior administrator roles, particularly in the president’s cabinet, at a member institution of the Association of Public and Land-Grant Universities (APLU) in Alabama describe their experiences of developing an authentic leadership style. Following previous studies and recommendations for future research (Davis, 2016; Milner, 2006; Pace, 2017; Robinson, 2017; Wiggs-Harris, 2011), the following research question guides this work: How do African American women senior administrators describe their experiences of developing a leadership style? The results of this study revealed six common themes that are related to the authentic leadership style development of African American women. Code-switching was also an interesting element that emerged from some of the interviews, which may impact how some of them may present themselves and are perceived by others. In relation to the findings, theories of authentic leadership and intersectionality are discussed along with suggestions for future research.
ENVIRONMENTAL SENSITIVITY OF MITOCHONDRIAL GENE EXPRESSION IN FISH

ii Co-Authorship . iv Acknowledgements . vi List of Figures . xi List of Tables . xii List of Abbreviations . xiii Chapter 1 : General introduction . 1 1.1 Mitochondria . 2 1.1.1 A brief history . 2 1.1.2 The powerhouse of the cell . 3 1.1.3 Cytochrome c oxidase structure and function . 5 1.2 The regulation of aerobic energy metabolism . 8 1.2.1 The control of aerobic energy metabolism by cytochrome c oxidase . 10 1.3 Control of mitochondrial biogenesis . 13 1.3.1 Transcriptional control of COX genes . 13 1.3.2 Control of PGC-1α levels and activity . 17 1.3.3 What determines (COX subunit) transcript levels? 19 1.4 Cytochrome c oxidase across the animal kingdom and why we are interested in fish . 25 1.5 Questions . 27 Chapter 2 : Origins of variation in muscle cytochrome c oxidase activity within and between fish species . 30 2.1 Abstract . 30 2.2 Introduction . 31 2.3 Materials and methods . 33 2.3.1 Fish . 33 2.3.2 Acclimation experiment . 35 2.3.3 Cytochrome c oxidase activity . 36 2.3.4 RNA extraction and reverse transcription . 37 2.3.5 Real-time PCR . 37 2.3.6 Statistics . 40 ix 2.4 Results . 40 2.4.1 COX activity . 40 2.4.2 Transcription factors and coactivator mRNA levels . 42 2.5 Discussion . 44 2.5. 1 Species-specific seasonal thermal response in enzyme activity . 44 2.5. 2 Acclimation versus acclimatization . 46 2.5. 3 Control of mitochondrial oxidative capacity . 48 2.6 Acknowledgements . 52 Chapter 3 : Transcriptional regulation of temperature-induced remodeling of muscle bioenergetics in goldfish . 53 3.1 Abstract . 53 3.2 Introduction . 54 3.3 Materials and methods . 57 3.3.1 Fish and experimental setup . 57 3.3.2 COX activities . 58 3.3.3 RNA analyses . 59 3.3.4 Protein levels . 61 3.3.5 Statistics . 64 3.4 Results . 64 3.4.1 Yield of RNA and nuclear protein . 64 3.4.2 COX activity and transcript patterns . 65 3.4.3 Protein levels . 70 3.5 Discussion . 71 3.5. 1 Transcriptional regulators . 72 3.5. 2 DNA-binding proteins . 73 3.5. 2.1 NRFs . 73 3.5. 2.2 ERRα, TRα-1, PPARs, and RXRα . 74 3.5. 3 Significance of changes in RNA and nuclear protein per gram tissue . 79 3.5. 4 Perspectives and significance . 80 3.6 Acknowledgments . 81 Chapter 4 : mRNA degradation: an underestimated factor on steady-state transcript levels of cytochrome c oxidase subunits? 82 x 4.1 Abstract . 82 4.2 Introduction . 83 4.3 Materials and methods . 86 4.3.1 Fish and experimental setup . 86 4.3.2 Cytochrome c oxidase activities . 87 4.3.3 Decay assay and RNA extraction . 88 4.3.4 Real-time PCR . 89 4.3.5 Data analysis .
Cumulation of Tabernanthe Iboga alkaloid and its metabolite in organs of mice

The accumulation of Tabernanthe Iboga alkaloid ibogaine and its metabolite noribogaine in liver, kidney, spleen, heart, brain and muscle after administration directly into the stomach in white laboratory mice were studied. For this purpose a high-performance liquid chromatography (HPLC) method with fluorescein as internal standart were chosen. Solid phase extraction (SPE) method was employed to isolate the tested substances from the internal organs. Separation of the analytes was performed on a reversed-phase XTerra RP18 analytical column (3×150 mm, particle size 3.5 µm) using a gradient, the mobile phase consisted of a mixture acetonitril and 0.1% TFA in water. The total run cycle was 25 min. The flow rate was 0.4 ml/min, and injection volume was 10 µl. The excitation wavelength was set at 230 nm and emission wavelength at 336 nm. Excitation wavelength of internal standard (fluoresceine) was set at 440 nm and emission wavelength at 514 nm. Experiment demonstrated that highest concentration of ibogaine and noribogaine have been obtained in spleen and the lower one – in muscle of the animal after the direct administration into the mice stomach. Key words: Tabernanthe Iboga, ibogaine, noribogaine, solid phase extraction, distribution in mice organs, HPLC.
Selection for higher three week body weight in Japanese quail:2. Estimation of genetic parameters.

Data on pedigree and performance records of 480 Japanese quails progeny of 81 sires and 200 dams maintained at Avian Research and Training Centre, University of Veterinary and Animal Sciences, Lahore selected for three generations for higher body weight were used to estimate some genetic parameters for body weight, egg production performance, egg quality and hatching traits. The generation, sex and genetic groups were included as fixed effects in the model for univariate analysis through WOMBAT computer software for Restricted Maximum Likelihood (REML) procedure. The heritability estimates of body weight at the age of 3, 4 and 6 weeks were 0.0126, 0.0315 and 0.20, respectively. For egg production traits including age at 1 egg, total eggs produced and average feed consumed per egg, heritability estimates were 0.20, 0.20 and 0.0047, respectively. Whereas for fertility and clear eggs %, heritability estimates were almost negligible indicating the impact of environment more pronounced than genetics on hatching traits. Breeding values for growth performance in selected birds at the age of three weeks ranged between, -0.1845 to 0.4102, -0.2309 to 0.471 and -0.0908 to 0.5373 in generation 1, 2 and 3, respectively. For random-bred control birds the values ranged between -0.845 to 0.6384, -1.2542 to 0.6713 and -1.3781 to 0.7623 for 1, 2 and 3 generation, respectively. Genetic trend lines indicated positive response to selection as the generations progressed.