Miracle-dz/UniFAR-FTUs huggingface dataset:
Symbiodinium (Dinophyceae) community patterns in invertebrate hosts from inshore marginal reefs of the southern Great Barrier Reef, Australia

The broad range in physiological variation displayed by Symbiodinium spp. has proven imperative during periods of environmental change and contribute to the survival of their coral host. Characterizing how host and Symbiodinium community assemblages differ across environmentally distinct habitats provides useful information to predict how corals will respond to major environmental change. Despite the extensive characterizations of Symbiodinium diversity found amongst reef cnidarians on the Great Barrier Reef (GBR) substantial biogeographic gaps exist, especially across inshore habitats. Here, we investigate Symbiodinium community patterns in invertebrates from inshore and mid‐shelf reefs on the southern GBR, Australia. Dominant Symbiodinium types were characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Twenty one genetically distinct Symbiodinium types including four novel types were identified from 321 reef‐invertebrate samples comprising three sub‐generic clades (A, C, and D). A range of host genera harbored C22a, which is normally rare or absent from inshore or low latitude reefs in the GBR. Multivariate analysis showed that host identity and sea surface temperature best explained the variation in symbiont communities across sites. Patterns of changes in Symbiodinium community assemblage over small geographic distances (100s of kilometers or less) indicate the likelihood that shifts in Symbiodinium distributions and associated host populations, may occur in response to future climate change impacting the GBR.
Oral HHV‐8 replication among women in Mombasa, Kenya

Human herpesvirus‐8 (HHV‐8) replication in the oropharynx may play an important role in HHV‐8 transmission and contribute to the development of Kaposi sarcoma (KS) in some individuals. Studies in the United States and Europe report high rates of HHV‐8 DNA detection in saliva of HHV‐8 infected men, but little is known about the natural history of HHV‐8 among persons in sub‐Saharan Africa, where prevalence of HHV‐8 infection and KS is greatest. To address this gap, this study evaluated oral HHV‐8 replication in a cohort of 40 HHV‐8 seropositive Kenyan women. Study clinicians collected daily oral swabs from participants for up to 30 consecutive days, and swab samples were tested for HHV‐8 DNA using quantitative, real‐time polymerase chain reaction. HHV‐8 was detected at least once in 27 (68%) participants, and the overall shedding rate was 23%. On days with HHV‐8 detection, mean HHV‐8 quantity was 4.5 log10 copies/ml. Among HIV‐infected women, CD4 count ≥500 cells/mm3 versus <500 cells/mm3 was associated with higher HHV‐8 copy number (4.8 log10 copies/ml vs. 3.4 log10 copies/ml; coef 1.2 [95% CI, 0.5–1.9]; P = 0.001) and a higher HHV‐8 shedding rate (49% vs.12%; RR, 4.2 [95% CI, 0.8–21.4]; P = 0.08). No other factors were associated with HHV‐8 shedding rate or copy number. The study demonstrates high rates and quantity of HHV‐8 in the oropharynx of HHV‐8 seropositive African women. These findings support the observation that oral replication is an essential feature of HHV‐8 infection, with likely implications for HHV‐8 transmission and KS pathogenesis. J. Med. Virol. 86: 1759–1765, 2014. © 2014 Wiley Periodicals, Inc.
Enhanced phenylpyruvic acid production with Proteus vulgaris in fed-batch and continuous fermentation

ABSTRACT Phenylpyruvic acid is a deaminated form of phenylalanine and is used in various areas such as development of cheese and wine flavors, diagnosis of phenylketonuria, and to decrease excessive nitrogen accumulation in the manure of farm animals. However, reported phenylpyruvic acid fermentation studies in the literature have been usually performed at shake-flask scale with low production. In this study, phenylpyruvic acid production was evaluated in bench-top bioreactors by conducting fed-batch and continuous fermentation for the first time. As a result, maximum phenylpyruvic acid concentrations increased from 1350 mg/L (batch fermentation) to 2958 mg/L utilizing fed-batch fermentation. Furthermore, phenylpyruvic acid productivity was increased from 48 mg/L/hr (batch fermentation) to 104 and 259 mg/L/hr by conducting fed-batch and continuous fermentation, respectively. Overall, this study demonstrated that fed-batch and continuous fermentation significantly improved phenylpyruvic acid production in bench-scale bioreactor production.
Mammary Epithelial Cells Cultured onto Non-Woven Nanofiber Electrospun Silk-Based Biomaterials to Engineer Breast Tissue Models

xvi CHAPTER 1: INTRODUCTION 1 1.1. Abstract 1 1.2. Introduction 1 1.3. Biological Features of the Breast Tissue 5 1.3. 1. Anatomy and Structure of the Breast Tissue 5 1.3. 2. Mechanical Properties of the Breast Tissue 6 1.3. 3. Breast Development 7 1.3. 4. Cancer Development & Progression 8 1.4. Breast Tissue Modeling 9 1.4. 1. Clinical Potential and Other Uses 9 1.4. 2. 2D vs. 3D In Vitro Models 11 1.4. 3. Biomaterial Properties and Suitability for Tissue Regeneration 11 1.4. 4. Early 3D Breast Models 13 1.4. 5. Epithelial Cell Interactions with ECM Proteins 14
Number of Limit cycles of some Polynomial LiéNard Systems

In this paper, we study the number of limit cycles of some polynomial Lienard systems. Using the methods of the Melnikov functions and Hopf, homoclinic and heteroclinic bifurcation theory, we prove that H(2, 5) ≥ 4, H(6, 5) ≥ 7, H(10, 5) ≥ 11.
Variations in tropospheric submicron particle size distributions across the European continent 2008-2009

Cluster analysis of particle number size distributions from background sites across Europe is presented. This generated a total of nine clusters which could be further combined into two main groups, namely: a South to North category (four clusters) and a West to East category (five clusters). The first category was identified as most fre-quently being detected inside and around Northern Germany and neighbouring coun- tries, showing clear evidence of local afternoon nucleation and growth events that could be linked to movement of air masses from South-to-North arriving ultimately at the Arc-tic resulting in Arctic Haze. The second group of particle size spectra proved to have narrower size distributions and collectively showed a dependence of modal diame- ter upon the longitude of the site (West to East) at which they were most frequently detected. These clusters indicated regional nucleation (at the coastal sites) growing to larger modes further inland. The apparent growth rate of the modal diameter was around 1–3 nmh−1. Four specific air mass back trajectories were successively taken as case studies to examine in real time the evolution of aerosol size distributions across Europe. While aerosol growth processes can be observed as aerosol traverses Europe, the processes are often obscured by the addition of aerosol by emissions en route. This study re-vealed that some of the 24 stations exhibit more complex behaviour than others, es- pecially when impacted by local sources or a variety of di erent air masses. Overall, the aerosol size distribution clustering analysis greatly simplifies the complex dataset and allows a description of aerosol aging processes, which reflects the longer-term av-erage development of particle number size distributions as air masses advect across Europe.
The experience of seeking, gaining and maintaining employment after traumatic spinal cord injury and the vocational pathways involved.

BACKGROUND Vocational potential in people with spinal cord injury (SCI) are unrealised with rates of employment substantially lower than in the labour force participation of the general population and the pre-injury employment rates. OBJECTIVES To understand the experience and pathway of people achieving employment outcome after traumatic spinal cord injury by; classifying participants into employment outcome groups of stable, unstable and without employment; identifying pre and post-injury pathways for participants in each group and, exploring the experiences of people of seeking, gaining and maintaining employment. METHODS Thirty-one participants were interviewed. Mixed methods approach including interpretive phenomenological analysis and vocational pathway mapping of quantitative data. RESULTS The most common pathway identified was from study and work pre-injury to stable employment post-injury. Four super-ordinate themes were identified from the interpretive phenomenological analysis; expectations of work, system impacts, worker identity and social supports. Implications for clinical practice include fostering cultural change, strategies for system navigation, promotion of worker identity and optimal use of social supports. CONCLUSIONS The findings increase insight and understanding of the complex experience of employment after spinal cord injury. There is opportunity to guide experimental research, policy development and education concerning the complexity of the return to work experience and factors that influence pathways.
The effect of measurement method on static weight distribution to all legs in dogs using the Quadruped Biofeedback System

Summary An application to measure static quadruped load distribution would be highly beneficial in the assessment of rehabilitation and lameness in many small animal patients. The scope of this study was to analyze the effects of confinement, location and local environment on the measurement of static quadruped load distribution as measured by the Quadruped Biofeedback System in normal dogs in order to better prescribe the use of this system. A prospective study of 20 healthy adult dogs was performed to evaluate effects on measurement on quadruped load distribution. Data collection in the form of mean load per extremity was recorded four times in five positions for a total of 20 measurements for each limb. A replicated cross-over design in which a mixed effect, repeated measures analysis of variance was used to test for main effects of treatment and end as well as their interaction. The effects of right vs. left within each end and for each end was analyzed for each treatment and significance of p<0.01 was established. Measurements were taken from 20 healthy adult dogs with no obvious lameness at the time of data collection. Analysis by end suggests that measurements were affected in similar manners in comparable locations. Each method demonstrated consistency in measurement without any significant influence by day or session, suggesting that one standardized method be established for measurement. With standardization, the Quadruped Biofeedback System has potential use as a reliable instrument for the measurement of quadruped load distribution in dogs.
Evidencing a place for the hippocampus within the core scene processing network

Functional neuroimaging studies have identified several “core” brain regions that are preferentially activated by scene stimuli, namely posterior parahippocampal gyrus (PHG), retrosplenial cortex (RSC), and transverse occipital sulcus (TOS). The hippocampus (HC), too, is thought to play a key role in scene processing, although no study has yet investigated scene‐sensitivity in the HC relative to these other “core” regions. Here, we characterised the frequency and consistency of individual scene‐preferential responses within these regions by analysing a large dataset (n = 51) in which participants performed a one‐back working memory task for scenes, objects, and scrambled objects. An unbiased approach was adopted by applying independently‐defined anatomical ROIs to individual‐level functional data across different voxel‐wise thresholds and spatial filters. It was found that the majority of subjects had preferential scene clusters in PHG (max = 100% of participants), RSC (max = 76%), and TOS (max = 94%). A comparable number of individuals also possessed significant scene‐related clusters within their individually defined HC ROIs (max = 88%), evidencing a HC contribution to scene processing. While probabilistic overlap maps of individual clusters showed that overlap “peaks” were close to those identified in group‐level analyses (particularly for TOS and HC), inter‐individual consistency varied across regions and statistical thresholds. The inter‐regional and inter‐individual variability revealed by these analyses has implications for how scene‐sensitive cortex is localised and interrogated in functional neuroimaging studies, particularly in medial temporal lobe regions, such as the HC. Hum Brain Mapp 37:3779–3794, 2016. © 2016 Wiley Periodicals, Inc.
The complete mitochondrial genome of the invasive Ponto-Caspian goby Ponticola kessleri obtained from high-throughput sequencing using the Ion Torrent Personal Genome Machine

Abstract We report the first complete mitochondrial genome (mitogenome) of an invasive Ponto-Caspian goby, Ponticola kessleri (bighead goby, Günther 1891). Ion Torrent PGM sequencing of total DNA from two individuals yielded a contig of 16,971 bp, with overlapping ends located in the repetitive control region, which was validated using Sanger sequencing. The final mitogenome of Ponticola kessleri has a size of 16,890 bp and contains the expected gene configuration of 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. In a comparison with complete mitogenomes from other goby species, we identified a translocation of tRNA-Glu in the mitogenome of P. kessleri. Rearrangements are unique and rare events, and can thus provide phylogenetic information.
Host serum factor triggers germination of Clostridium perfringens spores lacking the cortex hydrolysis machinery.

Clostridium perfringens type A is the causative agent of a variety of histotoxic and enteric diseases. The ability of C. perfringens spores to germinate in vivo might be due to the presence of nutrient germinants in the host tissue and blood. In the current study, we investigated the ability of spores of C. perfringens wild-type and mutation strains to germinate in blood. Results indicate that spores of all three surveyed C. perfringens wild-type isolates germinated better in blood than in brain heart infusion (BHI) broth. However, as expected, spores lacking germinant receptor (GR) protein GerAA or GerKB germinated like wild-type spores in BHI broth and blood. Strikingly, while spores lacking GR proteins GerKA and GerKC showed significantly decreased germination in BHI broth, these spores germinated well in blood, suggesting that blood factor(s) can trigger spore germination through a GR-independent pathway. Using C. perfringens spores lacking cortex lytic enzymes (ΔcspB or ΔsleC ΔsleM), we were able to identify a host serum germination factor with peptidoglycan hydrolysing activity that (i) restored the colony-forming efficiencies of ΔcspB and ΔsleC ΔsleM spores up to ~5-20% of that of total colony-forming spores; (ii) increased the number of c.f. u. of decoated ΔcspB and ΔsleC ΔsleM spores to ~99% of that of colony-forming spores; (iii) and finally lost enzymic activity after heat inactivation, consistent with serum germination factor being an enzyme. Further characterization demonstrated that serum germination factor is very likely lysozyme, which can form a stable high molecular mass complex of ~120 kDa in serum. In conclusion, the current study indicates that a host serum germination factor with peptidoglycan hydrolysing activity is capable of triggering germination of C. perfringens spores by directly degrading the spore peptidoglycan cortex. Collectively, this study contributes to our understanding of the mechanism of in vivo germination of spores of C. perfringens.
Farmers’ knowledge and use of soil fauna in agriculture: a worldwide review

General knowledge of the small, invisible, or hidden organisms that make soil one of the most biodiverse habitats on Earth is thought to be scarce, despite their importance in food systems and agricultural production. We provide the first worldwide review of high-quality research that reports on farmers’ knowledge of soil organisms in agriculture. The depth of farmers’ knowledge varied; some farming communities held detailed local taxonomies and observations of soil biota, or used soil biological activity as indicators of soil fertility, while others were largely unaware of soil fauna. Elicitation of soil biota knowledge was often incidental to the main research goal in many of the reviewed studies. Farmers are rarely deliberately or deeply consulted by researchers on their existing knowledge of soil biota, soil ecology, or soil ecological processes. Deeper understanding of how farmers use and value soil life can lead to more effective development of collaborative extension programs, policies, and management initiatives directed at maintaining healthy, living soils.
Antiviral Antibodies Are Necessary To Prevent Cytotoxic T-Lymphocyte Escape in Mice Infected with a Coronavirus

ABSTRACT Mutation within virus-derived CD8 T-cell epitopes can effectively abrogate cytotoxic T-lymphocyte (CTL) recognition and impede virus clearance in infected hosts. These so-called “CTL escape variant viruses” are commonly selected during persistent infections and are associated with rapid disease progression and increased disease severity. Herein, we tested whether antiviral antibody-mediated suppression of virus replication and subsequent virus clearance were necessary for preventing CTL escape in coronavirus-infected mice. We found that compared to wild-type mice, B-cell-deficient mice did not efficiently clear infectious virus, uniformly developed clinical disease, and harbored CTL escape variant viruses. These data directly demonstrate a critical role for antiviral antibody in protecting from the selective outgrowth of CTL escape variant viruses.
Delayed Presentation of Turner Syndrome: Challenge to Optimal Management

Background: Turner syndrome (TS) is a chromosomal disorder associated with dysmorphic features and comorbidities, with recent trends focusing on early diagnosis for adequate management. Aim: The aim is to study the age and mode of presentation of TS, associated comorbidities and look for any correlation with the genotype. Material and Methods: This was a retrospective analysis of girls with TS attending the endocrinology clinic of a tertiary care center. Their age, mode of presentation, and clinical features were noted. All participants underwent ear examination, echocardiography, and ultrasonography of the abdomen. Laboratory investigations included serum T4, thyroid-stimulating hormone, thyroid peroxidase antibodies, follicle-stimulating hormone, fasting, and 2-h plasma glucose after 75 g glucose load and a karyotype. Simple descriptive statistical methods were used. Results: Seventeen cases of TS were seen with a median age of presentation of 18 years (range 14–42 years). Primary amenorrhea was the most common reason for seeking medical attention (76.4%) followed by short stature and diabetes mellitus (11.8% each). The mean height at presentation was 137.5 ± 5.4 cm. Monosomy of X chromosome (45,X) was the most common karyotype obtained in 58.8% of the patients, followed by 45,X/46, XX in 17.6%, 45,X/46X,i(X)(q10) in 11.8%, and 45,X/47,XXX and 46X,delXp11.2 in 5.9% patients each. Bicuspid aortic valve was seen in two patients having a 45,X/46,XX karyotype. Conclusion: Primary amenorrhea is the most common presenting feature in girls with TS leading to a delayed age of presentation. Short stature and dysmorphic features are often overlooked in infancy and childhood due to socioeconomic factors. This late age of presentation is a cause of concern as early detection and management is important for height outcomes, bone health, and psychosocial support. Assessment of comorbidities becomes important in this setting.
Clinical efficacy of polyspecific intravenous immunoglobulin therapy in patients with streptococcal toxic shock syndrome: a comparative observational study.

BACKGROUND Streptococcal toxic shock syndrome (STSS) and necrotizing fasciitis are the 2 most severe invasive manifestations caused by group A Streptococcus (GAS). Intravenous immunoglobulin (IVIG) therapy has been suggested as adjunctive treatment with a beneficial effect on mortality. However the clinical evidence is limited. Here we aim to further document the clinical efficacy of administered IVIG therapy in a comparative observational study of well-defined patients with STSS. METHODS The effect of IVIG was evaluated in patients with STSS prospectively identified in a nationwide Swedish surveillance study conducted between April 2002 and December 2004. Detailed data on symptoms, severity of disease, treatment, and outcome were obtained from 67 patients. Crude and adjusted analyses with logistic regression were performed. RESULTS Twenty-three patients received IVIG therapy compared with 44 who did not. No significant difference in comorbidities, severity of disease, organ failures, or sex was seen, but the IVIG group was slightly younger and had a higher degree of necrotizing fasciitis (56% vs 14%). The primary endpoint was 28-day survival. Adjusted analysis revealed that factors influencing survival in STSS were Simplified Acute Physiology Score II (odds ratio [OR], 1.1; P = .007), clindamycin (OR, 8.6; P = .007), and IVIG (OR, 5.6; P = .030). CONCLUSIONS This comparative observational study of prospectively identified STSS patients demonstrates that both IVIG and clindamycin therapy contribute to a significantly improved survival in STSS.
Is pregnancy the time to change alcohol consumption habits in France?

BACKGROUND Although it is well known that France has a cultural history of alcohol use, no recent French data on alcohol consumption during pregnancy in a large sample are available. METHODS To determine the alcohol consumption patterns among pregnant women in France, we analyzed data from a 1-year multicenter self-survey. Sociodemographic profile, obstetrical history, neonatal data, and a self-report for assessing drinking patterns during pregnancy including AUDIT were recorded from women who delivered recently. Cases of fetal alcohol syndrome (FAS) were also reported. RESULTS A total of 837 pregnant women have described all parameters. The mean age at delivery of our sample was 29.7 years (SD = 4.8 years). A total of 52.2% of women indicated that they had consumed alcohol at least once during their pregnancy, and among abstainers 54.5% had a positive AUDIT score. Of the pregnant women who consumed alcohol, 13.7% reported at least one binge drinking episode (5 or more drinks on 1 occasion) during pregnancy. Binge drinking is significantly more frequent than regular alcohol consumption (at least 1 drink more than 1 time per week) during pregnancy. A prevalence rate of FAS of 1.8 per 1,000 live births was observed. CONCLUSIONS There is a large population of women who still drink alcohol during pregnancy, particularly in binge drinking episodes. This underlines the need to clearly inform women of childbearing age about the dangers of alcohol during pregnancy as related to all types of consumption. Moreover, acting to prevent alcohol consumption prior to pregnancy may also greatly influence prenatal drinking.