Miracle-dz/UniFAR-FTUs huggingface dataset:
Disciplining transnationality? The impact of study abroad educational experiences on Turkish returnee scholars’ lives, careers and identity

Using the literature on transnationalism, this article explores overseas-trained Turkish scholars’ experiences and whether these have had any effects on their identity construction/transformation, professional and personal lives after returning home. This exploration is informed by quantitative and qualitative data collected from Turkish scholars who completed their MA and/or PhD degrees in English-speaking countries and are now working in universities as academics. Besides highlighting the differences between educational values and practices in Turkey and Western countries, this article also examines how these differences influence professional trajectories and negotiations of identities among overseas-trained academics, with follow-up references to the author’s autoethnography as a Western-trained scholar to spotlight the commonalities in the lived experiences of returnees. The results highlight the dynamic nature of overseas experiences and returning home with new competences, skills and a broadened worldview which results in returnees’ distinguishing themselves from those around them in their personal and professional transactions.
Blood Lymphocyte Subsets for Early Identification of Non-Remission to TNF Inhibitors in Rheumatoid Arthritis

Background: TNF inhibitors (TNFis) are widely used for the treatment of rheumatoid arthritis (RA), although the response rates to this therapy in patients with RA remains heterogeneous and < 50% achieve remission (REM). Objective: To analyze baseline peripheral blood leukocytes profiles in order to search for biomarkers identifying patients who will most likely not achieve REM under TNFi treatment. Methods: A prospective bi-center pilot study including 98 RA patients treated with TNFis and followed-up during 6 months. Patients were classified according to DAS28 as follows: those who achieved REM (DAS28 ≤ 2.6) and those who did not (DAS28 > 2.6) at 6 months after starting TNFis. These rates were also assessed by simplified disease activity index (SDAI ≤ 3.3 and SDAI > 3.3, respectively). Peripheral blood immune cells were studied by flow cytometry before treatment initiation. Results: At 6 months, 61 or 80% of patients did not achieve REM by DAS28 or SDAI, respectively. Basal leukocyte profiles differed between REM vs. non-REM patients. Non-REM patients showed lower percentages of total and naïve B cells at baseline than REM subjects. A B lymphocyte/CD4+ lymphocyte ratio (BL/CD4 ratio) <0.2 clearly associated with a higher probability of non-REM status based on DAS28 at 6 months (OR = 9.2, p = 0.006). These data were confirmed when patient response was evaluated by SDAI index. Conclusion: Our results strongly suggest that BL/CD4 ratio could be considered as a useful biomarker for the early identification of non-remitters to TNFi in clinical practice.
The Proteome and Secretome of Cortical Brain Cells Infected With Herpes Simplex Virus

Infections of the brain with herpes simplex virus type 1 (HSV-1) cause life-threatening Herpes simplex encephalitis (HSE) characterized by viral replication in neurons and neuro-inflammation including an infiltration of peripheral immune cells. HSV-1 reprograms host cells to foster its own replication and for immune evasion, but eventually the immune responses clear the infection in most patients. However, many survivors suffer from long-term neuronal damage and cannot regenerate all brain functions. HSV-1 influences the physiology of neurons, astrocytes, oligodendrocytes and microglia, and significantly changes their protein expression and secretion pattern. To characterize temporal changes upon HSV-1 infection in detail, we inoculated mixed primary cultures of the murine brain cortex, and performed quantitative mass spectrometry analyses of the cell-associated proteome and the secretome. We identified 28 differentially regulated host proteins influencing inflammasome formation and intracellular vesicle trafficking during endocytosis and secretion. The NIMA-related kinase 7 (NEK7), a critical component of the inflammasome, and ArfGap1, a regulator of endocytosis, were significantly up-regulated upon HSV-1 infection. In the secretome, we identified 71 proteins including guidance cues regulating axonal regeneration, such as semaphorin6D, which were enriched in the conditioned media of HSV-1 infected cells. Modulation of inflammasome activity and intracellular membrane traffic are critical for HSV-1 cell entry, virus assembly, and intracellular spread. Our proteome analysis provides first clues on host factors that might dampen the inflammasome response and modulate intracellular vesicle transport to promote HSV infection of the brain. Furthermore, our secretome analysis revealed a set of proteins involved in neuroregeneration that might foster neuronal repair processes to restore brain functions after clearance of an HSV-1 infection.
Local Scale Thermal Environment and Limited Gene Flow Indicates Vulnerability of Warm Edge Populations in a Habitat Forming Macroalga

Species inhabiting warm-edge populations of their distribution are suggested to be at the forefront of global warming due to reduced fitness, limited gene flow and living close to their physiological thermal limits. Determining the scale that governs thermal niche and the functional responses of habitat-forming species to environmental stressors is critical for successful conservation efforts, particularly as coastal ecosystems are impacted by global change. Here, we examine the susceptibility of warm-edge populations to warming, in the habitat-forming macroalga, Hormosira banksii, from south-eastern Australia. We use a quantitative breeding design to quantify intraspecific variation in thermal performance (growth, ontogenic development and photosynthetic efficiency) of different genotypes sourced from sites at the equatorward distributional edge (warm-edge) and those toward the center of its distribution (non-edge). The genetic diversity and structure of H. banksii was also examined using microsatellite markers amongst the same sites. Our results found variable responses in thermal performance for growth and development. Warm-edge germlings grew optimally in lower temperatures tested and had narrower thermal breadth compared to non-edge germlings which grew in higher and more broader temperatures. Warm-edge germlings however, showed greater plasticity to tolerate high light indicated by a greater proportion of energy being dissipated as regulated non-photochemical quenching [Y(NPQ)] than non-regulated non-photochemical quenching [Y(NO)]. Overall genetic diversity was lower at the warm-edge location with evidence of increased structuring and reduced gene flow in comparison to the non-edge location. Evidence of genetic structuring was not found locally between high and low shore within sites. Together, these data suggest that non-edge populations may be “thermally buffered” from increased temperatures associated with ocean warming. Warm-edge populations of H. banksii, however, may be vulnerable to warming, due to narrower thermal breadth and sensitivity to higher temperatures, with genetic impoverishment through loss of individuals likely to further reduce population viability.
The Use of Marine Algae for Evaluation of Heavy Metal Pollution

The phytoplankton species Chlorella stigmatophora was used to monitor the effect of lead (as lead chloride). In order to standardise the toxicity assay, initial low concentrations of algae were used during optimal supply with nutrients, to avoid the problem of light shading. The growth rates of control algae were compared during 3–4 doubling periods with those exposed to 98-980nM lead. Since heavy metals may influence enzymic activities, e.g. of selenium-containing glutathione peroxidase by precipitating selenium as selenium selenide, the growth rate was compared with the specific glutathione peroxidase activity. Our data demonstrate that it is possible to monitor for lead toxicity (and other heavy metal toxicity) both by decrease in growth rate and by inhibition of enzymic activity. Since cultivation of unicellular algae is relatively simple, it should be possible to use such systems for ecotoxicological screening.
A revision of the genus Podaena Ordish (Insecta: Coleoptera: Hydraenidae)

The New Zealand endemic genus Podaena Ordish, 1984 is revised. Eleven species are recognized of which four are described as new, and the remainder redescribed. The new species are: Podaena aotea from Great Barrier Island, Podaena hauturu from Little Barrier Island, Podaena mariae from the west coast of the South Island, and Podaena moanaiti from Lake Waikaremoana. The most useful characters to separate species are the shape of the maxillary palps and the shape and chaetotaxy of the foretibiae in males; these characters are illustrated for all the species. Unlike most genera of Hydraenidae, male genitalia in Podaena are not diagnostic for all species. The known geographical distribution of some species is expanded, and the complete collecting data for the type series of all the species described by Ordish (1984) are given, together with distribution maps.
The Racialized and Gendered Workplace: Applying an Intersectional Lens to a Field Experiment on Hiring Discrimination in Five European Labor Markets

We draw on a field experiment conducted in five European countries to analyze hiring discrimination on the basis of gender and race. We adopt an intersectional perspective and relate existing theories on gender and racial discrimination to recent work on the gendered stereotype content of different races. We find that employers prefer hiring white women over men for female-typed jobs. By contrast, women of color do not have any advantage over men of the same race. Moreover, black and Middle Eastern men encounter the strongest racial discrimination in male-typed jobs, where it is possible that their stereotyped masculinity, made salient by the occupational context, is perceived as threatening. Overall, we argue that the employment chances of applicants of different gender and racial backgrounds are highly dependent on their perceived congruence (or lack thereof) with the feminine or masculine traits of the job they apply to.
Bruton’s Tyrosine Kinase (BTK) Inhibitor RN486 Overcomes ABCB1-Mediated Multidrug Resistance in Cancer Cells

Overexpression of ATP-binding cassette subfamily B member 1 (ABCB1) remains one of the most vital factors leading to multidrug resistance (MDR). It is important to enhance the effect and bioavailability of chemotherapeutic drugs that are substrates of ABCB1 transporter in ABCB1-overexpression cancer cells and reverse ABCB1-mediated MDR. Previous, we uncovered that the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib is a potent reversal agent to overcomes paclitaxel resistance in ABCB1-overexpressing cells and tumors. In this study, we explored whether RN486, another BTK inhibitor, was competent to surmount ABCB1-mediated MDR and promote relevant cancer chemotherapy. We found that RN486 significantly increased the efficacy of paclitaxel and doxorubicin in both drug-selected carcinoma cells and transfected cells overexpressing ABCB1. Mechanistic studies indicated that RN486 dramatically attenuated the drug efflux activity of ABCB1 transporter without altering its expression level or subcellular localization. The ATPase activity of ABCB1 transporter was not affected by low concentrations but stimulated by high concentrations of RN486. Moreover, an interaction between RN486 with ABCB1 substrate-binding and inhibitor binding sites was verified by in silico docking simulation. The results from our study suggest that RN486 could be a reversal agent and could be used in the novel combination therapy with other antineoplastic drugs to conquer MDR-mediated by ABCB1 transporter in clinics.
Assessment of Implementation of Antimicrobial Resistance Surveillance and Antimicrobial Stewardship Programs in Tanzanian Health Facilities a Year After Launch of the National Action Plan

Introduction: Antimicrobial resistance (AMR) is a current global health threat and a challenge to the treatment of infectious diseases. The WHO advocates a strategy of antibiotic stewardship programs (ASP) in optimizing antimicrobial use in hospitals. This study aimed at assessing the existence of AMR surveillance and ASP implementation in health facilities in Tanzania in the year following the launch of the National Action Plan (NAP). Methodology: From December 2017 through July 2018, a descriptive cross-sectional study was conducted using a structured questionnaire administered online. A total of 199 health facilities in Tanzania mainland whose contacts was obtained from the Ministry of Health Community Development Gender Elderly and Children (MoHCDGEC) were reached by phone and thereafter, a survey was sent via text or e-mail to focal persons in the corresponding facilities. Results: Only 39 (32.5%) responses from contacted facilities were received and analyzed. Thirty (76.9%) of the facilities were government-owned. Of the 39 respondents surveyed, 13 (35.9%) declared to have implemented some sort of coordinated ASP to promote the rational use of antimicrobials at their facilities. The respondents reported the presence of guidelines for the implementation of ASP at variable proportions, whereas the presence of a committee for Infection Prevention and Control was reported by 27 (69.2%). Twenty-four (61.5%) had a Medical and Therapeutic Committee. Although all 39 (100%) respondents were aware of the presence of AMR in Tanzania, only 26 (66.7%) were aware of the presence of the Tanzanian NAP for AMR. Hospital antibiotic policy document was present in 6 (15.4%) facilities. Only 7 (17.9%) facilities conducted prescription auditing; 9 (23.1%) had a hospital formulary; 14 (35.9%) had standard hospital prescription. 9 (23.1%) had software for data storage about AMR. Only 7 (17.9%) facilities conducted microorganisms' susceptibility tests and kept the record of the microorganism susceptibility testing. Conclusion: Our study found the existence of AMR surveillance activities and ASP implementation in Tanzania, albeit at a low level. The implementation was inconsistent across the surveyed facilities. These data have identified areas of improvement in addressing AMR in Tanzania through the NAP.
Analysis of T and B Cell Epitopes to Predict the Risk of de novo Donor-Specific Antibody (DSA) Production After Kidney Transplantation: A Two-Center Retrospective Cohort Study

Risk prediction of de novo donor specific antibody (DSA) would be very important for long term graft outcome after organ transplantation. The purpose of this study was to elucidate the association of eplet mismatches and predicted indirectly recognizable HLA epitopes (PIRCHE) scores with de novo DSA production. Our retrospective cohort study enrolled 691 living donor kidney transplantations. HLA-A, B, DRB and DQB eplet mismatches and PIRCHE scores (4 digit of HLA-A, B, DR, and DQ) were determined by HLA matchmaker (ver 2.1) and PIRCHE-II Matching Service, respectively. Weak correlation between eplet mismatches and PIRCHE scores was identified, although both measurements were associated with classical HLA mismatches. Class II (DRB+DQB) eplet mismatches were significantly correlated with the incidence of de novo class II (DR/DQ) DSA production [8/235 (3.4%) in eplet mismatch ≤ 13 vs. 92/456 (20.2%) in eplet mismatch ≥ 14, p < 0.001]. PIRCHE scores were also significantly correlated with de novo class II DSA production [26/318 (8.2%) in PIRCHE ≤ 175 vs. 74/373 (19.8%) in PIRCHE ≥ 176, p < 0.001]. Patients with low levels of both class II eplet mismatches and PIRCHE scores developed de novo class II DSA only in 4/179 (2.2%). Analysis of T cell and B cell epitopes can provide a beneficial information on the design of individualized immunosuppression regimens for prevention of de novo DSA production after kidney transplantation.
Phenotypic Variability in a Coinfection With Three Independent Candida parapsilosis Lineages

The human pathogenic yeast Candida parapsilosis has gained significant importance over the past decades as one of the principal causes of fungal bloodstream infections. Isolates of C. parapsilosis are known to be able to switch between several different colony morphologies in vitro, which are correlated with different cell shapes, altered cell surface properties, and thus different capacities to form biofilms on indwelling medical devices. In a set of six clinical specimens from a single surgery patient yielding stable smooth- as well as crepe-morphology isolates, we investigated the differences between five of them on a phenotypic and genomic level. In contrast to the initial assumption that they were switched forms of a clonal strain, karyotyping and genome sequencing showed that the patient was colonized by at least three distinct linages. Statistical analysis placed these groups distantly across the population of C. parapsilosis. Interestingly the single blood culture isolate was of smooth morphology and matched with an isolate from the patient’s nose of similar morphology. Strong variation between the isolates was seen in adhesin-encoding genes, where repeat regions showed significant variation in length and repeat-numbers, most strikingly in HWP1 of the smooth isolates. Although no differences in drug susceptibility were evident, the high phylogenetic distance separating the individual strains highlights the need for testing of multiple colonies in routine practice. The absence of biofilm formation in the blood stream isolate indicates a lack of respective adhesins in the cell wall, in turn pointing toward lack of adhesion as a positively contributing factor for dissemination.
An Update on Autophagy in Prion Diseases

Autophagy is a dynamic intracellular mechanism involved in protein and organelle turnover through lysosomal degradation. When properly regulated, autophagy supports normal cellular and developmental processes, whereas defects in autophagic degradation have been associated with several pathologies, including prion diseases. Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of fatal neurodegenerative disorders characterized by the accumulation of the pathological misfolded isoform (PrPSc) of the physiological cellular prion protein (PrPc) in the central nervous system. Autophagic vacuoles have been described in experimental models of TSE and in the natural disease in humans. The precise connection of this process with prion-related neuropathology, or even whether autophagy is completely beneficial or pathogenic during neurodegeneration, is poorly understood. Thus, the biological role of autophagy in these diseases is still open to debate. During the last years, researchers have used a wide range of morphological, genetic and biochemical methods to monitor and manipulate the autophagic pathway and thus determine the specific role of this process in TSE. It has been suggested that PrPc could play a crucial role in modulating the autophagic pathway in neuronal cells, and the presence of abnormal autophagic activity has been frequently observed in several models of TSE both in vitro and in vivo, as well as in human prion diseases. Altogether, these findings suggest that autophagy is implicated in prion neuropathology and points to an impairment or failure of the process, potentially contributing to the pathogenesis of the disease. Additionally, autophagy is now emerging as a host defense response in controlling prion infection that plays a protective role by facilitating the clearance of aggregation-prone proteins accumulated within neurons. Since autophagy is one of the pathways of PrPSc degradation, and drug-induced stimulation of autophagic flux (the dynamic process of autophagic degradation activity) produces anti-prion effects, new treatments based on its activation have been tested to develop therapeutic strategies for prion diseases. In this review, we summarize previous and recent findings concerning the role of autophagy in TSE.
Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields

Breeding for grain yield (GY) in bread wheat at the International Maize and Wheat Improvement Center (CIMMYT) involves three-stage testing at Obregon, Mexico in different selection environments (SEs). To understand the efficiency of selection in the SEs, we performed a large retrospective quantitative genetics study using CIMMYT’s yield trials evaluated in the SEs (2013–2014 to 2017–2018), the South Asia Bread Wheat Genomic Prediction Yield Trials (SABWGPYTs) evaluated in India, Pakistan, and Bangladesh (2014–2015 to 2017–2018), and the Elite Spring Wheat Yield Trials (ESWYTs) evaluated in several sites globally (2003–2004 to 2016–2017). First, we compared the narrow-sense heritabilities in the Obregon SEs and target sites and observed that the mean heritability in the SEs was 44.2 and 92.3% higher than the mean heritabilities in the SABWGPYT and ESWYT sites, respectively. Second, we observed significant genetic correlations between a SE in Obregon and all the five SABWGPYT sites and 65.1% of the ESWYT sites. Third, we observed high ratios of response to indirect selection in the SEs of Obregon with a mean of 0.80 ± 0.21 and 2.6 ± 5.4 in the SABWGPYT and ESWYT sites, respectively. Furthermore, our results also indicated that for all the SABWGPYT sites and 82% of the ESWYT sites, a response greater than 0.5 can be achieved by indirect selection for GY in Obregon. We also performed genomic prediction for GY in the target sites using the performance of the same lines in the SEs of Obregon and observed moderate mean prediction accuracies of 0.24 ± 0.08 and 0.28 ± 0.08 in the SABWGPYT and ESWYT sites, respectively using the genotype x environment (GxE) model. However, we observed similar accuracies using the baseline model with environment and line effects and no advantage of modeling GxE interactions. Overall, this study provides important insights into the suitability of the Obregon SEs in breeding for GY, while the variable genomic predictabilities of GY and the high year-to-year GY fluctuations reported, highlight the importance of multi-environment testing across time and space to stave off GxE induced uncertainties in varietal yields.