Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of Neurospora crassa mitochondrial DNA using quantitative real‐time PCR

The filamentous fungus Neurospora crassa is a popular model organism used in a wide range of biochemical and genetic studies and vastly used in mitochondrial research. Despite the relevance of mitochondria in N. crassa biology, no method for quantification of mitochondrial DNA (mtDNA) is currently available. Quantitative real‐time PCR (qPCR) is a powerful tool, with a wide range of applications, and has been used for the quantification of nucleic acids in humans and a few other species. Here we present a new qPCR assay for relative quantification of N. crassa mtDNA. Three sets of qPCR primers targeting different regions of the mitochondrial genome were tested for mtDNA quantification. The qPCR was successfully validated in N. crassa strains from different geographical locations, representing the vast genetic diversity of this species, and knockout mutant strains. Moreover the assay proved to be efficient in templates with varied amounts of mitochondria, obtained through different DNA extraction methods. The qPCR performed well in all tested samples revealing a higher amount of mtDNA than nuclear DNA in all cases. This technique will facilitate the characterization of mtDNA of N. crassa in future studies and can be used as a tool to validate methods of mitochondria isolation.
Serum creatinine in cirrhotic patients: a cornerstone

In arecent issue of Hepatology , Cullaro et al. highlighted, in apopulation of cirrhotic patients listed for liver transplant, the associationbetween patient’ s basal serum creatinine level, including “normal rangevalues” and the occurrence of acute kidney injury (AKI), the persistent kidneyinjury after AKI, and the death/delisting risk (1). In this retrospective singlecenter study involving 385 patients, they showed thanks to a competing riskanalysis, that each 1mg/dL increase of basal serum creatinine was associatedwith a 62 % higher risk of mortality. If these results confirm the crucialprognosis impact of an impaired renal function in cirrhotic patients, they alsoencourage us to stay alert to changes in creatinine values within the normalrange. This paper leads to key reflections on creatinine role in cirrhosismanagement.
Roles of Sorcin in Drug Resistance in Cancer: One Protein, Many Mechanisms, for a Novel Potential Anticancer Drug Target

The development of drug resistance is one of the main causes of failure in anti-cancer treatments. Tumor cells adopt many strategies to counteract the action of chemotherapeutic agents, e.g., enhanced DNA damage repair, inactivation of apoptotic pathways, alteration of drug targets, drug inactivation, and overexpression of ABC (Adenosine triphosphate-binding cassette, or ATP-binding cassette) transporters. These are broad substrate-specificity ATP-dependent efflux pumps able to export toxins or drugs out of cells; for instance, ABCB1 (MDR1, or P-glycoprotein 1), overexpressed in most cancer cells, confers them multidrug resistance (MDR). The gene coding for sorcin (SOluble Resistance-related Calcium-binding proteIN) is highly conserved among mammals and is located in the same chromosomal locus and amplicon as the ABC transporters ABCB1 and ABCB4, both in human and rodent genomes (two variants of ABCB1, i.e., ABCB1a and ABCB1b, are in rodent amplicon). Sorcin was initially characterized as a soluble protein overexpressed in multidrug (MD) resistant cells and named “resistance-related” because of its co-amplification with ABCB1. Although for years sorcin overexpression was thought to be only a by-product of the co-amplification with ABC transporter genes, many papers have recently demonstrated that sorcin plays an important part in MDR, indicating a possible role of sorcin as an oncoprotein. The present review illustrates sorcin roles in the generation of MDR via many mechanisms and points to sorcin as a novel potential target of different anticancer molecules.
Why Patients Miss Their Appointments - A Survey

Introduction: Patient’s missing their appointments is a problem all dental practitioners face and which can immensely affect the productivity of their work. Patients may report with a variety of reasons to explain their tardiness and hope for immunity. This study embarked upon the aim to ascertain what reasons a patient would prioritize over a dental visit. Materials and Methods: This study focused on patients visiting the University hospital at Riyadh, Kingdom of Saudi Arabia. A total of 477 complete questionnaires were analyzed. The survey consisted of questions pertaining to reasons that influenced patients to miss their appointments. Results: Among the participants, it was seen that the most significant reasons (p<0.05) for patients to miss their appointments were; the quality of treatment rendered, duration of appointments, satisfaction with clinic personnel, ease of communication with receptionist, accuracy of SMS reminders, unavailability of babysitters, personal health status and religious obligations. Conclusions: Patients considered being treated by a dental student under the guidance of an instructor to be very relevant in their decision to miss a dental appointment. Unavailability of Childcare showed to be one among the least important reasons to miss one’s appointment. The Holy month of Ramadan or other religious obligations were not a major factor for missing appointments but mostly affected patients above the age of 36 years in the present study. Cost of treatment at the University was also not relevant to cause patients to miss their appointments. The long duration of treatment and lack of issuance of sick leave forms were considered important factors for those patients living outside Riyadh.
The effects of co-morbidities on blood transcriptomes in tuberculosis patients before and during treatment

The blood transcriptome in tuberculosis (TB) has been well described, it is distinct from healthy controls and other diseases, and is being developed as a biomarker for risk of disease progression, disease severity and treatment response. But TB patients, especially those from high TB-burden countries, often have comorbidities, so the described transcriptomic signature may not be an accurate representation of a typical population. Whether this signature remains constant in different patient phenotypes is an important question. The effect of HIV-1 and also type 2 diabetes (T2DM) on the transcriptomic profile of TB was investigated, using microarray and RNA-seq technology, respectively. Both comorbidities increase the risk of developing active TB, but the underlying mechanism in T2DM is unknown. The potentially beneficial effects of the anti-diabetes drug metformin, on the transcriptome of healthy donors, were also investigated, as existing reports indicate it could behave as an adjuvant for TB therapy. The effect on the TB blood transcriptome signature of HIV-1 coinfection was studied in collaboration with the PanACEA consortium, and T2DM (HbA1c > 6:5) and prediabetes (HbA1c > 5:7 & < 6:5) in the TANDEM consortium. It was found that the TB treatment response transcriptomic signatures could still be observed with HIV-1 coinfection. Both T2DM and pre-diabetes affected the blood transcriptome: increased in ammatory profile with down-regulated type I interferon response genes. This could be indicative of an enhanced immunopathological response in TB/DM and of the important role of type I interferons in susceptibility to TB. Because patients with pre-diabetes had similar transcriptomes to TB/DM, albeit of lower magnitude, it shows that even at intermediate levels of hyperglycaemia there is an immune dysfunction. Metformin had an anti-in ammatory effect in healthy donors in the context of M. tuberculosis stimulation, indicating its potentially beneficial role in TB/DM treatment.
Multiparametric MR-PET Imaging Predicts Pharmacokinetics and Clinical Response to GDC-0084 in Patients with Recurrent High-Grade Glioma

Purpose: GDC-0084 is an oral, brain-penetrant small-molecule inhibitor of PI3K and mTOR. Because these two targets alter tumor vascularity and metabolism, respectively, we hypothesized multiparametric MR-PET could be used to quantify the response, estimate pharmacokinetic (PK) parameters, and predict progression-free survival (PFS) in patients with recurrent malignant gliomas. Patients and Methods: Multiparametric advanced MR-PET imaging was performed to evaluate physiologic response in a first-in-man, multicenter, phase I, dose-escalation study of GDC-0084 (NCT01547546) in 47 patients with recurrent malignant glioma. Results: Measured maximum concentration (Cmax) was associated with a decrease in enhancing tumor volume (P = 0.0287) and an increase in fractional anisotropy (FA; P = 0.0418). Posttreatment tumor volume, 18F-FDG uptake, Ktrans, and relative cerebral blood volume (rCBV) were all correlated with Cmax. A linear combination of change in 18F-FDG PET uptake, apparent diffusion coefficient (ADC), FA, Ktrans, vp, and rCBV was able to estimate both Cmax (R2 = 0.4113; P < 0.0001) and drug exposure (AUC; R2 = 0.3481; P < 0.0001). Using this composite multiparametric MR-PET imaging response biomarker to predict PK, patients with an estimated Cmax > 0.1 μmol/L and AUC > 1.25 μmol/L*hour demonstrated significantly longer PFS compared with patients with a lower estimated concentration and exposure (P = 0.0039 and P = 0.0296, respectively). Conclusions: Results from this study suggest composite biomarkers created from multiparametric MR-PET imaging targeting metabolic and/or physiologic processes specific to the drug mechanism of action may be useful for subsequent evaluation of treatment efficacy for larger phase II–III studies.
Pay communication, justice, and affect: The asymmetric effects of process and outcome pay transparency on counterproductive workplace behavior.

Grounded on uncertainty management theory, the current research examines the role of employee justice perceptions in explaining the distinct effects of two forms of pay transparency-process versus outcome pay transparency-on counterproductive workplace behavior (CWB). Study 1, a field study of 321 employees, revealed that process pay transparency is inversely related to CWB targeting the organization (i.e., less CWB-O), with this effect explained by enhanced employee procedural justice perceptions. It also indicated, however, that among employees perceiving their pay position as being lower than that of referent others, outcome pay transparency is positively associated with both CWB-O and CWB-I (i.e., CWB targeting other employees), with this effect explained by reduced employee distributive justice perceptions. Study 2, using an online simulation-based experiment conducted on 394 employees and assessing actual deception behaviors (targeting both the agency sponsoring the study and other participants in the study), replicated these findings and extended our understanding of the negative consequences of outcome pay transparency on CWB. Specifically, when pay allocations were transparent (vs. secretive) and participant's pay was manipulated to be lower (vs. higher) than that of teammates, participants reported lower distributive justice perceptions leading to heightened deception behaviors, with this effect explained by a more negative emotional state. Theoretical and practical implications of both the positive and negative consequences of pay transparency on CWB are discussed. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
Poultry nutrition for economic egg and meat production: A review

Poultry industry of India, though one of the fastest growing segments of animal hushandry sector uncertainly prevails in the mind of poultry entrepreneurs because of chronic and acute problems high feeding cost. emerging and remerging diseases, vaccine failure and fluctuating market prices of meat and eggs. Economizing the cost of feeding is one of the effective tools, which can make poultry farming a sustainable enterprise. The present review highlights certain burning issues related to feeding and nutrition, their present status and scope ahead for economizing production of safe foods from poultry birds with due consideration for their welfare and environment based on latest research carried out in the country and elsewhere. Reduction of feed cost, encompassing judicious use of available feed resources, precise nutrient supply and augmenting nutrient utilization through processing, supplementation of deficient nutrients and suitable feed additives. are continuous processes. Close relation exists among nutrition, immunity and health of poultry. However, the effects are more pronounced in high producing stock. Nutrition, disease management and flock management must be considered together to ensure maximum profitability in poultry production. As the imnmunostimulation effects of various nutrients are observed at much higher levels than those actually recommended for optimum production, it is necessary to give due considerations to the economic aspects of the whole exercise.
GILT in Thymic Epithelial Cells Facilitates Central CD4 T Cell Tolerance to a Tissue-Restricted, Melanoma-Associated Self-Antigen

Key Points GILT expression in thymic APCs enhances the negative selection of CD4+ T cells. GILT facilitates MHC class II–restricted presentation by thymic APCs. GILT expression in mTECs preferentially facilitates negative selection. Central tolerance prevents autoimmunity, but also limits T cell responses to potentially immunodominant tumor epitopes with limited expression in healthy tissues. In peripheral APCs, γ-IFN–inducible lysosomal thiol reductase (GILT) is critical for MHC class II–restricted presentation of disulfide bond–containing proteins, including the self-antigen and melanoma Ag tyrosinase-related protein 1 (TRP1). The role of GILT in thymic Ag processing and generation of central tolerance has not been investigated. We found that GILT enhanced the negative selection of TRP1-specific thymocytes in mice. GILT expression was enriched in thymic APCs capable of mediating deletion, namely medullary thymic epithelial cells (mTECs) and dendritic cells, whereas TRP1 expression was restricted solely to mTECs. GILT facilitated MHC class II–restricted presentation of endogenous TRP1 by pooled thymic APCs. Using bone marrow chimeras, GILT expression in thymic epithelial cells (TECs), but not hematopoietic cells, was sufficient for complete deletion of TRP1-specific thymocytes. An increased frequency of TRP1-specific regulatory T (Treg) cells was present in chimeras with increased deletion of TRP1-specific thymocytes. Only chimeras that lacked GILT in both TECs and hematopoietic cells had a high conventional T/Treg cell ratio and were protected from melanoma challenge. Thus, GILT expression in thymic APCs, and mTECs in particular, preferentially facilitates MHC class II–restricted presentation, negative selection, and increased Treg cells, resulting in a diminished antitumor response to a tissue-restricted, melanoma-associated self-antigen.
The POU Transcription Factor POU-M2 Regulates Vitellogenin Receptor Gene Expression in the Silkworm, Bombyx mori

Vitellogenin receptors (VgRs) play critical roles in egg formation by transporting vitellogenin (Vg) into oocytes in insects. Although the function of VgR in insects is well studied, the transcriptional regulation of this gene is still unclear. Here, we cloned the promoter of the VgR gene from Bombyx mori (BmVgR), and predicted many POU cis-response elements (CREs) in its promoter. Electrophoretic mobility shift and chromatin immunoprecipitation assays showed that the POU transcription factor POU-M2 bound directly to the CREs of the promoter. Overexpression of POU-M2 in an ovarian cell line (BmNs) enhanced BmVgR transcription and promoter activity detected by quantitative reverse transcription PCR and luciferase reporter assays. Analyses of expression patterns indicated that POU-M2 was expressed in ovary at day two of wandering stage initially, followed by BmVgR. RNA interference of POU-M2 significantly reduced the transcription of BmVgR in ovary and egg-laying rate. Our results suggest a novel function for the POU factor in silkworm oogenesis by its involvement in BmVgR regulation and expands the understanding of POU factors in insect VgR expression.
Antimicrobial resistance, virulence genes and molecular subtypes of S. Enteritidis isolated from children in Shanghai.

INTRODUCTION Antimicrobial resistance of Salmonella poses a key threat to public health worldwide. Salmonella Enteritidis (S. Enteritidis) (119 isolates) from children under 10 years old with diarrhea in Shanghai from 2010-2012 were characterized for antimicrobial susceptibility, virulence gene profiles and pulsed field gel electrophoresis (PFGE) patterns. METHODOLOGY The minimum inhibitory concentration for the 119 S. Enteritidis isolates was determined using an agar dilution method. The presence of virulence genes was detected by polymerase chain reaction (PCR). All the isolates with antimicrobial resistance were subjected to PFGE analysis. RESULTS Among these isolates, 71.4% (85) were resistant to sulfafurazole, 59.7% (71) were resistant to ampicillin, 47.1% (56) were resistant to streptomycin, 7.6% (9) were resistant to ceftiofur and 3.4% (4) were resistant to ceftriaxone. Multidrug resistance (MDR) was found in 63.9% (76) of the isolates; 23 resistance profiles were identified. All isolates harbored the ssaQ and sopE virulence genes in the 16 virulence profiles (VPs); VP1 accounted for 70.59% of the 119 isolates. There were 57 PFGE patterns among the 92 isolates tested, mainly grouped into five clusters (A to E). All of the 76 MDR isolates carried multiple virulence genes. CONCLUSIONS Our study provides useful microbiological data for the successful treatment of S. Enteritidis infections in Shanghai. Although broad spectrum antimicrobials may be useful in the treatment of invasive S. Enteritidis infections, clinicians need to be aware of common microbiological traits, because of the high prevalence of MDR.
Acute effects of haemodialysis on circulating microparticles

Abstract Background Microparticles (MPs) are small cell membrane-derived vesicles regarded as both biomarkers and mediators of biological effects. Elevated levels of MPs have previously been associated with endothelial dysfunction and predict cardiovascular death in patients with end-stage renal disease. The objective of this study was to measure change in MP concentrations in contemporary haemodialysis (HD). Methods Blood was sampled from 20 consecutive HD patients before and 1 h into the HD session. MPs were measured by flow cytometry and phenotyped based on surface markers. Results Concentrations of platelet (CD41+) (P = 0.039), endothelial (CD62E+) (P = 0.004) and monocyte-derived MPs (CD14+) (P < 0.001) significantly increased during HD. Similarly, endothelial- (P = 0.007) and monocyte-derived MPs (P = 0.001) expressing tissue factor (TF) significantly increased as well as MPs expressing Klotho (P = 0.003) and receptor for advanced glycation end products (RAGE) (P = 0.009). Furthermore, MPs expressing platelet activation markers P-selectin (P = 0.009) and CD40L (P = 0.045) also significantly increased. The increase of endothelial (P = 0.034), monocyte (P = 0.014) and RAGE+ MPs (P = 0.032) as well as TF+ platelet-derived MPs (P = 0.043) was significantly higher in patients treated with low-flux compared with high-flux dialysers. Conclusion Dialysis triggers release of MPs of various origins with marked differences between high-flux and low-flux dialysers. The MPs carry surface molecules that could possibly influence coagulation, inflammation, oxidative stress and endothelial dysfunction. The clinical impact of these findings remains to be established in future studies.
KDM6A-Mediated Expression of the Long Noncoding RNA DINO Causes TP53 Tumor Suppressor Stabilization in Human Papillomavirus 16 E7-Expressing Cells

Viral oncoproteins, including HPV16 E6 and E7, have been instrumental in elucidating the activities of cellular signaling networks, including those governed by the TP53 tumor suppressor. Our study demonstrates that the long noncoding RNA DINO is the long-sought missing link between HPV16 E7 and elevated TP53 levels. Importantly, the TP53-stabilizing DINO plays a critical role in the cell death response of HPV16 E7-expressing cells to metabolic stress or DNA damage. ABSTRACT Human papillomavirus 16 (HPV16) E7 has long been known to stabilize the tumor suppressor TP53. However, the molecular mechanism of TP53 stabilization by HPV16 E7 has remained obscure, and this stabilization can occur independently of the E2F-regulated MDM2 inhibitor p14ARF. Here, we report that the damage-induced noncoding (DINO) lncRNA (DINOL) is the “missing link” between HPV16 E7 and increased TP53 levels. DINO levels are decreased in cells where TP53 is inactivated, either by HPV16 E6, by expression of a dominant negative TP53 minigene, or by TP53 depletion. DINO levels are increased in HPV16 E7-expressing cells. HPV16 E7 causes increased DINO expression independently of RB1 degradation and E2F1 activation. Similar to what is seen with the adjacent CDKN1A locus, DINO expression is regulated by the histone demethylase KDM6A. DINO stabilizes TP53 in HPV16 E7-expressing cells, and as it is a TP53 transcriptional target, DINO levels further increase. As with expression of other oncogenes, such as adenovirus E1A or MYC, HPV16 E7-expressing cells are sensitized to cell death under conditions of metabolic stress, which in the case of E7 has been linked to TP53 activation. Consistent with earlier studies, we show that HPV16 E7-expressing keratinocytes are highly sensitive to metabolic stress induced by starvation or the antidiabetic drug metformin. Sensitivity of HPV16 E7-expressing cells to metabolic stress is rescued by DINO depletion. Moreover, DINO depletion decreases sensitivity to the DNA damage-inducing chemotherapy agent doxorubicin. This work identifies DINO as a critical mediator of TP53 stabilization and activation in HPV16 E7-expressing cells. IMPORTANCE Viral oncoproteins, including HPV16 E6 and E7, have been instrumental in elucidating the activities of cellular signaling networks, including those governed by the TP53 tumor suppressor. Our study demonstrates that the long noncoding RNA DINO is the long-sought missing link between HPV16 E7 and elevated TP53 levels. Importantly, the TP53-stabilizing DINO plays a critical role in the cell death response of HPV16 E7-expressing cells to metabolic stress or DNA damage.
Exemplar models and support for older carers and carers of people with dementia: informing commissioning

In May 2017 NHS England commissioned a project to support its Commitment to Carers programme. The focus of the work was to scope exemplar models of support for older carers, and for carers of people with dementia (of any age). The work took place between May 2017 and March 2018, and included a consultation workshop in February 2018. A full report of the findings is available, but this brief summary has been prepared primarily to give feedback to the people who contributed to the project and shared their experience with us. Our conclusions and recommendations should inform the further development of NHS England’s Commitment to Carers, but more widely they also point to gaps in which new approaches might be further developed and tested, building on the experiences and exemplars discussed.