Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered Distribution of Peripheral Blood Memory B Cells in Humans Chronically Infected with Trypanosoma cruzi

Numerous abnormalities of the peripheral blood T cell compartment have been reported in human chronic Trypanosoma cruzi infection and related to prolonged antigenic stimulation by persisting parasites. Herein, we measured circulating lymphocytes of various phenotypes based on the differential expression of CD19, CD4, CD27, CD10, IgD, IgM, IgG and CD138 in a total of 48 T. cruzi-infected individuals and 24 healthy controls. Infected individuals had decreased frequencies of CD19+CD27+ cells, which positively correlated with the frequencies of CD4+CD27+ cells. The contraction of CD19+CD27+ cells was comprised of IgG+IgD-, IgM+IgD- and isotype switched IgM-IgD- memory B cells, CD19+CD10+CD27+ B cell precursors and terminally differentiated CD19+CD27+CD138+ plasma cells. Conversely, infected individuals had increased proportions of CD19+IgG+CD27-IgD- memory and CD19+IgM+CD27-IgD+ transitional/naïve B cells. These observations prompted us to assess soluble CD27, a molecule generated by the cleavage of membrane-bound CD27 and used to monitor systemic immune activation. Elevated levels of serum soluble CD27 were observed in infected individuals with Chagas cardiomyopathy, indicating its potentiality as an immunological marker for disease progression in endemic areas. In conclusion, our results demonstrate that chronic T. cruzi infection alters the distribution of various peripheral blood B cell subsets, probably related to the CD4+ T cell deregulation process provoked by the parasite in humans.
MIG-7 and phosphorylated prohibitin coordinately regulate lung cancer invasion/metastasis

Growth factors and COX-2/PGE2 enhance lung cancer invasion/metastasis via PI3K/Akt and RAS/Raf. Here, we explored their mechanism of action further. We found first that higher levels of migration inducting gene-7 protein (MIG-7) and PHB phosphorylated at threonine 258 (phospho-PHBT258) are positively correlated with advanced stages of human lung cancer in tissue microarray. PGE2 or growth factors such as EGF, HGF and IGF-1 increased complex formation of phospho-PHBT258 with Ras, phospho-AktS473, phospho-Raf-1S338, MEKK1 and IKKα/βS176/180 in the raft domain transiently within 1 hour and MIG-7 in the cytosol 12-24 hours later. Association of phospho-PHBT258 with MEKK1 but not MEKK3 activates IKK/IκB/NF-κB and MEK/ERK to increase cellular COX-2/PGE2 and an E-cadherin suppressor Snail leading to enhancement of epithelial-mesenchymal transition (EMT) and lung cancer migration/invasion. MIG-7, on the other hand, was induced by growth factors and PGE2 via Akt/GSK-3β in a phospho-PHBT258 independent manner. MIG-7 increased two E-cadherin suppressors ZEB-1 and Twist to enhance EMT and cancer migration/invasion. Downregulating phospho-PHBT258 and MIG-7 had an additive effect on attenuating lung cancer invasion/metastasis and prolonging the survival of xenograft mice. Phospho-PHBT258 and MIG-7 may thus play complementary roles in the initiation and sustainment of the effects of growth factors and COX-2/PGE2 on cancer invasion/metastasis.
Problems with the graduated frequency approach to measuring alcohol consumption: results from a pilot study in Toronto, Canada.

AIMS To evaluate advantages and disadvantages of the graduated frequency (GF) approach, which asks about the frequency of alcohol consumption at mutually exclusive quantity levels (i.e. 12 or more drinks, at least eight drinks but less than 12, etc.). METHODS Telephone survey of 464 adults aged 18 and older in Toronto, Canada, using random digit dialing and computer-assisted telephone interviewing. RESULTS Respondents reported higher frequency and volume of drinking on the GF compared to overall and beverage-specific quantity-frequency type measures; however, at least 16% of GF responses included double counting on their frequency estimates using the GF. When these cases were excluded or corrected, differences between the GF and quantity-frequency measures mostly disappeared. The GF was superior to quantity-frequency measures for identifying heavy episodic drinkers. However, the GF had little advantage over the weekly recall method except for identifying very infrequent (i.e. less often than twice a month) heavy drinkers. CONCLUSIONS Because the GF has a high rate of response errors in terms of measuring frequency of alcohol consumption, other combinations of measures, including alternate measures of heavy episodic drinking should be considered.
Transition processes for junction vortex flow

The details of the start-up transient vortex structure that forms near the junction of an impulsively started plate and a stationary plate where a step jump in velocity occurs at the plate surfaces are investigated. Numerical simulations have been conducted in a geometry representative of recent experiments of this flow. The experiments did not have access to data at very early times following the impulsive start, but they did suggest that the flow undergoes transitions from a viscous-dominated phase to an inertia-dominated phase. The numerical simulations presented here are designed to explore the early viscous-dominated transients. The simulations show that when the non-dimensional time, τ = tU2/ν (t is the time that the plate has been in motion and ν is the kinematic viscosity), is less than 100, the development process is dominated by viscous forces. In this regime similarity scaling is used to collapse the data, which scale as $\sqrt{t}$. The simulation results at low τ, when evaluated using entrainment diagrams, show an unsteady transition process consisting of the following stages. Initially, the flow consists of a non-rotating vorticity front with a single critical point for τ < 40. For 40 < τ < 50, the flow has three critical points, two nodes and a saddle. A rotational leading jet head develops for τ > 50 as the outermost node evolves into a spiral focus. The simulations span the viscous range to the inertial range. In the inertial range, for τ > 103, the flow structure scales as t5/6, as was observed in the experiments.
Recent advances in understanding and treating nephrotic syndrome

Idiopathic nephrotic syndrome (INS) is one of the most common glomerular diseases in children and adults, and the central event is podocyte injury. INS is a heterogeneous disease, and treatment is largely empirical and in many cases unsuccessful, and steroids are the initial mainstay of therapy. Close to 70% of children with INS have some response to steroids and are labelled as steroid-‘sensitive’, and the rest as steroid-‘resistant’ (also termed focal segmental glomerulosclerosis), and single-gene mutations underlie a large proportion of the latter group. The burden of morbidity is enormous, both to patients with lifelong chronic disease and to health services, particularly in managing dialysis and transplantation. The target cell of nephrotic syndrome is the glomerular podocyte, and podocyte biology research has exploded over the last 15 years. Major advances in genetic and biological understanding now put clinicians and researchers at the threshold of a major reclassification of the disease and testing of targeted therapies both identified and novel. That potential is based on complete genetic analysis, deep clinical phenotyping, and the introduction of mechanism-derived biomarkers into clinical practice. INS can now be split off into those with a single-gene defect, of which currently at least 53 genes are known to be causative, and the others. Of the others, the majority are likely to be immune-mediated and caused by the presence of a still-unknown circulating factor or factors, and whether there is a third (or more) mechanistic group or groups remains to be discovered. Treatment is therefore now being refined towards separating out the monogenic cases to minimise immunosuppression and further understanding how best to stratify and appropriately direct immunosuppressive treatments within the immune group. Therapies directed specifically towards the target cell, the podocyte, are in their infancy but hold considerable promise for the near future.
Effect of carcinogen dose on the dynamics of neoplastic development in rat tracheal epithelium.

The aim of our studies was to analyze carcinogen dose effects on the development of “carcinogen-altered” preneoplastic epithelial cell populations in rat tracheas following exposure to 7,12-dimethylbenz( a )anthracene. As described previously (Cancer Res., 39: 4003–4010, 1979), cells appear in the tracheal epithelium upon exposure to carcinogen which are distinguishable from the majority of the epithelial cells by a markedly enhanced in vitro growth capacity. In normal tracheal epithelium, most of the clonogenic cells have only a limited replicative capacity. After a limited number of population doublings, tracheal epithelial cell cultures cease to proliferate and senesce. In contrast, cultures established from carcinogenexposed epithelium contain clonogenic cells which proliferate extensively, forming expanding epithelial foci (EF) in late primary cultures. These altered clonogenic units are designated EF-forming units (EFFU). They often escape senescence permanently, thus giving rise to epithelial cell lines. Some of these become neoplastic after repeated subculturing. There are clonogenic units giving rise to subculturable progeny (EFFUs) and those giving rise to progeny which became anchorage independent (EFFUs,ag+). In the tracheal cell culture system, anchorage-independent growth is highly correlated with oncogenicity in vivo . In the present study, tracheas were exposed in vivo for 4 weeks to carcinogen doses ranging from 5 to 335 µg of 7,12′-dimethylbenz( a )anthracene. Tracheal cells were harvested by enzymatic procedures at 0, 4, 16, and 52 weeks after the end of exposure and were assayed in vitro in the epithelial focus assay (EF assay) for the frequency of different types of EFFU. Control tracheas contained less than one EFFU per 105 cells. Exposure to 7,12-dimethylbenz( a )anthracene resulted in a 100- to 500-fold increase. We were unable to detect any definitive carcinogen dose-response effect on the number of clonogenic cells forming EF or subculturable EF (EFFU or EFFUs), although there was some indication that the latter might be increasing with increasing dose. In contrast, there was a marked carcinogen dose effect on the frequency and rate of appearance of EFFUs,ag+. For example, at 16 weeks after exposure, the frequencies of EFFUs,ag+ (as the percentage of all EFFUs) were 4, 24, and 70% in the tracheas treated with 50, 162, and 335 µg of 7,12-dimethylbenz( a )anthracene, respectively. The data suggest that the carcinogen dose affects either the rate of growth of EFFUs,ag+, the cell compartment with neoplastic potential, or the conversion rate of EFFUs to EFFUs,ag+.
Does Participation in Physical Therapy Student-Run Free Clinics Relate to Altruism, Social Responsibility, and Cultural Competency Post-Graduation? A Pilot Study

Introduction: The American Physical Therapy Association Code of Ethics and Vision Statement encourage physical therapists to provide pro bono services to the economically disadvantaged, uninsured, and underinsured. Despite professional socialization during professional education, physical therapists and physical therapy students consistently indicate the need for improvement in social responsibility and altruism. The purpose of this study is to identify if participation in student-run free clinics (SRFC) as student physical therapists correlates with high values of altruism, social responsibility, and cultural competency as practicing physical therapists. Methods: An electronic survey was distributed to practicing therapists who had the opportunity to participate in SRFCs as physical therapy students. The survey consisted of 48 questions divided into six sections: SRFC involvement; value on providing pro bono services, altruism, social responsibility, cultural competency; demographics. Results: Eighty-five practicing physical therapists completed the survey. A significant correlation was found between hours volunteered in a SRFC and valuing altruism (rs=0.32, p=0.003) and hours volunteered and valuing providing pro bono services (rs=0.56, p<0.001). A significant correlation was also found between holding a leadership position in a SRFC and valuing providing pro bono services (rs=0.45, p<0.001). Of those who previously volunteered, 86.3% (n=63) indicated that they never to occasionally provide pro bono services in their current practice. In addition, 52.1% (n=38) indicated that they never to occasionally provide physical therapy services to underserved and underrepresented populations in their current practice. Conclusion: Practicing physical therapists are lacking demonstration of social responsibility and altruism despite participation in SRFCs as physical therapy students.
Natural Actions, Concurrency and Continuous Time in the Situation Calculus

Our focus in this paper is on natural exoge-nous actions (Pinto 23]), namely those which occur in response to known laws of physics, like a ball bouncing at times determined by Newtonian equations of motion. The property of such actions that we wish to capture is that they must occur at their predicted times, provided no earlier actions (natural or agent initiated) prevent them from occurring. Because several such actions may occur simultaneously, we need a theory of concur-rency. Because such actions may be modeled by equations of motion, we need to represent continuous time. This paper shows how to gracefully accommodate all these features within the situation calculus, without sacri-cing the simple solution to the frame problem of Reiter 25]. One nice consequence of this approach is a situation calculus speci-cation of deductive planning, with continuous time and true concurrency, and where the agent can incorporate external natural event occurrences into her plans.
Can Vascular Endothelial Growth Factor and Microvessel Density Be Used as Prognostic Biomarkers for Colorectal Cancer? A Systematic Review and Meta-Analysis

Background. Vascular endothelial growth factor (VEGF) and microvessel density (MVD) are associated with greater incidence of metastases and decreased survival. Whether they can be used as prognostic indicators of colorectal cancer (CRC) is still controversial. Methods. The authors performed a meta-analysis using the results of a literature search of databases of PubMed and EMBASE, and the references of articles included in the analysis. Meta-analysis was performed using random effects model and hazard ratios (HRs) and 95% confidence intervals (CIs) as effect measures. Results. Twenty studies contributed to the analysis of VEGF, of which 16 were used for overall survival (OS) and 9 for disease-free survival (DFS). High VEGF levels has a relationship with unfavorable survival (OS: HR = 1.98, 95% CI: 1.30–3.02; DFS: HR = 2.10, 95% CI: 1.26–3.49) and a 4.22-fold increase in the rate of distant metastases. Analysis was performed on 18 studies for MVD; the results showed that patients with high MVD expression in tumors appeared to have poorer overall survival (HR = 1.39, 95% CI: 1.22–1.58) and were at a greater risk of having unfavorable clinical characteristics related to prognosis. Corresponding results were obtained from quantitative and/or qualitative analysis of clinicopathological. Conclusions. The meta-analysis demonstrates that VEGF and MVD can be used as prognostic biomarkers for CRC patients.
Questionable Research Practices, Preregistration, and More – Exploring Self-Report Opinions of Swedish and Dutch PhD Students

For this exploratory study, I reached out to all 302 individuals that were listed as PhD students at the psychology departments of all Swedish and Dutch “Top 100” universities. The final 111 participants (37.9% response rate) were asked to indicate how often they encountered questionable research practices (QRPs) and replied to items asking about the impact of QRPs on themselves and their environment, thoughts of leaving academia, implications of the “replication crisis”, and knowledge and use of preregistrations. The results indicated that QRPs were common, but that the type of QRP mattered. While only 3.7% of participants considered leaving academia because of fear of “replication bullies”, 23.9% considered leaving academia because they were disillusioned by the problems revealed by the replication crisis. Results also indicated that the more QRPs a student encountered, the higher the chance that they had thought of leaving because of being disillusioned. Preregistration was widely known, but the majority had never preregistered a project. The study provides first insights in the situation of PhD students in Sweden and the Netherlands and can serve as a foundation for confirmatory research in the future. (Less)
The Composition of International Capital Flows: Risk Sharing Through Foreign Direct Investment

Evidence on international capital flows suggests that foreign direct investment (FDI) is less volatile than other financial flows. To explain this finding, I model international capital flows under the assumptions of imperfect enforcement of financial contracts and inalienability of FDI. Imperfect enforcement of contracts leads to endogenous financing constraints and the pricing of default risk. Inalienability implies that it is not as advantageous to expropriate FDI relative to other flows. These features combine to give a risk sharing advantage to FDI over other capital flows. This risk sharing advantage of FDI translates into a lower default premium and lower sensitivity to changes in a country's financing constraint. The model offers the new implication that financially constrained countries should borrow relatively more through FDI. This is because FDI is harder to expropriate and not because FDI is more productive or less volatile. Using several creditworthiness and country risk ratings to measure financing constraints, I present new evidence linking FDI and financing constraints. Moreover, numerical simulations of the model generate stronger serial correlation for FDI than for other flows into developing countries. This corroborates the view that non-FDI flows are more short-term and more likely to change direction.
Evaluating the association between endometrial cancer and polycystic ovary syndrome.

BACKGROUND Given the current lack of clarity in the published literature, we performed a systematic review of the literature to determine the exact strength of the association between polycystic ovary syndrome (PCOS) and endometrial cancer (EC). METHODS All published studies on the association between PCOS and EC identified through MEDLINE (1966-April 2011), EMBASE (1980-April 2011) and Cochrane (1998-April 2011). Original data were abstracted where available and summarized on a separate Microsoft Excel (2007) database for analysis. A total of 14 studies comparative and non-comparative were identified and included. RESULTS The non-comparative and comparative data suggested that women with PCOS were more likely to develop EC. A meta-analyses of five comparative studies showed an increased risk of EC in women with an odds ratio of 2.89 with a 95% confidence interval of 1.52-5.48. CONCLUSIONS Women with PCOS are about three times more likely to develop EC compared with women without it. This translates into a 9% lifetime risk of EC in Caucasian women with PCOS compared with 3% in women without it. Although most women (91%) with PCOS will not develop endometrial cancer, our study has shown that they are more likely at increased risk. More studies are required to clarify the exact molecular mechanisms, determine the best way of screening and preventing disease progression.
Correlation between nitrogen fixation rate and alginate productivity of an indigenous Azotobacter vinelandii from Iran

Background and Objectives Azotobacter vinelandii, a gamma-proteobacterium, is an obligate aerobic free-living gram-negative soil bacterium capable of fixing nitrogen. Oxygen transfer rate into the cell is reduced by the increase of alginate concentrations during the course of A. vinelandii cultivation. This phenomenon provides a low intracellular oxygen concentration needed for nitrogenase activity. The aim of this study was to design a simple strategy to explain the alginate production, cell growth and nitrogenase activity correlation in A. vinelandii under aerobic conditions. Material and Methods Thirty-five different soil samples were taken from the rhizosphere of agricultural crops of Iran. Enrichment and isolation strategies were employed for microbial isolation. Physiological and biochemical characteristics were determined. Molecular identification was performed using selective nifH-g1 primers. Alginate production and nitrogenase activity assay by each isolate of Azotobacter were carried out. Bacterial growth, alginate production and Nitrogenase activity were conducted by time-coursed quantitative measurements. Results Total of 26 isolates were selected after enrichment, isolation, and screening. The isolate was identified by molecular tests as A. vinelandii. The highest alginate productions of 1.02 g/l and 0.91g/l were noted after 4 days in 8 isolates, cell biomass of which were estimated 4.88-5.26 g/l. Six of 8 isolates were able to fix atmospheric N2 on nitrogen-free medium. Rates obtained in isolates were in the range of 12.1 to 326.4 nmol C2H4 h-1 vial-1. Conclusions Nitrogen fixation and alginate production yielded significant and positive Pearson's correlation coefficient of R2 = 0.760, p ∼ 0.02. Finally association between bacterial growth, alginate production and nitrogenase activity almost noticeable yielded significant and positive Pearson's correlation coefficient R2= 0.723, p ∼ 0.04.
Culture Change in Skilled Nursing: An Exploratory Comparison of a Traditional Home to a New Model

Abstract The culture change movement has pushed for reform for more than two decades to align policy, the long-term care industry, and resident preferences with regard to care. Evidence from research indicates that culture change has the potential to improve quality in nursing homes. There is no one-size-fits-all way to implement culture change; however, there are key elements and associated concepts and models. A common thread is that they run counter to the medical model, typically found in nursing homes, where care is provided in a hospital-like setting according to the schedules and routines of physicians and staff with little resident input. This qualitative study looks for evidence of culture change in a traditional model of care compared to a newer culture change model, by describing the differences in practices associated with the medical model, person-centered care, and person-directed care between the two settings. Our results indicate that there is evidence of person-directed care in one model of culture change—the Green House home—but not in the traditional nursing home. Future studies should examine other culture change models to compare the differences in the utilization of person-directed care. This information will help to clarify the definitions and concepts of culture change, along with developing best practices for future culture change models.