Miracle-dz/UniFAR-FTUs huggingface dataset:
Seroprevalence and Risk Factors for Coxiella burnetii (Q Fever) Seropositivity in Dairy Goat Farmers' Households in The Netherlands, 2009–2010

Community Q fever epidemics occurred in the Netherlands in 2007–2009, with dairy goat and dairy sheep farms as the implicated source. The aim of the study was to determine the seroprevalence and risk factors for seropositivity in dairy goat farmers and their household members living or working on these farms. Sera of 268 people living or working on 111 dairy goat farms were tested for Coxiella burnetii IgG and IgM antibodies using immunofluorescence assay. Seroprevalences in farmers, spouses and children (12–17 years) were 73.5%, 66.7%, and 57.1%, respectively. Risk factors for seropositivity were: performing three or more daily goat-related tasks, farm location in the two southern provinces of the country, proximity to bulk milk-positive farms, distance from the nearest stable to residence of 10 meters or less, presence of cats and multiple goat breeds in the stable, covering stable air spaces and staff not wearing farm boots. Goat farmers have a high risk to acquire this occupational infection. Clinicians should consider Q fever in this population presenting with compatible symptoms to allow timely diagnosis and treatment to prevent severe sequelae. Based on the risk factors identified, strengthening general biosecurity measures is recommended such as consistently wearing boots and protective clothing by farm staff to avoid indirect transmission and avoiding access of companion animals in the goat stable. Furthermore, it provides an evidence base for continuation of the current vaccination policy for small ruminants, preventing spread from contaminated farms to other farms in the vicinity. Finally, vaccination of seronegative farmers and household members could be considered.
The Study of External Dose Rate and Retained Body Activity of Patients Receiving 131I Therapy for Differentiated Thyroid Carcinoma

Radiation safety is an integral part of targeted radionuclide therapy. The aim of this work was to study the external dose rate and retained body activity as functions of time in differentiated thyroid carcinoma patients receiving 131I therapy. Seventy patients were stratified into two groups: the ablation group (A) and the follow-up group (FU). The patients’ external dose rate was measured, and simultaneously, their retained body radiation activity was monitored at various time points. The equations of the external dose rate and the retained body activity, described as a function of hours post administration, were fitted. Additionally, the release time for patients was calculated. The reduction in activity in the group receiving a second or subsequent treatment was more rapid than the group receiving only the initial treatment. Most important, an expeditious method was established to indirectly evaluate the retained body activity of patients by measuring the external dose rate with a portable radiation survey meter. By this method, the calculated external dose rate limits are 19.2, 8.85, 5.08 and 2.32 μSv·h−1 at 1, 1.5, 2 and 3 m, respectively, according to a patient’s released threshold level of retained body activity <400 MBq. This study is beneficial for radiation safety decision-making.
Transcriptome-Wide RNA Interaction Profiling Reveals Physical and Functional Targets of hnRNP L in Human T Cells

ABSTRACT The RNA processing factor hnRNP L is required for T cell development and function. However, the spectrum of direct targets of hnRNP L activity in T cells has yet to be defined. In this study, we used cross-linking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq) to identify the RNA binding sites of hnRNP L within the transcriptomes of human CD4+ and cultured Jurkat T cells. We find that hnRNP L binds preferentially to transcripts encoding proteins involved in RNA processing and in Wnt and T cell receptor (TCR) signaling. This binding is largely conserved across both quiescent and activated T cells, in agreement with the critical role of hnRNP L throughout T cell biology. Importantly, based on the binding profile of hnRNP L, we validate numerous instances of hnRNP L-dependent alternative splicing of genes critical to T cell function. We further show that alternative exons with weak 5′ splice site sequences specifically show a strong correlation between hnRNP L binding and hnRNP L-dependent splicing regulation. Together, these data provide the first transcriptome-wide analysis of the RNA targets of hnRNP L in lymphoid cells and add to the functional understanding of hnRNP L in human biology.
Using electronic health record clinical decision support is associated with improved quality of care.

OBJECTIVES To determine whether clinical decision support (CDS) is associated with improved quality indicators and whether disabling CDS negatively affects these. STUDY DESIGN/METHODS Using the 2006-2009 National Ambulatory and National Hospital Ambulatory Medical Care Surveys, we performed logistic regression to analyze adult primary care visits for the association between the use of CDS (problem lists, preventive care reminders, lab results, lab range notifications, and drug-drug interaction warnings) and quality measures (blood pressure control, cancer screening, health education, influenza vaccination, and visits related to adverse drug events). RESULTS There were an estimated 900 million outpatient primary care visits to clinics with EHRs from 2006-2009; 97% involved CDS, 77% were missing at least 1 CDS, and 15% had at least 1 CDS disabled. The presence of CDS was associated with improved blood pressure control (86% vs 82%; OR 1.3; 95% CI, 1.1-1.5) and more visits not related to adverse drug events (99.9% vs 99.8%; OR 3.0; 95% CI, 1.3-7.3); these associations were also present when comparing practices with CDS against practices that had disabled CDS. Electronic problem lists were associated with increased odds of having a visit with controlled blood pressure (86% vs 80%; OR 1.4; 95% CI, 1.3-1.6). Lab result notification was associated with increased odds of ordering cancer screening (15% vs 10%; OR 1.5; 95% CI, 1.03-2.2). CONCLUSIONS The use of CDS was associated with improvement in some quality indicators. Not having at least 1 CDS was common; disabling CDS was infrequent. This suggests that meaningful use standards may improve national quality indicators and health outcomes, once fully implemented.
Productive Entry of HIV-1 during Cell-to-Cell Transmission via Dynamin-Dependent Endocytosis

ABSTRACT HIV-1 can be transmitted as cell-free virus or via cell-to-cell contacts. Cell-to-cell transmission between CD4+ T cells is the more efficient mode of transmission and is predominant in lymphoid tissue, where the majority of virus resides. Yet the cellular mechanisms underlying productive cell-to-cell transmission in uninfected target cells are unclear. Although it has been demonstrated that target cells can take up virus via endocytosis, definitive links between this process and productive infection remain undefined, and this route of transmission has been proposed to be nonproductive. Here, we report that productive cell-to-cell transmission can occur via endocytosis in a dynamin-dependent manner and is sensitive to clathrin-associated antagonists. These data were obtained in a number of CD4+ T-cell lines and in primary CD4+ T cells, using both CXCR4- and CCR5-tropic virus. However, we also found that HIV-1 demonstrated flexibility in its use of such endocytic pathways as certain allogeneic transmissions were seen to occur in a dynamin-dependent manner but were insensitive to clathrin-associated antagonists. Also, depleting cells of the clathrin accessory protein AP180 led to a viral uptake defect associated with enhanced infection. Collectively, these data demonstrate that endosomal uptake of HIV-1 during cell-to-cell transmission leads to productive infection, but they are also indicative of a flexible model of viral entry during cell-to-cell transmission, in which the virus can alter its entry route according to the pressures that it encounters.
Activation of Liver X Receptor Decreases Atherosclerosis in Ldlr−/− Mice in the Absence of ATP-Binding Cassette Transporters A1 and G1 in Myeloid Cells

Objective—Liver X receptor (LXR) activators decrease atherosclerosis in mice. LXR activators (1) directly upregulate genes involved in reverse cholesterol transport and (2) exert anti-inflammatory effects mediated by transrepression of nuclear factor-&kgr;B target genes. We investigated whether myeloid cell deficiency of ATP-binding cassette transporters A1 and G1 (ABCA1/G1), principal targets of LXR that promote macrophage cholesterol efflux and initiate reverse cholesterol transport, would abolish the beneficial effects of LXR activation on atherosclerosis. Approach and Results—LXR activator T0901317 substantially reduced inflammatory gene expression in macrophages lacking ABCA1/G1. Ldlr−/− mice were transplanted with Abca1−/−Abcg1−/− or wild-type bone marrow (BM) and fed a Western-type diet for 6 weeks with or without T0901317 supplementation. Abca1/g1 BM deficiency increased atherosclerotic lesion complexity and inflammatory cell infiltration into the adventitia and myocardium. T0901317 markedly decreased lesion area, complexity, and inflammatory cell infiltration in the Abca1−/−Abcg1−/− BM–transplanted mice. To investigate whether this was because of macrophage Abca1/g1 deficiency, Ldlr−/− mice were transplanted with LysmCreAbca1fl/flAbcg1fl/fl or Abca1fl/flAbcg1fl/fl BM and fed Western-type diet with or without the more specific LXR agonist GW3965 for 12 weeks. GW3965 decreased lesion size in both groups, and the decrease was more prominent in the LysmCreAbca1fl/flAbcg1fl/fl group. Conclusions—The results suggest that anti-inflammatory effects of LXR activators are of key importance to their antiatherosclerotic effects in vivo independent of cholesterol efflux pathways mediated by macrophage ABCA1/G1. This has implications for the development of LXR activators that lack adverse effects on lipogenic genes while maintaining the ability to transrepress inflammatory genes.
Topological relics of symmetry breaking: winding numbers and scaling tilts from random vortex–antivortex pairs

I show that random distributions of vortex–antivortex pairs (rather than of individual vortices) lead to scaling of typical winding numbers 𝒲 trapped inside a loop of circumference 𝒞 with the square root of that circumference, W ∼ C ? > , when the expected winding numbers are large, |𝒲| ≫ 1. Such scaling is consistent with the Kibble–Zurek mechanism (KZM), with 〈𝒲2〉 inversely proportional to ξ ˆ ? > , the typical size of the domain that can break symmetry in unison. (The dependence of ξ ˆ ? > on quench rate is predicted by KZM from critical exponents of the phase transition.) Thus, according to KZM, the dispersion ⟨ W 2 ⟩ ? > scales as C / ξ ˆ ? > for large 𝒲. By contrast, a distribution of individual vortices with randomly assigned topological charges would result in the dispersion scaling with the square root of the area inside 𝒞 (i.e., ⟨ W 2 ⟩ ∼ C? > ). Scaling of the dispersion of 𝒲 as well as of the probability of detection of non-zero 𝒲 with 𝒞 and ξ ˆ ? > can be also studied for loops so small that non-zero windings are rare. In this case I show that dispersion varies not as 1 / ξ ˆ ? > , but as 1 / ξ ˆ ? > , which results in a doubling of the scaling of dispersion with the quench rate when compared to the large |𝒲| regime. Moreover, the probability of trapping of non-zero 𝒲 becomes approximately equal to 〈𝒲2〉, and scales as 1 / ξ ˆ 2 ? > . This quadruples—as compared with ⟨ W 2 ⟩ ≃ C / ξ ˆ ? > valid for large 𝒲—the exponent in the power law dependence of the frequency of trapping of |𝒲| = 1 on ξ ˆ ? > when the probability of |𝒲| > 1 is negligible. This change of the power law exponent by a factor of four—from 1 / ξ ˆ ? > for the dispersion of large 𝒲 to 1 / ξ ˆ 2 ? > for the frequency of non-zero 𝒲 when |𝒲| > 1 is negligibly rare—is of paramount importance for experimental tests of KZM.
An Application of Bayesian Approach in Modeling Risk of Death in an Intensive Care Unit

Background and Objectives There are not many studies that attempt to model intensive care unit (ICU) risk of death in developing countries, especially in South East Asia. The aim of this study was to propose and describe application of a Bayesian approach in modeling in-ICU deaths in a Malaysian ICU. Methods This was a prospective study in a mixed medical-surgery ICU in a multidisciplinary tertiary referral hospital in Malaysia. Data collection included variables that were defined in Acute Physiology and Chronic Health Evaluation IV (APACHE IV) model. Bayesian Markov Chain Monte Carlo (MCMC) simulation approach was applied in the development of four multivariate logistic regression predictive models for the ICU, where the main outcome measure was in-ICU mortality risk. The performance of the models were assessed through overall model fit, discrimination and calibration measures. Results from the Bayesian models were also compared against results obtained using frequentist maximum likelihood method. Results The study involved 1,286 consecutive ICU admissions between January 1, 2009 and June 30, 2010, of which 1,111 met the inclusion criteria. Patients who were admitted to the ICU were generally younger, predominantly male, with low co-morbidity load and mostly under mechanical ventilation. The overall in-ICU mortality rate was 18.5% and the overall mean Acute Physiology Score (APS) was 68.5. All four models exhibited good discrimination, with area under receiver operating characteristic curve (AUC) values approximately 0.8. Calibration was acceptable (Hosmer-Lemeshow p-values > 0.05) for all models, except for model M3. Model M1 was identified as the model with the best overall performance in this study. Conclusion Four prediction models were proposed, where the best model was chosen based on its overall performance in this study. This study has also demonstrated the promising potential of the Bayesian MCMC approach as an alternative in the analysis and modeling of in-ICU mortality outcomes.
Using Automatic Process Clustering for Design Recovery and Distributed Debugging

Distributed applications written in Hermes typically consist of a large number of sequential processes. The use of a hierarchy of process clusters can facilitate the debugging of such applications. Ideally, such a hierarchy should be derived automatically. This paper discusses two approaches to automatic process clustering, one analyzing runtime information with a statistical approach and one utilizing additional semantic information. Tools realizing these approaches were developed and a quantitative measure to evaluate process clusters is proposed. The results obtained under both approaches are compared, and indicate that the additional semantic information improves the cluster hierarchies derived. We demonstrate the value of automatic process clustering with an example. It is shown how appropriate process clusters reduce the complexity of the understanding process, facilitating program maintenance activities such as debugging. >
Tumor-associated and immunochemotherapy-dependent long-term alterations of the peripheral blood NK cell compartment in DLBCL patients

Natural Killer (NK) cells are a key component of tumor immunosurveillance and thus play an important role in rituximab-dependent killing of lymphoma cells via an antibody-dependent cellular cytotoxicity (ADCC) mechanism. We evaluated the phenotypic and functional assets of peripheral blood NK cell subsets in 32 newly-diagnosed diffuse large B-cell lymphoma (DLBCL) patients and in 27 healthy controls. We further monitored long-term modifications of patient NK cells for up to 12 months after rituximab-based immunochemotherapy. At diagnosis, patients showed a higher percentage of CD56dim and CD16+ NK cells, and a higher frequency of GrzB+ cells in CD56dim, CD56bright, and CD16+ NK cell subsets than healthy controls. Conversely, DLBCL NK cell killing and interferon γ (IFNγ) production capability were comparable to those derived from healthy subjects. Notably, NK cells from refractory/relapsed patients exhibited a lower “natural” cytotoxicity. A marked and prolonged therapy-induced reduction of both “natural” and CD16-dependent NK cytotoxic activities was accompanied by the down-modulation of CD16 and NKG2D activating receptors, particularly in the CD56dim subset. However, reduced NK cell killing was not associated with defective lytic granule content or IFNγ production capability. This study firstly describes tumor-associated and therapy-induced alterations of the systemic NK cell compartment in DLBCL patients. As these alterations may negatively impact rituximab-based therapy efficacy, our work may provide useful information for improving immunochemotherapeutic strategies.
Simplified quantitative methods for bacteriuria and pyuria

Although pyelonephritis is a common disease, it escapes clinical detection in an undesirably high proportion of patients. The present unsatisfactory diagnostic position would be much improved by widespread screening of patients by simple yet reasonably accurate methods. Bacterial counts by the pour-plate technique and estimates of the white cell excretion per hour or day, while undoubtedly of diagnostic value, are probably unsuitable for use on a wide scale. In an attempt to find more convenient procedures a simplified stroke-plate method of bacterial counting and a simplified quantitative white cell count method were devised and applied to over 1,000 mid-stream urine samples from 398 patients. Good correlation was obtained between the simpler stroke-plate method of bacterial counting and the more time-consuming pour-plate method. The quantitative white cell procedure was a much more sensitive index of pyuria than wet-film microscopy, and comparison with the bacterial count results showed that it gave a useful indication of urinary infection. It is suggested that a quantitative bacterial count should replace non-quantitative culture methods when urinary infection is suspected and that the quantitative white cell count should be performed as a routine part of the initial clinical and laboratory assessment of all patients, followed by a bacterial count if pyuria is revealed. Experience has shown that routine urine microscopy by a precise method leads to the detection of many cases of occult urinary infection.
Propagation and Root Zone Management for Controlled Environment Cannabis Production

PROPAGATION AND ROOT ZONE MANAGEMENT FOR CONTROLLED ENVIRONMENT CANNABIS PRODUCTION Deron Caplan University of Guelph, 2018 Advisors: Dr. Youbin Zheng Dr. Mike Dixon Cannabis producers lack reliable information on the horticultural management of their crops. This thesis research was designed to improve horticultural practices for controlled environment cannabis production; topics included propagation, growing substrates, fertilization, and irrigation. To optimize the procedures for taking vegetative stem cuttings in cannabis, several factors were evaluated on how they affect rooting success and quality (Chapter Two). These included number of leaves, leaf tip removal, basal/apical position of cutting on the stock plant, and type of rooting hormone. Removing leaf tips reduced rooting success and cuttings with three fully-expanded leaves had higher rooting success and quality than those with two. Also, a 0.2% indole-3-butyric gel was more effective than a 0.2% willow extract gel to stimulate rooting and cutting position had no effect on rooting. Coir-based substrates with different physical properties were evaluated during the vegetative and flowering stage of cannabis production; optimal organic fertilizer rates were established for each substrate (Chapters Three and Four). During the vegetative stage, cannabis performed well in both tested substrates despite the ≈11% difference in container capacity (CC) between them. During the flowering stage, the substrate with lower CC increased floral dry weight (yield) and the concentration and/or yield of some cannabinoids, including THC, compared to the substrate with higher CC. The optimal organic fertilizer rate varied by substrate during the flowering stage but not during the vegetative stage; higher fertilizer rate during the flowering stage increased growth and yield but diluted some cannabinoids. Finally, the effects of controlled drought stress timing and frequency during the flowering stage were explored on floral dry weight and secondary metabolism (Chapters Five and Six). When drought was applied during week seven of the flowering stage, through gradual substrate drying over eleven days, floral concentration and content per unit growing area of major cannabinoids were increased. When drought was applied over a period of ≈8 days during week seven, cannabinoid content was similar to a well-watered control; though, dependent on drought timing, the content of some terpenoids varied. This research provided evidence-based information that can help growers improve the quality and yield of their cannabis crops.
The effects of anxiety and strategic planning on visual search behaviour

The past decade has witnessed increased interest in the visual search behaviour of athletes. Little is known, however, about the relationship between anxiety and eye movements in sport performers or about the extent to which athletes' planned and actual visual search strategies correspond. To address these issues, we conducted two studies. In Study 1, eight expert female gymnasts were presented with three digital slides of a model performing a skill that is known to be anxiety-provoking in this sport - namely, the 'back flip' on the beam. By varying the height of the beam and the presence or absence of safety mats, the slides differed in the amount of anxiety that they elicited vicariously in the viewer. In the study, the gymnasts were asked to imagine themselves in the position of the depicted model and to describe the anxiety that they felt. As they viewed the slides, their eye movements were recorded. As predicted, anxiety was associated with an increase in the number of fixations to peripheral areas. In addition, the more 'threatening' slides elicited significantly more fixations than the less feared images. In Study 2, the plans of 15 equestrian performers (5 expert, 5 intermediate and 5 novice) were elicited as they engaged in a virtual 'walk' around a computerized show-jumping course. Contrary to expectations, the congruence between intended and actual search behaviour was not significantly greater for expert riders than for the less skilled groups. Also, the fact that the top riders allocated more fixations to slides than the less skilled performers challenged the prediction that expertise would be associated with economy of visual search. Finally, as expected, the expert riders were significantly less dependent on the overall 'course plan' than the intermediate and novice equestrian performers when inspecting the fences.