Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors associated with loss to follow-up among multidrug-resistant tuberculosis patients in Georgia.

SETTING Georgia, a country with a high-burden of multi-drug-resistant tuberculosis (MDR-TB). OBJECTIVE To determine the proportion of loss to follow-up (LFU) among MDR-TB patients treated nationwide from 2009 to 2011, and associated risk factors. DESIGN Retrospective cohort study involving a review of the National Tuberculosis Programme electronic surveillance database. A Cox proportional hazards model was used to assess risk factors for time to LFU. RESULTS Among 1593 patients, 458 (29%) were lost to follow-up. A total of 1240 MDR-TB patients were included in the final analysis (845 treatment success, 395 LFU). Over 40% of LFU occurred during the first 8 months of MDR-TB treatment; 40% of patients had not achieved culture conversion at the time of LFU. In multivariate analysis, the factors associated with LFU included male sex, illicit drug use, tobacco use, history of previous anti-tuberculosis treatment, site of TB disease, and place and year of initiating treatment. CONCLUSION LFU was high among MDR-TB patients in Georgia and posed a significant public health risk, as many were culture-positive at the time of LFU. A multi-pronged approach is needed to address the various patient- and treatment-related characteristics associated with LFU.
Improved Model-Free Predictive Current Control for Synchronous Reluctance Motor Drives

An improved model-free predictive current control (IMFPCC) method for synchronous reluctance motor (SynRM) drives is presented in this paper. The main advantages of previous MFPCC are that it does not require specific SynRM models and it requires neither motor parameters nor back-EMF estimations. However, this approach has two disadvantages: 1) two current measurements are required in each sampling period, which may lead to the detection of undesirable current spikes caused by instantaneous switching inside the inverter, and 2) an unresolved problem of stagnant current-variation updates, which undermines the prediction performance. This paper intends to eliminate these two drawbacks while retaining all the merits of MFPCC. The proposed IMFPCC is simple and easy to realize. Furthermore, no pulsewidth modulation (PWM) technique is required. A 32-bit microprocessor, TMS320F2809, is utilized to implement both the proposed IMFPCC and the model-based predictive current control (MBPCC) for a performance comparison. Experiment results are provided to validate the proposed method and verify its feasibility.
Prevalence of high-risk human papillomavirus infection (HPV) and correlation with postmenopausal hormonal therapy in Thai women aged more than 45 years old.

OBJECTIVE To determine the prevalence of high-risk HPV infection and to evaluate the association between high-risk HPV infection and hormone replacement therapy in Thai women 45 years old and older. MATERIAL AND METHOD The present cross-sectional study was performed in 600 women aged 45 years old and older who attended the menopausal clinic of Phramongkutklao Hospital. There were 191 hormone users and 392 non-hormone users. The HPV DNA was studied in cellular residual from liquid-based collection tube and analyzed with a hybrid capture two techniques using a mix of high risk viral RNA probe. RESULTS The prevalence of high-risk HPV infection was 34 (5.67%) of 600 participants. When divided by status of hormone users, the prevalence of this infection in non-users, past user group, and current user group was 5.36%, 4.96%, and 10.00% respectively There was non-significantly elevated risk among past (adjusted odd ratio (OR) = 0.92, 95% confidence interval (CI) = 0.36-2.34) and current (adjusted OR = 1.96, 95% CI = 0.80-4.81) hormonal users compared to never users. However, women who currently used unopposed estrogen orally had a statistically significant higher risk of high-risk HPV detection (adjusted OR = 9.82, 95% CI = 3.02-31.89). CONCLUSION The prevalence of high-risk HPV infection in Thai women 45 years old and older was 5.67%. The oral, unopposed estrogen was associated with a higher incidence of high-risk HPV infection, but a small number of hormonal users. Further investigations are needed.
Divergent drivers of tree community composition in lowland and highland forests of the northern tropical Andes, Colombia

Identificar los determinantes de la composicion de especies arboreas entre tipos de bosques tropicales altitudinalmente contrastantes incrementaran nuestro conocimiento de los principales factores y procesos que controlan los patrones de diversidad y distribucion de las especies. El area de estudio se localiza en la region noroeste de Colombia, principalmente en el departamento de Antioquia. Se empleo el analisis de redundancia (RDA) y un modelo semi-logaritmico linealizado para analizar la influencia del clima, fertilidad del suelo, y procesos espaciales, tales como la limitacion en dispersion, sobre la composicion de la comunidad arborea. Se encontraron tres tipos de bosques: uno en tierras altas y dos en tierras bajas. En las tierras bajas, ambos modelos, el RDA y el modelo semi-logaritmico linealizado, identificaron las concentraciones de calcio como la variable que mejor explica la composicion de especies (R2 adj = 0,24; p= 0,001 y RMantel = 0,68; p = 0,006, respectivamente). En las tierras altas, el RDA solo identifico la longitud como una variable explicativa significativa (R2 adj = 0,24; p = 0,001), determinada principalmente por la ubicacion biogeografica de los bosques en la cordillera Occidental o Central de los Andes. En estos bosques neotropicales, los factores que determinan la composicion de especies de arboles entre tierras bajas y altas vario en magnitud y naturaleza. En general, nuestros resultados no apoyan la idea que existe una mayor especializacion de habitat en tierras altas que en tierras bajas debido a mayor variacion geomorfologica y edafica. Los ecosistemas tropicales andinos y en particular los bosques de tierras altas, han recibido menos atencion que sus contrapartes de tierras bajas; nuestros hallazgos ayudan a ampliar el conocimiento actual de los factores y procesos que determinan la composicion de las comunidades de los bosques montanos tropicales.
A Visualization Tool for Mining Large Correlation Tables: The Association Navigator

The Association Navigator is an interactive visualization tool for viewing large tables of correlations. The basic operation is zooming and panning of a table that is presented in graphical form, here called a “blockplot”. The tool is really a tool box that includes, among other things: (1) display of p-values and missing value patterns in addition to correlations, (2) mark-up facilities to highlight variables and sub-tables as landmarks when navigating the larger table, (3) histograms/barcharts, scatterplots and scatterplot matrices as “lenses” into the distributions of variables and variable pairs, (4) thresholding of correlations and p-values to show only strong and highly significant p-values, (5) trimming of extreme values of the variables for robustness, (6) “reference variables” that stay in sight at all times, and (7) wholesale adjustment of groups of variables for other variables. The tool has been applied to data with nearly 2,000 variables and associated tables approaching a size of 2,000×2,000. The usefulness of the tool is less in beholding gigantic tables in their entirety and more in searching for interesting association patterns by navigating manageable but numerous and interconnected sub-tables.
Signal Transduction Targeting TBK 1 Inhibits Migration and Resistance to MEK Inhibitors in Mutant NRAS Melanoma

Melanoma is a devastating form of skin cancer with limited therapeutic options. Fifteen to 20% of patients with melanoma have an activating mutation in the GTPase, NRAS. The major downstream effectors of RAS are RAFs (ARAF, BRAF, and CRAF), phosphoinositide 3-kinase (PI3K), and the Ral guanine exchange factors (RalGEF). TANK-binding kinase 1 (TBK1) is an atypical IkB kinase family member that acts downstream of RalGEFs. Whereas many studies have analyzed RAF and PI3K signaling in mutantNRASmelanoma, the role of RalGEF/Ral is understudied and TBK1 has not been examined. To address this, TBK1 was modulated with knockdown approaches and targeted therapies to determine the role of TBK1 in motility, apoptosis, and signaling. In melanoma, NRAS overexpression increased TBK1 phosphorylation. TBK1 depletion inhibited migration and invasion, whereas its constitutive overexpression led to an increase in invasion. In three-dimensional systems that mimic the dermal microenvironment, TBK1 depletion or inhibition cooperated with MEK inhibitors to promote apoptosis, particularly in the context of MEK-insensitive mutant NRAS. This effect was absent in melanoma cells that are wild-type forNRAS. These results suggest the utility of TBK1 inhibitors as part of a treatment regimen for patients with mutant NRAS melanoma, for whom there are no current effective therapies. Implications: TBK1 promotes the malignant properties of NRAS-mutant melanoma and its targeting, in combination with MEK, promotes apoptosis, thus providing a potential novel targeted therapeutic option. Mol Cancer Res; 12(10); 1509–19. 2014 AACR.
Assembly and disassembly of spliceosomes along a specific pre‐messenger RNP fiber.

Transcriptionally active Balbiani ring (BR) genes in the salivary glands of the dipteran Chironomus tentans were studied by immunoelectron microscopy to establish the distribution of spliceosome components along a specific pre‐messenger ribonucleoprotein (pre‐mRNP) fiber. The BR genes are 35‐40 kb in size with three introns close to the 5′ end and one close to the 3′ end; a very large middle portion lacks introns. As a rule the 5′ introns are spliced concomitant with transcription in the promoter proximal third of the gene, while the 3′ intron is spliced post‐transcriptionally. The BR genes with growing pre‐mRNPs were visualized in situ, while completed and released pre‐mRNPs were isolated from the nucleoplasm and studied unfolded on a grid surface. An anti‐snRNP antibody (Y12) bound mainly to the promoter proximal third of the BR gene (86%) and only to a minor extent to the middle and distal thirds (7 and 7% respectively). An antibody to an hnRNP protein reacted with the proximal, middle and distal regions to an increasing extent (17, 38 and 45% respectively), reflecting the increase in size of the growing transcription product. In the nucleoplasmic pre‐mRNP particle only one end of the RNP fiber was labeled by Y 12, presumably the 3′ end; the anti‐hnRNP antibody decorated the entire RNP fiber. Thus, the snRNPs do not associate along the whole pre‐mRNP fiber but rather bind to the 5′ and 3′ ends, i.e. the regions containing the introns. The results also imply that the spliceosomes both assemble and disassemble rapidly on the pre‐mRNP fiber.
Thalamic single‐unit and local field potential activity in Tourette syndrome

Deep brain stimulation (DBS) of the ventralis oralis (VO) complex of the thalamus improves tics in patients with Tourette syndrome (TS). To neurophysiologically describe the VO complex we recorded, in seven patients with TS undergoing DBS electrode implantation, single‐unit activity during surgery and local field potentials (LFPs) a few days after surgery. Single unit recordings showed that the VO complex is characterized by a localized pattern of bursting neuronal activity. LFP spectra demonstrated that VO of TS patients has a prominent oscillatory activity at low frequencies (2–7 Hz) and in the α‐band (8–13 Hz), and a virtually absent beta activity. In each patient, the main LFP frequency significantly correlated with single‐unit interburst frequency. In conclusion, we observed an oscillatory bursting activity in the VO as target region in patients with severe TS undergoing DBS surgery. © 2010 Movement Disorder Society
Chloroquine transport in Plasmodium falciparum. 2. Analysis of PfCRT-mediated drug transport using proteoliposomes and a fluorescent chloroquine probe.

Mutations in the PfCRT protein cause chloroquine resistance (CQR), and earlier studies from our laboratory using plasma membrane inside-out vesicles (ISOV) prepared from yeast expressing recombinant PfCRT [Zhang, H. , et al. (2004) Biochemistry 43, 8290-8296] suggested that the putative transporter mediates downhill facilitated diffusion of charged chloroquine (CQ). However, more recent experiments with a fluorescent CQ probe (NBD-CQ) presented in the accompanying paper (DOI 10.1021/bi901034r ) indicated that the CQR phenotype in live parasites is associated with a reduced rate of ATP-dependent CQ uptake into the digestive vacuole (DV). An altered rate constant for uptake has multiple interpretations. To further investigate this phenomenon, PfCRT proteins found in chloroquine-sensitive (CQS) and CQR strains of Plasmodium falciparum were purified from yeast engineered to express "yeast optimized" pfcrt genes, reconstituted into proteoliposomes (PL), and efflux of NBD-CQ was measured from these PL. A membrane-impermeant quencher was used to distinguish intra-PL NBD-CQ from extra-PL NBD-CQ vs time as well as resolve initial rates and rate constants for efflux. Efflux was investigated at a range of NBD-CQ concentrations, in the presence vs absence of pH gradients (DeltapH) and transmembrane potentials (DeltaPsi). Explicit turnover numbers for apparent PfCRT-mediated transport were then calculated under these conditions. Our data are consistent with a model wherein PfCRT catalyzes electrochemically downhill diffusion of NBD-CQ out of the DV, in response to DeltaPsi or DeltapH, at a rate that can partially compete with the ATP-dependent uptake of NBD-CQ by CQS parasites described in the previous paper. These data allow us to propose a refined model for altered CQ accumulation in CQR malarial parasites.
remote sensing Comment We Must All Pay More Attention to Rigor in Accuracy Assessment : Additional Comment to “ The Improvement of Land Cover Classification by Thermal Remote Sensing ”

Despite recent calls for statistically robust and transparent accuracy assessment [1], further attention to rigor is still needed. Here I take the opportunity of a disputed accuracy assessment recently published in Remote Sensing [2–4] to highlight some issues regarding sampling design, response design and analysis that I often find as a reviewer, and that I too have neglected in the past, among them: (i) use of a sampling design that is purposive instead of probability based; (ii) use of suboptimal label allocation procedures for reference data; and (iii) incorrect computation of accuracy estimates and lack of reporting of confidence intervals. Following the good practices in [1] will enhance the scientific credibility of our discipline.
Hybrid Search Strategies for Heterogeneous Search Spaces

Recently, there has been much interest in enhancing purely combinatorial formalisms with numerical information. For example, planning formalisms can be enriched by taking resource constraints and probabilistic information into account. The Mixed Integer Programming (MIP) paradigm from operations research provides a natural tool for solving optimization problems that combine such numeric and non-numeric information. The MIP approach relies heavily on linear program relaxations and branch-and-bound search. This is in contrast with depth-first or iterative deepening strategies generally used in artificial intelligence. We provide a detailed characterization of the structure of the underlying search spaces as explored by these search strategies. Our analysis shows that much can be gained by combining different search strategies for solving hard MIP problems, thereby leveraging each strategy's strength in terms of the combinatorial and numeric information.
Presence of Epstein–Barr virus and human herpesvirus 6B DNA in multiple sclerosis patients: associations with disease activity

Objective – To assess the presence of Epstein–Barr virus (EBV) and human herpesvirus 6B (HHV‐6B) DNA in saliva and plasma from multiple sclerosis (MS) patients enrolled in a randomized, double‐blind, placebo‐controlled valacyclovir treatment study.
EFFECTS OF cAMP ON ERK MITOGEN‐ACTIVATED PROTEIN KINASE ACTIVITY IN HEPATOCYTES DO NOT PARALLEL THE BIDIRECTIONAL REGULATION OF DNA SYNTHESIS

Previous studies have indicated that cAMP has bidirectional effects on epidermal growth factor (EGF)‐induced DNA synthesis in cultured hepatocytes, acting to stimulate soon after plating (early G1) and to inhibit at later stages (nearer the G1/S transition). In this study we examined the role of the extracellular signal‐regulated kinase (ERK) subgroup (p42/p44) of the mitogen activated protein (MAP) kinases both at growth‐stimulatory and growth‐inhibitory conditions. When added at low concentrations early during culturing, glucagon and 8‐chlorophenylthio‐cAMP (8‐CPT‐cAMP) did not increase MAP kinase activity, but enhanced the subsequent DNA synthesis. However, when administered at 24h, glucagon and 8‐CPT‐cAMP decreased basal and EGF‐induced MAP kinase activity and also inhibited EGF‐induced DNA synthesis. Thus, although MAP kinase might play a role in the growth‐inhibitory effect, it does not seem to be involved in growth‐promoting regulation by cAMP in hepatocytes.
by Carel Muller - Using farmers’ records to determine genetic parameters for fertility traits for South African Holstein cows

In South Africa little attention has been given towards the improvement of fertility in dairy cows. Cows not becoming pregnant are culled because of infertility. This could be due to environmental effects (management) or a change in the genetic make-up of cows. At present, routine analyses for fertility traits for Holstein and Jersey cows are based on calving interval (CI). A study has been conducted to determine the possibility of using farmers’ AI records to determine the fertility of dairy cows. Farmers routinely collect insemination (AI) dates and results from pregnancy diagnosis tests for herd management purposes. All artificial insemination (AI) records (n = 69 181) in 24 646 lactations of 9 046 cows calving down in 14 South African Holstein herds were used to determine alternative fertility traits. Traits included the interval from calving to first service (CFS), the interval from calving to conception (DO), services per conception (SPC) and whether first service was within 80 days after calving (FS80d), whether cows became pregnant within 100 (PD100d) or 200 days (PD200d) after calving. Traits were significantly affected by herd, calving year, calving season and lactation number. Heritability (h²) estimates for these traits varied between 0.04 and 0.08 but were in agreement with results from the literature. The genetic correlations between CFS and DO and CFS and PD100d were positive, 0.56 and 0.64 respectively. Selection for dairy cow fertility, despite being lowly heritable, would be aided by high levels of phenotypic variation. A fertility index could be derived from a combination of these traits.
The Pleasing and the Awesome: On the Beauty of Humans in the Old Testament

Profiting from the OT research programme held at the University of South Africa during August 2010, this paper further investigates different aspects of the concept of beauty in the Old Testament (OT). The use of the concept of human beauty and the beauty of human achievement is investigated in a broad variety of text types. Representative texts are examined where the concept occurs as a literary motif. It is found that human beauty, both erotic and non-erotic, as well as the metaphorical use of the concept are intertwined with descriptions of awe not only in the terminology, but also in the actual use to which it is put in texts from practically all genres. It is concluded that a coherent aesthetic is found in OT texts from different periods, which remains stable despite diverging historical and theological contexts. The contours emerging from the texts seem to square with the Kantian concept of the beautiful and Goethe’s view of the awesome. A INTRODUCTION
General aviation accidents in degraded visibility: a case control study of 72 accidents.

BACKGROUND Accidents in degraded visibility continue to account for a disproportionately large number of fatal crashes and fatalities in general aviation (GA). However, the relatively small percentage of these crashes annually suggests that even a small reduction in the number of crashes can result in a large reduction in associated fatalities. OBJECTIVE This study identified risk factors associated with GA accidents that occur in degraded visibility. METHODS Data collected during 72 National Transportation Safety Board investigations of GA accidents were compared with data collected from 135 control flights matched on weather conditions, location, time, and rules of flight. Study variables included pilot demographics, experience, testing and accident histories, and the purpose and length of flights. Initial comparisons were conducted using Chi-square analyses, followed by the development of a logistic regression model. RESULTS Univariate analyses identified significant differences in pilot age at accident, age at initial certification, certificate level, instrument rating, testing performance, and previous accident involvement. There were also significant differences between groups related to aircraft ownership, purpose of flight, and intended flight length. The logistic regression revealed significant increased risk for pilots initially certified after age 25 [odds ratio (OR) 4.5, 95% confidence interval (CI) 1.9-10.81, without instrument ratings (OR 4.8, 95% CI 1.8-12.8), with prior accidents/incidents (OR 3.1, 95% CI 1.1-8.7), and for intended flights longer than 300 nmi (OR 4.6, 95% CI 1.6-13.8). CONCLUSIONS Certain risk factors (e.g., instrument rating) were consistent with previous research, while others (e.g., age at certification) raise questions for future research.
Anesthetic Approach to High-Risk Patients and Prolonged Awake Craniotomy Using Dexmedetomidine and Scalp Block

Background: Awake craniotomy with intraoperative speech or motor testing is relatively contraindicated in cases requiring prolonged operative times and in patients with severe medical comorbidities including anxiety, anticipated difficult airway, obesity, large tumors, and intracranial hypertension. The anesthetic management of neurosurgical patients who possess these contraindications but would be optimally treated by an awake procedure remains unclear. Methods: We describe a new anesthetic approach for awake craniotomy that did not require any airway manipulation, utilizing a bupivacaine-based scalp nerve block, and dexmedetomidine as the primary hypnotic-sedative agent. Using this technique, we provided optimal operative conditions to perform awake craniotomy facilitating safe tumor resection, while utilizing intraoperative electrocorticography for motor and speech mapping in a cohort of 10 patients at a high risk for airway compromise and complications associated with patient comorbidities. Results: All patients underwent successful awake craniotomy, intraoperative mapping, and tumor resection with adequate sedation for up to 9 hours (median 3.5 h, range 3 to 9 h) without any loss of neurological function, airway competency, or the need to provide any active rescue airway management. We report 4 of these cases that highlight our experience: 1 case required prolonged surgery because of the complexity of tumor resection and 3 patients had important medical comorbidities and/or relative contraindication for an awake procedure. Conclusions: Dexmedetomidine, with concurrent scalp block, is an effective and safe anesthetic approach for awake craniotomy. Dexmedetomidine facilitates the extension procedure complexity and duration in patients who might traditionally not be considered to be candidates for this procedure.