Miracle-dz/UniFAR-FTUs huggingface dataset:
Human pulmonary infections with bovine and environment (atypical) mycobacteria in jos, Nigeria.

SUMMARY OBJECTIVES To examine sputum specimens from patients with persistent bronchopulmonary disorders for mycobacterium species and to characterize the recovered isolates with a view to determining the extent of involvement of environmental mycobacteria in pulmonary infections. DESIGN Analytical study using standard microscopy, culture and biochemical test for the identification of mycobacterium species. SETTING Jos University Teaching Hospital (JUTH) and 2 referral hospitals: Plateau Specialist Hospital and Evangelical Churches of West Africa (ECWA) Evangel Hospital in Jos, Nigeria. PARTICIPANTS Three hundred and twenty nine (329) volunteer new patients seen at the chest clinic and general out patient departments with broncho-pulmonary disorders. Patients already on anti-tuberculosis were excluded from the study. INTERVENTIONS Subjects were administered antituberculosis drugs and or other treatment regimes after proper diagnosis RESULTS Sixty-five (65) mycobacterial isolates were obtained and differentiated into human tubercle bacilli, bovine and or environmental (atypical) mycobacteria on the basis of nine identification tests. Of the 65 mycobacterial isolates subjected to the tests, 40 (61.54%) were identified as mycobacterium tuberculosis, 10 (15.38%) as M. bovis and 15 (23.08%) as environmental mycobacteria. Among the environmental group, 9 (20.69%) were classified as M. avium 3 (3.45%) each as M. kansasi and M. fortuitum. CONCLUSIONS The study confirms the involvement of bovine and environmental mycobacteria in pulmonary infections. This may be related to the rising prevalence of HIV/AIDS globally. The need for adequate bacteriological analysis in current-day diagnosis of pulmonary tuberculosis in indicated.
A Distal Enhancer in Il12b Is the Target of Transcriptional Repression by the STAT3 Pathway and Requires the Basic Leucine Zipper (B-ZIP) Protein NFIL3*

Deregulated IL-12 and IL-23 production from activated myeloid lineage cells is a key driver of numerous T cell-dependent autoimmune and inflammatory diseases. IL-12 and IL-23 share a common p40 subunit encoded by Il12b, which is negatively regulated at the transcriptional level by the STAT3 (signal transducer and activator of transcription 3)-activating anti-inflammatory cytokine IL-10. We found that IL-10 targets an enhancer 10 kb upstream of the Il12b transcriptional start site. Within the enhancer, a single 10-bp site is required for the inhibitory effects of IL-10 and is bound by NFIL3 (nuclear factor, interleukin 3-regulated), a B-ZIP transcription factor. Myeloid cells lacking NFIL3 produce excessive IL-12p40 and increased IL-12p70. Thus, the STAT3-dependent expression of NFIL3 is a key component of a negative feedback pathway in myeloid cells that suppresses proinflammatory responses.
Oxidized LDL and malondialdehyde-modified LDL in patients with acute coronary syndromes and stable coronary artery disease.

BACKGROUND The association between oxidative modifications of LDL and coronary artery disease (CAD) is suspected but not established. Therefore, the association between plasma levels of oxidized LDL and malondialdehyde (MDA)-modified LDL and acute coronary syndromes and stable CAD was investigated. METHODS AND RESULTS The study population contained 63 patients with acute coronary syndromes (45 with acute myocardial infarction and 18 with unstable angina pectoris), 35 nontransplanted patients with angiographically confirmed stable angina, 28 heart transplant patients with posttransplant CAD, 79 heart transplant patients without CAD, and 65 control subjects. After correction for age, sex, and LDL and HDL cholesterol, plasma levels of oxidized LDL and MDA-modified LDL were significantly higher in patients with CAD than in individuals without CAD (r2=0.57 and r2=0.26, respectively; both P=0.0001). Plasma levels of MDA-modified LDL were significantly higher in patients with acute coronary syndromes than in individuals with stable CAD (r2=0.65; P=0.0001) and were associated with increased levels of troponin I and C-reactive protein (r2=0.39 and r2=0.34, respectively; both P=0.0001). Plasma levels of oxidized LDL were not associated with increased levels of troponin I and C-reactive protein (r2=0.089 and r2=0.063, respectively). CONCLUSIONS Elevated plasma levels of oxidized LDL are associated with CAD. Elevated plasma levels of MDA-modified LDL suggest plaque instability and may be useful for the identification of patients with acute coronary syndromes.
Comparison of HDAC inhibitors in clinical development

Objective: We aimed to compare the potential for inducing HIV production and the effect on T-cell activation of potent HDAC inhibitors undergoing clinical investigation. Design: In vitro study Methods: The latently infected cell lines ACH2 and U1 were treated with the HDAC inhibitors panobinostat, givinostat, belinostat, vorinostat and valproic acid. Viral induction was estimated by p24 production. Peripheral blood mononuclear cells from uninfected donors were treated with the HDAC inhibitors and the expression of activation markers on T-cell phenotypes was measured using flow cytometry. Finally, the ability of givinostat, belinostat and panobinostat to reactivate latent HIV-1 expression in primary T-cells was investigated employing a CCL19-induced latent primary CD4+ T cell infection model. Results: The various HDAC inhibitors displayed significant potency differences in stimulating HIV-1 expression from the latently infected cell lines with panobinostat > givinostat ≈belinostat > vorinostat > valproic acid. Panobinostat was significantly more potent than all other HDAC inhibitors and induced virus production even in the very low concentration range 8–31 nM. The proportion of primary T-cells expressing the early activation marker CD69 increased moderately in all HDAC inhibitor-treated cells compared with untreated cells. Finally, proof was obtained that panobinostat, givinostat and belinostat induce virus production in latently infected primary cells at therapeutic concentrations with panobinostat being the most potent stimulator. Conclusion: At therapeutic concentrations panobinostat stimulate HIV-1 expression in latently infected cells with greater potency than other HDAC inhibitors undergoing clinical investigation. These findings warrant further investigation and panobinostat is now being advanced into clinical testing against latent HIV infection.
Cobordisms of maps with singularities of given class

We prove that the diagonal of the transition probabilities for the d-dimensional Bessel processes on (0, 1], reflected at 1, which we denote by $p_R^N(t, r,r)$, is an increasing function of r for d>2 and that this is false for d=2.
Assessing Stability of Coastal Bluffs Due to Combined Actions of Waves and Changing Ambient Temperatures in the Arctic

The main objective of this thesis is the development of a numerical model with the software Plaxis, which simulates the thermodenudation, an erosion process in the Arctic which is mainly caused by the thawing of the permafrost soil. The developed model is a combination of a thermo-hydraulic model, which considers the cryogenic suction as an important process within frozen soil, coupled with a mechanical model via Python program codes to allow the analysis of slope stability and coastal retreat rates. The model was calibrated and partly validated to the coastline of Baydara Bay in western Russia, showing good results regarding the active layer thickness, the coastal retreat rate and the volume of eroded soil, which were close to the measured data. To investigate the effects of climate change on this coastline and the applicability of the model for such a purpose, a temperature increase was simulated, according to predictions of the Intergovernmental Panel on Climate Change. The calculated results were reasonable and complied with predicted developments. Additionally, also the bearing capacity of the bluff at Baydara Bay was determined and the effects of a thermosyphon as a coastal protection measure were simulated, whereby the coastal erosion could be significantly reduced. A parameter variation was also conducted to identify modelling parameters with a high importance for the modelling results, which were the unit weight, the slope angle of the bluff and the positions of the boundary conditions and the water level. In a conclusion, the limitations of the model are outlined and further research possibilities are proposed. Report Title: Assessing Stability of Coastal Bluffs Due to Combined Action of Waves and Changing Ambient Temperatures in the Arctic Date: Number of pages (incl. appendices): 91 Master Thesis X Project Work Name: Agnes Schneider Professor in charge/supervisor: Prof. Raed Lubbad Other external professional contacts/supervisors: Dr. Ivan Depina, Dr. Mohammad Saud Afzal
Extension of a genetic network model by iterative experimentation and mathematical analysis

From a closer and purer league betweenythe experimental and the rationalymuch may be hoped. (Bacon, 1620) Although Francis Bacon proposed the benefits of interdisciplinary science in 1620, only recently have molecular biologists and mathematicians talked with any frequency. Although no modern biologist would deny the validity of computational approaches in biology—just look at the burgeoning field of Genomics—how useful mathematical modeling will be to biologists remains debated (Lawrence, 2004; Tyson, 2004). An answer may be here with a study in this issue of MSB by Locke et al (2005), which highlights the advantages of being able to work effectively with models and molecules. The study by Locke et al (2005) focuses on circadian rhythms, daily rhythms of behavior and physiology found in most organisms. These rhythms range from human sleep/ wake cycles to leaf movements in plants. The cyclical nature and the precision of these internally driven rhythms has intrigued mathematicians and biologists alike. Yet despite working on the same questions for decades, most circadian molecular biologists have not embraced mathematical modeling. The following dialogue highlights similarities and differences in the views of a biologist (B) and a mathematician (M):
Managing cardiovascular risk in patients with inflammatory arthritis: practical considerations

Patients with inflammatory arthritis, such as rheumatoid arthritis, psoriatic arthritis, or ankylosing spondylitis, have higher rates of cardiovascular mortality. While the increased cardiovascular risk is only explained to some extent, a lot of research is currently conducted to improve our understanding of its pathogenesis, risk stratification, and optimal cardiovascular risk management. This review sought to report epidemiological data pertaining to the cardiovascular disease burden in patients with inflammatory arthritis, underlying mechanisms accounting for excessive cardiovascular risk, along with recommendations regarding risk assessment and management in this patient population.
Polymorphisms in Cyclooxygenase-2 and Epidermal Growth Factor Receptor Are Associated with Progression-Free Survival Independent of K-ras in Metastatic Colorectal Cancer Patients Treated with Single-Agent Cetuximab

Purpose: Recently, an objective response rate of 12% was reported in a phase II study of cetuximab in patients with epidermal growth factor receptor (EGFR)-expressing metastatic colorectal cancer (mCRC) refractory to fluoropyrimidine-, oxaliplatin-, and irinotecan-based chemotherapy (IMC-0144). In this large molecular correlates study, we tested whether K-ras mutation status and polymorphisms in genes involved in the EGFR-signaling pathway were associated with clinical outcome in IMC-0144. Experimental Design: We analyzed all available tissue samples from 130 of 346 mCRC patients enrolled in the IMC-0144 phase II clinical trial of cetuximab. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor tissues, and K-ras mutation status and the genotypes were analyzed using PCR-RFLP, direct DNA-sequencing, and 5′-end [γ-33P] ATP–labeled PCR-protocols. Results: The PFS of patients with cyclooxygenase-2 (COX-2) −765 G>C [C/C; risk ratio (RR), 0.31; 95% confidence interval (95% CI), 0.12-0.84; P = 0.032], COX-2 +8473 T>C (C/C; RR, 0.67; 95% CI, 0.40-1.13; P = 0.003), EGF +61 A>G (G/G; RR, 0.57; 95% CI, 0.34-0.95; P = 0.042), and EGFR +497 G>A (A/G; RR, 0.82; 95% CI, 0.56-1.20; P = 0.017) genotypes was significantly longer compared with those with other genotypes. In addition, patients whose tumors did not have K-ras mutations showed better RR, PFS, and overall survival than patients with K-ras mutations. In multivariable analysis, COX-2 +8473 T>C (adjusted P = 0.013) and EGFR +497 G>A (adjusted P = 0.010) remained significantly associated with progression-free survival, independent of skin rash toxicity, K-ras mutation status, and Eastern Cooperative Group performance status. Conclusions: Polymorphisms in COX-2 and EGFR may be useful independent molecular markers to predict clinical outcome in patients with mCRC treated with single-agent cetuximab, independent of skin rash toxicity, K-ras mutation, and Eastern Cooperative Oncology Group performance status.
Cytoadherence in paediatric malaria: ABO blood group, CD36, and ICAM1 expression and severe Plasmodium falciparum infection

As a leading cause of childhood mortality worldwide, selection pressure by Plasmodium falciparum continues to shape the human genome. Severe disturbances within the microcirculation result from the adhesion of infected erythrocytes to host receptors on monocytes, platelets, and endothelium. In this prospective study, we compared expression of all major host cytoadhesion receptors among Ugandan children presenting with uncomplicated malaria (n = 1078) versus children with severe malaria (n = 855), including cerebral malaria (n = 174), severe anaemia (n = 522), and lactic acidosis (n = 154). We report a significant survival advantage attributed to blood group O and increased monocyte expression of CD36 and ICAM1 (CD54). The high case fatality rate syndromes of cerebral malaria and lactic acidosis were associated with high platelet CD36 expression and thrombocytopenia, and severe malaria anaemia was characterized by low ICAM1 expression. In a logistic regression model of disease severity, odds ratios for the mitigating effects of blood group O, CD36, and ICAM1 phenotypes were greater than that of sickle haemoglobin. Host genetic adaptations to Plasmodium falciparum suggest new potential malaria treatment strategies.
Erectile dysfunction as a sentinel symptom of cardiovascular autonomic neuropathy in heavy drinkers

Abstract Because autonomic neuropathy (AN) is not routinely assessed in chronic alcoholism, its features and relationship with other disease parameters remain undefined. The very existence of true alcohol‐related autonomic dysfunction, in the absence of alcoholic hepatopathy, is even controversial. We aimed this study at evaluating the frequency and pattern of AN in a population of heavy drinkers without liver dysfunction. We also investigated the putative risk factors for AN as well as its relationship to peripheral neuropathy (PN). Autonomic function was evaluated in 70 detoxified alcoholics and 70 well‐matched controls by heart‐rate response to deep breathing, heart‐rate response to standing from lying position, and blood pressure response to standing up. PN was assessed by electroneurography (ENG). Detailed information about sensorimotor and autonomic symptoms, nutritional status, and parameters reflecting alcohol intake were recorded. No patients showed signs of caloric/protein malnutrition. PN was found in 74% and AN (abnormal test results in two of three tests performed) in 26%; abnormalities in at least one autonomic test were found in 62%. All patients with PN were symptomatic, mainly due to sensory disturbances. In line with this, ENG abnormalities were more evident at sural nerves. AN was symptomatic in 10 of 18 patients, and its sole clinical expression was impotence: indeed, the pattern of autonomic involvement was mainly parasympathetic. AN did not correlate with PN, nor with any parameter reflecting the amount of alcohol intake; only performances on heart‐rate response to standing from lying position were related to the duration of abuse. The lack of correlation between PN and AN may suggest a different pathophysiology for these two complications. Unlike PN, AN is often asymptomatic. Among symptomatic patients (55%), erectile dysfunction seems to be the sole symptom, in line with the higher degree of parasympathetic damage.
Slow filament dynamics and viscoelasticity in entangled and active actin networks

This paper deals with correlations between the viscoelastic impedance of entangled actin networks and the slow conformational dynamics and diffusive motions of single filaments. The single filament dynamics is visualized and analysed by analysing the Brownian motion of attached colloidal beads, which enables independent measurements of characteristic viscoelastic response times such as the entanglement and reptation times. We further studied the frequency–dependent viscoelastic impedance of active actin–heavy–meromyosin II networks by magnetic–tweezers microrheometry to gain insight into the effect of such highly dynamic and force–generating crosslinkers (exhibiting bond lifetimes of less than 1 s) on the rheological properties. We show that at high frequencies (higher than 1 Hz) the viscoelastic loss modulus is slightly increased relative to the entangled network (associated with an increase in the energy dissipated during mechanical excitations), while at low frequencies the plateau of the impedance spectrum becomes more pronounced as a consequence of the cross–linking of the network and the suppression of the terminal regime. Our data provide evidence that the myosin motor protein may play a role as softener of the actin cortex, enabling the adaptive reduction of the yield stress of cells and thus facilitating cellular deformations.
A new control method for shunt active filters based on sinusoidal signal integrators

In this paper, a new integral-proportional controller based control method using sinusoidal signal integrator (SSI) controller is proposed to control the shunt active filters. In the proposed technique, the harmonic components is transferred to the synchronous rotating reference frame with +ω and −ω rotation speeds and the output signals are applied to controllers tuned at 6, 12, and 18 times of the fundamental frequency. Therefore, it is possible to detect odd harmonic components exist in negative and positive sequences. One of the advantageous of the proposed technique in compare with other methods applying SSI is complete detection of odd harmonics in positive and negative sequences and consequently, the compensation process can be completely accomplished, particularly on loads the harmonics sequence is important. The advantageous of the proposed technique over the conventional approaches is confirmed by presenting simulation results in PSCAD/EMTDC.
Biotransformation of melatonin in human breast cancer cell lines: role of sulfotransferase 1A1

Abstract: The biologically active melatonin metabolite, 6‐hydroxymelatonin (6‐OHMel), is conjugated to form 6‐hydroxymelatonin sulfate (6‐OHMelS). To elucidate the role of the sulfotransferase (SULT) enzyme 1A1, considerably expressed in normal and malignant human breast cells, we measured the formation of 6‐OHMelS by ELISA in hormone‐dependent MCF‐7 and hormone‐independent MDA‐MB231 (MDA) breast cancer cell lines after stable transfection with SULT1A1. In parent MDA cells, low SULT1A1 mRNA expression was associated with moderate 6‐OHMelS formation as determined after application (24 hr) of 0.1 μm 6‐OHMel. As expected, overexpression of SULT1A1 in MDA cells resulted in a 2.9‐ and 110‐fold increase in 6‐OHMelS in the cytosol and cellular supernatant respectively. Furthermore, 6.3‐ and 115‐fold increases were observed after 0.5 μm, and 12.6‐ and 101‐fold increases after 1 μm 6‐OHMel respectively. In MCF‐7 cells, because of high basal SULT1A1 expression, only two‐ to threefold increases in 6‐OHMelS were observed after transfection with the enzyme. In total, 866 and 539 pmol/mg protein 6‐OHMelS were formed from 1 μm 6‐OHMel in SULT1A1 overexpressing MDA and MCF‐7 cells, respectively, whereas application of 1 μm melatonin produced only <1% of 6‐OHMelS. Possible interactions with the SULT1A1 substrate tamoxifen (tam), an anti‐estrogen applied in the therapy of breast cancer, were also studied. A concentration of 1 μm tam increased 6‐OHMelS formation by approximately threefold in the presence of 1 μm melatonin or 1 μm 6‐OHMel respectively. However, no alterations were detected after application of 1 μm 4‐hydroxy‐tamoxifen. In summary, we demonstrate the importance of SULT1A1 for the biotransformation of 6‐OHMel in human breast cancer cells. Our data further suggest that tam can modulate melatonin biotransformation.
Lexical Phonology and the Lexicon

It would be a time-consuming but straightforward task to compile a complete list of exceptions, at least for the rules of word-level phonology. Given the purposes of this study such an effort would be beside the point unless it were to lead to the formulation of new and deeper rules that explained the exceptions or to a different theory that accounted both for the regularities that our rules express and for some of their defects and limitations. Chomsky and Halle (1968:ix) 2 CONTENTS
Natural Language Processing (Almost) from Scratch

We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This versatility is achieved by trying to avoid task-specific engineering and therefore disregarding a lot of prior knowledge. Instead of exploiting man-made input features carefully optimized for each task, our system learns internal representations on the basis of vast amounts of mostly unlabeled training data. This work is then used as a basis for building a freely available tagging system with good performance and minimal computational requirements.
The Response of Local Precipitation and Sea Level Pressure to Hadley Cell Expansion

Numerous lines of observational evidence suggest that Earth's tropical belt has expanded over the past 30–40 years. It is natural to expect that this poleward displacement should be associated with drying on the poleward margins of the subtropics, but it is less clear to what degree the drying should be zonally symmetric. This study tests the degree to which poleward motion of the Hadley cell boundary is associated with changes in local precipitation or sea level pressure and the degree to which those changes are zonally symmetric. Evidence from both reanalysis data and global climate models reveals that the local changes associated with Hadley cell expansion are mostly confined to certain centers of action which lie primarily over oceans. Consequently, the tropical expansion measured by zonally averaged variables is not associated with systematic drying over subtropical land regions, as is often assumed.
Discussion: The Dantzig selector: Statistical estimation when p is much larger than n

1. Introduction. This is a fascinating paper on an important topic: the choice of predictor variables in large-scale linear models. A previous paper in these pages attacked the same problem using the “LARS” algorithm (Efron, Hastie, Johnstone and Tibshirani [3]); actually three algorithms including the Lasso as middle case. There are tantalizing similarities between the Dantzig Selector (DS) and the LARS methods, but they are not the same and produce somewhat different models. We explore this relationship with the Lasso and LARS here. 2. Dantzig selector and the Lasso. The definition of the Dantzig selector (DS) in (1.7) can be re-expressed as