Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation, identification and DNA fingerprinting of Mycobacterial Isolates from AIDS patients

ARTICLE INFO ABSTRACT Article history: Received 10 October 2010 Accepted 7 February 2011 Available online 11 April 2011 Tuberculosis (TB) is one of the most important AIDS associated infectious diseases worldwide. It is a leading cause of illness and death among people with HIV/AIDS in resource-poor areas of the world. The annual incidence of TB among indigenous Iranians stands at 14 cases per 100,000 inhabitants. This study aimed to identify Mycobacterium infection among Iranian HIV positive patients. Two sputum specimens were collected from smear positive AIDS patients. Samples were cultured on Lowenstein-Jensen media for three weeks. DNA was extracted from two samples based on van Embden protocol. To identify Mycobacterium tuberculosis complex, a PCR was conducted to amplify a 245 bp fragment of IS6110 element, followed by RD12 method to confirm PCR result. Whole DNARFLP with PvuII restriction enzyme was employed to genotype the cultured isolates. The results obtained by colonial morphology, PCR, and RD12 methods showed that both isolates were belonging to M. tuberculosis, and Genotyping of the isolates by RFLP technique displayed that two isolates were belonging to different strains of M. tuberculosis.
Characterization of the human biliverdin reductase gene structure and regulatory elements: promoter activity is enhanced by hypoxia and suppressed by TNF‐α‐activated NF‐κB

hBVR is a Ser/Thr/Tyr kinase/scaffold protein/transcription factor/intracellular transporter of regulators. hBVR is an upstream activator of the insulin/IGF‐1/MAPK/PI3K signaling pathway, and of NF‐κB. As a reductase, it converts biliverdin to the antioxidant, bilirubin. hBVR gene has 8 exons; exon 1 is not translated. We report the characterization of hBVR promoter and its negative and positive regulation, respectively, by TNF‐α and hypoxia. The 5′ end of exon 1 was defined by primer extension analyses; deletion of an inhibitor sequence 350–425 bp upstream of this exon enhanced the promoter activity. One of two NF‐κB binding sites in the 836‐bp promoter was functional; the P65 subunit of NF‐κB and TNF‐α acted as inhibitors. On the basis of EMSA and ChIP assays, TNF‐α treatment increases binding of NF‐κB to its regulatory element. Overexpression of IκB increased hBVR mRNA. Biliverdin, but not bilirubin, was as effective as TNF‐α in inhibiting hBVR promoter activity. Only one of 4 hypoxia responsive elements (HREs) bound to HIF‐1α and ARNT expressed in HEK293A cells. An abasic site was introduced at the 3′ G of the HRE. This element bound HIF‐1 in the gel shift and in in‐cell luciferase assays. hBVR was detected in the nucleus at 1, 2, and 4 h after hypoxia (1% O2), at which times its kinase and reductase activities were increased. Because hypoxia positively influences hBVR promoter and phosphorylation and TNF‐α activated NF‐κB inhibits the promoter, while biliverdin inhibits both NF‐κB activity and hBVR promoter, we propose a regulatory mechanism for NF‐κB by hypoxia and TNF‐α centered on hBVR/biliverdin. —Gibbs, P. E. M. , Miralem, T. , Maines, M. D. Characterization of the human biliverdin reductase gene structure and regulatory elements: promoter activity is enhanced by hypoxia and suppressed by TNF‐α‐activated NF‐κB. FASEB J. 24, 3239–3254 (2010). www.fasebj. org
Techniques for Improving Performance of Hybrid Snooping Cache Protocols

Bus-based multiprocessors constitute a cost-effective class of shared-memory multiprocessors. Private caches are the key to an efficient utilization of the shared bus, and most such systems use a write-invalidate cache-coherence protocol to keep the caches coherent. Two important factors that limit the performance of the system are cache misses that lead to long-latency reads and bus congestion because of read misses and coherence traffic. While hybrid write-invalidate/write-update snooping protocols lead to fewer read misses than write-invalidate protocols, previous studies have shown them to be incapable of providing consistent performance improvements because of heavily increased coherence traffic. In this paper, we analyze how the deficiencies of hybrid snooping protocols can be dramatically reduced by using write caches and read snarfing (also called read-broadcast) under release consistency. Our performance evaluation is based on program-driven simulation and a set of five scientific applications with different sharing behaviors including migratory sharing as well as producer? consumer sharing. We show that one of the evaluated hybrid protocols, extended with write caches as well as read snarfing, manages to reduce the number of coherence misses by between 83 and 93% as compared to a write-invalidate protocol for all five applications in this study. In addition, the number of bus transactions is reduced substantially. However, we also show that read snarfing and hybrid snooping protocols might lead to higher cache occupancy because of increased sharing. Because of the small implementation cost of the hybrid protocol and the two extensions, we believe the combination to be an effective approach to boosting the performance of bus-based multiprocessors.
Probing the statistical properties of Anderson localization with quantum emitters

Wave propagation in disordered media can be strongly modified by multiple scattering and wave interference. Ultimately, the so-called Anderson-localized regime is reached when the waves become strongly confined in space. So far, Anderson localization of light has been probed in transmission experiments by measuring the intensity of an external light source after propagation through a disordered medium. However, discriminating between Anderson localization and losses in these experiments remains a major challenge. In this paper, we present an alternative approach where we use quantum emitters embedded in disordered photonic crystal waveguides as light sources. Anderson-localized modes are efficiently excited and the analysis of the photoluminescence spectra allows us to explore their statistical properties, for example the localization length and average loss length. With increasing the amount of disorder induced in the photonic crystal, we observe a pronounced increase in the localization length that is attributed to changes in the local density of states, a behavior that is in stark contrast to entirely random systems. The analysis may pave the way for accurate models and the control of Anderson localization in disordered photonic crystals.
Cocaine increases dopamine uptake and cell surface expression of dopamine transporters.

In HEK 293 cells expressing the human dopamine transporter (DAT), a 10-min incubation with 10 microM cocaine followed by extensive washing resulted in a 30% increase in [3H]dopamine (DA) uptake as well as an increase in cell surface DAT in biotinylation experiments. Consistent with this novel regulation, [3H]DA uptake into synaptosomes prepared from the nucleus accumbens of rats sacrificed 30 min after a single cocaine injection (30 mg/kg) was significantly increased compared to controls (56% increase in V(max), no change in K(m)). In addition, DA clearance in the striatum of anesthetized rats was increased after local application of a low (3 pmol) but not high (65 pmol) dose of cocaine, presumably as a result of mobilization of DAT to the cell surface. Cocaine-induced increases in cell surface expression of DAT and associated changes in DA clearance represent a novel mechanism that may play a role in its addictive properties.
Splicing precedes polyadenylation during Drosophila E74A transcription

The E74 gene is one of a small set of early genes induced by the steroid hormone ecdysone at the onset of metamorphosis in the fruit fly, Drosophila melanogaster. This complex gene directs the synthesis of a 60-kilobase (kb) primary transcript that is spliced to form the 6-kb E74A mRNA. In a previous study, we found that ecdysone directly activates the E74A promoter and determined that RNA polymerase II transcribes this gene at a rate of approximately 1.1 kb/min. This elongation rate accounts for most of the 1-hour delay seen between the addition of ecdysone and the appearance of cytoplasmic E74A mRNA (C. S. Thummel, K. C. Burtis, and D. S. Hogness, Cell 61:101-111, 1990). We show here that nascent E74A transcripts are spliced, and we propose a model for the order of that splicing. This study provides, for the first time, direct biochemical evidence for splicing of a low-abundance cellular RNA before transcription termination and polyadenylation.
Is there a role for combination anti-remodelling therapy for heart failure secondary to chronic rheumatic mitral regurgitation?

Summary Introduction: The value of combination anti-remodelling therapy for heart failure (HF) secondary to mitral regurgitation (MR) is unknown. We studied the effect of anti-remodelling therapy on clinical and echocardiographic parameters in patients with severe chronic rheumatic mitral regurgitation (CRMR) presenting in HF. Methods: Thirty-one patients (29 females) at Chris Hani Baragwanath Academic Hospital, treated with combination therapy for HF due to CRMR and New York Heart Association functional class II–III symptoms, underwent prospective six-month follow up. Results: Mean age was 50.7 ± 8.5 years. No patients died or were hospitalised for HF during the study period. No worsening of clinical symptoms or functional status, or left and right ventricular echocardiographic parameters (p > 0.05) was noted. Peak left atrial systolic strain improved at six months (18.7 ± 7.7 vs 23.6 ± 8.5%, p = 0.02). Conclusion: This preliminary analysis suggests that combination anti-remodelling therapy may be beneficial for HF secondary to CRMR. We had no HF-related admissions or deaths, and no deterioration in echocardiographic parameters of ventricular size and function.
Ultramicroscopic Examination of the Ovine Tonsillar Epithelia

As solid morphological knowledge of ovine tonsillar epithelia might contribute to a better understanding of the pathogenesis of several diseases including prion diseases, the epithelia of all tonsils of 7 one‐year‐old Texel sheep were examined using scanning and transmission electron microscopy. Major parts of the pharyngeal and tubal tonsils were covered by pseudostratified columnar ciliated epithelia that were interrupted by patches of epithelium containing cells with densely packed microfolds or microvilli, and cells with both microvilli and cilia. Smaller parts were covered by either flattened polygonal cells with densely packed microvilli or microfolds, squamous epithelial cells, or patches of reticular epithelium. The palatine and paraepiglottic tonsils were mainly lined by squamous epithelial cells with apical microplicae or short knobs. Additionally, regions of reticular epithelium containing epithelial cells with apical microvilli were seen. The lingual tonsil was uniformly covered by a keratinized squamous epithelium and devoid of microvillous cells and patches of reticular epithelium. The rostral half of the tonsil of the soft palate was lined by a pseudostratified columnar ciliated epithelium with characteristics of the pharyngeal and tubal tonsils. The epithelium of the caudal part resembled the epithelia of the palatine and paraepiglottic tonsils. Putative M cells, mainly characterized by apical microvilli or microfolds and a close association with lymphoid cells, seem manifestly present on the nasopharyngeal tonsils. The reticular epithelium of the palatine and paraepiglottic tonsils also harbor cells with small apical microvilli. The exact nature of these presumptive M cells should, however, be elucidated in functional studies. Anat Rec, 2010. © 2010 Wiley‐Liss, Inc.
Enzymes, Trophoblasts, and Cancer: The Afterlife of an Idea (1924-2008)

In the early 20th century, advocacy of the enzyme therapy of cancer was primarily the work of one man, John Beard, DSc (1858-1924). He and his collaborators made a determined effort to establish this mode of therapy, especially in the years 1905 to 1911. Despite a brief flowering of international interest, Beard's efforts came to naught. During the 20th century, there was a succession of American researchers who continued to investigate this topic. This included Marshall William McDuffie, MD (1882-1945), Frank LeForest Morse, MD (1876-1953), Franklin Lloyd Shively, MD (1887-1971), and William Donald Kelley (1926-2005). In central Europe, India, and other parts of the globe, the use of pancreatic enzymes as an adjuvant treatment for cancer has become a fairly routine practice, at least among those doctors who utilize complementary and alternative medicine (CAM). It is also a well-established method for reducing inflammation and mitigating the adverse effects of cytotoxic treatment.
Ecology of Paracoccidioides brasiliensis, P. lutzii and related species: infection in armadillos, soil occurrence and mycological aspects

Abstract Paracoccidioides brasiliensis and the related species P. americana, P. restrepiensis, P. venezuelensis, and P. lutzii (Ascomycota, Ajellomycetaceae) are the etiological agents of paracoccidoidoimycosis (PCM), one of the most important systemic mycoses in Latin America. They are dimorphic fungi, with a mycelial life cycle in soil and a yeast phase associated with tissues of mammalian hosts. This study aimed to detect Paracoccidioides spp. in armadillo tissues and associated soil samples in three well‐defined geographic areas, including the Alta Floresta, an area not only endemic for PCM in the central region of Brazil but also of probable P. lutzii occurrence, whose ecology and geographic distribution are poorly elucidated. The isolates were genotyped by sequencing ITS‐rDNA and the gp43‐exon‐2 region, and by PCR‐RFLP of alpha tubulin (tub1) gene; mycological aspects such as yeast‐to‐mycelial transition, growth and conidial production in soil extract agar were also evaluated. We confirmed that while armadillos are highly infected by P. brasiliensis, including multiple infections by distinct genotypes or species (P. brasiliensis and P. americana) in the same animal, the same does not hold true for P. lutzii, which in turn seems to present less capacity for mycelial growth and conidial production, when developing in a soil‐related condition.
Control of interferon‐τ secretion by in vitro‐derived bovine blastocysts during extended culture and outgrowth formation

A series of experiments was conducted to examine the pattern of interferon‐τ (IFN‐τ) secretion by bovine blastocysts during extended culture in vitro. In the first experiment, blastocysts were cultured individually for three 48‐hour periods. The day of blastocyst formation affected how much IFN‐τ was produced during the first two culture periods, but not during the third period. The overall secretion of IFN‐τ during the 6‐day period increased significantly and well beyond what could be accounted for by the concomitant increase in cell numbers. In the second experiment, blastocysts were initially cultured in individual droplets for 48 hr, then plated into 48‐well plates. Medium concentrations of IFN‐τ were determined after 48 hr and again after 6 and 12 days of culture. Initial IFN‐τ secretion did not affect the ability to form outgrowths or their final size, and initial differences in secretion between groups of blastocysts had disappeared by the second and third analyses. In the third experiment, blastocysts were cultured individually for 48 hr in droplets containing the medium that had been flushed through the uteri of non‐pregnant sheep on days 10, 12, and 15 of the estrous cycle. Culture in the medium obtained from the Day 15 flush significantly increased the number of cells that blastocysts contained, as well as IFN‐τ secretion. Mol. Reprod. Dev. 58:390–397, 2001. © 2001 Wiley‐Liss, Inc.
Direct electron beam writing of optical devices on Ge-doped flame hydrolysis deposited silica

Electron beam irradiation of silica is a very flexible technique for the fabrication and trimming of optical circuits for the telecommunications and biosensing areas. In this paper, we review the effects induced by electron beam irradiation of germanium-doped, flame-hydrolysis deposited (FHD) silica. The structural modifications were studied with Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS). The compaction of the material was characterized by profilometry and the refractive index variation and index distribution of channel waveguides were characterized using the m-line technique and microreflectivity, respectively. Finally, some optical devices were fabricated using this technique with application in optical fluorescence sensing. The technique appears as a very interesting way of fabrication low-loss optical waveguides in silica.
Effect of electrical activity feedback on cognition

The goal of physiological computing, i.e. brain-computer interface (BCI) is to transform bioelectrical signals from the human nervous system into computer in order to enhance and enrich the interactive experience. In this line, effect of electroencephalographic rhythm feedback (EEG biofeedback) has been investigated on different domains of cognitive functioning of Attention-deficit/hyperactivity disorder (ADHD). This approach is argued to be an effective method for treating children with ADHD. This study was performed to evaluate the effectiveness of this method. Participants were 26 children with ADHD aged between 7–12 years. Via electrical activity feedback, thirteen children were trained to enhance the power of the beta1 activity (15–18 Hz) and decrease the power of the theta activity (4–8 Hz), and 13 of which were treated with methylphenidate alone. Neuropsychological and experimental tests were administered before and after intervention. Both methods were associated with improvements on the variability and accuracy measures of computerized test. Intellectual ability increased also by both methods.
Tumour characteristics and surgical treatment of renal cell carcinoma in Sweden 2005–2010: a population-based study from the National Swedish Kidney Cancer Register

Abstract Objective. Tumour characteristics, preoperative work-up and surgical treatment in patients diagnosed with renal cell carcinoma (RCC) between 2005 and 2010, and changes over time were studied in a national population-based cohort. Material and methods. The National Swedish Kidney Cancer Register (NSKCR) contains information on histopathology, Fuhrman grade and clinical stage at presentation, and on the preoperative work-up and surgical treatment of patients with RCC. Between 2005 and 2010, 5553 RCC patients were registered in the NSKCR, 99% of those registered in the National Cancer Registry. Results. During the study period the mean tumour size decreased from 70 to 64 mm (p = 0.024) and the frequency of metastatic RCC decreased from 22% to 15% (p < 0.001). The use of preoperative chest computed tomography increased from 59% to 84%. In total, 4229 (76%) patients were treated with curative intent, 3453 (82%) underwent radical nephrectomy, 606 (14%) partial nephrectomy (PN) and 170 (4%) cryotherapy or radiofrequency ablation. In tumours up to 4 cm, PN was performed in 33% of the surgically treated patients. PN irrespective of size increased from 8% to 20% and laparoscopic nephrectomy increased from 6% to 17% during the period. In patients with metastatic RCC, 55% underwent cytoreductive nephrectomy. Conclusions. The NSKCR explores population-based data on the clinical handling of patients with RCC. This study, between 2005 and 2010, shows significant decrease in tumour size and metastatic RCC at presentation, a more complete preoperative work-up, and significantly increased use of PN and laparoscopic nephrectomy in Sweden.
Ubiquitin-mediated Proteolysis of a Short-lived Regulatory Protein Depends on Its Cellular Localization*

In this study we demonstrate that the Deg1 degradation signal of the transcriptional repressor Matα2 confers compartment-specific turnover to a reporter protein. Rapid degradation of a Deg1-containing fusion protein is observed only when the reporter is efficiently imported into the nucleus. In contrast, a reporter that is constantly exported from the nucleus exhibits an extended half-life. Furthermore, nuclear import functions are crucial for both Deg1-induced degradation as well as for the turnover of the endogenous Matα2 protein. The conjugation of ubiquitin to a Deg1-containing reporter protein is abrogated in mutants affected in nuclear import. Obviously, the Deg1 signal initiates rapid proteolysis within the nucleoplasm, whereas in the cytosol it mediates turnover via a slower pathway. In both pathways the ubiquitin-conjugating enzymes Ubc6p/Ubc7p play a pivotal role. These observations imply that both the cellular targeting of a substrate and the compartment-specific activity of components of the ubiquitin-proteasome system define the half-life of naturally short-lived proteins.
Development of magnetic coupling with variable thrust structure for flywheel energy storage system in long lifetime UPS

This paper introduces the flywheel energy storage system (FESS) in a long lifetime uninterruptible power supply. The first prototype FESS (3.0-MJ) uses low cost ball bearings and general purpose induction motor in terms of cost reduction. From the experimental results, it is confirmed that the charge and discharge efficiency of the FESS is 60.7% (charge 80.7%, discharge 75.1%). In order to improve the efficiency and lifetime, a permanent magnet synchronous motor, a spherical spiral groove bearing and a magnetic coupling with variable thrust structure are applied to the second prototype. The estimated charging efficiency is achieved to 86.9% and the estimated discharging efficiency is achieved to 82.8% at the second prototype. Then, the thrust of the proposed magnetic coupling is analyzed by the finite element method (FEM). As a result, the thrust can be changed by 11.1% with the electromagnet. In addition, the thrust analysis results are evaluated by using the prototype electromagnet.
MO2TOS: Multi-Fidelity Optimization with Ordinal Transformation and Optimal Sampling

Simulation optimization can be used to solve many complex optimization problems in automation applications such as job scheduling and inventory control. We propose a new framework to perform efficient simulation optimization when simulation models with different fidelity levels are available. The framework consists of two novel methodologies: ordinal transformation (OT) and optimal sampling (OS). The OT methodology uses the low-fidelity simulations to transform the original solution space into an ordinal space that encapsulates useful information from the low-fidelity model. The OS methodology efficiently uses high-fidelity simulations to sample the transformed space in search of the optimal solution. Through theoretical analysis and numerical experiments, we demonstrate the promising performance of the multi-fidelity optimization with ordinal transformation and optimal sampling (MO2TOS) framework.