Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Sialic Acid and Complex Carbohydrate Biosynthesis in Biofilm Formation by Nontypeable Haemophilus influenzae in the Chinchilla Middle Ear

ABSTRACT Nontypeable Haemophilus influenzae (NTHI) is an important pathogen in respiratory tract infections, including otitis media (OM). NTHI forms biofilms in vitro as well as in the chinchilla middle ear, suggesting that biofilm formation in vivo might play an important role in the pathogenesis and chronicity of OM. We've previously shown that SiaA, SiaB, and WecA are involved in biofilm production by NTHI in vitro. To investigate whether these gene products were also involved in biofilm production in vivo, NTHI strain 2019 and five isogenic mutants with deletions in genes involved in carbohydrate biosynthesis were inoculated into the middle ears of chinchillas. The wild-type strain formed a large, well-organized, and viable biofilm; however, the wecA, lsgB, siaA, pgm, and siaB mutants were either unable to form biofilms or formed biofilms of markedly reduced mass, organization, and viability. Despite their compromised ability to form a biofilm in vivo, wecA, lsgB, and siaA mutants survived in the chinchilla, inducing culture-positive middle ear effusions, whereas pgm and siaB mutants were extremely sensitive to the bactericidal activity of chinchilla serum and thus did not survive. Lectin analysis indicated that sialic acid was an important component of the NTHI 2019 biofilm produced in vivo. Our data suggested that genes involved in carbohydrate biosynthesis and assembly play an important role in the ability of NTHI to form a biofilm in vivo. Collectively, we found that when modeled in a mammalian host, whereas biofilm formation was not essential for survivability of NTHI in vivo, lipooligosaccharide sialylation was indispensable.
Potential Residential Exposure to Toxics Release Inventory Chemicals during Pregnancy and Childhood Brain Cancer

Background Although the susceptibility of the developing fetus to various chemical exposures is well documented, the role of environmental chemicals in childhood brain cancer etiology is not well understood. Objectives We aimed to evaluate whether mothers of childhood brain cancer cases had greater potential residential exposure to Toxics Release Inventory (TRI) chemicals than control mothers during pregnancy. Methods We included 382 brain cancer cases diagnosed at < 10 years of age from 1993 through 1997 who were identified from four statewide cancer registries. One-to-one matched controls were selected by random-digit dialing. Computer-assisted telephone interviews were conducted. Using residential history of mothers during pregnancy, we measured proximity to TRI facilities and exposure index, including mass and chemicals released. We calculated odds ratios (ORs) and 95% confidence intervals (CIs) using conditional logistic regression to estimate brain cancer risk associated with TRI chemicals. Results Increased risk was observed for mothers living within 1 mi of a TRI facility (OR = 1.66; 95% CI, 1.11–2.48) and living within 1 mi of a facility releasing carcinogens (OR = 1.72; 95% CI, 1.05–2.82) for having children diagnosed with brain cancer before 5 years of age, compared to living > 1 mi from a facility. Taking into account the mass and toxicity of chemical releases, we found a nonsignificant increase in risk (OR = 1.25; 95% CI, 0.67–2.34) comparing those with the lowest versus highest exposure index. Conclusions Risk of childhood brain cancers may be associated with living near a TRI facility; however, this is an exploratory study and further studies are needed.
Genetic variability affects the development of brown adipocytes in white fat but not in interscapular brown fats⃞ Published, JLR Papers in Press, October 14, 2006.

Cold exposure induces brown adipocytes in retroperitoneal fat (RP) of adult A/J mice but not in C57BL/6J (B6) mice. In contrast, induction of the mitochondrial uncoupling protein 1 gene (Ucp1) in interscapular brown adipose tissue (iBAT) shows no strain dependence. We now show that unlike iBAT, in which Ucp1 was expressed in the fetus and continued throughout life, in RP, Ucp1 was transiently expressed between 10 and 30 days of age and then disappeared. Similar to the lack of genetic variation in the expression of Ucp1 in iBAT during cold induction of adult mice, no genetic variation in Ucp1 expression in iBAT was detected during development. In contrast, UCP1-positive multilocular adipocytes, together with corresponding increases in Ucp1 expression, appeared in RP at 10 days of age in A/J and B6 mice, but with much higher expression in A/J mice. At 20 days of age, brown adipocytes represent the major adipocyte present in RP of A/J mice. The disappearance of brown adipocytes by 30 days of age suggested that tissue remodeling occurred in RP. Genetic variability in Ucp1 expression could not be explained by variation in the expression of selective transcription factors and signaling molecules of adipogenesis. In summary, the existence of genetic variability between A/J and B6 mice during the development of brown adipocyte expression in RP, but not in iBAT, suggests that developmental mechanisms for the brown adipocyte differentiation program are different in these adipose tissues.
Energy-efficient and SLA-aware management of IaaS clouds

Cloud computing utilizes arbitrary mega-scale computing infrastructures and is currently revolutionizing the ICT landscape by allowing remote access to computing power and data over the Internet. Besides the huge economical impact Cloud technology exhibits a high potential to be a cornerstone of a new generation of sustainable and energy-efficient ICT. The challenging issue thereby is the energy-efficient utilization of physical machines (PMs) and the resource-efficient management of virtual machines (VMs) while attaining promised non-functional qualities of service expressed by means of Service Level Agreements (SLAs). Currently, there exist solutions for PM power management, VM migrations, and dynamic reconfiguration of VMs. However, most of the existing approaches consider each of them alone, and only use rudimentary concepts for migration costs or disrespect the nature of the highly volatile workloads. In this paper we present an integrated approach for VM migration and reconfiguration, and PM power management. Thereby, we incorporate an autonomic management loop, where proactive actions are suggested for all three areas in a hierarchically structured way. We evaluate our approach with both, synthetic workload data and real-word monitoring data of a Next Generation Sequencing (NGS) application used for the protein folding in the bioinformatics area. The efficacy of our approach is evaluated by considering classical algorithms like First Fit, Monte Carlo and Vector Packing, adapted for energy-efficient reallocation. The results show energy savings up to 61.6% while keeping acceptably low SLA violation rates.
The redshift distribution of gamma-ray bursts revisited

In this Letter, we calculate the redshift distribution of gamma-ray bursts assuming that they trace (i) the globally averaged star formation rate or (ii) the average metallicity in the Universe. While at redshifts 5 and below both the star formation rate and the metallicity are observationally determined modulo some uncertainties, at higher redshifts there are few constraints. We extrapolate the star formation rate and metallicity to higher redshifts and explore models that are broadly consistent with bounds on the optical depth from WMAP results. In addition, we also include parametric descriptions of the luminosity function, and the typical spectrum for gamma-ray bursts (GRBs). With these essential ingredients included in the modelling, we find that a substantial fraction (75 per cent) of GRBs are expected to originate at redshifts below 4, in variance with some previous estimates. Conversely, if we assume as expected for the collapsar model that gamma-ray bursts favour a low-metallicity environment, and therefore relate the GRB rate to a simple model of the average metallicity as a function of redshift, we find that a higher fraction of bursts, about 40 per cent, originate from z > 4. We conclude with the implications of Swift GRB detections.
MicroRNA Expression and Clinical Outcome of Small Cell Lung Cancer

The role of microRNAs in small-cell lung carcinoma (SCLC) is largely unknown. miR-34a is known as a p53 regulated tumor suppressor microRNA in many cancer types. However, its therapeutic implication has never been studied in SCLC, a cancer type with frequent dysfunction of p53. We investigated the expression of a panel of 7 microRNAs (miR-21, miR-29b, miR-34a/b/c, miR-155, and let-7a) in 31 SCLC tumors, 14 SCLC cell lines, and 26 NSCLC cell lines. We observed significantly lower miR-21, miR-29b, and miR-34a expression in SCLC cell lines than in NSCLC cell lines. The expression of the 7 microRNAs was unrelated to SCLC patients' clinical characteristics and was neither prognostic in term of overall survival or progression-free survival nor predictive of treatment response. Overexpression or downregulation of miR-34a did not influence SCLC cell viability. The expression of these 7 microRNAs also did not predict in vitro sensitivity to cisplatin or etoposide in SCLC cell lines. Overexpression or downregulation of miR-34a did not influence sensitivity to cisplatin or etoposide in SCLC cell lines. In contrast to downregulation of the miR-34a target genes cMET and Axl by overexpression of miR-34a in NSCLC cell lines, the intrinsic expression of cMET and Axl was low in SCLC cell lines and was not influenced by overexpression of miR-34a. Our results suggest that the expression of the 7 selected microRNAs are not prognostic in SCLC patients, and miR-34a is unrelated to the malignant behavior of SCLC cells and is unlikely to be a therapeutic target.
Contrasting Effects of Selection on Sequence Diversity and Linkage Disequilibrium at Two Phytoene Synthase Loci Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012526.

We investigated the effects of human selection for yellow endosperm color, representing increased carotenoid content, on two maize genes, the Y1 phytoene synthase and PSY2, a putative second phytoene synthase. Multiple polymorphic sites were identified at Y1 and PSY2 in 75 white and yellow maize inbred lines. Many polymorphic sites showed strong association with the endosperm color phenotype at Y1, but no detectable association was found at PSY2. Nucleotide diversity was equivalent for whites and yellows at PSY2 but was 19-fold less in yellows than in whites at Y1, consistent with the white ancestral state of the gene. The strong sequence haplotype conservation within yellows at Y1 and a significant, negative Tajima's D both verified positive selection for yellow endosperm. We propose that two independent gain-of-function events associated with insertions into the promoter of the Y1 gene and upregulation of expression in endosperm have been incorporated into yellow maize.
Selenium disrupts estrogen receptor α signaling and potentiates tamoxifen antagonism in endometrial cancer cells and tamoxifen-resistant breast cancer cells

Tamoxifen, a selective estrogen receptor (ER) modulator, is the most widely prescribed hormonal therapy treatment for breast cancer. Despite the benefits of tamoxifen therapy, almost all tamoxifen-responsive breast cancer patients develop resistance to therapy. In addition, tamoxifen displays estrogen-like effects in the endometrium increasing the incidence of endometrial cancer. New therapeutic strategies are needed to circumvent tamoxifen resistance in breast cancer as well as tamoxifen toxicity in endometrium. Organic selenium compounds are highly effective chemopreventive agents with well-documented benefits in reducing total cancer incidence and mortality rates for a number of cancers. The present study shows that the organic selenium compound methylseleninic acid (MSA, 2.5 μmol/L) can potentiate growth inhibition of 4-hydroxytamoxifen (10−7 mol/L) in tamoxifen-sensitive MCF-7 and T47D breast cancer cell lines. Remarkably, in tamoxifen-resistant MCF-7-LCC2 and MCF7-H2Δ16 breast cancer cell lines and endometrial-derived HEC1A and Ishikawa cells, coincubation of 4-hydroxytamoxifen with MSA resulted in a marked growth inhibition that was substantially greater than MSA alone. Growth inhibition by MSA and MSA + 4-hydroxytamoxifen in all cell lines was preceded by a specific decrease in ERα mRNA and protein without an effect on ERβ levels. Estradiol and 4-hydroxytamoxifen induction of endogenous ER-dependent gene expression (pS2 and c-myc) as well as ER-dependent reporter gene expression (ERE2e1b-luciferase) was also attenuated by MSA in all cell lines before effect on growth inhibition. Taken together, these data strongly suggest that specific decrease in ERα levels by MSA is required for both MSA potentiation of the growth inhibitory effects of 4-hydroxytamoxifen and resensitization of tamoxifen-resistant cell lines.
Departement Elektrotechniek ESAT-SISTA / TR 2003-49 Linear and Decision-Feedback Per Tone Equalization for DMT-based Transmission over IIR Channels 1

The per-tone equalizer (PTEQ) has been presented as an attractive alternative for the classical timedomain equalizer (TEQ) in discrete multitone (DMT) based systems, such as ADSL systems. The PTEQ is based on a linear minimum mean-square-error (L-MMSE) equalizer design for each separate tone. In this paper, we reconsider DMT modulation and equalization in the ADSL context under the realistic assumption of an infinite impulse response (IIR) model for the wireline channel. First, optimum linear zero-forcing (L-ZF) block equalizers for arbitrary IIR model orders and cyclic prefix (CP) lengths are developed. It is shown that these L-ZF block equalizers can be decoupled per tone, hence they lead to an L-ZF PTEQ. Then, based on the L-ZF PTEQ, low-complexity L-MMSE PTEQ extensions are developed: the linear PTEQ extension exploits frequency-domain transmit redundancy from pilot and unused tones; alternatively, a closely related decision-feedback PTEQ extension can be applied. The PTEQ extensions then add flexibility to a DMT-based system design: the CP overhead can be reduced by exploiting frequency-domain transmit redundancy instead, so that a similar bitrate as with the original PTEQ is achieved at a lower memory and computational cost or, alternatively, a higher bitrate is achieved without a considerable cost increase. Both PTEQ extensions are also shown to improve the receiver’s robustness to narrow-band interference. Index Terms Discrete Multitone, Digital Subscriber Lines, Per-Tone Equalization, Linear Equalization, DecisionFeedback Equalization, Narrow-Band Interference Suppression
Magnetic resonance elastography (MRE) of the human brain: technique, findings and clinical applications

Neurological disorders are one of the most important public health concerns in developed countries. Established brain imaging techniques such as magnetic resonance imaging (MRI) and x-ray computerised tomography (CT) have been essential in the identification and diagnosis of a wide range of disorders, although usually are insufficient in sensitivity for detecting subtle pathological alterations to the brain prior to the onset of clinical symptoms—at a time when prognosis for treatment is more favourable. The mechanical properties of biological tissue provide information related to the strength and integrity of the cellular microstructure. In recent years, mechanical properties of the brain have been visualised and measured non-invasively with magnetic resonance elastography (MRE), a particularly sensitive medical imaging technique that may increase the potential for early diagnosis. This review begins with an introduction to the various methods used for the acquisition and analysis of MRE data. A systematic literature search is then conducted to identify studies that have specifically utilised MRE to investigate the human brain. Through the conversion of MRE-derived measurements to shear stiffness (kPa) and, where possible, the loss tangent (rad), a summary of results for global brain tissue and grey and white matter across studies is provided for healthy participants, as potential baseline values to be used in future clinical investigations. In addition, the extent to which MRE has revealed significant alterations to the brain in patients with neurological disorders is assessed and discussed in terms of known pathophysiology. The review concludes by predicting the trends for future MRE research and applications in neuroscience.
Special Section—Behavioral symptoms of dementia: their measurement and intervention. Predictors of circadian sleep-wake rhythm maintenance in elders with dementia

Minimal data exists to predict which elders with dementia in nursing homes will maintain circadian sleep-wake rhythms during senescence and which elders with dementia in nursing homes will experience sleep-wake rhythm deterioration. This circadian deterioration is one of the background factors identified in the Needs-driven Dementia-compromised Behavior Model. The objective of this study was to determine predictors of circadian sleep-wake rhythm maintenance in elders with dementia residing in nursing homes. This secondary analysis identifies predictors of maintaining circadian sleep-wake rhythm in a convenience sample of 171 elders with dementia residing in seven nursing homes in the Southern United States. An autocorrelogram of the circadian sleep-wake rhythm for each participant determined whether or not the rhythm had deteriorated. Using measures of depression, cognitive function, physical and psychosocial activity, medications, and sleep apnea, as well as demographic characteristics of the sample, logistic regression determined the best predictors of rhythm maintenance. The best predictors of circadian sleep-wake rhythm maintenance in elders with dementia residing in nursing homes were physical activity (p = 0.00) and psychosocial activity (p = 0.00). The interaction term between these variables was not significant (p = 0.24). These findings suggest that providing meaningful daytime physical and psychosocial activity may assist in maintaining circadian sleep-wake rhythmicity. Additional research is needed to determine if these interventions would improve circadian sleep-wake rhythm in elders with dementia residing in nursing homes.
Association of Race/Ethnicity, Inflammation, and Albuminuria in Patients With Diabetes and Early Chronic Kidney Disease

OBJECTIVE African Americans (AAs) and Hispanics have higher diabetes and end-stage renal disease but similar or lower early chronic kidney disease (CKD) compared with whites. Inflammation plays a critical role in the pathogenesis of diabetes-related CKD. We postulated that in contrast to the general population, AAs and Hispanics have a higher prevalence of early diabetic CKD and systemic inflammatory markers compared with whites. RESEARCH DESIGN AND METHODS We analyzed the National Health and Nutrition Examination Survey 1999–2008 of 2,310 diabetic patients aged ≥20 years with fasting plasma glucose (FPG) ≥126 mg/dL. We performed multiple linear regression among patients with early CKD (urinary albumin excretion [UAE] ≥30 μg/mL and estimated glomerular filtration rate ≥60 mL/min/1.73 m2) to test the relationship between UAE and C-reactive protein (CRP) by race/ethnicity, adjusting for demographics, diabetes duration, FPG, hemoglobin A1c, uric acid, white blood cell count, medication use, cardiovascular disease, and related parameters. RESULTS In patients with diabetes, the prevalence of early CKD was greater among Hispanics and AAs than whites (P < 0.0001). AAs had higher adjusted odds ratio (AOR) for CRP ≥0.2 mg/dL (AOR 1.81 [95% CI 1.19–2.78]), and Hispanics had higher AOR for UAE ≥30 μg/mL (AOR 1.65 [1.07–2.54]). In a regression model adjusted for confounding variables, there was a significant association between UAE and CRP in the mid-CRP tertile (CRP 0.20–0.56 mg/dL, P = 0.001) and highest CRP tertile (CRP ≥0.57 mg/dL, P = 0.01) for Hispanics, but only in the mid-CRP tertile (P = 0.04) for AAs, compared with whites. CONCLUSIONS AAs and Hispanics with diabetes have a higher prevalence of early CKD compared with whites, which is significantly associated with UAE and/or CRP.
A rapid and simple method for the isolation of apoptotic DNA fragments.

During development different cells of multicellular organisms die by a physiological process referred to as programmed cell death or apoptosis (1). In difference to necrosis the apoptotic death requires de novo protein synthesis (2) and is therefore often called cellular suicide. Besides cell morphology fragmentation of chromatin into units of single or multiple nucleosomes is specific for apoptosis and one of the easiest ways to distinguish programmed cell death and toxic necrosis.
Effects of dexmedetomidine in combination with fentanyl-based intravenous patient-controlled analgesia on pain attenuation after open gastrectomy in comparison with conventional thoracic epidural and fentanyl-based intravenous patient-controlled analgesia

Background: This study was investigated the effects of dexmedetomidine in combination with fentanyl-based intravenous patient-controlled analgesia (IV-PCA) on pain attenuation in patients undergoing open gastrectomy in comparison with conventional thoracic epidural patient-controlled analgesia (E-PCA) and IV-PCA. Methods: One hundred seventy-one patients who planned open gastrectomy were randomly distributed into one of the 3 groups: conventional thoracic E-PCA (E-PCA group, n = 57), dexmedetomidine in combination with fentanyl-based IV-PCA (dIV-PCA group, n = 57), or fentanyl-based IV-PCA only (IV-PCA group, n = 57). The primary outcome was the postoperative pain intensity (numerical rating scale) at 3 hours after surgery, and the secondary outcomes were the number of bolus deliveries and bolus attempts, and the number of patients who required additional rescue analgesics. Mean blood pressure, heart rate, and adverse effects were evaluated as well. Results: One hundred fifty-three patients were finally completed the study. The postoperative pain intensity was significantly lower in the dIV-PCA and E-PCA groups than in the IV-PCA group, but comparable between the dIV-PCA group and the E-PCA group. Patients in the dIV-PCA and E-PCA groups needed significantly fewer additional analgesic rescues between 6 and 24 hours after surgery, and had a significantly lower number of bolus attempts and bolus deliveries during the first 24 hours after surgery than those in the IV-PCA group. Conclusions: Dexmedetomidine in combination with fentanyl-based IV-PCA significantly improved postoperative analgesia in patients undergoing open gastrectomy without hemodynamic instability, which was comparable to thoracic E-PCA. Furthermore, this approach could be clinically more meaningful owing to its noninvasive nature.