Miracle-dz/UniFAR-FTUs huggingface dataset:
Decreased Expression of Type 1 Fimbriae by a pst Mutant of Uropathogenic Escherichia coli Reduces Urinary Tract Infection

ABSTRACT The pstSCAB-phoU operon encodes the phosphate-specific transport system (Pst). Loss of Pst constitutively activates the Pho regulon and decreases bacterial virulence. However, specific mechanisms underlying decreased bacterial virulence through inactivation of Pst are poorly understood. In uropathogenic Escherichia coli (UPEC) strain CFT073, inactivation of pst decreased urinary tract colonization in CBA/J mice. The pst mutant was deficient in production of type 1 fimbriae and showed decreased expression of the fimA structural gene which correlated with differential expression of the fimB, fimE, ipuA, and ipbA genes, encoding recombinases, mediating inversion of the fim promoter. The role of fim downregulation in attenuation of the pst mutant was confirmed using a fim phase-locked-on derivative, which demonstrated a significant gain in virulence. In addition, the pst mutant was less able to invade human bladder epithelial cells. Since type 1 fimbriae contribute to UPEC virulence by promoting colonization and invasion of bladder cells, the reduced bladder colonization by the pst mutant is predominantly attributed to downregulation of these fimbriae. Elucidation of mechanisms mediating the control of type 1 fimbriae through activation of the Pho regulon in UPEC may open new avenues for therapeutics or prophylactics against urinary tract infections.
Music induces universal emotion-related psychophysiological responses: comparing Canadian listeners to Congolese Pygmies

Subjective and psychophysiological emotional responses to music from two different cultures were compared within these two cultures. Two identical experiments were conducted: the first in the Congolese rainforest with an isolated population of Mebenzélé Pygmies without any exposure to Western music and culture, the second with a group of Western music listeners, with no experience with Congolese music. Forty Pygmies and 40 Canadians listened in pairs to 19 music excerpts of 29–99 s in duration in random order (eight from the Pygmy population and 11 Western instrumental excerpts). For both groups, emotion components were continuously measured: subjective feeling (using a two- dimensional valence and arousal rating interface), peripheral physiological activation, and facial expression. While Pygmy music was rated as positive and arousing by Pygmies, ratings of Western music by Westerners covered the range from arousing to calming and from positive to negative. Comparing psychophysiological responses to emotional qualities of Pygmy music across participant groups showed no similarities. However, Western stimuli, rated as high and low arousing by Canadians, created similar responses in both participant groups (with high arousal associated with increases in subjective and physiological activation). Several low-level acoustical features of the music presented (tempo, pitch, and timbre) were shown to affect subjective and physiological arousal similarly in both cultures. Results suggest that while the subjective dimension of emotional valence might be mediated by cultural learning, changes in arousal might involve a more basic, universal response to low-level acoustical characteristics of music.
Nominal Rigidities and Asset Pricing

This paper examines the asset-pricing implications of nominal rigidities. I find that firms that adjust their product prices infrequently earn a cross-sectional return premium of more than 4% per year. Merging confidential product price data at the firm level with stock returns, I document that the premium for sticky-price firms is a robust feature of the data and is not driven by other firm and industry characteristics. The consumption-wealth ratio is a strong predictor of the return differential in the time series, and differential exposure to systematic risk fully explains the premium in the cross section. The sticky-price portfolio has a conditional market beta of 1.3, which is 0.4 higher than the beta of the flexible-price portfolio. The frequency of price adjustment is therefore a strong determinant of the cross section of stock returns. To rationalize these facts, I develop a multi-sector production-based asset-pricing model with sectors differing in their frequency of price adjustment.
The Legacy of Empires on Political Outcomes in Romania

This paper investigates the discontinuity in political outcomes at the former HabsburgOttoman border in contemporary Romania. Historically Romania consisted of three provinces which were divided between the Habsburg and Ottoman Empires. The country united in the beginning of the 20-th century and was turned into a national unitary state with a highly centralized economy. We posit that the striking institutional differences between two parts of the country in the 18 and 19 centuries could persist and influence political attitudes of people nowadays despite the fact that there was convergence in economic development across its regions and it has homogeneous institutions today. We test this hypothesis by merging data on historical borders between Habsburg and Ottoman Empires with data on voting in elections in Romania at the municipality level in the 1990s and 2000s. We find that on average within Romania the former Habsburg affiliation is associated with an increase in the percentage of votes for the major “right” parties by 3.5% and a decrease in the percentage of votes for the major “left” party by 4.5%. This is a remarkable effect taking into account that we identify these differences in political attitudes around the former border in a country which united a century ago and where during the Communist period the authorities tried to eliminate any regional differences. We do not find evidence that these differences might be explained by past ethnic diversity or geographical isolation. 1 The author is from Duke University. Address for correspondence: roman.levkin@duke.edu; Duke University, Department of Economics, 213 Social Sciences, Box 90097, Durham, NC, 27708-0097 Acknowledgements: The author is especially grateful to Timur Kuran, Erica Field, Charles Becker, Robert Garlick, and Cosmin Ilut for invaluable comments.
Five-year follow-up of a randomized, prospective trial of topical methyl aminolevulinate photodynamic therapy vs surgery for nodular basal cell carcinoma.

OBJECTIVE To compare 5-year lesion recurrence rates in primary nodular basal cell carcinoma treated with topical methyl aminolevulinate photodynamic therapy (PDT) or simple excision surgery. DESIGN Prospective, randomized, multicenter study. SETTING University hospital dermatology departments. PATIENTS A total of 97 patients, 50 with 53 lesions treated with methyl aminolevulinate PDT and 47 with 52 lesions treated by excision surgery, were included in the per protocol analysis. Of the lesions treated with methyl aminolevulinate PDT and surgery, 49 and 52, respectively, showed complete clinical response at 3 months after treatment and were observed for long-term outcome evaluation. INTERVENTIONS Topical methyl aminolevulinate cream, 160 mg/g, applied for 3 hours before illumination (75 J/cm(2) of red light at 570 to 670 nm) on 2 or 4 occasions (12 [23%] of 53 lesions); or excision surgery. MAIN OUTCOME MEASURES Histologically confirmed lesion recurrence, sustained lesion complete response rate (time-to-event analysis), and investigator assessment of cosmetic outcome, 5 years after the last treatment. RESULTS At 5 years, recurrence was documented in 7 (14%) of 49 lesions (95% confidence interval [CI], 6%-27%) treated with methyl aminolevulinate PDT vs 2 (4%) of 52 lesions (95% CI, 1%-13%) treated with excision surgery (P = .09). Estimated sustained lesion complete response rates were 76% (95% CI, 59%-87%) and 96% (95% CI, 84%-99%), respectively (P = .01). More patients treated with methyl aminolevulinate PDT than surgery had an excellent or good cosmetic outcome: 27 (87%) of 31 patients (95% CI, 70%-96%) vs 19 (54%) of 35 patients (95% CI, 37%-71%) (P = .007). CONCLUSIONS Long-term follow-up indicates superior efficacy of surgery to methyl aminolevulinate PDT in nodular basal cell carcinoma. However, methyl aminolevulinate PDT is also an effective treatment for this indication and exhibits a more favorable cosmetic outcome.
Nitrogen removal performance of intermitTENTly aerated membrane bioreactor treating black water

The study investigated the effect of intermitTENT aeration on the nitrogen removal performance of a membrane bioreactor (MBR) treating black water. A pilot-scale MBR with an effective volume of 630 L operating as a sequencing batch reactor (SBR) with intermitTENT aeration was used in the experiments. Substrate feeding was limited to the initial non-aerated phase. The MBR unit was sustained at a steady state at a sludge age of 60 d with a biomass concentration of around 10,000 mg/L for 3 months. The treated black water could be characterized with an average COD of 950 mg/L and total nitrogen of 172 mg/L, corresponding to a low COD/N ratio of 5.5. The selected MBR scheme was quite effective, reducing COD down to 26 mg/L, providing effective nitrification and yielding a total oxidized nitrogen concentration under 10 mg N/L. The nitrogen removal performance was substantially better than the level predicted by process stoichiometry, due to multiple anoxic configuration inducing additional nitrogen removal. Dissolved oxygen profiles associated with the cyclic operation of the system suggested that the incremental nitrogen removal could be attributed to simultaneous nitrification-denitrification, a commonly observed mechanism in MBR systems sustained at high biomass concentrations.
Asynchronous Stochastic Coordinate Descent: Parallelism and Convergence Properties

We describe an asynchronous parallel stochastic proximal coordinate descent algorithm for minimizing a composite objective function, which consists of a smooth convex function added to a separable convex function. In contrast to previous analyses, our model of asynchronous computation accounts for the fact that components of the unknown vector may be written by some cores simultaneously with being read by others. Despite the complications arising from this possibility, the method achieves a linear convergence rate on functions that satisfy an optimal strong convexity property and a sublinear rate ($1/k$) on general convex functions. Near-linear speedup on a multicore system can be expected if the number of processors is $O(n^{1/4})$. We describe results from implementation on 10 cores of a multicore processor.
Power Allocation for Maximizing the Minimum Rate With QoS Constraints

Max-min fair power allocation brings higher average throughput and better utilization of the resources than a work-conserving equal-sharing policy. In this paper, instead of achieving a common maximum sum-rate objective, an optimal power-allocation design for maximizing the minimum rate of the reverse link of code-division multiple-access (CDMA) systems with quality-of-service (QoS) constraints is investigated. To avoid the difficulty of directly solving a nonconvex optimization problem, we split the original problem into two successive steps. First, we try to derive the structure of the optimum solution via majorization theory. Then, based on this result, we propose a very efficient search method to find the max-min fair solution, which reduces the search space from a 1-D space into a finite set of points. Compared with existing methods, a much lighter computational complexity is required by our method.
Human immunodeficiency virus type 1 Nef binds directly to Lck and mitogen-activated protein kinase, inhibiting kinase activity

It is now well established that human immunodeficiency virus type I (HIV-1) Nef contributes substantially to disease pathogenesis by augmenting virus replication and markedly perturbing T-cell function. The effect of Nef on host cell activation could be explained in part by its interaction with specific cellular proteins involved in signal transduction, including at least a member of the src family kinase, Lck, and the serine/threonine kinase, mitogen-activated protein kinase (MAPK). Recombinant Nef directly interacted with purified Lck and MAPK in coprecipitation experiments and binding assays. A proline-rich repeat sequence [(Pxx)4] in Nef occurring between amino acid residues 69 to 78 is highly conserved and bears strong resemblance to a defined consensus sequence identified as an SH3 binding domain present in several proteins which can interact with the SH3 domain of various signalling and cytoskeletal proteins. Binding and coprecipitation assays with short synthetic peptides corresponding to the proline-rich repeat sequence [(Pxx)4] of Nef and the SH2, SH3, or SH2 and SH3 domains of Lck revealed that the interaction between these two proteins is at least in part mediated by the proline repeat sequence of Nef and the SH3 domain of Lck. In addition to direct binding to full-length Nef, MAPK was also shown to bind the same proline repeat motif. Nef protein significantly decreased the in vitro kinase activity of Lck and MAPK. Inhibition of key members of signalling cascades, including those emanating from the T-cell receptor, by the HIV-1 Nef protein undoubtedly alters the ability of the infected T cell to respond to antigens or cytokines, facilitating HIV-1 replication and contributing to HIV-1-induced disease pathogenesis.
The Need to Know Caregiver Perspectives Toward Using Smart Home Technology

This article reviews the literature on adults with serious mental illness, their caregivers, and smart home technology. The article provides compelling evidence for social workers to undertake research aimed at investigating caregivers' perceptions toward using smart home technology for care of adult family members or friends with a serious mental illness. Empirical support for using smart home technologies with adults with serious mental illness is provided, and recommendations for future social work research are offered.
Towards an elastic distributed SDN controller

Distributed controllers have been proposed for Software Defined Networking to address the issues of scalability and reliability that a centralized controller suffers from. One key limitation of the distributed controllers is that the mapping between a switch and a controller is statically configured, which may result in uneven load distribution among the controllers. To address this problem, we propose ElastiCon, an elastic distributed controller architecture in which the controller pool is dynamically grown or shrunk according to traffic conditions and the load is dynamically shifted across controllers. We propose a novel switch migration protocol for enabling such load shifting, which conforms with the Openflow standard. We also build a prototype to demonstrate the efficacy of our design.
Prevalence and Follow-Up of Occult HCV Infection in an Italian Population Free of Clinically Detectable Infectious Liver Disease

Background Occult hepatitis C virus infection (OCI) is a recently described phenomenon characterized by undetectable levels of HCV-RNA in serum/plasma by current laboratory assays, with identifiable levels in peripheral blood mononuclear cells (PBMCs) and/or liver tissue by molecular tests with enhanced sensitivity. Previous results from our group showed an OCI prevalence of 3.3% in a population unselected for hepatic disease. The present study aimed to evaluate OCI prevalence in a larger cohort of infectious liver disease-free (ILDF) subjects. Clinical follow-up of OCI subjects was performed to investigate the natural history of the infection. Methods and Findings 439 subjects referred to a Turin Blood Bank for phlebotomy therapy were recruited. They included 314 ILDF subjects, 40 HCV-positive subjects and 85 HBV-positive subjects, of whom 7 were active HBV carriers. Six subjects (4/314 ILDF subjects [1.27%] and 2/7 active HBV carriers [28%]) were positive for HCV-RNA in PBMCs, but negative for serological and virological markers of HCV, indicating OCI. HCV genotypes were determined in the PBMCs of 3/6 OCI subjects two had type 1b; the other had type 2a/2c. OCI subjects were followed up for at least 2 years. After 12 months only one OCI persisted, showing a low HCV viral load (3.73×101 UI/ml). By the end of follow-up all OCI subjects were negative for HCV. No seroconversion, alteration of liver enzyme levels, or reduction of liver synthesis occurred during follow-up. Conclusions This study demonstrated the existence of OCI in ILDF subjects, and suggested a high OCI prevalence among active HBV carriers. Follow-up suggested that OCI could be transient, with a trend toward the decrease of HCV viral load to levels undetectable by conventional methods after 12–18 months. Confirmation studies with a longer follow-up period are needed for identification of the OCI clearance or recurrence rates, and to characterize the viruses involved.
Vitrectorhexis versus forceps posterior capsulorhexis in pediatric cataract surgery

This study was done to compare the results of posterior continuous curvilinear capsulorhexis created using forceps with those created using vitrector in eyes suffering from congenital cataract. Vitrectorhexis term was first used by Wilson et al in 1999. [1] Fifty eyes with congenital and developmental cataract were included in this study. The posterior capsulorhexis was created using utrata forceps in 17 eyes or through a vitrector in 33 eyes. Forceps capsulorhexis was performed before IOL implantation, while vitrectorhexis was performed after IOL implantation in the bag. The results of both the surgery were compared using the following criteria: incidence of extension of rhexis, ability to achieve posterior rhexis of appropriate size, ability to implant the IOL in the bag, the surgical time, and learning curve. Vitrectorhexis after IOL implantation was an easy to learn alternative to manual posterior continuous curvilinear capsulorhexis in pediatric cataract surgery. It was more predictable and reproducible, with a short learning curve and lesser surgical time.
Kidney disease is an independent risk factor for adverse fetal and maternal outcomes in pregnancy.

BACKGROUND Kidney disease has long been recognized to adversely affect fetal and maternal outcomes during pregnancy. The goal of this study is to better describe the population of women with kidney disease and provide a contemporary assessment of their risk for adverse events caused by kidney disease after adjustment for other contributing factors. METHODS We used Colorado birth and death certificate data for 1989 to 2001. Of 747,368 births during this period, 911 births from women with kidney disease were identified, and 4,606 births from women without kidney disease were randomly selected for comparison. Adverse fetal outcomes included fetal prematurity, low birth weight, or neonatal death, whereas adverse maternal outcomes included preeclampsia, eclampsia, or abruptio placenta. RESULTS Women with kidney disease were more likely to have comorbid illnesses, including chronic hypertension, anemia, diabetes, and lung and cardiac disease. Women with kidney disease had a greater frequency of adverse fetal (18.2% versus 9.5%) and maternal outcomes (13.7% versus 4.3%) compared with women without kidney disease (P < 0.0001). The presence of kidney disease independently increased the likelihood of adverse fetal outcomes (adjusted odds ratio [OR], 1.76; 95% confidence interval [CI], 1.40 to 2.21) and occurrence of adverse maternal outcomes, especially in the middle 1990s, among nulliparous women (adjusted OR, 4.07; 95% CI, 2.17 to 7.66). CONCLUSION This analysis shows that independent of other risk factors, kidney disease significantly increases the likelihood of unfavorable pregnancy outcomes for both mother and child.
Mutation-targeted therapy with sunitinib or everolimus in patients with advanced low-grade or intermediate-grade neuroendocrine tumours of the gastrointestinal tract and pancreas with or without cytoreductive surgery: protocol for a phase II clinical trial

Introduction Finding the optimal management strategy for patients with advanced, metastatic neuroendocrine tumours (NETs) of the gastrointestinal tract and pancreas is a work in progress. Sunitinib and everolimus are currently approved for the treatment of progressive, unresectable, locally advanced or metastatic low-grade or intermediate-grade pancreatic NETs. However, mutation-targeted therapy with sunitinib or everolimus has not been studied in this patient population. Methods and analysis This prospective, open-label phase II clinical trial was designed to determine if mutation-targeting therapy with sunitinib or everolimus for patients with advanced low-grade or intermediate-grade NETs is more effective than historically expected results with progression-free survival (PFS) as the primary end point. Patients ≥18 years of age with progressive, low-grade or intermediate-grade locally advanced or metastatic NETs are eligible for this study. Patients will undergo tumour biopsy (if they are not a surgical candidate) for tumour genotyping. Patients will be assigned to sunitininb or everolimus based on somatic/germline mutations profile. Patients who have disease progression on either sunitinib or everolimus will crossover to the other drug. Treatment will continue until disease progression, unacceptable toxicity, or consent to withdrawal. Using the proposed criteria, 44 patients will be accrued within each treatment group during a 48-month period (a total of 88 patients for the 2 treatments), and followed for up to an additional 12 months (a total of 60 months from entry of the first patient) to achieve 80% power in order to test whether there is an improvement in PFS compared to historically expected results, with a 0.10 α level one-sided significance test. Ethics and dissemination The study protocol was approved by the institutional review board of the National Cancer Institute (NCI-IRB Number 15C0040; iRIS Reference Number 339636). The results will be published in a peer-reviewed journal and shared with the worldwide medical community. Trial registration number NCT02315625.
Association analyses of single nucleotide polymorphisms in bovine stearoyl-CoA desaturase and fatty acid synthase genes with fatty acid composition in commercial cross-bred beef steers.

Two previously reported non-synonymous coding single nucleotide polymorphisms (SNPs) of bovine stearoyl-CoA desaturase (delta-9-desaturase) (SCD) (c.878C>T) and fatty acid synthase (FASN) (g:17924A>G) were assessed for their associations with 72 individual and 12 groups of fatty acids in brisket adipose tissue of 223 Canadian commercial cross-bred beef steers. It was found that the 'CC' genotype of the SCD SNP was significantly associated with lower concentrations of saturated fatty acids (SFA) including 10:0, 14:0 and 20:0, higher concentrations of monounsaturated fatty acids including 9c-14:1, 12c-16:1 and 13c-18:1, higher concentrations of polyunsaturated fatty acids (PUFA) including 9c,15c-18:2, 10c,12c-18:2, 11c,13t-18:2 and 12c,14t-18:2, but lower concentrations of other PUFA of 9c,13t/8t,12c and 20:2n-6 (P < 0.05). The 'AA' genotype of the FASN SNP was significantly associated with higher concentrations of SFAs of 10:0, 12:0, 13:0, 14:0 and 15:0, lower concentrations of unsaturated fatty acids of 9c-18:1 and 20:3n-6, and higher concentrations of unsaturated fatty acids of 9c-14:1 and 12c-16:1 (P < 0.05). Significant epistatic effects between the SCD and FASN SNP genotypes were also found for several fatty acids including 10:0, 23:0, 6t/7t/8t-18:1, 12t-18:1, 13t/14t-18:1, 16t-18:1, total trans18:1 and 9c,13t/8t,12c-18:2 (P < 0.05). These results further suggest that SCD and FASN are strong candidate genes influencing fatty acid composition in beef cattle.