Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrospective Analysis of Antimicrobial Susceptibility Trends (2000–2009) in Neisseria gonorrhoeae Isolates from Countries in Latin America and the Caribbean Shows Evolving Resistance to Ciprofloxacin, Azithromycin and Decreased Susceptibility to Ceftriaxone

Background The emergence of resistance and treatment failures to third generation cephalosporins prompted the revitalization of the global Gonococcal Antimicrobial Surveillance Program (GASP) to ensure that information regarding trends of the antimicrobial susceptibility of Neisseria gonorrhoeae isolates is up-to-date. Accordingly, former and potential GASP participants in Latin America and the Caribbean were contacted to reinitiate the GASP network in the region and to undertake a retrospective analysis of the antimicrobial susceptibility of N. gonorrhoeae isolates between 2000 and 2009. Methods Eleven countries participated in this retrospective analysis reporting on the susceptibility of N. gonorrhoeae isolates to up to 6 antibiotics as well as national treatment guidelines over the period. Antimicrobial susceptibility determination was carried out using combination of agar dilution and disk diffusion (Clinical Laboratory and Standards Institute) or Etest. Antimicrobial susceptibility data from each country were aggregated and analyzed for antimicrobial resistance trends in the region. Results More than 11,400 N. gonorrhoeae isolates were tested for antimicrobial susceptibility: 6 countries tested N. gonorrhoeae over the entire period and 5 countries tested sporadically. Decreased susceptibility to ceftriaxone was reported from 1 country (7 isolates, MICs >0.25 &mgr;g/ml) in 2007. No resistance to spectinomycin was reported. From 2000 to 2009, aggregated ciprofloxacin resistance increased from 2% (19/784) to 31% (311/1015) in 9 countries and azithromycin resistance increased from 6% (39/646) to 23% (225/962) in 4/6 reporting countries. Overall, resistance to penicillin and tetracycline decreased from 35% (441/1241) to 26% (258/975) and from 60% (476/792) to 35% (323/931), respectively. In 2009, resistance to gentamicin (3%, 4/122), chloramphenicol (5%, 6/120), and ofloxacin (2%, 6/120) was reported from 1 country. Conclusions The report of ceftriaxone-resistant isolates coupled with the emergence and spread of resistance to ciprofloxacin and azithromycin in Latin America and the Caribbean in the 2000s indicates the importance of active surveillance of N. gonorrhoeae antimicrobial susceptibility to determine antimicrobial resistance emerging trends so as to promptly inform and guide the development of effective treatment options for gonococcal infections.
Impulse Response Modeling for Underwater Wireless Optical Communication Links

In underwater wireless optical communication (UWOC) links, multiple scattering may cause temporal spread of beam pulse characterized by the impulse response, which therefore results in inter-symbol interference (ISI) and degrades system error performance. The impulse response of UWOC links has been investigated both theoretically and experimentally by researchers but has not been derived in simple closed-form to the best of our knowledge. In this paper, we analyze the optical characteristics of seawater and present a closed-form expression of double Gamma functions to model the channel impulse response. The double Gamma functions model fits well with Monte Carlo simulation results in turbid seawater such as coastal and harbor water. The bit-error-rate (BER) and channel bandwidth are further evaluated based on this model for various link ranges. Numerical results suggest that the temporal pulse spread strongly degrades the BER performance for high data rate UWOC systems with on-off keying (OOK) modulation and limits the channel bandwidth in turbid underwater environments. The zero-forcing (ZF) equalization designed based on our channel model has been adopted to overcome ISI and improve the system performance. It is plausible and convenient to utilize this impulse response model for performance analysis and system design of UWOC systems.
Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods.

BACKGROUND An obvious difference between breast-fed and formula-fed newborn infants is the development of the intestinal flora, considered to be of importance for protection against harmful micro-organisms and for the maturation of the intestinal immune system. In this study, novel molecular identification methods were used to verify the data obtained by traditional culture methods and to validate the culture independent fluorescent in situ hybridization (FISH) technique. METHODS From each of six breast-fed and six formula-fed newborn infants, six fecal samples were obtained during the first 20 days of life. The microbial compositions of the samples were analyzed by culturing on specific media and by FISH, by using specific 16S rRNA-targeted oligonucleotide probes. The colonies growing on the media were identified by random amplified polymorphic DNA pattern analysis and by polymerase chain reaction amplification and subsequent analysis of the 16S rRNA gene. RESULTS Molecular identification of the colonies showed that the selective media are insufficiently selective and unsuitable for quantitative analyses. Qualitative information from the culturing results combined with the data obtained by the FISH technique revealed initial colonization in all infants of a complex (adult-like) flora. After this initial colonization, a selection of bacterial strains began in all infants, in which Bifidobacterium strains played an important role. In all breast-fed infants, bifidobacteria become dominant, whereas in most formula-fed infants similar amounts of Bacteroides and bifidobacteria (approximately 40%) were found. The minor components of the fecal samples from breast-fed infants were mainly lactobacilli and streptococci; samples from formula-fed infants often contained staphylococci, Escherichia coli, and clostridia. CONCLUSIONS This study confirms the differences in development of intestinal flora between breast-fed and formula-fed infants. The results obtained from the FISH technique were consistent. Although the repertoire of probes for this study was not yet complete, the FISH technique will probably become the method of reference for future studies designed to develop breast-fed-like intestinal flora in formula-fed infants.
Evaluation of renal cortical perfusion by noninvasive power Doppler ultrasound during vascular occlusion and reperfusion.

BACKGROUND Urine output, a frequently used resuscitation end point, is presumed to represent renal cortical perfusion. However, no noninvasive method for direct measurement of renal perfusion exists. Power Doppler ultrasound (PDUS) is a method that reportedly is sensitive to low-velocity and microvascular blood flow and can depict it. This study aimed to develop a quantitative technique for PDUS image analysis, and to evaluate the ability of PDUS to quantify cortical perfusion during renal ischemia induced by vascular occlusion. METHODS A method was developed to determine the mean gray-scale intensity of PDUS images from within the renal cortex (PDUS image intensity). This index was hypothesized to represent renal cortical microvascular blood flow. Renal cortical blood flow was determined using fluorescent microspheres in five swine. Renal artery flow was measured with an ultrasonic flow probe. Power Doppler ultrasound was performed at baseline; at 75%, 50%, and 25% of baseline renal artery flow; and during reperfusion. RESULTS Subjectively, PDUS images showed decreases in image intensity corresponding to renal artery occlusion and increases after reperfusion. Cortical blood flow correlated well with renal artery flow (n = 25; r2 = 0.868) and with PDUS image intensity (n = 25; r2 = 0.844). CONCLUSION Noninvasive power Doppler ultrasound image intensity correlated well with invasively measured renal cortical blood flow, and may be useful during resuscitation of injured and critically ill patients.
Promoter DNA methylation is associated with KLF11 expression in epithelial ovarian cancer

As a transforming growth factor‐β (TGF‐β)‐inducible gene, the expression of Krüppel‐like transcription factor 11 (KLF11) is altered in several types of cancer. In the current study, through using human 9K CpG island array, KLF11 was identified as one of hypermethylated genes in RAS‐transformed ovarian T29H cells. Methylation of the KLF11 promoter was also observed in ovarian cancer tissue samples accompanied by significantly reduced KLF11 gene expression. Interestingly, the expression of SMAD2, SMAD3, and SMAD7 genes was reduced in the tumour, whilst no change was found in TGF‐β expression. Our data suggest a relationship between promoter DNA methylation and KLF11 gene expression in ovarian cancer tumorigenesis. © 2015 Wiley Periodicals, Inc.
Waves of novelties in the expansion into the adjacent possible

The emergence of novelties and their rise and fall in popularity is an ubiquitous phenomenon in human activities. The coexistence of popular evergreens with novel and sometimes ephemeral trends pervades technological, scientific and artistic production. Though this phenomenon is very intuitively captured by our common sense, a comprehensive explanation of how waves of novelties are not hampered by well established old-comers is still lacking. Here we first quantify this phenomenology by empirically looking at different systems that display innovation at very different levels: the creation of hashtags in Twitter, the evolution of online code repositories, the creation of texts and the listening of songs on online platforms. In all these systems surprisingly similar patterns emerge as the non-trivial outcome of two contrasting forces: the tendency of retracing already explored avenues (exploit) and the inclination to explore new possibilities. These findings are naturally explained in the framework of the expansion of the adjacent possible, a recently introduced theoretical framework that postulates the restructuring of the space of possibilities conditional to the occurrence of innovations. The predictions of our theoretical framework are borne out in all the phenomenologies investigated, paving the way to a better understanding and control of innovation processes.
Adalimumab for long-term treatment of psoriatic arthritis: forty-eight week data from the adalimumab effectiveness in psoriatic arthritis trial.

OBJECTIVE To evaluate the efficacy and safety of treatment with adalimumab, a fully human anti-tumor necrosis factor (anti-TNF) monoclonal antibody, over 48 weeks in patients with moderate to severe psoriatic arthritis (PsA). METHODS Patients who completed the Adalimumab Effectiveness in Psoriatic Arthritis Trial (ADEPT), a 24-week, double-blind study of adalimumab versus placebo in PsA, could elect to receive open-label adalimumab, 40 mg subcutaneously every other week after week 24. Radiographs were obtained at week 48 and were read with radiographs obtained previously. Clinical and radiographic efficacy data were analyzed overall and in patient subsets. Safety data were collected over 48 weeks. RESULTS At week 48, patients from the adalimumab arm of ADEPT (n = 151) had achieved American College of Rheumatology 20% improvement (ACR20), ACR50, and ACR70 response rates of 56%, 44%, and 30%, respectively. Among those evaluated with the Psoriasis Area and Severity Index (PASI) (n = 69), PASI50, PASI75, PASI90, and PASI100 response rates (> or =50%, > or =75%, > or =90%, and 100% reduction in PASI scores, respectively) were 67%, 58%, 46%, and 33%, respectively (ACR and PASI response rates were analyzed using nonresponder imputation). Improvements in disability, as measured by the Disability Index of the Health Assessment Questionnaire (mean change in score -0.4) were sustained from week 24 to week 48. At week 24 and week 48, the mean changes from baseline in the modified total Sharp score were -0.1 and 0.1, respectively, for patients who received adalimumab for 48 weeks (n = 133), and 0.9 and 1.0, respectively, for patients who received placebo for 24 weeks followed by adalimumab for 24 weeks (n = 141). Adalimumab demonstrated clinical and radiographic efficacy regardless of whether patients were receiving methotrexate (MTX) at baseline. Adalimumab was generally safe and well tolerated through week 48. CONCLUSION Adalimumab improved joint and skin manifestations, reduced disability, and inhibited radiographic progression over 48 weeks in patients with PsA who were participants in ADEPT. MTX use at baseline was not required for clinical or radiographic efficacy. Adalimumab had a good safety profile through week 48.
Chronic blockade of angiotensin II action prevents glomerulosclerosis, but induces graft vasculopathy in experimental kidney transplantation

Long‐term renin–angiotensin system blockade is beneficial in a variety of renal diseases. This study examines the long‐term (34 weeks) effects of the angiotensin‐converting enzyme inhibitor lisinopril and the angiotensin II receptor type I blocker L158,809 in the Fisher to Lewis rat model of chronic renal transplant failure. Treatment in allografted rats with lisinopril or L158,809 was initiated 10 days after transplantation, or at the time when proteinuria exceeded 50 mg/24 h. Untreated allografts and syngrafts served as controls. In contrast to syngrafts, untreated allografts developed proteinuria, hypercholesterolaemia, interstitial damage, and glomerulosclerosis. Lisinopril or L158,809 treatment in allografts starting at day 10 after transplantation completely prevented this, with the exception of interstitial damage, but this treatment also caused a reduction in blood pressure and renal function. Moreover, the intimal surface area of the renal arteries was dramatically increased in allografts treated with either lisinopril or L158,809 compared with untreated allografted rats. Treatment once proteinuria had developed was less effective in preventing glomerulosclerosis, but also caused less intimal expansion. Thus, chronic renin–angiotensin system blockade preserves glomerular morphology in the absence of proteinuria, but enhances intimal hyperplasia and reduces renal function in experimental transplantation. In view of these results, it should be questioned whether such treatment benefits renal transplant patients in the long term. Copyright © 2001 John Wiley & Sons, Ltd.
Comparison of “Risk-Adjusted” Hospital Outcomes

Background— A frequent challenge in outcomes research is the comparison of rates from different populations. One common example with substantial health policy implications involves the determination and comparison of hospital outcomes. The concept of “risk-adjusted” outcomes is frequently misunderstood, particularly when it is used to justify the direct comparison of performance at 2 specific institutions. Methods and Results— Data from 14 Massachusetts hospitals were analyzed for 4393 adults undergoing isolated coronary artery bypass graft surgery in 2003. Mortality estimates were adjusted using clinical data prospectively collected by hospital personnel and submitted to a data coordinating center designated by the state. The primary outcome was hospital-specific, risk-standardized, 30-day all-cause mortality after surgery. Propensity scores were used to assess the comparability of case mix (covariate balance) for each Massachusetts hospital relative to the pool of patients undergoing coronary artery bypass grafting surgery at the remaining hospitals and for selected pairwise comparisons. Using hierarchical logistic regression, we indirectly standardized the mortality rate of each hospital using its expected rate. Predictive cross-validation was used to avoid underidentification of true outlying hospitals. Overall, there was sufficient overlap between the case mix of each hospital and that of all other Massachusetts hospitals to justify comparison of individual hospital performance with that of the remaining hospitals. As expected, some pairwise hospital comparisons indicated lack of comparability. This finding illustrates the fallacy of assuming that risk adjustment per se is sufficient to permit direct side-by-side comparison of healthcare providers. In some instances, such analyses may be facilitated by the use of propensity scores to improve covariate balance between institutions and to justify such comparisons. Conclusions— Risk-adjusted outcomes, commonly the focus of public report cards, have a specific interpretation. Using indirect standardization, these outcomes reflect a provider's performance for its specific case mix relative to the expected performance of an average provider for that same case mix. Unless study design or post hoc adjustments have resulted in reasonable overlap of case-mix distributions, such risk-adjusted outcomes should not be used to directly compare one institution with another.
The Influence of Gas-to-Liquids and Natural Gas Production Technology Penetration on the Crude Oil-Natural Gas Price Relationship

This work has been funded in part by BP, the MITEI ENI Energy Fellowship, the MITEI Martin Family Fellowship, and sponsors of MIT’s Joint Program on the Science and Policy of Global Change. The Joint Program on the Science and Policy of Global Change is funded by the U.S. Department of Energy, Office of Science under grants DE-FG02-94ER61937, DE-FG02- 08ER64597, DE-FG02-93ER61677, DE-SC0003906, DE-SC0007114, XEU-0-9920-01; the U.S. Department of Energy, Oak Ridge National Laboratory under Subcontract 4000109855; the U.S. Environmental Protection Agency under grants XA-83240101, PI-83412601-0, RD-83427901-0, XA-83505101-0, XA-83600001-1, and subcontract UTA12-000624; the U.S. National Science Foundation under grants AGS-0944121, EFRI-0835414, IIS-1028163, ECCS-1128147, ARC-1203526, EF-1137306, AGS-1216707, and SES-0825915; the U.S. National Aeronautics and Space Administration (NASA) under grants NNX06AC30A, NNX07AI49G, NNX11AN72G and Sub Agreement No. 08-SFWS-209365.MIT; the U.S. Federal Aviation Administration under grants 06-C-NE-MIT, 09-C-NE-MIT, Agmt. No. 4103-30368; the U.S. Department of Transportation under grant DTRT57-10-C-10015; the Electric Power Research Institute under grant EP-P32616/C15124, EP-P8154/C4106; the U.S. Department of Agriculture under grant 58-6000-2-0099, 58-0111-9-001; and a consortium of 35 industrial and foundation sponsors (for the complete list see: http://globalchange.mit.edu/sponsors/all).
Individual Differences in Subjective Utility and Risk Preferences: The Influence of Hedonic Capacity and Trait Anxiety

Individual differences in decision-making are important in both normal populations and psychiatric conditions. Variability in decision-making could be mediated by different subjective utilities or by other processes. For example, while traditional economic accounts attribute risk aversion to a concave subjective utility curve, in practice other factors could affect risk behavior. This distinction may have important implications for understanding the biological basis of variability in decision-making and for developing interventions to improve decision-making. Another aspect of decision-making that may vary between individuals is the sensitivity of subjective utility to counterfactual outcomes (outcomes that could have occurred, but did not). We investigated decision-making in relation to hedonic capacity and trait anxiety, two traits that relate to psychiatric conditions but also vary in the general population. Subjects performed a decision-making task, in which they chose between low- and high-risk gambles to win 0, 20, or 40 points on each trial. Subjects then rated satisfaction after each outcome on a visual analog scale, indicating subjective utility. Hedonic capacity was positively associated with the subjective utility of winning 20 points but was not associated with the concavity of the subjective utility curve (constructed using the mean subjective utility of winning 0, 20, or 40 points). Consistent with economic theory, concavity of the subjective utility curve was associated with risk aversion. Hedonic capacity was independently associated with risk seeking (i.e., not mediated by the shape of the subjective utility curve), while trait anxiety was unrelated to risk preferences. Contrary to our expectations, counterfactual sensitivity was unrelated to hedonic capacity and trait anxiety. Nevertheless, trait anxiety was associated with a self-report measure of regret-proneness, suggesting that counterfactual influences may occur via a pathway that is separate from immediate counterfactual processing biases. Taken together, our results show that hedonic capacity but not trait anxiety affects risk-taking through a mechanism that appears independent of the shape of the subjective utility curve, while hedonic capacity and trait anxiety do not affect the influence of counterfactual outcomes on subjective utility. The results have implications for understanding the underlying mechanisms of variable decision-making and for developing interventions to improve decision-making.
Expression of Cutaneous Lymphocyte-Associated Antigen Regulated by a Set of Glycosyltransferases in Human T Cells: Involvement of α1,3-Fucosyltransferase VII and β1,4-Galactosyltransferase I

Cutaneous lymphocyte-associated antigen (CLA), which plays a key part in skin homing of human CD4 + memory T cells via CLA/E-selectin binding, is upregulated by IL-12 and downregulated by IL-4. Although α1,3-fucosyltransferase VII is essential for synthesis of the CLA carbohydrate epitope, little is known about how the CLA expression is regulated by a number of glycosyltransferases. A 6 wk long-term culture for the in vitro differentiation of naive Th cells to memory Th1 cells was employed. By repeated activation in the presence of IL-12, naive T cells differentiated into memory Th1 cells, resulting in the upregulation of CLA expression. The switching of cytokine from IL-12 to IL-4 at three cycles resulted in a marked downregulation of CLA. The transcript levels of 16 glycosyltransferases and P-selectin glycoprotein ligand-1, all considered to be potentially involved in CLA synthesis, were determined after each cycle. The level of CLA expression was well correlated with the amounts of α1,3-fucosyltransferase VII and β1,4-galactosyltransferase I. Both were upregulated by IL-12 and downregulated by IL-4. In particular, α1,3-fucosyltransferase VII levels decreased markedly in the presence of IL-4. P-selectin glycoprotein ligand-1 and Core 2 β1,6- N -acetylglucosaminyltransferase were progressively up-regulated by repeated IL-12 stimulation, but they were not downregulated by IL-4. The transcript levels of some genes examined were constitutive without any correlation to CLA expression. These results suggest that the level of CLA expression is determined by α1,3-fucosyltransferase VII and β1,4-galactosyltransferase I, the other enzymes merely participating in the synthesis of CLA. In peripheral blood mononuclear cells, IL-12 and IL-4 profoundly upregulated and downregulated the α1,3-fucosyltransferase VII transcripts, respectively, but not the β1,4-galactosyltransferase I ones, within only 2 h of in vitro culture. This suggested that α1,3-fucosyltransferase VII is transcriptionally regulated directly by IL-12 and IL-4.
Precise outage specifications for first-order PMD

Advanced simulations show that closed-form outage predictions for first-order polarization-mode dispersion (PMD) can be inaccurate in practical communication systems. We adapt the two-step method to obtain outage probabilities for arbitrary optical signals and receiver designs. The approach is free of restrictive assumptions and allows for direct experimental testing, required for accurate PMD outage specifications.