Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of IS1515, a Functional Insertion Sequence in Streptococcus pneumoniae

ABSTRACT We describe the characterization of a new insertion sequence, IS1515, identified in the genome of Streptococcus pneumoniae I41R, an unencapsulated mutant isolated many years ago (R. Austrian, H. P. Bernheimer, E. E. B. Smith, and G. T. Mills, J. Exp. Med. 110:585–602, 1959). A copy of this element located in the cap1EI41R gene was sequenced. The 871-bp-long IS1515 element possesses 12-bp perfect inverted repeats and generates a 3-bp target duplication upon insertion. The IS encodes a protein of 271 amino acid residues similar to the putative transposases of other insertion sequences, namely IS1381 from S. pneumoniae, ISL2from Lactobacillus helveticus, IS702 from the cyanobacterium Calothrix sp. strain PCC 7601, and IS112 from Streptomyces albus G. IS1515 appears to be present in the genome of most type 1 pneumococci in a maximum of 13 copies, although it has also been found in the chromosome of pneumococcal isolates belonging to other serotypes. We have found that the unencapsulated phenotype of strain I41R is the result of both the presence of an IS1515 copy and a frameshift mutation in the cap1EI41Rgene. Precise excision of the IS was observed in the type 1 encapsulated transformants isolated in experiments designed to repair the frameshift. These results reveal that IS1515 behaves quite differently from other previously described pneumococcal insertion sequences. Several copies of IS1515 were also able to excise and move to another locations in the chromosome ofS. pneumoniae. To our knowledge, this is the first report of a functional IS in pneumococcus.
Tolerance and Pharmacokinetics of Single‐Dose Atorvastatin, a Potent Inhibitor of HMG‐CoA Reductase, in Healthy Subjects

Tolerance and pharmacokinetics after single‐dose administration of atorvastatin, an investigational inhibitor of HMG‐CoA reductase, were examined in 22 healthy volunteers in a three‐period, partially‐blinded study. Participants received capsule and solution doses of atorvastatin (0.5 to 120 mg) and placebo at weekly intervals. Atorvastatin was well tolerated at doses as high as 80 mg. The adverse event profile was similar after administration of atorvastatin capsules and placebo. Atorvastatin solution was slightly less well tolerated. The most common side effect after administration of capsules and solution was headache, followed by sporadic reports of diarrhea, flatulence, and nausea. At the 120‐mg solution dose, one participant experienced mild, transient restlessness, euphoria, and mental confusion that were considered to be dose‐limiting side effects. Mean concentrations of atorvastatin, maximum concentration (Cmax), and area under the concentration—time curve from time 0 to the time of the last detectable concentration (AUC0‐tldc) increased with increasing dose. Plasma elimination half‐life (t1/2) ranged from 14.7 to 57.6 hours. The bioavailability of atorvastatin capsules was similar to that of solution. These results suggest that atorvastatin is well tolerated after single doses as high as 80 mg, and may require administration only once daily.
Stride Angle as a Novel Indicator of Running Economy in Well-Trained Runners

Abstract Santos-Concejero, J, Tam, N, Granados, C, Irazusta, J, Bidaurrazaga-Letona, I, Zabala-Lili, J, and Gil, SM. Stride angle as a novel indicator of running economy in well-trained runners. J Strength Cond Res 28(7): 1889–1895, 2014—The main purpose of this study was to investigate the relationship between a novel biomechanical variable, the stride angle, and running economy (RE) in a homogeneous group of long-distance athletes. Twenty-five well-trained male runners completed 4-minute running stages on a treadmill at different set velocities. During the test, biomechanical variables such as stride angle, swing time, ground contact time, stride length, stride frequency, and the different sub-phases of ground contact were recorded using an optical measurement system. V[Combining Dot Above]O2 values at velocities below the lactate threshold were measured to calculate RE. Stride angle was negatively correlated with RE at every speed (p < 0.001, large effect sizes). Running economy was also negatively correlated with swing phase and positively correlated with ground contact time and running performance according to the best 10-km race time (p ⩽ 0.05, moderate and large effect sizes). Last, stride angle was correlated with ground contact time at every speed (p < 0.001, large effect sizes). In conclusion, it seems that optimal execution of stride angle allows runners to minimize contact time during ground contact, whereby facilitating a better RE. Coaches and/or athletes may find stride angle a useful and easily obtainable measure to track and make alterations to running technique, because changes in stride angle may influence the energy cost of running and lead to improved performance.
A Novel Approach for Phishing URLs Detection

Seeking sensitive user data in the form of online banking user-id and passwords or credit card information, which may then be used by ‘phishers’ for their own personal gain is the primary objective of the phishing. With the increase in the online trading activities, there has been a phenomenal increase in the phishing scams which have now started achieving monstrous proportions. This paper gives strategies for distinguishing phishing sites by dissecting different components of phishing URLs by Machine learning systems. It talks about the systems utilized for identification of phishing sites in view of lexical features. We consider different data mining approaches for assessment of the features to show signs of improvement comprehension of the structure of URLs that spread phishing. We use KNN, Regression and SVM classifiers.
Calcification of the Arctic coralline red algae Lithothamnion glaciale in response to elevated CO2

Rising atmospheric CO2 concentrations could cause a calcium carbonate subsaturation of Arctic surface waters in the next 20 yr, making these waters corrosive for calcareous organisms. It is presently unknown what effects this will have on Arctic calcifying organisms and the ecosystems of which they are integral components. So far, acidification effects on crustose coralline red algae (CCA) have only been studied in tropical and Mediterranean species. In this work, we investigated calcification rates of the CCA Lithothamnion glaciale collected in northwest Svalbard in laboratory experiments under future atmospheric CO2 concentrations. The algae were exposed to simulated Arctic summer and winter light conditions in 2 separate experiments at optimum growth temperatures. We found a significant negative effect of increased CO2 levels on the net calcification rates of L. glaciale in both experiments. Annual mean net dissolution of L. glaciale was estimated to start at an aragonite saturation state between 1.1 and 0.9 which is projected to occur in parts of the Arctic surface ocean between 2030 and 2050 if emissions follow ‘business as usual’ scenarios (SRES A2; IPCC 2007). The massive skeleton of CCA, which consist of more than 80% calcium carbonate, is considered crucial to withstanding natural stresses such as water movement, overgrowth or grazing. The observed strong negative response of this Arctic CCA to increased CO2 levels suggests severe threats of the projected ocean acidification for an important habitat provider in the Arctic coastal ocean.
Caring for Mom and Neglecting Yourself? The Health Effects of Caring for an Elderly Parent

We examine the physical and mental health effects of providing care to an elderly mother on the adult child caregiver. We address the endogeneity of the selection in and out of caregiving using an instrumental variable approach, using the death of the care recipient and sibling characteristics. We also carefully control for baseline health and work status of the adult child. We explore flexible specifications, such as Arellano-Bond estimation techniques. Continued caregiving over time increases depressive symptoms and decreases self-rated health for married women and married men. In addition, the increase in depressive symptoms is persistent for married women. While depressive symptoms for single men and women are not affected by continued caregiving, there is evidence of increased incidence of heart conditions for single men, and that these effects are persistent. Robustness checks indicate that these health changes can be directly attributable to caregiving behavior, and not due to a direct effect of the death of the mother. The initial onset of caregiving has modest immediate negative effects on depressive symptoms for married women and no immediate effects on physical health. Negative physical health effects emerge 2 years later, however, suggesting that there are delayed effects on health that would be missed with a short recall period. Initial caregiving does not affect health of married men.
Prediction of the growth response in children with various growth disorders treated with growth hormone: analyses of data from the Kabi Pharmacia International Growth Study

Analyses to predict the growth response to recombinant human growth hormone (GH) in prepubertal children during the first year of treatment were performed on data from 472 patients with idiopathic GH deficiency (IGHD), 202 children with Turner's syndrome, 327 children with idiopathic short stature (ISS) and 135 children with intrauterine growth retardation (IUGR). In IGHD, 56% of the variability of the response could be predicted from a model based on six variables. These variables could be ranked in order of importance as follows: target height SDS minus height SDS, chronological age, frequency of GH injections, dose of GH, weight‐for‐height index, and birth weight SDS. When the model for IGHD was applied to Turner's syndrome, ISS and IUGR, there was a high degree of similarity between the predicted and achieved growth response in ISS and IUGR. However, an uneven distribution within the plot of Studentized residuals in ISS and IUGR suggested heterogeneity within these populations. Prediction of growth in Turner's syndrome was greatly exaggerated by the model for IGHD, suggesting a different pathogenesis as the basis of the growth disorder. Specific prediction models were therefore developed for Turner's syndrome, ISS and IUGR. In all three disorders, the dose of GH was found to be the most important predictor, suggesting that, in contrast to IGHD, first‐year growth is governed less by the difference between height and the presumed genetically determined target height. Again, in contrast to IGHD, this suggests that catch‐up phenomena are not involved. As the predictability of the variation in growth response in Turner's syndrome, ISS and IUGR did not exceed 32% (for ISS), the search for new predictors should continue in these disorders.
Forensic Psychiatry and Elderly People — A Retrospective Review

Elderly offenders have rarely been studied. We describe a population of elderly offenders referred to a forensic psychiatric service over a 20-year period (1972–1992). Patients over 65 years charged with a criminal offence were eligible for inclusion. For the purpose of the study they were divided into four study groups. Demographic data, forensic and psychiatric history, alcohol abuse, charge and psychiatric diagnosis are reported. The possible reasons for the high proportion of sex offences are discussed. Difficulties were encountered in the transfer of longstay elderly offenders back to their local area. Finally, we recommend that most of the elderly patients referred to the forensic service for treatment would best be cared for in their local catchment area hospital rather than in a high security hospital.
Thoracoplasty for the Treatment of Rib Prominence in Thoracic Scoliosis

Objectives The authors evaluated the reduction of fib prominence in patients who underwent thoraco plasty wersus matched control patients who underwent fuaion without thoracoplasty. Summary of Background Data Correction in rib prominence with thoracoplasty is not well quantified in the literature. The role of rib bone graft as an alternative to iliac crest is unknown. Methods Fifty patients who underwent thoracoplasty were revlewed and compared with 26 patients who underwent fuaion without thoracoplacty. Rib prominerca, dinical data, and patient outcome were evaluated. Results The mean reduction in rib prominence was 71% in the thoracoplasty group and 17% in the control group. There was no difference in estimated blood loss, operative time, and length of hospitalization. Satisfaction with thoracoplasty was high. Conclusions Thoracoplasty is more effective than fusion alone for reduction of rib prominence in thoracic scoliosis; it provides ample, effective bone graft for fusion.
Prevention of Postherniorrhaphy Urinary Retention with Prazosin

Urinary retention that necessitates catheterization after herniorrhaphy is a well known, but usually ignored, situation. Increased sympathetic activity resulting from surgery may be the contributing factor. Blockade of a receptors in the bladder neck and urethral sphinchter may prevent postoperative urinary retention. In this prospective placebo-controlled study, the efficacy of prazosin in preventing postoperative urinary retention after herniorrhaphy was investigated in 156 patients. Patients were randomized into two groups. Patients in Group I (control) were given placebo orally 12 hours before surgery, just before surgery, and 12 and 24 hours after surgery. In Group II, 1 mg of prazosin was given in the same manner of placebo. Nine of 84 patients (10.8%) in the prazosin group and 18 of 72 patients (25%) in the placebo group developed urinary retention. Catheterization was required in only 3 patients (3.5%) in the prazosin group compared to 10 patients (13.8%) in placebo-treated group (P < 0.05). In conclusion, prophylactic use of prazosin after herniorrhaphy significantly reduced the incidence of urinary retention and catheterization.
Gains of 12q are the most frequent genomic imbalances in adult fibrosarcoma and are correlated with a poor outcome

Comparative genomic hybridization was used to analyze 41 adult fibrosarcomas from 34 patients. Thirty‐one patients showed in their tumors DNA sequence copy number changes (mean 11, range 3–25). The minimal common regions for the most frequent gains were narrowed down to 12q21 (18 cases); 12q14–q15 and 14q22 (16 cases each); 4q22, 7q31, and 14q23–q24 (15 cases each); and 4q21, 4q23–q24, 8q22, and 12q22 (14 cases each). Twenty‐five high‐level amplifications were observed in 12 samples. 12q21 and 18p were affected three times each; and 1p21, 4q31.3, 7p21, 12q14–q15, Xp22.1–p22.2, and Xq22–q23 two times each. Losses were less frequent than gains. Early stages of adult fibrosarcomas were characterized by frequent gains of chromosomes 2, 4q, and 14q, whereas gains of chromosomes 7 and 8q were associated with progression. Gains of 12q were frequent in all of the developmental steps of this soft‐tissue sarcoma. By investigation of several tumors of the same patient, a number of corresponding changes were always detected. Adult fibrosarcomas from patients who died during the observation time showed statistically significant more frequent gains of 8q, 12q, 13q, and 15q compared to the fibrosarcomas of patients who are alive. Gains and high‐level amplifications of 12q14–q22, which were the most frequent genomic imbalances, partly reflected an MDM2 amplification, indicating the importance of this region in the tumorigenesis of sarcomas. In adult fibrosarcomas, a gain of 12q22 correlated significantly (P = 0.028) with a poor overall survival rate. © 2002 Wiley‐Liss, Inc.
Neuregulin expression modulates clinical response to trastuzumab in patients with metastatic breast cancer.

PURPOSE Human epidermal growth factor receptor 2 (HER-2) overexpression has been associated with the genesis and progression of a subset of breast cancers. The function of HER-2 may be upregulated by overexpression or by the availability of neuregulins (NRGs), a group of transmembrane growth factors. Transmembrane NRGs strongly activated HER-2 and cell proliferation in breast cancer cells that did not overexpress HER-2, and treatment with trastuzumab prevented the proliferative action of transmembrane NRG. This raised the relevant clinical question of whether patients considered as HER-2 negative, but expressing transmembrane NRG, may benefit from treatment with trastuzumab. PATIENTS AND METHODS MCF7 cells expressing transmembrane NRG (MCF7-NRG2c) were injected into mice, and their sensitivity to trastuzumab was assessed. A retrospective study of 124 patients with early-stage or metastatic breast cancer was conducted. Expression of transmembrane NRG was evaluated by immunohistochemistry. In 11 patients, Western blot for NRGs was also carried out. Statistics were performed to analyze possible correlations between NRG expression and response to trastuzumab-based therapies, event-free survival, and overall survival (OS). RESULTS Trastuzumab inhibited tumor growth in mice injected with MCF7-NRG2c cells. Transmembrane NRG was frequently expressed in breast cancer patients. Overexpression of transmembrane NRG significantly correlated with a longer event-free survival and OS in patients with low or normal HER-2 expression who were treated with trastuzumab-based therapies but not in patients with HER-2 overexpression. CONCLUSION We suggest that the spectrum of patients who may benefit from trastuzumab-based therapies may be widened to include patients with metastatic breast cancer without HER-2 amplification but who express transmembrane NRGs.
Stabilization of Switched Linear Systems with Multiple Time-Varying Delays

This paper considers the problem of stabilization via state feedback and/or state-based switching for switched linear systems with multiple time-varying delays. The main contribution of this paper is that we proved the switched linear delay system will be stabilizable via state feedback and/or switching for an appropriate upper bound of delays if the corresponding (closed-loop) system with zero delays has a Hurwitz stable convex combination. Particularly, the maximal allowable upper bound of delays can be obtained from some feasible linear matrix inequalities (LMIs)
How do Very Open Economies Absorb Large Immigration Flows? Recent Evidence from Spanish Regions

In recent years, Spain has received unprecedented immigration flows. Between 2001 and 2006 the fraction of the population born abroad more than doubled, increasing from 4.8% to 10.8%. For Spanish provinces with above-median inflows (relative to population), immigration increased by 24% the number of high school dropouts while only increasing college graduates by 11%. We study different channels by which regional labor markets have absorbed the large increase in relative supply of low educated workers. We identify the exogenous supply shock using historical immigrant settlement patterns by country of origin. Using data from the Labor Force Survey and the decennial Census, we find a large expansion of employment in high immigration regions. Disaggregating by industry, the absorption operated through large increases in the share of low-educated workers, compared to the same industry in low-immigration regions. We do not find changes in sectoral specialization. Overall, and perhaps surprisingly, the pattern of absorption is very similar to the one found in the US.
Getting the Query Right for Crisis Informatics Design Issues for Web-Based Analysis Environments

Web-based data analysis environments are powerful platforms for exploring large data sets. To ensure that these environments meet the needs of analysts, a human-centered design perspective is needed. Interfaces to these platforms should provide flexible search, support user-generated content, and enable collaboration. We report on our efforts to design and develop a web interface for a custom analytics platform—EPIC Analyze— which provides interactive search over large Twitter data sets collected during crisis events. We performed seven think-aloud sessions with researchers who regularly analyze crisis data sets and compiled their feedback. They identified a need for a "big picture" view of an event, flexible querying capabilities, and user-defined coding schemes. Adding these features allowed EPIC Analyze to meet the needs of these analysts and enable exploratory research on crisis data. In performing this work, we identified an opportunity to migrate the software architecture of EPIC Analyze to one based on microservices. We report on the lessons learned in performing this migration and the impact it had on EPIC Analyze's capabilities. We also reflect on the benefits a microservices approach can have on the design of data-intensive software systems like EPIC Analyze.
Enhancing Retirement Security Through the Tax Code: The Efficacy of Tax-Based Subsidies in Life Annuity Markets

Abstract The under-development of existing annuity markets coupled with the secular trend away from traditional pensions towards defined contribution accounts in the U.S. raises significant concerns about the adequacy of retirement income for future retirees. We develop dynamic programming techniques to evaluate the efficacy of policies designed to address this concern by encouraging annuitization. Our analysis suggests that policies providing monetary incentives through the tax code can indeed significantly enhance annuitization among retirees: our central estimates suggest that tax-exemption based policies which have been recently proposed in Congress have the potential to increase annuitization by as much as $50,000 for each retired household, at a relatively modest revenue cost to the government. Similar sized policies based instead on refundable tax credits may be more desirable from both efficiency and distributional perspectives.
[Prevention of post-ERCP acute pancreatitis with octreotide].

Acute pancreatitis is one of the most serious complications in endoscopic cholangio-pancreatography (ERCP) and endoscopic sphincterotomy (EPT). Many attempts to avoid such complication have proved to be unsuccessful. The aim of this study was to evaluate the therapeutic effect of octreotide acetate in preventing acute pancreatitis following ERCP. The study was carried out over 100 patients, randomly allocated in two groups. The first group of patients (50 pt.) received 0.1 mg of octreotide acetate s.c. 45 minutes before the ERCP, followed by another dose given 6 hours later. The second group received placebo s.c.
DEM resolution dependencies of terrain attributes across a landscape

This paper documents resolution dependencies in terrain analysis and describes how they vary across landform location. Six terrain attributes were evaluated as a function of DEM resolution—slope, plan curvature, profile curvature, north–south slope orientation, east–west slope orientation, and topographic wetness index. The research highlights the effect of varying spatial resolution through a spatial sampling/resampling scheme while maintaining sets of indexed sample points at various resolutions. Tested sample points therefore coincide exactly between two directly compared resolutions in terms of their location and elevation value. An unsupervised landform classification procedure based on statistical clustering algorithms was employed to define landform classes in a reproducible manner. Correlation and regression analyses identified sensitive and consistent responses for each attribute as resolution was changed, although the tested terrain attributes responded in characteristically different ways. These responses displayed distinguishable patterns among various landform classes, a conclusion that was further verified by a series of two‐sample, two‐tailed t‐tests.