Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Mycoplasma pneumoniae Genome Sequences from Strains Isolated from Symptomatic and Asymptomatic Patients

Mycoplasma pneumoniae is a common cause of respiratory tract infections (RTIs) in children. We recently demonstrated that this bacterium can be carried asymptomatically in the respiratory tract of children. To identify potential genetic differences between M. pneumoniae strains that are carried asymptomatically and those that cause symptomatic infections, we performed whole-genome sequence analysis of 20 M. pneumoniae strains. The analyzed strains included 3 reference strains, 3 strains isolated from asymptomatic children, 13 strains isolated from clinically well-defined patients suffering from an upper (n = 4) or lower (n = 9) RTI, and one strain isolated from a follow-up patient who recently recovered from an RTI. The obtained sequences were each compared to the sequences of the reference strains. To find differences between strains isolated from asymptomatic and symptomatic individuals, a variant comparison was performed between the different groups of strains. Irrespective of the group (asymptomatic vs. symptomatic) from which the strains originated, subtype 1 and subtype 2 strains formed separate clusters. We could not identify a specific genotype associated with M. pneumoniae virulence. However, we found marked genetic differences between clinical isolates and the reference strains, which indicated that the latter strains may not be regarded as appropriate representatives of circulating M. pneumoniae strains.
Total Internal Reflection Fluorescence Quantification of Receptor Pharmacology

Total internal reflection fluorescence (TIRF) microscopy has been widely used as a single molecule imaging technique to study various fundamental aspects of cell biology, owing to its ability to selectively excite a very thin fluorescent volume immediately above the substrate on which the cells are grown. However, TIRF microscopy has found little use in high content screening due to its complexity in instrumental setup and experimental procedures. Inspired by the recent demonstration of label-free evanescent wave biosensors for cell phenotypic profiling and drug screening with high throughput, we had hypothesized and demonstrated that TIRF imaging is also amenable to receptor pharmacology profiling. This paper reviews key considerations and recent applications of TIRF imaging for pharmacology profiling.
Using simulation to evaluate prediction techniques [for software]

The need for accurate software prediction systems increases as software becomes larger and more complex. A variety of techniques have been proposed, but none has proved consistently accurate. The underlying characteristics of the data set influence the choice of the prediction system to be used. It has proved difficult to obtain significant results over small data sets; consequently, we required large validation data sets. Moreover, we wished to control the characteristics of such data sets in order to systematically explore the relationship between accuracy, choice of prediction system and data set characteristics. Our solution has been to simulate data, allowing both control and the possibility of large validation cases. We compared regression, rule induction and nearest neighbours (a form of case-based reasoning). The results suggest that there are significant differences depending upon the characteristics of the data set. Consequently, researchers should consider the prediction context when evaluating competing prediction systems. We also observed that the more "messy" the data and the more complex the relationship with the dependent variable, the more variability in the results. This became apparent since we sampled two different training sets from each simulated population of data. In the more complex cases, we observed significantly different results depending upon the training set. This suggests that researchers will need to exercise caution when comparing different approaches and utilise procedures such as bootstrapping in order to generate multiple samples for training purposes.
Cardiovascular risk factors in children and adolescents with anxiety disorders and their association with disease severity.

INTRODUCTION Studies suggest that anxiety is an independent predictor of adverse cardiovascular events. However, few studies have investigated the association between cardiovascular risk factors (RF) and severity of anxiety disorders (AD) in childhood and adolescents. OBJECTIVES To assess the prevalence of cardiovascular RF in children and adolescents with anxiety disorders and their association with disease severity. METHOD Cross-sectional study assessing nutritional and anthropometric RF, as well as % body fat (BF), blood pressure (BP), physical activity level, anxiety symptoms and severity of the anxiety disorder of children and adolescents. RESULTS A total of 65 children and adolescents (8.6 } 1.7 years) took part in the study. Excess saturated fatty acid intake (52.3%), high body mass index (50.8%), high BP (50.8%) and physical inactivity (50.0%) were the most prevalent cardiovascular RF. There was a significant association between the severity of the anxiety and the presence of ≥ 6 RF per patient (p=0.026), excess abdominal body fat as assessed by waist circumference (p=0.019) and conicity index (p=0,053), and excess % BF (p=0.035). Generalized anxiety disorder was significantly associated with high BP (p=0.044). CONCLUSION A high prevalence of cardiovascular RF was found in the present sample, and individuals with more severe anxiety had greater cardiovascular risk. The characterization of the cardiovascular risk in young populations, especially in individuals with AD who are therefore more susceptible to CVD, is crucial for the development of lifestyle interventions in these patients.
Tuning garbage collection for reducing memory system energy in an embedded java environment

Java has been widely adopted as one of the software platforms for the seamless integration of diverse computing devices. Over the last year, there has been great momentum in adopting Java technology in devices such as cellphones, PDAs, and pagers where optimizing energy consumption is critical. Since, traditionally, the Java virtual machine (JVM), the cornerstone of Java technology, is tuned for performance, taking into account energy consumption requires reevaluation, and possibly redesign of the virtual machine. This motivates us to tune specific components of the virtual machine for a battery-operated architecture. As embedded JVMs are designed to run for long periods of time on limited-memory embedded systems, creating and managing Java objects is of critical importance. The garbage collector (GC) is an important part of the JVM responsible for the automatic reclamation of unused memory. This article shows that the GC is not only important for limited-memory systems but also for energy-constrained architectures.This article focuses on tuning the GC to reduce energy consumption in a multibanked memory architecture. Tuning the GC is important not because it consumes a sizeable portion of overall energy during execution, but because it influences the energy consumed in the memory during application execution. In particular, we present a GC-controlled leakage energy optimization technique that shuts off memory banks that do not hold live data. Using two different commercial GCs and a suite of thirteen mobile applications, we evaluate the effectiveness of the GC-controlled energy optimization technique and study its sensitivity to different parameters such as bank size, the garbage collection frequency, object allocation style, compaction style, and compaction frequency. We observe that the energy consumption of an embedded Java application can be significantly more if the GC parameters are not tuned appropriately. Further, we notice that the object allocation pattern and the number of memory banks available in the underlying architecture are limiting factors on how effectively GC parameters can be used to optimize the memory energy consumption.
Error-Related EEG Potentials Generated During Simulated Brain–Computer Interaction

Brain-computer interfaces (BCIs) are prone to errors in the recognition of subject's intent. An elegant approach to improve the accuracy of BCIs consists in a verification procedure directly based on the presence of error-related potentials (ErrP) in the electroencephalogram (EEG) recorded right after the occurrence of an error. Several studies show the presence of ErrP in typical choice reaction tasks. However, in the context of a BCI, the central question is: ldquoAre ErrP also elicited when the error is made by the interface during the recognition of the subject's intent? rdquo We have thus explored whether ErrP also follow a feedback indicating incorrect responses of the simulated BCI interface. Five healthy volunteer subjects participated in a new human-robot interaction experiment, which seem to confirm the previously reported presence of a new kind of ErrP. However, in order to exploit these ErrP, we need to detect them in each single trial using a short window following the feedback associated to the response of the BCI. We have achieved an average recognition rate of correct and erroneous single trials of 83.5% and 79.2%, respectively, using a classifier built with data recorded up to three months earlier.
Long-Term Results of Transapical Versus Transfemoral TAVI in a Real World Population of 1000 Patients With Severe Symptomatic Aortic Stenosis

Background—Transapical transcatheter aortic valve implantation is generally perceived to be associated with increased morbidity compared with transfemoral transcatheter aortic valve implantation. We aimed to compare access-related complications and survival using propensity score matching. Methods and Results—Prospective, single-center registry of 1000 consecutive patients undergoing transapical and transfemoral transcatheter aortic valve implantation between May 2008 and April 2012. Transapical was performed in 413 patients and transfemoral in 587 patients. Patients with transapical access were less often women and less had pulmonary hypertension. Further they had more peripheral arterial disease, coronary artery disease, carotid stenosis, and recurrent surgery and a higher logistic EuroSCORE I (24.3%±16.2% for transapical versus 22.2%±16.2% for transfemoral; P<0.01). After building 2 propensity score–matched groups of 354 patients each with either access route (total 708 patients), baseline characteristics were comparable. In this analysis, there was no significant difference in 30 day mortality (5.9% transapical versus 8.5% transfemoral; P=0.19), the rate of myocardial infarction (2.5% transapical versus 2.0% transfemoral; P=0.61), stroke (2.0% transapical versus 2.3% transfemoral; P=0.79), bleeding complications, pacemaker implantation rates, or moderate aortic insufficiency. Stage 1 renal complications were more common in transapical patients (odds ratio, 2.81; 95% confidence interval, 1.93–4.09), whereas major vascular complications were less common (odds ratio, 0.14; 95% confidence interval, 0.06–0.29). Survival probability over the long term was not statistically different (hazard ratio, 0.89; 95% confidence interval, 0.72–1.10; log-rank Test, P=0.27). Conclusions—The data demonstrate that in an experienced multidisciplinary heart team, either access route can be performed with comparable results.
DateFinder : detecting date regions on handwritten document images based on positional expectancy

Whereas Optical Character Recognition (OCR) technology is used for many documents, such as check, passport, bank statement and receipt, there is a showing interest on modelling of occurrence and location of visual items. However, this source of information attracts much less attention in general OCR. For instance, there are many specific visual items (e.g., dates, writer signatures, calligraphy, author markings, schematic drawings, glyphs and even graffiti) that can be used to explain the underlying meaning and origin of documents. Among the aforementioned visual items, dates play a very important role in many documents (e.g., bank cheques, letters, postal mails, bills and diaries), which can provide time-related clues for readers. Also, the date is central to many administrative applications such as document indexing, translation and retrieval. In this thesis, we propose a method called DateFinder for detecting date regions on handwritten document images based on a four-step processing sequence. Firstly, we perform pre-processing operations on original scanned images, which aim to extract appropriate proposed date blocks. Secondly, a positional expectancy model is used for ‘date’ text blocks to measure how much an unknown region is similar to a date region based on its position. Thirdly, feature representation and classification techniques are used to extract features from an extracted block and compute the probability this block is a date region. Finally, we combine the scores of the positional expectancy model and classification to determine whether an extracted block is a date region. In the experiments, we have obtained encouraging results for detecting date regions in our dataset. However, there are still ample opportunities to improve the proposed DateFinder method, which can be considered for future work.
Photometric parameters of edge-on galaxies from 2MASS observations

To analyze the vertical structure of edge-on galaxies, we have used images of a large uniform sample of flat galaxies that have been taken during the 2MASS all-sky survey. The photometric parameters, such as the radial scale length, the vertical scale height, and the deprojected central surface brightness of galactic disks have been obtained. We find a strong correlation between the central surface brightness and the ratio of the vertical scale height to the vertical scale length: the thinner the galaxy, the lower the central surface brightness of its disk. The vertical scale height does not increase systematically with the distance from the galaxy center in the frames of this sample.
Recurrent patellar dislocation: reappraising our approach to surgery.

INTRODUCTION The management of recurrent traumatic patellar dislocation includes surgical realignment. There is no clear distinction whether proximal soft tissue or distal procedures produce superior results. However, distal realignment procedures are commonly associated with greater morbidity. We advocate a distal procedure only for cases which are more severe, such as the presence of patellar maltracking. MATERIALS AND METHODS Between January 2002 and June 2007, all patients who had a history of traumatic patellar dislocation with recurrent symptoms and failed conservative management underwent surgical realignment. Patients who had evidence of lateral patellar subluxation on computed tomography (CT) scan were offered a distal realignment procedure using the Elmslie-Trillat or Roux Goldthwaite procedure. All other patients underwent proximal soft tissue medial patellofemoral ligament (MPFL) reconstruction. Pre and postoperative functional International Knee Documentation Committee (IKDC), Lysholm and Tegner score assessments were performed for a minimum follow-up period of 6 months. The mean scores for each group were analysed using the Wilcoxon Matched-Pairs Signed-Ranks test and the Mann-Whitney U test was used to evaluate the difference between the groups. RESULTS A total of 23 patients underwent surgery for patellar realignment. Of whom, 14 patients had a distal realignment procedure while 9 patients had a proximal procedure of MPFL reconstruction. There was greater morbidity reported with distal realignment procedures. Pre and postoperative IKDC, Lysholm and Tegner scores showed significant improvement for both treatment arms. However, there was no significant difference between the improvement scores for both groups. CONCLUSION Patients with significant patellar maltracking following traumatic patellar dislocation would benefit from distal realignment using the Elmslie-Trillat or Roux Goldthwaite procedure. Otherwise, a proximal soft tissue procedure involving MPFL reconstruction would be adequate. A management algorithm is proposed for clinical use.
Accelerate Stochastic Subgradient Method by Leveraging Local Error Bound

In this paper, we propose two accelerated stochastic {\bf subgradient} methods for stochastic non-strongly convex optimization problems by leveraging a generic local error bound condition. The novelty of the proposed methods lies at smartly leveraging the recent historical solution to tackle the variance in the stochastic subgradient. The key idea of both methods is to iteratively solve the original problem approximately in a local region around a recent historical solution with size of the local region gradually decreasing as the solution approaches the optimal set. The difference of the two methods lies at how to construct the local region. The first method uses an explicit ball constraint and the second method uses an implicit regularization approach. For both methods, we establish the improved iteration complexity in a high probability for achieving an $\epsilon$-optimal solution. Besides the improved order of iteration complexity with a high probability, the proposed algorithms also enjoy a logarithmic dependence on the distance of the initial solution to the optimal set. When applied to the $\ell_1$ regularized polyhedral loss minimization (e.g., hinge loss, absolute loss), the proposed stochastic methods have a logarithmic iteration complexity.
Granulocyte Elastase as a Sensitive Diagnostic Parameter of Silent Male Genital Tract Inflammation *

Summary: Elastase, a specific inflammatory parameter of polymorphonuclear (PMN) granulocytes, was quantified with a sensitive enzyme immunoassay in the ejaculates of 188 patients consulting the andrological outpatient service. Correlations of the elastase concentrations to other parameters used up to now for the diagnosis of silent male genital tract inflammation were statistically evaluated by the CHI2‐test. A correlation was found neither to the percentage of morphologically intact spermatozoa in the differential sper‐miocytogram and the total number of spermatozoa nor to the pH‐value and viscosity of the ejaculate. However, release of elastase into the ejaculates was clearly associated with the occurrence of bacteria in native and stained smears or with the numbers of round cells present. Moreover, leukocyte counts in stained smears as well as an inflammation coefficient were highly significantly correlated to elastase concentrations. Obviously, quantification of granulocyte elastase in seminal plasma enables a rapid diagnosis of silent male genital tract inflammation, since even a single determination gives a reliable criterion and sequential determinations may allow the control of the course of the disease during therapy.
Glypican-3–Deficient Mice Exhibit Developmental Overgrowth and Some of the Abnormalities Typical of Simpson-Golabi-Behmel Syndrome

Glypicans are a family of heparan sulfate proteoglycans that are linked to the cell surface through a glycosyl–phosphatidylinositol anchor. One member of this family, glypican-3 (Gpc3), is mutated in patients with the Simpson-Golabi-Behmel syndrome (SGBS). These patients display pre- and postnatal overgrowth, and a varying range of dysmorphisms. The clinical features of SGBS are very similar to the more extensively studied Beckwith-Wiedemann syndrome (BWS). Since BWS has been associated with biallelic expression of insulin-like growth factor II (IGF-II), it has been proposed that GPC3 is a negative regulator of IGF-II. However, there is still no biochemical evidence indicating that GPC3 plays such a role. Here, we report that GPC3-deficient mice exhibit several of the clinical features observed in SGBS patients, including developmental overgrowth, perinatal death, cystic and dyplastic kidneys, and abnormal lung development. A proportion of the mutant mice also display mandibular hypoplasia and an imperforate vagina. In the particular case of the kidney, we demonstrate that there is an early and persistent developmental abnormality of the ureteric bud/collecting system due to increased proliferation of cells in this tissue element. The degree of developmental overgrowth of the GPC3-deficient mice is similar to that of mice deficient in IGF receptor type 2 (IGF2R), a well characterized negative regulator of IGF-II. Unlike the IGF2R-deficient mice, however, the levels of IGF-II in GPC3 knockouts are similar to those of the normal littermates.
Lessons from the Bristol case

News p 1691 Papers pp 1697, 1701, 1705 Education and debate pp 1734, 1736, 1740 Personal view p 1756 Medicine and the media p 1757 Cardiac surgery has changed within living memory from desperate attempts to achieve miracles for a few to the present situation where there is high expectation of a good result for tens of thousands of patients each year. It is easy to recall the surgeons who performed the first heart operations, who used cardiopulmonary bypass while it was still in its infancy, or who started transplantation — all undertaken with a high initial mortality. They worked on doggedly, in the face of doubt, scepticism, and often widely publicised criticism. They are now remembered with respect as having had “the courage to fail. ” Many others, equally determined, did fail and are not remembered.1 Some of that determination, in the face of possible failure, is necessary in every surgeon. But the congenital heart surgery undertaken in Bristol in the past 10 years — the subject of the General Medical Council's most recent, and arguably most important, disciplinary case (p 1691, 1740) 2 3 — was within the realms of routine practice, for which there are known and well established standards. In heart surgery accountability supplemented doggedness a long time ago. The present arrangements, however — which rely on local monitoring of results, clinician based judgments about acceptable standards, and continuing referrals — failed to avert the situation in Bristol, which we have seen spelt out in distressing detail before the General Medical Council and the …
Fanout optimization under a submicron transistor-level delay model

We present a new fanout optimization algorithm which is particularly suitable for digital circuits designed with submicron CMOS technologies. Restricting the class of fanout trees to the so-called bipolar LT-trees, the topology of the optimal fanout tree is found by means of a dynamic programming algorithm. The buffer selection is in turn performed by using a continuous buffer sizing technique based on a very accurate delay model especially developed for submicron CMOS processes. The fanout trees can distribute a signal with arbitrary polarity from the root of the tree to a set of sinks with arbitrary required time, required minimum signal slope, polarity and capacitive load. These trees can be constructed to maximize the required time at the root or to minimize the total buffer area under a required time constraint at the root. The performance of the algorithm shows several improvements with respect to conventional fanout optimization methods. More precisely, the area and delay improvements are 28% and 7%, respectively, when the algorithm is applied to entire circuits.