Miracle-dz/UniFAR-FTUs huggingface dataset:
Guidelines for the management of atrial fibrillation: the Task Force for the Management of Atrial Fibrillation of the European Society of Cardiology (ESC).

Guidelines summarize and evaluate all currently available evidence on a particular issue with the aim of assisting physicians in selecting the best management strategy for an individual patient suffering from a given condition, taking into account the impact on outcome, as well as the risk–benefit ratio of particular diagnostic or therapeutic means. Guidelines are no substitutes for textbooks. The legal implications of medical guidelines have been discussed previously. A large number of Guidelines have been issued in recent years by the European Society of Cardiology (ESC) as well as by other societies and organizations. Because of the impact on clinical practice, quality criteria for development of guidelines have been established in order to make all decisions transparent to the user. The recommendations for formulating and issuing ESC Guidelines can be found on the ESC Web Site (http://www.escardio.org/knowledge/guidelines/rules). In brief, experts in the field are selected and undertake a comprehensive review of the published evidence for management and/or prevention of a given condition. A critical evaluation of diagnostic and therapeutic procedures is performed, including assessment of the risk–benefit ratio. Estimates of expected health outcomes for larger societies are included, where data exist. The level of evidence and the strength of recommendation of particular treatment options are weighed and graded according to pre-defined scales, as outlined in Tables 1 and 2 . View this table: Table 1 Classes of recommendations View this table: Table 2 Levels of evidence The experts of the writing panels have provided disclosure statements of all relationships they may have that might be perceived as real or potential sources of conflicts of interest. These disclosure forms are kept on file at the European Heart House, headquarters of the ESC. Any changes in conflict of interest that arise during the writing period must be notified to the ESC. The Task Force report received its entire financial support from …
Mining Coding Patterns to Detect Crosscutting Concerns in Java Programs

A coding pattern is a frequent sequence of method calls and control statements to implement a particular behavior. Coding patterns include copy-and-pasted code, crosscutting concerns and implementation idioms. Duplicated code fragments and crosscutting concerns that spread across modules are problematic in software maintenance. In this paper, we propose a sequential pattern mining approach to capture coding patterns in Java programs. We have defined a set of rules to translate Java source code into a sequence database for pattern mining, and applied PrefixSpan algorithm to the sequence database. As a case study, we have applied our tool to six open-source programs and manually investigated the resultant patterns. We report coding patterns that are candidates of aspects and several logging patterns that are well-known crosscutting concerns but hard to modularize.
The mechanics of active muscle

When a frog’s or toad’s sartorius is rapidly released during a maintained isometric contraction its tension drops immediately and is redeveloped later. The extent of release required to reduce the tension to zero is 3 to 4 % of the length of the muscle. This is much less than the 10 to 15 % originally stated by Gasser & Hill: the difference is explained. The amount of work done during release by the passive elastic element in series with the contractile element is affected only very slightly by speed of release: the damping of this element is small. The redevelopment of tension after release has been compared with the original development of tension when the stimulus began. Minor and variable differences only have been observed, and these are probably due to redistribution of length, during isometric contraction, between different regions of the muscle. At greater initial extensions the rise of tension during an isometric tetanus is much slower than at smaller initial extensions. This also is attributed to redistribution of length, within the muscle. At an initial extension not greater than that at which the developed tension is a maximum the system is ‘stable’ and the tension reaches its full value sharply: at extensions on the outer side of the maximum the system is ‘unstable’ and a long slow creep of rising tension occurs. The apparent complexity of the time-course of the heat production in an isometric twitch is discussed.
Quantification of plasma cell-free DNA in patients with gastric cancer.

BACKGROUND The circulating DNA concentration and integrity was examined by a quantitative polymerase chain reaction (qPCR) in the plasma from patients with gastric cancer and their diagnostic value for the detection of gastric cancer assessed. PATIENTS AND METHODS Plasma samples were collected preoperatively from 53 patients with gastric cancer and 21 healthy controls. qPCR was performed using two different primer sets for the beta-actin gene, amplifying short and long segments. DNA integrity was calculated as the ratio of concentrations in both assays. RESULTS The DNA concentrations in the short and long assays of the gastric cancer patients were significantly higher (p=0.03 and p<0.0001, respectively) than those of the control group. The DNA integrity was also higher in cancer patients than that of the controls, however the difference was not significant (p=0.07). CONCLUSION The plasma DNA concentration assay may serve as a new diagnostic marker for the screening and monitoring of patients with gastric cancer.
Effects of titanium surface topography on bone integration: a systematic review.

AIM To analyse possible effects of titanium surface topography on bone integration. MATERIALS AND METHODS Our analyses were centred on a PubMed search that identified 1184 publications of assumed relevance; of those, 1064 had to be disregarded because they did not accurately present in vivo data on bone response to surface topography. The remaining 120 papers were read and analysed, after removal of an additional 20 papers that mainly dealt with CaP-coated and Zr implants; 100 papers remained and formed the basis for this paper. The bone response to differently configurated surfaces was mainly evaluated by histomorphometry (bone-to-implant contact), removal torque and pushout/pullout tests. RESULTS AND DISCUSSION A huge number of the experimental investigations have demonstrated that the bone response was influenced by the implant surface topography; smooth (S(a)<0.5 microm) and minimally rough (S(a) 0.5-1 mum) surfaces showed less strong bone responses than rougher surfaces. Moderately rough (S(a)>1-2 microm) surfaces showed stronger bone responses than rough (S(a)>2 microm) in some studies. One limitation was that it was difficult to compare many studies because of the varying quality of surface evaluations; a surface termed 'rough' in one study was not uncommonly referred to as 'smooth' in another; many investigators falsely assumed that surface preparation per se identified the roughness of the implant; and many other studies used only qualitative techniques such as SEM. Furthermore, filtering techniques differed or only height parameters (S(a), R(a)) were reported. CONCLUSIONS * Surface topography influences bone response at the micrometre level. * Some indications exist that surface topography influences bone response at the nanometre level. * The majority of published papers present an inadequate surface characterization. * Measurement and evaluation techniques need to be standardized. * Not only height descriptive parameters but also spatial and hybrid ones should be used.
Subcellular distribution of acid DNase of rat submandibular gland.

A previous study (Yaegaki et al. 1982) indicated that acid DNase activity in hu man parotid saliva decreases with age. Acid DNase is generally a lysosomal enzyme, however its subcellular distribution in the salivary gland has not been studied. There fore, this study was undertaken to de termine the subcellular distribution of acid DNase in rat submandibular gland using micro slab electrophoresis.
Crystal structure of New Delhi metallo‐β‐lactamase reveals molecular basis for antibiotic resistance

β‐Lactams are the most commonly prescribed class of antibiotics and have had an enormous impact on human health. Thus, it is disquieting that an enzyme called New Delhi metallo‐β‐lactamase‐1 (NDM‐1) can confer Enterobacteriaceae with nearly complete resistance to all β‐lactam antibiotics including the carbapenams. We have determined the crystal structure of Klebsiella pneumoniae apo‐NDM‐1 to 2.1‐Å resolution. From the structure, we see that NDM‐1 has an expansive active site with a unique electrostatic profile, which we propose leads to a broader substrate specificity. In addition, NDM‐1 undergoes important conformational changes upon substrate binding. These changes have not been previously observed in metallo‐β‐lactamase enzymes and may have a direct influence on substrate recognition and catalysis.
Vascular and Thrombogenic Effects of Pulmonary Exposure to Libby Amphibole

Exposure to Libby amphibole (LA) asbestos is associated with increased incidences of human autoimmune disease and mortality related to cardiovascular diseases. However, the systemic and vascular impacts are less well examined because of the dominance of pulmonary disease. It was postulated that regardless of the type of exposure scenario, LA exposure might produce systemic and vascular inflammogenic and thrombotic alterations in healthy and cardiovascular compromised rat models. Samples from three independent studies were examined. In the first study, male Wistar Kyoto (WKY), spontaneously hypertensive (SH), and SH heart failure (SHHF) rats were intratracheally instilled once with 0 (vehicle), 0.25, or 1 mg/rat of LA. In the second study, F344 rats were instilled with vehicle or LA at 0.5, 1.5, or 5 mg/rat. In the third study, F344 rats were instilled with the same mass concentrations of LA delivered by biweekly multiple instillations over 3 mo to simulate an episodic subchronic exposure. Complete blood count, platelet aggregation, serum cytokines, and biomarkers of systemic and aortic effects were examined. LA reduced adenosine diphosphate (ADP)-induced platelet aggregation and decreased circulating platelets in WKY (1 mg/rat) and F344 (5 mg/rat) at the 3-mo time point but did not do so in SH or SHHF rats. A decline in circulating lymphocytes with age appeared to be exacerbated by LA exposure in F344 rats but the differences were not significant. Aorta mRNA expression for biomarkers of oxidative stress (HO-1, LOX-1), inflammation (MIP-2), and thrombosis (tPA, PAI-1, vWf) were increased at baseline in SH and SHHF relative to WKY. LA exposure upregulated several of these biomarkers and also those involved in aortic contractility of WKY rats at 3 mo, suggesting thrombogenic, vasocontractile, and oxidative stress-mediated impairments. The aorta changes in F344 rats were less remarkable than changes noted in WKY following LA exposure. In conclusion, exposure to LA decreased circulating platelets and platelet coagulability while increasing the expression of oxidative stress, thrombosis, and vasoconstriction biomarkers in the aorta of healthy rats. These changes were similar to those noted at baseline in SH and SHHF rats, suggesting that LA-induced pulmonary injury might increase the risk of developing cardiovascular disease in healthy individuals.
Interplay between miRNA regulation and mechanical stress for CUC gene expression at the shoot apical meristem

ABSTRACT The shoot apical meristem is the central organizer of plant aerial organogenesis. The molecular bases of its functions involve several cross-talks between transcription factors, hormones and microRNAs. We recently showed that the expression of the homeobox transcription factor STM is induced by mechanical perturbations, adding another layer of complexity to this regulation. Here we provide additional evidence that mechanical perturbations impact the promoter activity of CUC3, an important regulator of boundary formation at the shoot meristem. Interestingly, we did not detect such an effect for CUC1. This suggests that the robustness of expression patterns and developmental programs is controlled via a combined action of molecular factors as well as mechanical cues in the shoot apical meristem.
When the answer comes into question in question-answering: survey and open issues

Abstract The answer determines the success of a Question-Answering (QA) system. In redundancy-based QA systems, a common approach is to extract the candidate answers from the information sources and select the most frequent answers as the final answers. However, this strategy has some pitfalls. For instance, if a system is not able to detect equivalences between the candidate answers, their frequencies might be erroneously calculated. Moreover, the user who posed the question should also be taken into account when answering: different persons require different (correct) answers. This can involve the use of suitable vocabulary and/or information details. In these situations, the generation of a response can be a more suitable strategy, instead of the extraction and direct retrieval of the answer from the information sources. The present survey targets the state of the art in the answering task in QA under three different lines of research. First, we present several works that focus on relating candidate answers. Then, we recover the concept of cooperative answer – a correct, useful, and non-misleading answer – and we bring up attempts to address cooperative answering. Finally, we investigate the research community endeavors on response generation. We will also present our perspective on each of these three topics throughout this paper.
Early- and late-onset preeclampsia and the DNA methylation of circadian clock and clock-controlled genes in placental and newborn tissues

ABSTRACT The placenta is important in providing a healthy environment for the fetus and plays a central role in the pathophysiology of preeclampsia (PE). Fetal and placental developments are influenced by epigenetic programming. There is some evidence that PE is controlled to an altered circadian homeostasis. In a nested case–control study embedded in the Rotterdam Periconceptional Cohort, we obtained placental tissue, umbilical cord leukocytes (UCL), and human umbilical venous endothelial cells of 13 early-onset PE, 16 late-onset PE and 83 controls comprising 36 uncomplicated and 47 complicated pregnancies, i.e. 27 fetal growth restricted and 20 spontaneous preterm birth. To investigate the associations between PE and the epigenetics of circadian clock and clock-controlled genes in placental and newborn tissues, genome-wide DNA methylation analysis was performed using the Illumina HumanMethylation450K BeadChip and a candidate-gene approach using ANCOVA was applied on 939 CpGs of 39 circadian clock and clock-controlled genes. DNA methylation significantly differed in early-onset PE compared with spontaneous preterm birth at 6 CpGs in placental tissue (3.73E-5 ≤ p ≤ 0.016) and at 21 CpGs in UCL (1.09E-5≤ p ≤ 0.024). In early-onset PE compared with fetal growth restriction 2 CpGs in placental tissue (p < 0.05) and 8 CpGs in uncomplicated controls (4.78E-5≤ p ≤ 0.049) were significantly different. Moreover, significantly different DNA methylation in early-onset PE compared with uncomplicated controls was shown at 6 CpGs in placental tissue (1.36E-4≤ p ≤ 0.045) and 11 CpGs in uncomplicated controls (2.52E-6≤ p ≤ 0.009). No significant associations were shown with late-onset PE between study groups or tissues. The most differentially methylated CpGs showed hypomethylation in placental tissue and hypermethylation in uncomplicated controls. In conclusion, DNA methylation of circadian clock and clock-controlled genes demonstrated most differences in UCL of early-onset PE compared with spontaneous preterm birth. Implications of the tissue-specific variations in epigenetic programming for circadian performance and long-term health need further investigation.
CT of the ureteral wall.

T he normal anatomy and pathology of the ureter have been the subjects of several excellent reviews [1-81. However, these radiographic descriptions generally concentrate on the intraluminal manifestations of the disease, as revealed by direct opacification studies such as IV urography and retrograde ureteropyelography, rather than concentrating specifically on the ureteral wall and periureteral tissues. This study reviews the appearances of the ureteral wall and immediate periureteral tissues in normal and diseased states.
A Personal Use Program for Calculation of Aviation Route Doses

An Excel VBA program to calculate aviation route doses is developed for personal use by the general public. This program named as “JISCARD EX” runs on a personal computer installed with the Microsoft Excel 2003/2007. The JISCARD EX calculates instantaneously cut-off rigidities (Rc) and cosmic radiation dose rates at passing route points according to flight log data (latitude, longitude and altitude as a function of time). The Rc values for the Earth’s magnetosphere are calculated with the MAGNETOCOSMICS code developed at the University of Bern. Solar activity represented as a force field potential (FFP) is evaluated from the observed trend of selected neutron monitors at high latitude. Future FFP values up to December 2008 are predicted from recently observed fluctuation of sunspot numbers. Cosmic radiation dose rates in the atmosphere are calculated using a PHITS-based analytical radiation model in the atmosphere (PARMA) developed in Japan. Calculated results are automatically summarized in a report of another Excel worksheet containing airport names, flying time, route dose and time plots of altitude, Rc and effective dose rate. This program will be open to the public through a web site of the National Institute of Radiological Sciences.
Unlabeled-probe high-resolution melting to detect KRAS codon 12 and 13 mutations in pancreatic adenocarcinoma tissues

Abstract Background: The aim of our study was to establish an unlabeled-probe high-resolution melting (HRM) approach to the detection of Kirsten RAS (KRAS) codon 12 and 13 mutations in pancreatic adenocarcinoma (PA) tissues as a novel and effective diagnostic technique. Methods:We tested the sensitivity and specificity of this genotyping approach in cell lines with known KRAS mutations using 166 bp amplicons and 37 bp wild-type probe to detect KRAS codon 12 and 13 mutations. We screened 49 PA tissues to be subsequently sequenced to confirm the mutations. Simultaneously, we tested the specimens using Sanger sequencing and then used target-DNA cloning and sequencing for verification. Results: It was found that unlabeled-probe HRM was reliable in detecting 3% of mutant cell lines DNA diluted with that of the wild-type, whereas Sanger sequencing could only discriminate 20% mutant cell ratios. In detecting 49 specimens, the former was capable of detecting 23 mutations (46.9%); and the latter could observe 15 (30.6%). For further verification, T-A DNA cloning and sequencing was applied to the differences, with the results matching those of the unlabeled-probe HRM. Conclusions: It was concluded that the unlabeled-probe HRM approach can be a sensitive and accurate screening technique to detect KRAS codon 12 and 13 mutations in diagnosing and treating PA.
Changes in skin microcirculation during radiation therapy for breast cancer

Abstract Background: The majority of breast cancer patients who receive radiation treatment are affected by acute radiation-induced skin changes. The assessment of these changes is usually done by subjective methods, which complicates the comparison between different treatments or patient groups. This study investigates the feasibility of new robust methods for monitoring skin microcirculation to objectively assess and quantify acute skin reactions during radiation treatment. Material and methods: Laser Doppler flowmetry, laser speckle contrast imaging, and polarized light spectroscopy imaging were used to measure radiation-induced changes in microvascular perfusion and red blood cell concentration (RBC) in the skin of 15 patients undergoing adjuvant radiation therapy for breast cancer. Measurements were made before treatment, once a week during treatment, and directly after the last fraction. Results: In the treated breast, perfusion and RBC concentration were increased after 1–5 fractions (2.66–13.3 Gy) compared to baseline. The largest effects were seen in the areola and the medial area. No changes in perfusion and RBC concentration were seen in the untreated breast. In contrast, Radiation Therapy Oncology Group (RTOG) scores were increased only after 2 weeks of treatment, which demonstrates the potential of the proposed methods for early assessment of skin changes. Also, there was a moderate to good correlation between the perfusion (r = 0.52) and RBC concentration (r = 0.59) and the RTOG score given a week later. Conclusion: We conclude that radiation-induced microvascular changes in the skin can be objectively measured using novel camera-based techniques before visual changes in the skin are apparent. Objective measurement of microvascular changes in the skin may be valuable in the comparison of skin reactions between different radiation treatments and possibly in predicting acute skin effects at an earlier stage.
Plasmid DNA Supercoiling and Gyrase Activity in Escherichia coli Wild-Type and rpoS Stationary-Phase Cells

ABSTRACT Stationary-phase cells displayed a distribution of relaxed plasmids and had the ability to recover plasmid supercoiling as soon as nutrients became available. Preexisting gyrase molecules in these cells were responsible for this recovery. Stationary-phase rpoS cells showed a bimodal distribution of plasmids and failed to supercoil plasmids after the addition of nutrients, suggesting that rpoS plays a role in the regulation of plasmid topology during the stationary phase.
Residual force enhancement after stretch in striated muscle. A consequence of increased myofilament overlap?

Abstract When skeletal muscle is stretched above optimal sarcomere length during tetanic activity there is an increase in force that stays above the isometric force level throughout the activity period. This long‐lasting increase in contractile force, generally referred to as ‘residual force enhancement after stretch’ (FEresid), has been studied in great detail in various muscle preparations over more than half a century. Substantial evidence has been presented to show that non‐uniform sarcomere behaviour plays a major part in the development of FEresid. However, in a great number of recent studies the role of sarcomere non‐uniformity has been challenged and alternative mechanisms have instead been proposed to explain the increase in force such as enhancement of cross‐bridge function and/or strengthening of parallel elastic elements along the muscle fibres. This article presents a short review of the salient features of FEresid and provides evidence that non‐uniform sarcomere behaviour is indeed likely to play a major role in the development of FEresid. Electron microscopical studies of fibres rapidly fixed after active stretch demonstrate that, dispersed in the preparation, there are assymetrical length changes within the two halves of myofibrillar sarcomeres resulting in greater filament overlap in one half of the sarcomere than in the opposite sarcomere half. Sarcomere halves with increased filament overlap will consequently be in a situation where they are able to produce a greater force than that recorded in the isometric control. Weaker regions in series will be able to keep the enhanced force by recruitment of elastic elements.