Miracle-dz/UniFAR-FTUs huggingface dataset:
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing

MOTIVATION DNA methylation aberrations are now known to, almost universally, accompany the initiation and progression of cancers. In particular, the colon cancer epigenome contains specific genomic regions that, along with differences in methylation levels with respect to normal colon tissue, also show increased epigenetic and gene expression heterogeneity at the population level, i.e. across tumor samples, in comparison with other regions in the genome. Tumors are highly heterogeneous at the clonal level as well, and the relationship between clonal and population heterogeneity is poorly understood. RESULTS We present an approach that uses sequencing reads from high-throughput sequencing of bisulfite-converted DNA to reconstruct heterogeneous cell populations by assembling cell-specific methylation patterns. Our methodology is based on the solution of a specific class of minimum cost network flow problems. We use our methods to analyze the relationship between clonal heterogeneity and population heterogeneity in high-coverage data from multiple samples of colon tumor and matched normal tissues. AVAILABILITY AND IMPLEMENTATION http://github.com/hcorrada/methylFlow CONTACT hcorrada@umiacs.umd. edu SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION is available at Bioinformatics online.
Towards Transiently Secure Updates in Asynchronous SDNs

Software-Defined Networks (SDNs) promise to overcome the often complex and error-prone operation of tradi- tional computer networks, by enabling programmabil- ity, automation and verifiability. Yet, SDNs also in- troduce new challenges, for example due to the asyn- chronous communication channel between the logically centralized control platform and the switches in the data plane. In particular, the asynchronous commu- nication of network update commands (e.g., OpenFlow FlowMod messages) may lead to transient inconsisten- cies, such as loops or bypassed waypoints (e.g., fire- walls). One approach to ensure transient consistency even in asynchronous environments is to employ smart scheduling algorithms: algorithms which update subsets of switches in each communication round only, where each subset in itself guarantees consistency. In this demo, we show how to change routing policies in a transiently consistent manner. We demonstrate two al- gorithms, namely, Wayup [5] and Peacock [4], which partition the network updates sent from SDN controller towards OpenFlow software switches into multiple rounds as per respective algorithms. Later, the barrier mes- sages are utilized to ensure reliable network updates.
Application of parallelized multigrid method to solution of MHD equilibrium with MPI

The potential of applying the multigrid method (MGM) to magnetohydrodynamics (MHD) equilibrium analysis is investigated. The nonlinear eigenvalue problem often appears when the MHD equilibria are determined by solving the Grad-Shafranov equation numerically. After linearizing the equation, the problem is solved using an iterative procedure. Although the SOR method or the Gauss-Seidel method is often used for the solution of the linearized equation, it takes much CPU time to solve the problem. We introduced the use of MGM instead of the conventional method for solving the linear equation. The parallel processing by using message passing interface (MPI) on a PC cluster is adopted for implementation of the MGM to achieve higher performance.
Evidence-Based Medicine: Ultrasound Guidance for Truncal Blocks

We performed a systematic search of the medical literature and reviewed the evidence examining success rates and incidence of complications of ultrasound (US) guidance relative to traditional techniques for the following blocks: paravertebral, intercostal, transversus abdominis plane, rectus sheath, and ilioinguinal/iliohypogastric. We included studies of sufficient methodologic quality for review and excluded poor-quality studies. We then rated the strength of evidence for US guidance for each block using a system developed by the United States Agency for Health Care Policy and Research. Although relatively few studies have compared US guidance with established techniques, the available evidence suggests that the use of US guidance is a safe and effective means to facilitate correct needle placement and adequate spread of local anesthetic for truncal blocks. Further studies are needed to directly compare US guidance to traditional techniques and to clarify potential benefits and limitations of US guidance for truncal blocks.
Anwendung von Grundprinzipien der Physik bei der Magnetresonanzangiografie von Kopf und Hals: Erkennung von Artefakten

Zusammenfassung Bildgebende Untersuchungen von Nerven und Gefäßen zur Abklärung von Kopfschmerzen und psychischen Veränderungen, zum Workup nach einem Schlaganfall und zur Beurteilung der arteriovenösen Strukturen von Kopf und Hals gehören zur klinischen Routine. Derartige Untersuchungen werden immer häufiger durchgeführt, da der Anteil älterer Menschen an der Gesamtbevölkerung ständig wächst. Verschiedene Verfahren der Magnetresonanzangiografie sind in dieser Situation hilfreich. Jedoch erfordert die Beherrschung dieser Techniken ein tiefgehendes Verständnis der physikalischen Grundprinzipien, der komplexen Fließmuster und der Korrelation zwischen magnetresonanzangiografischen und konventionellen magnetresonanztomografischen Befunden. Zur Klärung schwieriger Fälle können mehrere Bildgebungsverfahren kombiniert werden, wobei jedes von ihnen spezifische Informationen liefert. Leider stellt die Integration der mit den verschiedenen Bildgebungsmodalitäten gewonnenen Befunde eine zusätzliche diagnostische Herausforderung dar. Um die Richtigkeit der Diagnosen zu gewährleisten, muss der Radiologe die Details all dieser Befunde sorgfältig im Lichte der physikalischen Grundprinzipien, der Grundlagen der verschiedenen Bildgebungstechniken und der Kenntnis häufiger Fehlerquellen bei der bildgebenden Untersuchung neurovaskulärer Strukturen würdigen.
LINQ: reconciling object, relations and XML in the .NET framework

Many software applications today need to handle data from different data models; typically objects from the host programming language along with the relational and XML data models. The ROX impedance mismatch makes programs awkward to write and hard to maintain.The . NET Language-Integrated Query (LINQ) framework, proposed for the next release of the . NET framework, approaches this problem by defining a pattern of general-purpose standard query operators for traversal, filter, and projection. Based on this pattern, any . NET language can define special query comprehension syntax that is subsequently compiled into these standard operators (our code examples are in VB). Besides the general query operators, the LINQ framework also defines two domain specific APIs that work over XML (XLinq) and relational data (DLinq) respectively. The operators over XML use a lightweight and easy to use in-memory XML representation to provide XQuery-style expressiveness in the host programming language. The operators over relational data provide a simple OR mapping by leveraging remotable queries that are executed directly in the back-end relational store.
Transformational change: governance interventions for climate change adaptation from a continuous change perspective

Although transformational change is a rather new topic in climate change adaptation literature, it has been studied in organisational theory for over 30 years. This paper argues that governance scholars can learn much from organisation theory, more specifically regarding the conceptualisation of change and intervention strategies. We reconceptualise the divide between transformational change and incremental change by questioning the feasibility of changes that are concurrently in-depth, large scale, and quick; and the assumption that incremental change is necessarily slow and can only result in superficial changes. To go beyond this dichotomy, we introduce the conceptualisation of continuous transformational change. Resulting intervention strategies include (1) providing basic conditions for enabling small in-depth wins; (2) amplifying small wins through sensemaking, coupling, and integrating; and (3) unblocking stagnations by confronting social and cognitive fixations with counterintuitive interventions. These interventions necessitate a modest leadership. Governing transformational change thus requires transformation of the governance systems themselves.
Total phenol, catechin, and caffeine contents of teas commonly consumed in the United kingdom.

Levels of total phenol, catechins, and caffeine in teas commonly consumed in the United Kingdom have been determined using reversed phase high-performance liquid chromatography. Tea bags or tea leaves were purchased from local supermarkets and extracted in boiling water for 5 min. The resulting data showed considerable variability in both total phenols [80.5-134.9 mg/g of dry matter (DM) in black teas and 87-106.2 mg/g of DM in green teas] and catechins (5.6-47.5, 51.5-84.3, and 8.5-13.9 mg/g of DM in black, green, and fruit teas, respectively); this was most probably a result of differing agronomic conditions, leaf age, and storage during and after transport, as well as the degree of fermentation. Caffeine contents of black teas (22-28 mg/g of DM) were significantly higher than in less fermented green teas (11-20 mg/g of DM). The relative concentration of the five major tea catechins ranked EGCG > ECG > EC > EGC > C. The estimated U.K. dietary intakes of total tea catechins, calculated on the basis of an average tea consumption of three cups of tea (200 mL cup, 1% tea leaves w/v), were 61.5, 92.7, and 405.5 mg/day from fruit teas, black teas, and green teas, respectively. The coefficients of variation were 19.4, 88.6, and 17.3%, respectively, indicating the wide variation in these intakes. The calculated caffeine intake ranged between 92 and 146 mg/day. In addition, many individuals will consume much larger quantities of tea, of various strengths (as determined by the brewing conditions employed). This broad spread of U.K. daily intakes further emphasizes the need for additional research to relate intake and effect in various population groups.
Antibiotic susceptibility of Listeria monocytogenes in Denmark 1958–2001

In order to see whether the susceptibility of Danish Listeria monocytogenes strains has changed over the years we examined a collection of human isolates from the period 1958–2001. We, furthermore, wanted to compare L. monocytogenes susceptibility testing using a disc diffusion assay with MIC measurements performed by the E‐test. 106 strains isolated predominantly from blood cultures and cerebrospinal fluids were examined together with three reference strains. Susceptibility to the following antibiotics was tested by the E‐test and by Oxoid discs using Iso‐sensitest agar: penicillin G, ampicillin, meropenem, gentamicin, sulphamethoxazole, trimethoprim, ciprofloxacin, erythromycin, vancomycin, linezolid, chloramphenicol and tetracycline. The strains were in the main sensitive to all antibiotics examined using both methods, except for ciprofloxacin, where the strains were intermediate sensitive. However, for penicillin, ampicillin and sulphamethoxazole, while the disc diffusion assay found the strains to be sensitive, MIC measurements generally placed the strains one dilution above the breakpoint for sensitivity in the intermediate sensitive group. Based on the MIC measurements, the antibiotic susceptibility of L. monocytogenes has not changed in Denmark from 1958 to 2001, and the multiresistant strains found in human infections elsewhere have not been found in Denmark.
Regulation of hypoxia‐inducible factor‐α isoforms and redox state by carotid body neural activity in rats

Rats exposed to chronic intermittent hypoxia (CIH) exhibited imbalanced expression of hypoxia‐inducible factor (HIF)‐α isoforms and oxidative stress in brainstem regions associated with the carotid body (CB) chemoreflex, and in the adrenal medulla, an end organ of the sympathetic nervous system. Selective ablation of the CB abolished the effects of CIH on HIF‐α isoform expression and oxidative stress. In the adrenal medulla, chemoreflex‐mediated sympathetic activation regulates HIF‐α isoform expression via muscarinic acetylcholine receptor‐mediated Ca2+ influx and the resultant activation of the mammalian target of rapamycin pathway and calpain proteases. Thus, CB neural activity regulates HIF‐α isoform expressions and redox state in the central and peripheral nervous system associated with the chemoreflex pathway under the setting of CIH.
Osteo-radio-necrosis (ORN) and bisphosphonate-related osteonecrosis of the jaws (BRONJ): the histopathological differences under the clinical similarities.

OBJECTIVES Both osteoradionecrosis (ORN) and bisphosphonate associated osteonecrosis of the jaws (BRONJ) present clinically as regions of exposed necrotic bone. The study aimed to demonstrate the histopathological differences behind the observed clinical similarities. STUDY DESIGN Ten ORN specimens and ten BRONJ specimens were used, as well as ten samples of normal mandibular bone as control. Two bone-specific stainings were used, i.e. Sirius Red for the study of the relative presence of collagen types I and III and toluidine blue for the study the osteon density. RESULTS The Red Green Blue (RGB)-analysis of the specimens stained with Sirius Red identified significant differences between the chromatic patterns observed in bone preparations of patients suffering from ORN when compared to both BRONJ and control samples. Moreover, the osteon density of the BRONJ samples was significantly lower when compared to ORN and normal bone samples. CONCLUSIONS The demonstrated differences in the bone architecture and in the bone collagen content between the two pathological conditions most likely reflect underlying pathophysiological differences.
PHYTOCHROME KINASE SUBSTRATE1 Regulates Root Phototropism and Gravitropism1[C][W][OA]

Light promotes the expression of PHYTOCHROME KINASE SUBSTRATE1 (PKS1) in the root of Arabidopsis thaliana, but the function of PKS1 in this organ is unknown. Unilateral blue light induced a negative root phototropic response mediated by phototropin 1 in wild-type seedlings. This response was absent in pks1 mutants. In the wild type, unilateral blue light enhanced PKS1 expression in the subapical region of the root several hours before bending was detectable. The negative phototropism and the enhanced PKS1 expression in response to blue light required phytochrome A (phyA). In addition, the pks1 mutation enhanced the root gravitropic response when vertically oriented seedlings were placed horizontally. The negative regulation of gravitropism by PKS1 occurred even in dark-grown seedlings and did not require phyA. Blue light also failed to induce negative phototropism in pks1 under reduced gravitational stimulation, indicating that the effect of pks1 on phototropism is not simply the consequence of the counteracting effect of enhanced gravitropism. We propose a model where the background level of PKS1 reduces gravitropism. After a phyA-dependent increase in its expression, PKS1 positively affects root phototropism and both effects contribute to negative curvature in response to unilateral blue light.
Albendazole versus thiabendazole as therapy for trichinosis: a retrospective study.

An outbreak of trichinosis caused by ingestion of horse meat occurred in December 1993 in France; more than 500 people were affected. We compared the immediate and midterm efficacy and tolerability of thiabendazole and albendazole as therapy for the 46 patients seen in our department. Forty-four patients (96%) were treated. The first 26 patients received thiabendazole therapy; the next 18 received albendazole therapy. All the patients were tested with prednisone. Eight relapses occurred (seven in the thiabendazole group and one in the albendazole group [not significant]). Side effects of treatment were reported by seven patients, all of whom were treated with thiabendazole (P = .01). Six months after treatment, 16 of the 31 patients who responded to a questionnaire still had symptoms, the most frequent of which were myalgias (81%) and fatigue (69%). No significant difference was observed between the two treatment groups. The immediate efficacy of thiabendazole and albendazole as therapy for trichinosis was comparable, but albendazole was better tolerated.
The Effects of Morphine and Fentanyl on the Inflammatory Response to Cardiopulmonary Bypass in Patients Undergoing Elective Coronary Artery Bypass Graft Surgery

BACKGROUND:Experimental data suggest that morphine has unique antiinflammatory properties. We hypothesized that morphine, when compared with fentanyl, would attenuate the perioperative inflammatory response to cardiopulmonary bypass (CPB) when administered as part of a balanced anesthetic technique. METHODS:Thirty patients undergoing elective coronary artery bypass graft surgery were randomized to receive, in a double-blind manner, either morphine (40 mg) or fentanyl (1000 &mgr;g) as part of a standardized opioid-isoflurane anesthetic. Serum concentrations of interleukin (IL)-6 and IL-8 and expression of neutrophil surface adhesion molecules (CD 11a, CD 11b, CD 11c, and CD 18) were measured perioperatively as indicators of the inflammatory response to surgery. Core temperatures were monitored in the intensive care unit to determine the incidence of postoperative hyperthermia (temperature >38.0°C). RESULTS:IL-6 and IL-8 concentrations increased in all patients after CPB. The increase in serum IL-6 levels was significantly attenuated in the morphine group compared to the fentanyl group at 3 and 24 h post-CPB (P < 0.05). Reductions in expression of neutrophil adhesion molecules were observed in both groups 15 min and 3 h post-CPB; however, a significantly larger reduction in CD 11b and CD 18 expression was noted in patients receiving morphine (P < 0.05). The incidence of postoperative hyperthermia was more frequent in the fentanyl group (73%) compared to the morphine group (0%, P < 0.05). CONCLUSIONS:Compared with fentanyl, the administration of morphine as part of balanced anesthetic technique suppressed several components the inflammatory response (IL-6, CD 11b, CD 18, postoperative hyperthermia) to cardiac surgery and CPB.
Effects of pentachlorophenol and some of its known and possible metabolites on different species of bacteria

The antibacterial activity of pentachlorophenol and 35 of its known or possible metabolites against 30 different species of bacteria was tested. In comparison with pentachlorophenol, no increase of inhibitory activity was found for any of the chlorinated anisoles tested (except for pentachloroanisole against Streptomyces spp.), 2-chlorophenol, 2,6-dichlorophenol, 2,3,6- and 2,4,6-trichlorophenol, 2,3,5,6-tetrachlorophenol, tetrachloro-1,4- and -1,3-benzenediol (except for the 1,3-isomer against Streptomyces spp.), tetrachloro-1,3-dimethoxybenzene, and tetrachloro-1,3-benzenediol diacetate. Two chlorophenols, five dichlorophenols, four trichlorophenols, two tetrachlorophenols, and tetrachloro-1,2-benzenediol were more active than pentachlorophenol against some, but not all, of the strains tested.
Perinatal mortality rate in 11 Jiangsu cities.

This prospective collaborative study investigated the perinatal mortality rate and causes of perinatal death in 11 cities in China's Jiangsu Province in the 1 year between September 1, 1980 and August 31, 1981. Of the 86,913 perinatals born during this period, there were 2131 deaths, including 1140 stillbirths and 991 early neonatal deaths, for a perinatal mortality rate of 24.52. Causes of perinatal mortality included hypoxia (37.5%), respiratory disturbance (25.0%), congenital anomaly (11.3%), birth trauma (8.5%), prematurity (6.1%), and miscellaneous or unknown causes (11.6%). These results indicate the importance of the prevention of hypoxia and respiratory disturbance, which together accounted for 62.5% all of perinatal deaths. In the hypoxic category, 54.2% of the deaths were due to umbilical cord factors; in the respiratory disturbance group, 45.6% of deaths were a result of asphyxia neonatorum. Setting up facilities to detect congenital anomalies and determine fetal maturity would further lower perinatal mortality, as would improved fetal monitoring and abandonment of methods of delivery such as version extraction. In the 5 cities south of the Yangzi River, where medical care and living standards are better, the perinatal mortality rate was 21.8-23.8 compared with 24.5-38.4 in the 6 northern cities of the province.
IFC-based Improved ACO for Multi-agent Path Planning in Web3D Mountain Environment

The path planning in Web3D for large-scale scenes is a fundamental problem. Especially, there are many agents searching for their optimal paths in a complex and large-scale mountain scene. This paper addresses a kind of method using an improved ant colony algorithm to find path for multi-agent in Web3D environment using HTML5. An improved leader-follower method is used to organize the Blue army soldiers to attach the Red army soldiers. Firstly, the paper proposes a kind of method using BIM information together with improved ACO algorithm to form a kind of Web3D path planning method. Secondly, the method is used in the reality experiment by using Egret Engine to find a multi-agent path when soldiers are marching or fighting in a mountain terrain. The result of the experiment displays that the convergence of the improved ACO algorithm is fast, and the Web3D path planning results are efficient, real time and precise.
Usability of assistive technologies in ageing and disabilities

Introduction Assistive technologies (AT) enable older and/or disabled people to age as long as possible in place by supporting them in various tasks and activities of daily living. AT range from low technologies such as walkers or book holders to high technologies, for instance alarm systems or voice-controlled computer input systems. Besides financial costs and accessibility, usability has the highest impact on actual technology use. Therefore, it is necessary to enhance effectiveness, efficacy and user satisfaction of the technical device. Review of the literature Research about awareness and perceptions considering AT and corresponding methodologies is relevant in order to investigate possible barriers and reasons for non-use. Psychological models emphasize the role of attitudes, social norms and self-efficacy. Prerequisites of acceptance and use will be discussed. Discussion Although there is a high number and variety of AT in Europe, little is known about acceptance and use of AT. Evidence-based-research is needed in order to enable cost-benefits-analysis of AT. Since enhancement of autonomy and competence of persons with disabilities should also be a matter of health care and social policies, political decisions are necessary for successful implementation of AT and rehabilitation.