Miracle-dz/UniFAR-FTUs huggingface dataset:
Guidelines for the management of inflammatory bowel disease in adults

The management of inflammatory bowel disease represents a key component of clinical practice for members of the British Society of Gastroenterology (BSG). There has been considerable progress in management strategies affecting all aspects of clinical care since the publication of previous BSG guidelines in 2004, necessitating the present revision. Key components of the present document worthy of attention as having been subject to re-assessment, and revision, and having direct impact on practice include: The data generated by the nationwide audits of inflammatory bowel disease (IBD) management in the UK in 2006, and 2008. The publication of ‘Quality Care: service standards for the healthcare of people with IBD’ in 2009. The introduction of the Montreal classification for Crohn's disease and ulcerative colitis. The revision of recommendations for the use of immunosuppressive therapy. The detailed analysis, guidelines and recommendations for the safe and appropriate use of biological therapies in Crohn's disease and ulcerative colitis. The reassessment of the role of surgery in disease management, with emphasis on the importance of multi-disciplinary decision-making in complex cases. The availablity of new data on the role of reconstructive surgery in ulcerative colitis. The cross-referencing to revised guidelines for colonoscopic surveillance, for the management of metabolic bone disease, and for the care of children with inflammatory bowel disease. Use of the BSG discussion forum available on the BSG website to enable ongoing feedback on the published document http://www.bsg. org.uk/forum (accessed Oct 2010). The present document is intended primarily for the use of clinicians in the United Kingdom, and serves to replace the previous BSG guidelines in IBD, while complementing recent consensus statements published by the European Crohn's and Colitis Organisation (ECCO) https://www.ecco-ibd.eu/index.php (accessed Oct 2010).
Calcium release‐activated calcium current in rat mast cells.

1. Whole‐cell patch clamp recordings of membrane currents and fura‐2 measurements of free intracellular calcium concentration ([Ca2+]i) were used to study the biophysical properties of a calcium current activated by depletion of intracellular calcium stores in rat peritoneal mast cells. 2. Calcium influx through an inward calcium release‐activated calcium current (ICRAC) was induced by three independent mechanisms that result in store depletion: intracellular infusion of inositol 1,4,5‐trisphosphate (InsP3) or extracellular application of ionomycin (active depletion), and intracellular infusion of calcium chelators (ethylene glycol bis‐N,N,N',N'‐tetraacetic acid (EGTA) or 1,2‐bis(2‐aminophenoxy)ethane‐N,N,N',N'‐tetraacetic acid (BAPTA)) to prevent reuptake of leaked‐out calcium into the stores (passive depletion). 3. The activation of ICRAC induced by active store depletion has a short delay (4‐14 s) following intracellular infusion of InsP3 or extracellular application of ionomycin. It has a monoexponential time course with a time constant of 20‐30 s and, depending on the complementary Ca2+ buffer, a mean normalized amplitude (at 0 mV) of 0.6 pA pF‐1 (with EGTA) and 1.1 pA pF‐1 (with BAPTA). 4. After full activation of ICRAC by InsP3 in the presence of EGTA (10 mM), hyperpolarizing pulses to ‐100 mV induced an instantaneous inward current that decayed by 64% within 50 ms. This inactivation is probably mediated by [Ca2+]i, since the decrease of inward current in the presence of the fast Ca2+ buffer BAPTA (10 mM) was only 30%. 5. The amplitude of ICRAC was dependent on the extracellular Ca2+ concentration with an apparent dissociation constant (KD) of 3.3 mM. Inward currents were nonsaturating up to ‐200 mV. 6. The selectivity of ICRAC for Ca2+ was assessed by using fura‐2 as the dominant intracellular buffer (at a concentration of 2 mM) and relating the absolute changes in the calcium‐sensitive fluorescence (390 nm excitation) with the calcium current integral. This relationship was almost identical to the one determined for Ca2+ influx through voltage‐activated calcium currents in chromaffin cells, suggesting a similar selectivity. Replacing Na+ and K+ by N‐methyl‐D‐glucamine (with Ca2+ ions as exclusive charge carriers) reduced the amplitude of ICRAC by only 9% further suggesting a high specificity for Ca2+ ions. 7. The current amplitude was not greatly affected by variations of external Mg2+ in the range of 0‐12 mM. Even at 12 mM Mg2+ the current amplitude was reduced by only 23%. 8. ICRAC was dose‐dependently inhibited by Cd2+. (ABSTRACT TRUNCATED AT 250 WORDS)
Ray Tracing Hardware System Using Plane-Sphere Intersections

Ray tracing is a global illumination based rendering method widely used in computer graphics. Although it generates photo-realistic images, it requires a large number of computations. In ray tracing, the ray-object intersection test is one of the dominant factors for the processing speed. To accelerate the intersection test, we propose a new method based on a plane-sphere intersection algorithm, and show a hardware system using an FPGA. The computations used in the method are highly pipelined and parallelized by optimizing the balance between the computation speed and the memory data bandwidth. As a result, the prototype makes full use of 512 DSP cores built in Xilinx Vertex-4 SX FPGA, and the average utilization of the DSP cores is close to 90%. The simulation results show that the proposed system running at 160MHz performs the intersection test a few hundred times faster than a commodity PC with a 3.4GHz Pentium 4
VIBRATION AND NOISE IN CENTRIFUGAL PUMPS - SOURCES AND DIAGNOSIS METHODS

In every centrifugal pump, dynamic forces of mechan ic l and hydraulic origin are present and a certain vibration and noise is therefore inevitable . To ensure the safety of the pump and associated plant components, the vibration and nois e must be kept within certain limits. If the mechanical state of the pump and its drive are good , the inflow conditions are in order and the duty point is admissible, these limits can be obser ved without difficulty. Higher vibrations ultimately results in decreased component life due to cyclic loads, lower bearing life, distortion to foundation, frequent seal failures etc. Similarl y noise has got huge impact on working environment and comfort conditions of an individual . Exact diagnosis of vibration and noise sources is very difficult in centrifugal pumps as t his may be generated due to system or the equipment itself. In this paper an attempt has been made to address some general causes of noise and vibrations, its diagnosis and remedies in centr ifugal pumps.
Fast Planning for Dynamic Preferences

We present an algorithm that quickly finds optimal plans for unforeseen agent preferences within graph-based planning domains where actions have deterministic outcomes and action costs are linearly parameterized by preference parameters. We focus on vehicle route planning for drivers with personal trade-offs for different types of roads, and specifically on settings where these preferences are not known until planning time. We employ novel bounds (based on the triangle inequality and on the the concavity of the optimal plan cost in the space of preferences) to enable the reuse of previously computed optimal plans that are similar to the new plan preferences. The resulting lower bounds are employed to guide the search for the optimal plan up to 60 times more efficiently than previous methods.
Accelerating compartmental modeling on a graphical processing unit

Compartmental modeling is a widely used tool in neurophysiology but the detail and scope of such models is frequently limited by lack of computational resources. Here we implement compartmental modeling on low cost Graphical Processing Units (GPUs), which significantly increases simulation speed compared to NEURON. Testing two methods for solving the current diffusion equation system revealed which method is more useful for specific neuron morphologies. Regions of applicability were investigated using a range of simulations from a single membrane potential trace simulated in a simple fork morphology to multiple traces on multiple realistic cells. A runtime peak 150-fold faster than the CPU was achieved. This application can be used for statistical analysis and data fitting optimizations of compartmental models and may be used for simultaneously simulating large populations of neurons. Since GPUs are forging ahead and proving to be more cost-effective than CPUs, this may significantly decrease the cost of computation power and open new computational possibilities for laboratories with limited budgets.
Complement subcomponent C1q secreted by cultured human monocytes has subunit structure identical with that of serum C1q.

An enzyme-linked immunosorbent assay (e.l.i.s.a.) that is capable of quantifying C1q concentrations as low as 2 ng/ml and a sensitive haemolytic assay were used to study the appearance of material that cross-reacts with human serum C1q as well as C1q haemolytic activity in human monocyte culture media. This material was detected in the medium after 10-14 days and continued to be secreted through to day 28 of culture, at which time the cultures were terminated. Material specifically immunoabsorbed with Sepharose-anti-C1q antibody from a culture medium of cells that was metabolically labelled with [3H] proline or [35S] methionine demonstrated a polypeptide pattern identical with that of serum C1q on SDS/polyacrylamide-gel electrophoresis. Under non-reducing conditions two protein bands were detected migrating with the same Rf values as the serum C1q A-B and C-C dimers. On reduction three bands were evident, which migrated identically with the A, B and C chains of serum C1q. The amount of radioactivity in these bands increased with time in culture, consistent with the e.l. i.s. a. and haemolytic C1q assays. These bands were reactive with monospecific anti-C1q antibody after transfer to nitrocellulose.
Sp1 Phosphorylation and Its Regulation of Gene Transcription

Sp1 is a ubiquitously expressed, prototypic C2H2-type zinc finger-containing DNA binding protein that can activate or repress transcription in response to physiologic and pathological stimuli. It was originally found to selectively transactivate the early and late simian virus 40 promoters without influencing numerous other promoters (16) and has since been shown to regulate the expression of thousands of genes implicated in the control of a diverse array of cellular processes, such as cell growth (26, 57), differentiation (48), apoptosis (26), angiogenesis (43), and immune response (25), to name just a few. Sp1 is a 785-amino-acid, 100- to 110-kDa nuclear transcription factor which regulates gene expression via multiple mechanisms. It binds GC-rich motifs (such as 5′-G/T-GGGCGG-G/A-G/A-C/T-3′ or 5′-G/T-G/A-GGCG-G/T-G/A-G/A-C/T-3′) with high affinity (4, 27, 28) and can regulate the expression of TATA-containing and TATA-less genes via protein-protein interactions or interplay with other transcription factors (47), such as Ets-1 (56), c-myc (51), c-Jun (44), Stat1 (6), and Egr-1 (31), and/or components of the basal transcriptional machinery. Sp1 has been linked to chromatin remodeling through interactions with chromatin-modifying factors such as p300 (62) and histone deacetylases (HDACs) (71). Sp1 was once thought to serve mainly as a constitutive activator of housekeeping genes. However, growing evidence indicates that phosphorylation, acetylation, sumoylation, ubiquitylation, and glycosylation are among the posttranslational modifications that can influence the transcriptional activity and stability of Sp1. Here we will discuss recent developments in our understanding of the role of posttranslational modifications influencing Sp1-dependent transcription, focusing mainly on phosphorylation.
Outcomes of anterolateral thigh‐free flaps and conversion from external to internal fixation with bone grafting in gustilo type IIIB open tibial fractures

The purpose of this study was to analyze the utility and the clinical outcomes of anterolateral thigh (ALT)‐free flaps and conversion from external to internal fixation with plating and bone grafting in Gustilo type IIIB open tibial fractures. A total of 21 patients were analyzed retrospectively. The mean follow‐up period was 18 months and the mean age was 46.7 years. There were 18 men and three women. The mean time from injury to flap coverage was 11.6 days. The mean size of flaps used was 15.3 × 8.2 cm. The mean size of bone defects was 2.26 cm. Segmental bone defects were observed in 5 five cases, for which bone transport or vascularized fibular graft were performed. When flaps were successful and the fracture sites did not have any evidence of infection, internal fixation with plates and bone grafting were performed. Flaps survived in 20 cases. In the 20 cases with successful flaps, two cases developed osteomyelitis, but the 20 cases achieved solid bone union at a mean of 8.6 months after the injury, salvaging the lower extremity in 100% of the cases. At the last follow‐up, 9 nine cases were measured excellent or good; 6, fair; and 6, poor in the functional assessment based on the method developed by Puno et al. ALT‐ free flaps to cover soft tissue defects in Gustilo type IIIB open tibial fractures are considered as useful option for the treatment of composite defects. In addition, conversion to internal fixation and bone grafting can be an alternative method in order to reduce the risk of complications and inconvenience of external fixators. © 2012 Wiley Periodicals, Inc. Microsurgery, 2012.
Biological Effects of Add-On Eicosapentaenoic Acid Supplementation in Diabetes Mellitus and Co-Morbid Depression: A Randomized Controlled Trial

Background Eicosapentaenoic acid (EPA) may reduce increased risks for (cardiovascular) morbidity and mortality in patients with diabetes mellitus (DM) and comorbid major depressive depression (MDD). Yet, effects of EPA-supplementation on biological risk factors for adverse outcomes have not been studied in DM-patients with MDD. Methods We performed a randomized, double-blind trial (n = 25) comparing add-on ethyl-EPA-supplementation to placebo on (I) oxidative stress, (II) inflammatory, (III) hypothalamic-pituitary-adrenal (HPA)-axis, (IV) one-carbon-cycle, (V) fatty acid metabolism and (VI) lipoprotein parameters during 12-weeks' follow-up. Results Besides increases in supplemented α-tocopherol [estimate (95% CI); 3.62 (1.14–6.11) µmol/l; p = 0.006] and plasma and erythrocyte EPA, the intervention did not influence other oxidative stress, inflammatory or one-carbon-cycle parameters compared to placebo. HPA-axis reactivity significantly decreased in the EPA-group (N = 12) [AUCi: −121.93 (−240.20–−3.47) min×nmol/l; p = 0.045], not in the placebo-group (N = 12). Furthermore, EPA-supplementation increased erythrocyte and plasma docosapentaenoic acid, and decreased plasma arachidonic acid (AA) concentrations [−1.61 (−3.10–−0.11) %; p = 0.036]. Finally, EPA had a multivariate influence on lipoprotein concentrations (p = 0.030), reflected by relative increases in high density lipoprotein [HDL; 0.30 (0.02–0.58) mmol/l; p = 0.039] and total cholesterol concentrations [1.01 (0.29–1.72) mmol/l; p = 0.008]. Conclusion Overall, add-on EPA-supplementation had limited effects on biological risk factors for adverse outcome in this sample of DM-patients with comorbid MDD. Besides increases in concentrations of supplemented α-tocopherol and EPA, AA decreased, and inconclusive effects on HPA-axis (re)activity and lipoprotein concentrations were observed. Therefore, further studies on the alleged beneficial effects of EPA-supplementation on biological risk factors for adverse outcome in DM-patients with comorbid MDD seem warranted, preferably using clinical outcomes such as (cardiovascular) DM-complications. Trial Registration Controlled-Trials.com ISRCTN30877831 ISRCTN30877831
Palaceology, or Palace-as-Methodology: Ethnographic Conceptualism, Total Urbanism, and a Stalinist Skyscraper in Warsaw

This article describes experiments with fieldwork methodology, carried out while researching the relationship between a Stalinist skyscraper (the Palace of Culture and Science) and the social life of contemporary Warsaw. Making use of three concepts of totality taken from social and art theory (the Maussian “total social fact,” the Wagnerian Gesamtkunstwerk , and anthropological holism), I show how the provocative style and public scale of “Palaceological” “ethnographic conceptualism”—which triangulates participant observation, artlike ethnographic interventions, and a quantitative survey—mirrors the bombastic manner and pervasive scope of the Palace’s presence in the social life of the city. This text does not argue that an urban Gesamtkunstwerk or an experiment with ethnographic methodology can actually achieve (descriptive or actual) totality. Rather, it illustrates how an “urban portrait”—the product of an aspiration to approximate and to measure the totality of an urban environment, rather than to embrace partiality as an end in itself—might be assembled. In English, extended summary in Russian.
Making polysomnography more "child friendly:" a family-centered care approach.

STUDY OBJECTIVE With the increasing recognition of pediatric sleep disorders, there is a growing demand for pediatric sleep medicine services, including polysomnography. The procedure of polysomnography can be particularly challenging in young children with limited ability to cooperate, especially when they have developmental disabilities or other medical complications. This article describes a family-centered care approach to polysomnography in children that is appropriate in any type of sleep laboratory setting. This approach emphasizes respect for the family, psychological preparation, adaptation of laboratory routines to the needs of the family, substitution of child-friendly terminology for medical jargon, coping strategies for the child and family during the procedure, positioning for comfort, utilization of distraction and medical play, modeling behavior for the parent, and continuous praise and reassurance for the child. In our experience with over 1000 studies in children of all ages with a broad range of comorbidities, implementation of this approach has minimized the burden of the polysomnography for the child, boosted the confidence of the sleep technologist, improved study quality for the diagnostician, and increased patient and family satisfaction.
Assessment of genotoxicity of Lannate-90® and its plant and animal metabolites in human lymphocyte cultures

Abstract This study evaluated direct and metabolic genotoxic effects caused by Lannate-90®, a methomyl-based formulation (90 % active ingredient), in human lymphocyte cultures using sister chromatid exchange assay (SCE). Two processes were used for the plant promutagens evaluation: in vivo activation, applying the insecticide systemically in plants for 4 h and subsequently adding plant metabolites containing extracts to lymphocyte cultures; and in vitro activation, where the insecticide was incubated with Vicia faba S10 mix plus human lymphocyte culture. Direct treatment with the insecticide significantly increased SCE frequency in human lymphocytes (250-750 mgL−1), with cellular death observed at 1000 mgL−1 concentration. Using the extracts of Vicia faba treated with Lannate-90® to treat human lymphocytes, a dose-response relationship was observed. In lymphocyte cultures treated directly with the insecticide for 2 h, a negative response was obtained. When S10 mix was added, SCE frequency did not change significantly. Meanwhile, a mixture of S9 mammalian metabolic mix and Lannate-90® increased the SCE frequency, with an observed concentration-dependent response. Although Lannate-90® induced cellular death at the highest concentrations, it did not cause a delay in cell proliferation in any of the treatments, confirming its genotoxic action. This study is one of the first to evaluate and compare the direct effect of Lannate-90® in two bioassays, animal and vegetal, and the effect of plant and animal metabolism on its genotoxic potential.
Effects of intermittent hypoxia on oxidative stress and protein degradation in molluscan mitochondria

ABSTRACT Oxygen fluctuations represent a common stressor in estuarine and intertidal environments and can compromise the mitochondrial integrity and function in marine organisms. We assessed the role of mitochondrial protection mechanisms (ATP-dependent and -independent mitochondrial proteases, and antioxidants) in tolerance to intermittent hypoxia or anoxia in three species of marine bivalves: hypoxia-tolerant hard clams (Mercenaria mercenaria) and oysters (Crassostrea virginica), and a hypoxia-sensitive subtidal scallop (Argopecten irradians). In clams and oysters, mitochondrial tolerance to hypoxia (18 h at 5% O2), anoxia (18 h at 0.1% O2) and subsequent reoxygenation was associated with the ability to maintain the steady-state activity of ATP-dependent and -independent mitochondrial proteases and an anticipatory upregulation of the total antioxidant capacity under the low oxygen conditions. No accumulation of end-products of lipid or protein peroxidation was found during intermittent hypoxia or anoxia in clams and oysters (except for an increase in protein carbonyl concentration after hypoxia–reoxygenation in oysters). In contrast, hypoxia/anoxia and reoxygenation strongly suppressed activity of the ATP-dependent mitochondrial proteases in hypoxia-sensitive scallops. This suppression was associated with accumulation of oxidatively damaged mitochondrial proteins (including carbonylated proteins and proteins conjugated with a lipid peroxidation product malondialdehyde) despite high total antioxidant capacity levels in scallop mitochondria. These findings highlight a key role of mitochondrial proteases in protection against hypoxia–reoxygenation stress and adaptations to frequent oxygen fluctuations in intertidal mollusks. Summary: Mitochondrial tolerance to intermittent hypoxia and anoxia correlates with the ability to maintain high activity of mitochondrial proteases and upregulate antioxidants in mollusks.
Signal processing for melody transcription

MT is a melody transcription system that accepts acoustic input, typically sung by the user, and displays it in standard music notation. It tracks the pitch of the input and segments the pitch stream into musical notes, which are labelled by their pitches relative to a reference frequency that adapts to the user’s tuning. This paper describes the signal processing operations involved, and discusses two applications that have been prototyped: a sightsinging tutor and a scheme for acoustically indexing a melody database.