Miracle-dz/UniFAR-FTUs huggingface dataset:
Extension Complexity of Independent Set Polytopes

We exhibit an n-node graph whose independent set polytope requires extended formulations of size exponential in Ω(n/log n). Previously, no explicit examples of n-dimensional 0/1-polytopes were known with extension complexity larger than exponential in Θ(√n). Our construction is inspired by a relatively little-known connection between extended formulations and (monotone) circuit depth.
Escherichia coli O157 outbreak associated with fresh unpasteurized goats' cheese

SUMMARY A family cluster of three cases of Escherichia coli O157 infection was identified in France. Two cases developed haemolytic–uraemic syndrome. The source was fresh unpasteurized goats' cheese, produced by an independent producer. Three E. coli O157 strains, isolated from one HUS case and faeces of one cow and one goat, were indistinguishable by toxin type and PFGE pattern.
A new assay method that detects only intact osteocalcin. Two-step non-invasive diagnosis to predict adynamic bone disease in haemodialysed patients.

BACKGROUND We studied the usefulness of a new assay method that detects only the intact human osteocalcin molecule in haemodialysed patients. METHODS Iliac bone biopsy specimens obtained from 62 haemodialysed patients were analysed. RESULTS Bone formation rates (BFR/BS) correlated positively with serum intact osteocalcin concentrations (n=62), osteocalcin concentrations assayed by a conventional method (n=31), parathyroid hormone (PTH) concentrations (n=62), and total alkaline phosphatase concentrations (r=0.602, 0. 588, 0.650, and 0.401 respectively). Based on ROC curve and Youden index analysis, the optimal cut-off value to distinguish adynamic bone disease from a mild lesion was 195 pg/ml of serum PTH concentration (Youden index=0.233) or 30 ng/ml of serum intact osteocalcin concentration (Youden index=0.628). The optimal cut-off value to distinguish between hyperparathyroid bone and a mild lesion was 455 pg/ml of serum PTH level (Youden index=0.63) or 50 ng=ml of serum intact osteocalcin concentration (Youden index=0.634). Since both ROC curve and Youden index suggested that the serum PTH concentration was not a good marker to distinguish adynamic bone from a mild lesion or hyperparathyroid bone, we designed a two-step procedure. The first step was the diagnosis of adynamic bone (cut-off: 65 pg/ml) or hyperparathyroid bone (cut-off: 455 pg/ml) according to serum PTH concentration. In a second step, we assessed serum intact osteocalcin concentration in patients with serum PTH concentrations between 65 and 455 pg/ml. The cut-off values for adynamic and hyperparathyroid bone in this diagnostic approach were 30 and 70 ng/ml respectively. As a result, 49 out of 62 patients were diagnosed properly. The Youden index of this two-step diagnosis was 0.527 and 0.661 for adynamic bone and hyperparathyroid bone respectively. Sensitivity markedly improved to 94.4% and 96.2% for adynamic bone and hyperparathyroid bone respectively, without sacrificing specificity (84.0 and 88.8% respectively). CONCLUSION Measurement of serum intact osteocalcin concentration is useful for the diagnosis of adynamic bone in haemodialysed patients. A two-step procedure involving also simultaneous measurement of serum PTH concentration further improved the sensitivity of each individual marker while maintaining specificity.
Rule Based Expert System for Diagnosis of Neuromuscular Disorders

In this paper, we discuss the implementation of a rule based expert system for diagnosing neuromuscular diseases. The proposed system is implemented as a rule based expert system in JESS for the diagnosis of Cerebral Palsy, Multiple Sclerosis, Muscular Dystrophy and Parkinson's disease. In the system, the user is presented with a list of questionnaires about the symptoms of the patients based on which the disease of the patient is diagnosed and possible treatment is suggested. The system can aid and support the patients suffering from neuromuscular diseases to get an idea of their disease and possible treatment for the disease.
A Statistical Model for Assessing Sample Size for Bacterial Colony Selection: A Case Study of Escherichia Coli and Avian Cellulitis

A general problem for microbiologists is determining the number of phenotypically similar colonies growing on an agar plate that must be analyzed in order to be confident of identifying all of the different strains present in the sample. If a specified number of colonies is picked from a plate on which the number of unique strains of bacteria is unknown, assigning a probability of correctly identifying all of the strains present on the plate is not a simple task. With Escherichia coli of avian cellulitis origin as a case study, a statistical model was designed that would delineate sample sizes for efficient and consistent identification of all the strains of phenotypically similar bacteria in a clinical sample. This model enables the microbiologist to calculate the probability that all of the strains contained within the sample are correctly identified and to generate probability-based sample sizes for colony identification. The probability of cellulitis lesions containing a single strain of E. coli was 95.4%. If one E. coli strain is observed out of three colonies randomly selected from a future agar plate, the probability is 98.8% that only one strain is on the plate. These results are specific for this cellulitis E. coli scenario. For systems in which the number of bacterial strains per sample is variable, this model provides a quantitative means by which sample sizes can be determined.
Peatland ditch blocking has no effect on dissolved organic matter (DOM) quality

The globally widespread drainage of peatlands has often been shown to lead to increased concentrations and fluxes of dissolved organic carbon (DOC) in streams and rivers. Elevated DOC concentrations have implications for carbon cycling, ecosystem functioning, and potable water treatment. Peatland rewetting, principally through ditch blocking, is often carried out with the expectation that this will reduce DOC concentrations. Uncertainty still remains as to whether drainage, or its reversal via ditch blocking, will also lead to changes in the molecular composition of DOC/dissolved organic matter (DOM), which have the potential to affect downstream processing and treatability of U.K. drinking water supplies. To investigate this question, we used a replicated experiment consisting of 12 parallel ditches on an upland bog and took samples of ditch water, pore water, and overland flow water for 4 years. After a brief preblocking baseline period, eight ditches were blocked using two methods. A complementary suite of optical metrics, chemical measurements, and analytical techniques revealed that ditch blocking had no consistent effect on DOM quality, up to 4 years after blocking. Where significant differences were found, effect size calculations demonstrated that these differences were small and would therefore have minimal impact upon water treatability. Furthermore, some differences between ditches were evident before blocking took place, highlighting the need for robust baseline monitoring before intervention. Based on our results from a hillslope‐scale experiment, we were unable to identify clear evidence that peatland ditch blocking will deliver benefits in terms of DOM treatability in potable water supplies, although we also did not find any evidence of short‐term deterioration in water quality during the restoration period. We conclude that, although peatland restoration can be expected to deliver other benefits such as reduced carbon loss and enhanced biodiversity, it is doubtful whether it will lead to improvements in drinking water treatability.
Towards Generic Semi-Automatic Transformation Process in MDA

The Model Driven Engineering (MDE) has been proposed to support the development, maintenance and evolution of software systems. In this context several approaches for transformation models have been proposed in the literature. They suffer from two major limitations: i) they have been tested on homogeneous metamodels (e.g., Ecore, UML, Minjava, Kermeta .), and ii) they use common notions and concepts, such as modeling, matching and processing models. In some approaches they do not distinguish between matching, mapping and transformation. This leads to confusion between these operations. Indeed, it is well recognized that model transformation is at the heart of approaches MDE and it is derived from the mapping model, itself obtained after performing a matching process. In this paper, we propose, in a first part, an extended architecture to semi-automate the process of transformation models. It is the separation of concerns by distinguishing the operations matching, mapping and transformation taking into account several factors (e.g., semantic resources, pre-matching efforts and post-matching efforts.). In the second part, and to test the heterogeneity of metamodels that will be taken as input by matching techniques, we introduce two new types of metamodels representing respectively the multi-agents system platform JADE, and the BPEL language for the web services orchestration. To validate our proposal, our architecture is implemented on a matching technique which details the various steps leading to a semi-automatic transformation process.
Cardiac Magnetic Resonance Assessment of Myocarditis

Symptoms consistent with myocarditis are a frequent cause of medical visits, especially in young and middleaged patients. Moreover, myocarditis was found to be the most frequent disease in patients with acute coronary syndrome yet normal coronary arteries. 1 Although many causes have been identified, acute cases are mostly because of myocardial involvement in systemic viral disease. 2,3 During the first days of viral myocarditis, there is direct cardiomyocyte injury, accompanied by edema, necrosis, and, depending on its spatial extent, regional, or even global contractile dysfunction. The tissue is typically cleared from the virus within 5 days; yet, reactive inflammation (clean-up) may last for several weeks. In uncomplicated disease, there is full tissue and functional recovery within 3 to 4 weeks, whereas more severe disease necrosis results in myocardial scarring. Prolonged autoimmune response or virus persistence may lead to chronic inflammation and is considered a frequent cause of dilated cardiomyopathy. 3 Symptoms are not specific; patients may present with chest pain, fatigue, dyspnea, or arrhythmia. ECG findings may include AV block, ventricular or supraventricular arrhythmia, and ST changes, including severe elevation mimicking acute myocardial infarction. Except for more severe cases, echocardiography typically shows normal systolic wall motion or just mild regional dysfunction. Serological markers for cardiomyocyte injury, such as troponin, may be normal. Because of the nonspecificity of its symptoms, signs and test findings, myocarditis is often diagnosed by exclusion of other cardiac diseases. The specific identification of an active nonischemic inflammatory process, therefore, is a clinical challenge, especially in patients presenting with acute chest pain and heart failure. Invasive endomyocardial biopsy is only recommended in patients with evidence for heart failure in combination with acute disease (<2 weeks, class I) or left ventricular dilatation (<3 months, class I) or specific other cases of heart failure (class IIa). 4 While nuclear imaging methods have not been proven useful, echocardiography and contrast-enhanced cardiovascular magnetic resonance (CMR) are standard imaging tools in patients with suspected myocarditis. Figures 1 to 3 present results of a 31-year-old male patient presenting with acute chest pain and a normal physical examination. Although ECG, coronary angiography, and echocardiography were either normal or nonspecific, CMR provided strong evidence for myocardial edema, hyperemia, and necrosis and thus allowed for establishing the diagnosis of acute myocarditis.
A subset of natural killer cells in peripheral blood displays a mature T cell phenotype

Normal human PBMC were analyzed for the presence of cells expressing both T3 and NKH1 antigens, using direct two-color immunofluorescence. In six individuals, NKH1+T3+ cells were found to represent 2.5% of PBMC and 24% of the total number of NKH1+ cells. Purified NKH1+T3+ cells were shown to have the typical morphology of large granular lymphocytes (LGL). NKH1+T3+ cells also exhibited spontaneous cytotoxicity against K562 target cells and this lytic activity could be inhibited by anti-T3 mAb. Similar results were obtained with NKH1+T3+ cells cultured in vitro in lymphocyte-conditioned medium. Taken together, these results indicate that NKH1+T3+ cells represent a unique population of NK-active cells in normal peripheral blood. Although these cells exhibit LGL morphology and NK activity, this appears to be mediated through a functional T cell-like receptor for target antigen.
Characterization of a Central Ca2+/Calmodulin-dependent Protein Kinase IIα/β Binding Domain in Densin That Selectively Modulates Glutamate Receptor Subunit Phosphorylation*

The densin C-terminal domain can target Ca2+/calmodulin-dependent protein kinase IIα (CaMKIIα) in cells. Although the C-terminal domain selectively binds CaMKIIα in vitro, full-length densin associates with CaMKIIα or CaMKIIβ in brain extracts and in transfected HEK293 cells. This interaction requires a second central CaMKII binding site, the densin-IN domain, and an “open” activated CaMKII conformation caused by Ca2+/calmodulin binding, autophosphorylation at Thr-286/287, or mutation of Thr-286/287 to Asp. Mutations in the densin-IN domain (L815E) or in the CaMKIIα/β catalytic domain (I205/206K) disrupt the interaction. The amino acid sequence of the densin-IN domain is similar to the CaMKII inhibitor protein, CaMKIIN, and a CaMKIIN peptide competitively blocks CaMKII binding to densin. CaMKII is inhibited by both CaMKIIN and the densin-IN domain, but the inhibition by densin is substrate-selective. Phosphorylation of a model peptide substrate, syntide-2, or of Ser-831 in AMPA receptor GluA1 subunits is fully inhibited by densin. However, CaMKII phosphorylation of Ser-1303 in NMDA receptor GluN2B subunits is not effectively inhibited by densin in vitro or in intact cells. Thus, densin can target multiple CaMKII isoforms to differentially modulate phosphorylation of physiologically relevant downstream targets.
A study of urgent and emergency referrals from NHS Direct within England

Objectives The presented study aimed to explore referral patterns of National Health Service (NHS) Direct to determine how patients engage with telephone-based healthcare and how telephone-based healthcare can manage urgent and emergency care. Setting NHS Direct, England, UK Participants NHS Direct anonymised call data (N=1 415 472) were extracted over a representative 1-year period, during the combined month periods of July 2010, October 2010, January 2011 and April 2011. Urgent and emergency calls (N=269 558; 19.0%) were analysed by call factors and patient characteristics alongside symptom classification. Categorical data were analysed using the χ2 test of independence with cross-tabulations used to test within-group differences. Primary and secondary outcome measures Urgent and emergency referrals to 999; accident and emergency or to see a general practitioner urgently, which are expressed as call rate per 100 persons per annum. Outcomes related to symptom variations by patient characteristics (age, gender, ethnicity and deprivation) alongside differences by patient characteristics of call factors (date and time of day). Results Urgent and emergency referrals varied by a range of factors relating to call, patient and symptom characteristics. For young children (0–4), symptoms related to ‘crying’ and ‘colds and flu’ and ‘body temperature change’ represented the significantly highest referrals to ‘urgent and emergency’ health services symptoms relating to ‘mental health’ alongside ‘pain’ and ‘sensation disorders’ represented the highest referrals to urgent and emergency health services for adults aged 40+ years. Conclusions This study has highlighted characteristics of ‘higher likelihood’ referrals to urgent and emergency care through the delivery of a national nurse-led telephone healthcare service. This research can help facilitate an understanding of how patients engage with both in and out of hours care and the role of telephone-based healthcare within the care pathway.
First Case of Human Babesiosis in Korea: Detection and Characterization of a Novel Type of Babesia sp. (KO1) Similar to Ovine Babesia

ABSTRACT We report on the first case of human babesiosis in Korea. The intraerythrocytic parasite (KO1) in the patient's blood mainly appeared as paired pyriforms and ring forms; but Maltese cross forms were not seen, and the parasite showed morphological features consistent with those of the genus Babesia sensu stricto. The sequence of the 18S rRNA gene of KO1 was closely related to that of Babesia spp. isolated from sheep in China (similarity, 98%). The present study provides the first evidence of the presence of a hitherto unidentified, new type of Babesia parasite capable of infecting humans.
SUMO proteomics to decipher the SUMO‐modified proteome regulated by various diseases

Small ubiquitin‐like modifier (SUMO1–3) conjugation is a posttranslational protein modification whereby SUMOs are conjugated to lysine residues of target proteins. SUMO conjugation can alter the activity, stability, and function of target proteins, and thereby modulate almost all major cellular pathways. Many diseases are associated with SUMO conjugation, including heart failure, arthritis, cancer, degenerative diseases, and brain ischemia/stroke. It is, therefore, of major interest to characterize the SUMO‐modified proteome regulated by these disorders. SUMO proteomics analysis is hampered by low levels of SUMOylated proteins. Several strategies have, therefore, been developed to enrich SUMOylated proteins from cell/tissue extracts. These include proteomics analysis on cells expressing epitope‐tagged SUMO isoforms, use of monoclonal SUMO antibodies for immunoprecipitation and epitope‐specific peptides for elution, and affinity purification with peptides containing SUMO interaction motifs to specifically enrich polySUMOylated proteins. Recently, two mouse models were generated and characterized that express tagged SUMO isoforms, and allow purification of SUMOylated proteins from complex organ extracts. Ultimately, these new analytical tools will help to decipher the SUMO‐modified proteome regulated by various human diseases, and thereby, identify new targets for preventive and therapeutic purposes.
Similarity-Guided Streamline Placement with Error Evaluation

Most streamline generation algorithms either provide a particular density of streamlines across the domain or explicitly detect features, such as critical points, and follow customized rules to emphasize those features. However, the former generally includes many redundant streamlines, and the latter requires Boolean decisions on which points are features (and may thus suffer from robustness problems for real-world data). We take a new approach to adaptive streamline placement for steady vector fields in 2D and 3D. We define a metric for local similarity among streamlines and use this metric to grow streamlines from a dense set of candidate seed points. The metric considers not only Euclidean distance, but also a simple statistical measure of shape and directional similarity. Without explicit feature detection, our method produces streamlines that naturally accentuate regions of geometric interest. In conjunction with this method, we also propose a quantitative error metric for evaluating a streamline representation based on how well it preserves the information from the original vector field. This error metric reconstructs a vector field from points on the streamline representation and computes a difference of the reconstruction from the original vector field.
Minimal coronary artery damage by myocardial electroporation ablation.

AIMS Radiofrequency catheter ablation is a successful treatment for cardiac arrhythmias, but may lead to major complications such as permanent coronary damage. Irreversible electroporation (IRE) is a new non-thermal ablation modality, but its effect on coronary arteries is still unknown. METHODS AND RESULTS In a porcine model, epicardial IRE lesions were created at the base of the left ventricle in four hearts (group A) and directly on the left anterior descending artery (LAD) in five hearts (group B). After 3 weeks, coronary arteries inside IRE lesions and in apparently undamaged myocardium next to the lesions were (immuno-)histologically studied. Two untreated hearts served as controls. Coronary damage was defined as intimal hyperplasia. Left anterior descending artery angiograms were obtained before ablation, directly after ablation, and before termination in group B. In group A, 103 arterial branches were studied. Of these, 5 of 56 arterial branches inside lesions and 1 of 47 outside lesions showed intimal hyperplasia, but all had <50% area stenosis. Targeted LADs (group B) did not reveal intimal hyperplasia and angiograms showed no signs of stenosis. Expression of connective tissue growth factor was observed in the scar tissue, but not in the fibrotic tissue directly around the arteries, confirming that the arteries are indeed spared from tissue damage and remodelling. CONCLUSION Coronary arteries remain free of clinically relevant damage 3 weeks after epicardial IRE ablation, even amid very large myocardial lesions. This suggests that IRE ablation can be applied safely near or even on coronary arteries. With IRE ablation, arterial blood flow does not appear to affect lesion formation.
Beyond Leptin: Emerging Candidates for the Integration of Metabolic and Reproductive Function during Negative Energy Balance

Reproductive status is tightly coupled to metabolic state in females, and ovarian cycling in mammals is halted when energy output exceeds energy input, a metabolic condition known as negative energy balance. This inhibition of reproductive function during negative energy balance occurs due to suppression of gonadotropin-releasing hormone (GnRH) release in the hypothalamus. The GnRH secretagogue kisspeptin is also inhibited during negative energy balance, indicating that inhibition of reproductive neuroendocrine circuits may occur upstream of GnRH itself. Understanding the metabolic signals responsible for the inhibition of reproductive pathways has been a compelling research focus for many years. A predominant theory in the field is that the status of energy balance is conveyed to reproductive neuroendocrine circuits via the adipocyte hormone leptin. Leptin is stimulatory for GnRH release and lower levels of leptin during negative energy balance are believed to result in decreased stimulatory drive for GnRH cells. However, recent evidence found that restoring leptin to physiological levels did not restore GnRH function in three different models of negative energy balance. This suggests that although leptin may be an important permissive signal for reproductive function as indicated by many years of research, factors other than leptin must critically contribute to negative energy balance-induced reproductive inhibition. This review will focus on emerging candidates for the integration of metabolic status and reproductive function during negative energy balance.