Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy in cutaneous malignant melanoma

We show that malignant melanoma cells display high levels of autophagy, a cytoplasmic process of protein and organelle digestion that provides an energy source in times of nutrient deprivation. In a panel of 12 cases of cutaneous malignant melanoma of the superficial spreading type, cells in florid melanoma in situ (MIS) and invasive cells in the dermis appeared to be undergoing autophagy. Autophagosomes were detected through immunohistochemistry using the marker LC3B (microtubule‐associated light chain 3B), and by electron microscopy. Some autophagosomes contained melanized melanosomes, accounting for the phenomenon of ‘coarse melanin’ in malignant melanoma. Autophagosomes also contained the Golgi 58k protein, a structural component of the Golgi apparatus, and β1, 6‐branched oligosaccharides, indicating that at least some of the autophagosomal proteins were glycosylated with these structures. The findings suggest that autophagy could be a constitutive metabolic state for invasive and metastatic melanoma cells. Interestingly, a similar phenotype was also expressed by tumor‐associated melanophages. The findings are consistent with previous reports that endoplasmic reticulum (ER) stress drives melanoma progression, since ER stress is known to trigger autophagy. The results suggest that therapies inhibiting autophagy may be effective for the treatment of malignant melanoma by depriving cells of an important energy source.
A Network-based Approach to Mining Competitor Relationships from Online News

Identifying competitors for an individual company or a group of companies is important for businesses. Although people can consult paid company profile resources such as Hoover’s and Mergent, these sources are incomplete in company relationship coverage. We present an approach that uses graph-theoretic measures and machine learning techniques to achieve automated discovery of competitor relationships on the basis of structure of an intercompany network derived from company citations (cooccurrence) in online news articles. We also estimate to what extent our approach could extend the competitor relationships available from the data sources, Hoover’s and Mergent.
Left Ventricular Rotational Mechanics in Children After Heart Transplantation

Background—Left ventricular (LV) dysfunction after orthotopic heart transplantation (OHT) is multifactorial and can be an indicator of graft rejection or coronary artery vasculopathy. Analysis of rotational mechanics may help in the early diagnosis of ventricular dysfunction. Studies describing the left ventricular rotational strain in children after OHT are lacking. It is important to establish the baseline rotational mechanics in pediatric OHT to pursue further studies in this population. Methods and Results—Rotational strain measured by speckle tracking was compared in 32 children after OHT, with no evidence of active rejection or coronary artery vasculopathy with 35 age-matched normal controls. Twelve OHT patients and 13 controls underwent moderate exercise with pre- and postexercise echocardiography. Torsion, slope of the systolic limb of the torsion–radial displacement loop, and the untwist rate were significantly higher in OHT patients (torsion: median 2.7°/cm [Q1–Q3, 2.3–3.2] versus 2.3°/cm [Q1–Q3, 1.9–2.7]; P=0.03, torsion–radial displacement loop: 2.7°/mm [Q1–Q3, 2.1–3.6] versus 2.0°/mm [Q1–Q3, 1.6–2.7]; P=0.008, indexed peak untwist rate: −21.6°/s/cm [Q1–Q3, −24.3 to −15.7] versus −17.1°/s/cm [Q1–Q3, −19.6 to −13.3]; P=0.01). Contrary to controls, OHT recipients were unable to increase torsion with exercise (OHT: 2.8°/cm [2.7–3.2] versus 3°/cm [2.4–3.5]; P=0.81, controls: 2.2°/cm [2–2.6] versus 3°/cm [2.4–3.7]; P=0.01, pre and post exercise, respectively). The systolic slope of the torsion–radial displacement loop relationship decreased with exercise in most OHT patients. Conclusions—Baseline rotational strain in OHT patients is higher than normal with a blunted response to exercise. The slope of torsion–radial displacement loop, and its response to exercise, may serve as a marker of left ventricular dysfunction in OHT patients.
Residual investigation: predictive and precise bug detection

We introduce the concept of “residual investigation” for program analysis. A residual investigation is a dynamic check installed as a result of running a static analysis that reports a possible program error. The purpose is to observe conditions that indicate whether the statically predicted program fault is likely to be realizable and relevant. The key feature of a residual investigation is that it has to be much more precise (i.e., with fewer false warnings) than the static analysis alone, yet significantly more general (i.e., reporting more errors) than the dynamic tests in the program's test suite pertinent to the statically reported error. That is, good residual investigations encode dynamic conditions that, when taken in conjunction with the static error report, increase confidence in the existence of an error, as well as its severity, without needing to directly observe a fault resulting from the error. We enhance the static analyzer FindBugs with several residual investigations, appropriately tuned to the static error patterns in FindBugs, and apply it to 7 large open-source systems and their native test suites. The result is an analysis with a low occurrence of false warnings (“false positives”) while reporting several actual errors that would not have been detected by mere execution of a program's test suite.
Multivariate miRNA signatures as biomarkers for non-ischaemic systolic heart failure.

AIMS Non-ischaemic heart failure is one of the today's most prevalent cardiovascular disorders. Since modern pharmacotherapy has proved to be very effective in delaying disease progression and preventing death, imaging modalities and molecular biomarkers play an important role in early identification and clinical management as well as risk assessment of patients. The present study evaluated for the first time whole peripheral blood miRNAs as novel biomarker candidates for non-ischaemic heart failure with reduced ejection fraction (HF-REF). METHODS AND RESULTS We assessed genome-wide miRNA expression profiles in 53 HF-REF patients and 39 controls. We could identify and validate several miRNAs that show altered expression levels in non-ischaemic HF-REF, discriminating cases from controls both as single markers or when combined in a multivariate signature. In addition, we demonstrate that the miRNAs of this signature significantly correlate with disease severity as indicated by left ventricular ejection fraction. CONCLUSION Our data further denote that miRNAs are potential biomarkers for systolic heart failure. Since their detection levels in whole blood are also related to the degree of left ventricular dysfunction, they may serve as objective molecular tools to assess disease severity and prognosis.
A verb lexicon model for deep sentiment analysis and opinion mining applications

This paper presents a lexicon model for subjectivity description of Dutch verbs that offers a framework for the development of sentiment analysis and opinion mining applications based on a deep syntactic-semantic approach. The model aims to describe the detailed subjectivity relations that exist between the participants of the verbs, expressing multiple attitudes for each verb sense. Validation is provided by an annotation study that shows that these subtle subjectivity relations are reliably identifiable by human annotators.
Diagnosis of bovine tuberculosis : review of main techniques

Bovine tuberculosis (BTB) remains an important economic and zoonotic problem in Latin America. Traditionally, the fight against BTB is initiated by the implementation of routine diagnostic tests for certification of free properties. The diagnosis of BTB can be made by direct and indirect methods, in which we can mention clinical, post mortem, histopathological, immunological, bacteriological and molecular methods. The renewal of scientific interest in tuberculosis in recent year has led to develop and improve methods of diagnosis, prevention, control and eradication of BTB. The aim of this review is to present and discuss different diagnosis methods of BTB.
Mass outflow from the X-ray binary X2127 + 119 in M15

The bright X-ray binary X2127 + 119 in the core of the globular cluster M15 has long been thought to be in an unusual evolutionary state, in which the binary is embedded in a common envelope. Support for this idea comes from the absorption lines of X2127 + 119, which are blueshifted at all orbital phases, indicating the existence of outflows from the system. A common-envelope scenario implies that the absorption lines should exhibit maximum blueshift near mid-eclipse (binary phase 0.0). We have re-analysed Isaac Newton Telescope spectra of X2127 + 119 obtained in 1986, 1987 and 1988 using the latest orbital ephemeris (substantially different from that used in the original analysis), and find that the orbital phase at which the absorption lines show a maximum blueshift is not 0.0, but rather 0.25-0.3. These results indicate that a common-envelope scenario for X2127 + 119 may not work. In addition, from spectrograms of the He II λ4686 line, we report the first tentative detection of the companion star of X2127 + 119.
Factors that influence the severity of post-stroke depression

Aim: The aim of this paper was to investigate whether the extent of neurological impairment, the location of ischemic lesions due to stroke are associated with the severity of post-stroke depression. Materials and methods: The study included 82 patients, who were diagnosed with acute ischemic stroke and post-stroke depression and were admitted to the Neurology Clinic of Cluj-Napoca County Emergency Hospital between 2009 and 2011. A head MRI was performed with a 1.5 Tesla. Psychometric assessment was performed by using several scales, including the Beck Depression Inventory and the Mini-Mental State Examination. The National Institutes of Health Stroke Scale (NIHSS) and the Barthel Index of Activities of Daily Living were used to produce a complete neurological assessment. Results: Patients with severe depression had a lower score on the Quality of Life Scale (QOLS) and higher scores for the Barthel index, NIHSS and MMSE. A stroke located in the basal nuclei increased the probability of severe depression. The patients with fewer lesions (1-2) had a greater chance of developing mild or moderate depression compared to the patients with 3-4 lesions. A frontal localization of the stroke was almost twice as common in patients with severe depression. If the stroke affected the left hemisphere, there was a higher probability of severe depression. In multivariate analysis, a basal nuclei lesion, a left hemisphere stroke location, and an NIHSS score >11 were all independently associated with severe depression. Conclusion: The location of the stroke and the NIHSS score could be related to the severity of post-stroke depression. Abbreviations: NIHSS = The National Institutes of Health Stroke Scale; QQL = Quality of life Scale; BDI = Beck Depression Inventory; MMSE = Mini-Mental State Examination; PSD = Post-stroke depression; MRI = Magnetic resonance imaging
Ischemic stroke risk with oral contraceptives: A meta-analysis.

CONTEXT The relationship between ischemic stroke and oral contraceptive (OC) use has been studied for 40 years, but disagreement about an association persists. OBJECTIVE To review available literature to determine whether OC use is associated with increased stroke risk. DATA SOURCES Studies published from January 1960 through November 1999 were identified from electronic databases (MEDLINE, BIOSIS, and Dissertation Abstracts Online), Index Medicus, bibliographies of pertinent review articles and pertinent original articles, textbooks, and expert consultation. STUDY SELECTION From 804 potentially relevant references retrieved, 73 were studies investigating risk of ischemic stroke with OC use. Two reviewers independently applied the following inclusion criteria: more than 10 stroke cases sampled, clear stroke subtype differentiation, concurrent controls included, adequate data included to determine relative risks (RRs) and confidence intervals (CIs), analysis controlled for age, and no later publication of identical data. A third investigator adjudicated disagreements. Sixteen studies met all inclusion criteria and were included in the meta-analysis. DATA EXTRACTION Two investigators independently extracted data, with disagreements resolved through discussion. DATA SYNTHESIS The 16 studies were analyzed using random effects modeling. Current OC use was associated with increased risk of ischemic stroke (RR, 2.75; 95% CI, 2.24-3.38). Smaller estrogen dosages were associated with lower risk (P=.01 for trend), but risk was significantly elevated for all dosages. Studies that did not control for smoking (P=.01) and those using hospital-based controls (P<.001) found higher RRs, but no other patient characteristics or elements of study design were important. The summary RR was 1.93 (95% CI, 1.35-2.74) for low-estrogen preparations in population-based studies that controlled for smoking and hypertension. This translates to an additional 4.1 ischemic strokes per 100,000 nonsmoking, normotensive women using low-estrogen OCs, or 1 additional ischemic stroke per year per 24,000 such women. The RR of stroke due to OC use was not different in women who smoked, had migraines, or had hypertension. CONCLUSIONS Summary results indicate that risk of ischemic stroke is increased in current OC users, even with newer low-estrogen preparations. However, the absolute increase in stroke risk is expected to be small since incidence is very low in this population. JAMA. 2000;284:72-78
The effect of passive stretching on delayed onset muscle soreness, and other detrimental effects following eccentric exercise

The aim of this study was to measure if passive stretching would influence delayed onset muscle soreness (DOMS), dynamic muscle strength, plasma creatine kinase concentration (CK) and the ratio of phosphocreatine to inorganic phosphate (PCr/Pi) following eccentric exercise. Seven healthy untrained women, 28–46 years old, performed eccentric exercise with the right m. quadriceps in an isokinetic dynamometer (Biodex, angle velocity: 60°. s−1) until exhaustion, in two different experiments, with an interval of 13‐23 months. In both experiments the PCr/Pi ratio, dynamic muscle strength, CK and muscle pain were measured before the eccentric exercise (day 0) and the following 7 d. In the second experiment daily passive stretching (3 times of 30 s duration, with a pause of 30 s in between) of m. quadriceps was included in the protocol. The stretching was performed before and immediately after the eccentric exercise at day 0, and before measurements of the dependent variables daily for the following 7 d. The eccentric exercise alone led to significant decreases in PCr/Pi ratio (P<0.001) and muscle strength (P<0.001), and an increase in CK concentration (P<0.01). All subjects reported pain in the right m. quadriceps with a peak 48 h after exercise. There was no difference in the reported variables between experiments one and two. It is concluded that passive stretching did not have any significant influence on increased plasma‐ CK, muscle pain, muscle strength and the PCr/Pi ratio, indicating that passive stretching after eccentric exercise cannot prevent secondary pathological alterations.
Practical algorithms for constructing HKZ and Minkowski reduced bases

In this paper, three practical lattice basis reduction algorithms are presented. The first algorithm constructs a Hermite, Korkine and Zolotareff (HKZ) reduced lattice basis, in which a unimodular transformation is used for basis expansion. Our complexity analysis shows that our algorithm is significantly more efficient than the existing HKZ reduction algorithms. The second algorithm computes a Minkowski reduced lattice basis. It is the first practical algorithm for Minkowski reduced bases for lattices of arbitrary dimensions. The third algorithm is an improvement of the second algorithm by drastically reducing the number of lattice points being searched. Since the original LLL algorithm is no longer applicable to the third algorithm, we propose a notion of quasi-LLL reduction to accelerate the computation.
A Context-Aware mHealth System for Online Physiological Monitoring in Remote Healthcare

Physiological or biological stress is an organism’s response to a stressor such as an environmental condition or a stimulus. The identification of physiological stress while performing the activities of daily living is an important field of health research in preventive medicine. Activities initiate a dynamic physiological response that can be used as an indicator of the overall health status. This is especially relevant to high risk groups; the assessment of the physical state of patients with cardiovascular diseases in daily activities is still very difficult. This paper presents a context-aware telemonitoring platform, IPM-mHealth, that receives vital parameters from multiple sensors for online, real-time analysis. IPM-mHealth provides the technical basis for effectively evaluating patients’ physiological conditions, whether inpatient or at home, through the relevance between physical function and daily activities. The two core modules in the platform include: 1) online activity recognition algorithms based on 3-axis acceleration sensors and 2) a knowledge-based, conditional-reasoning decision module which uses context information to improve the accuracy of determining the occurrence of a potentially dangerous abnormal heart rate. Finally, we present relevant experiments to collect cardiac information and upper-body acceleration data from the human subjects. The test results show that this platform has enormous potential for use in long-term health observation, and can help us define an optimal patient activity profile through the automatic activity analysis.
On correlated availability in Internet-distributed systems

As computer networks rapidly increase in size and speed, Internet-distributed systems such as P2P, volunteer computing, and Grid systems are increasingly common. A precise and accurate characterization of Internet resources is important for the design and evaluation of such Internet-distributed systems, yet our picture of the Internet landscape is not perfectly clear. To improve this picture, we measure and characterize the time dynamics of availability in a large-scale Internet-distributed system with over 110,000 hosts. Our characterization focuses on identifying patterns of correlated availability. We determine scalable and accurate clustering techniques and distance metrics for automatically detecting significant availability patterns. By means of clustering, we identify groups of resources with correlated availability that exhibit similar time effects. Then we show how these correlated clusters of resources can be used to improve resource management for parallel applications in the context of volunteer computing.
Potential Enhanced Survivorship of Crown of Thorns Starfish Larvae due to Near-Annual Nutrient Enrichment during Secondary Outbreaks on the Central Mid-Shelf of the Great Barrier Reef, Australia

The Great Barrier Reef (GBR) is currently experiencing widespread crown of thorns starfish (CoTS) outbreaks, as part of the fourth wave of outbreaks since 1962. It is believed that these outbreaks have become more frequent on the GBR and elsewhere in the Indo-Pacific and are associated with anthropogenic causes. The two widely accepted potential causes are (1) anthropogenic nutrient enrichment leading to the increased biomass of phytoplankton, the food of the planktonic stage of larval CoTS; and (2) the overfishing of predators in the juvenile to adult stages of CoTS, for example, commercially fished species such as coral trout. In this study, we show that the evidence for the nutrient enrichment causation hypothesis is strongly based on a large number of recent studies in the GBR. We also hypothesise that secondary outbreaks in the region between Cairns and Townsville can also be enhanced by nutrient enriched conditions associated with the annual nutrient discharge from Wet Tropics rivers.
CD40 and CD80/86 act synergistically to regulate inflammation and mortality in polymicrobial sepsis.

RATIONALE Costimulatory molecules, including the CD40-CD154 and CD80/86-CD28 dyads, play a prominent role in regulating inflammation in the adaptive immune response. Studies from our group and others suggest a potentially important role for these costimulatory cascades in innate immunity as well. OBJECTIVES To determine the role of CD80/86 alone and in combination with CD40 in lethal polymicrobial sepsis in mice and humans. METHODS The murine cecal ligation and puncture (CLP) model was used to determine the role of CD80/86 alone and in combination with CD40 using wild-type mice, CD80/86(-/-) mice, and novel CD40/80/86(-/-) mice. Expression of cell-bound and soluble costimulatory molecules was assessed in humans via ELISA and flow cytometry. MEASUREMENTS AND MAIN RESULTS Lethal CLP was associated with up-regulation of CD40 and CD80/86 and their respective ligands CD28 and CD154 on innate effector cells. Blockade or deletion of CD80/86 attenuated mortality and inflammatory cytokine production during CLP. CD40/80/86(-/-) mice exhibited further reductions in mortality, lung injury, and inflammatory cytokine production compared with CD80/86(-/-) mice. Finally, humans with sepsis had increased monocyte expression of CD40 and CD80 compared with healthy control subjects; with higher levels in subjects requiring vasopressor support. Levels of soluble CD28 and CD154 were significantly higher in patients who died compared with those who lived. CONCLUSIONS These data demonstrate a central role for CD40 and CD80/86 in the innate immune response and suggest that combined inhibition of CD40 and CD80/86 may improve mortality in sepsis. Expression of costimulatory molecules may serve as biomarkers for outcome in septic patients.
INTERCELLULAR ADHESION MOLECULE‐1 (ICAM‐1) IS EXPRESSED ON HUMAN NEUTROPHILS AND IS ESSENTIAL FOR NEUTROPHIL ADHERENCE AND AGGREGATION

This study investigated the expression and regulation of intercellular adhesion molecule-1 (ICAM-1) on human polymorphonuclear neutrophils (PMNs), and its potential role in PMN-PMN adherence and aggregation as observed during systemic inflammatory response syndrome. Normal human PMNs were found to express ICAM-1 with 90% positive population, and this expression was augmented by endotoxin (lipopolysaccharide, LPS) and tumor necrosis factor-α (TNF-α) stimulation. The presence of ICAM-1 mRNA in human PMNs was further detected by reverse transcription-polymerase chain reaction before and after LPS and TNF-α treatment. Furthermore, incubation of PMNs with LPS and TNF-α resulted in significant increases in PMN-PMN adherence and aggregation, while addition of either anti ICAM-1 mAb or anti CD11b/CD18 mAb significantly inhibited LPS and TNF-α-mediated PMN-PMN adherence and aggregation. These novel findings demonstrate that ICAM-1 is expressed on human PMNs and responsible for PMN aggregation, and suggest that the interaction between ICAM-1 and CD11b/CD18 may be the molecular basis for PMN aggregation and clumping in the microcirculation during systemic inflammatory response syndrome.
In migrating fibroblasts, recycling receptors are concentrated in narrow tubules in the pericentriolar area, and then routed to the plasma membrane of the leading lamella

By following the intracellular processing of recycling transferrin receptors and the selective sorting of a-2 macroglobulin in chick embryo fibroblasts, we have shown that the concentration of 60 nm diam tubules which surrounds the centrioles represents a distal compartment on the recycling pathway. In migrating cells transferrin receptor tracers can be loaded into this compartment and then chased to the cell surface. When they emerge the recycling transferrin receptors are distributed over the surface of the leading lamella.