Miracle-dz/UniFAR-FTUs huggingface dataset:
The Neutrophil’s Choice: Phagocytose vs Make Neutrophil Extracellular Traps

Neutrophils recognize particulate substrates of microbial or endogenous origin and react by sequestering the cargo via phagocytosis or by releasing neutrophil extracellular traps (NETs) outside the cell, thus modifying and alerting the environment and bystander leukocytes. The signals that determine the choice between phagocytosis and the generation of NETs are still poorly characterized. Neutrophils that had phagocytosed bulky particulate substrates, such as apoptotic cells and activated platelets, appear to be “poised” in an unresponsive state. Environmental conditions, the metabolic, adhesive and activation state of the phagocyte, and the size of and signals associated with the tethered phagocytic cargo influence the choice of the neutrophils, prompting either phagocytic clearance or the generation of NETs. The choice is dichotomic and apparently irreversible. Defects in phagocytosis may foster the intravascular generation of NETs, thus promoting vascular inflammation and morbidities associated with diseases characterized by defective phagocytic clearance, such as systemic lupus erythematosus. There is a strong potential for novel treatments based on new knowledge of the events determining the inflammatory and pro-thrombotic function of inflammatory leukocytes.
Evaluation of the PROSAIL Model Capabilities for Future Hyperspectral Model Environments: A Review Study

Upcoming satellite hyperspectral sensors require powerful and robust methodologies for making optimum use of the rich spectral data. This paper reviews the widely applied coupled PROSPECT and SAIL radiative transfer models (PROSAIL), regarding their suitability for the retrieval of biophysical and biochemical variables in the context of agricultural crop monitoring. Evaluation was carried out using a systematic literature review of 281 scientific publications with regard to their (i) spectral exploitation, (ii) vegetation type analyzed, (iii) variables retrieved, and (iv) choice of retrieval methods. From the analysis, current trends were derived, and problems identified and discussed. Our analysis clearly shows that the PROSAIL model is well suited for the analysis of imaging spectrometer data from future satellite missions and that the model should be integrated in appropriate software tools that are being developed in this context for agricultural applications. The review supports the decision of potential users to employ PROSAIL for their specific data analysis and provides guidelines for choosing between the diverse retrieval techniques.
Stark-Zeeman Line Shape Modeling for Magnetic White Dwarf and Tokamak Edge Plasmas: Common Challenges

The shape of atomic spectral lines in plasmas contains information on the plasma parameters, and can be used as a diagnostic tool. Under specific conditions, the plasma located at the edge of tokamaks has parameters similar to those in magnetic white dwarf stellar atmospheres, which suggests that the same line shape models can be used. A problem common to tokamak and magnetic white dwarfs concerns the modeling of Stark broadening of hydrogen lines in the presence of an external magnetic field and the related Zeeman effect. In this work, we focus on a selection of issues relevant to Stark broadening in magnetized hydrogen plasmas. Various line shape models are presented and discussed through applications to ideal cases.
Linking named entities in Tweets with knowledge base via user interest modeling

Twitter has become an increasingly important source of information, with more than 400 million tweets posted per day. The task to link the named entity mentions detected from tweets with the corresponding real world entities in the knowledge base is called tweet entity linking. This task is of practical importance and can facilitate many different tasks, such as personalized recommendation and user interest discovery. The tweet entity linking task is challenging due to the noisy, short, and informal nature of tweets. Previous methods focus on linking entities in Web documents, and largely rely on the context around the entity mention and the topical coherence between entities in the document. However, these methods cannot be effectively applied to the tweet entity linking task due to the insufficient context information contained in a tweet. In this paper, we propose KAURI, a graph-based framework to collectively link all the named entity mentions in all tweets posted by a user via modeling the user's topics of interest. Our assumption is that each user has an underlying topic interest distribution over various named entities. KAURI integrates the intra-tweet local information with the inter-tweet user interest information into a unified graph-based framework. We extensively evaluated the performance of KAURI over manually annotated tweet corpus, and the experimental results show that KAURI significantly outperforms the baseline methods in terms of accuracy, and KAURI is efficient and scales well to tweet stream.
Alcohol Intake in Pregnancy Increases the Child's Risk of Atopic Dermatitis. The COPSAC Prospective Birth Cohort Study of a High Risk Population

Background Atopic dermatitis has increased four-fold over the recent decades in developed countries, indicating that changes in environmental factors associated with lifestyle may play an important role in this epidemic. It has been proposed that alcohol consumption may be one contributing risk factor in this development. Objective To analyze the impact of alcohol intake during pregnancy on the development of atopic dermatitis during the first 7 years of life. Method The COPSAC cohort is a prospective, longitudinal, birth cohort study of 411 children born to mothers with a history of asthma, followed up for 7 years with scheduled visits every 6 months as well as visits for acute exacerbations of atopic dermatitis. Risk of atopic dermatitis from any alcohol consumption during pregnancy was analyzed as time-to-diagnosis and adjusted for known risk factors. Results 177 of 411 children developed atopic dermatitis before age 7 years. We found a significant effect of alcohol intake during pregnancy on atopic dermatitis development (HR 1.44, 95% CI 1.05–1.99 p = 0.024). This conclusion was unaffected after adjustment for smoking, mother's education and mother's atopic dermatitis. Limitations The selection of a high-risk cohort, with all mothers suffering from asthma, and all children having a gestational age above 35 weeks with no congenital abnormality, systemic illness, or history of mechanical ventilation or lower airway infection. Conclusion Alcohol intake by pregnant women with a history of asthma, is significantly associated with an increased risk for the child for developing atopic dermatitis during the first 7 years of life.
Detection and Genotyping of Human Papillomavirus DNA Using Polymerase Chain Reaction Short PCR Fragment 10–Line Probe Assay in Abnormal Papanicolaou-Stained Cervicovaginal Smears

OBJECTIVE To evaluate the effectiveness of the short PCR fragment 10-line probe assay (SPF10-LiPA) system in detection of human papillomavirus (HPV) in abnormal Papanicolaou-stained cervicovaginal smears. STUDY DESIGN We included 20 abnormal Papanicolaou-stained cervicovaginal smears. Samples were tested for HPV DNA detection and genotyping using the SPF10-LiPA system. RESULTS All samples amplified the INF150 gene control. In 2 of 20 cases, amplification of the viral sequences was negative. Of processed samples, 18 of 20 presented HPV infection; of them, 56% showed only 1 type of HPV infection; the remaining presented > or = 2 types of HPV (multiple infections). HPV16 was the most frequent specific viral in 60%, in single and multiple infections, followed by HPV18 (20%), HPV6 (10%) and HPV58 (10%). We also found HR-HPV45, 52, 58 and 68 and LR-HPV6, 11 and 70 viral DNA types. These multiple infections were detected with greater frequencies in atypical squamous cells of undetermined significance and in the low-grade squamous intraepithelial lesions. CONCLUSION The SPF10-LiPA system is efficient, sensitive, fast and simple for detecting and genotyping HPV DNA in abnormal Papanicolaou-stained cervicovaginal smears, which could be enormously useful in routine investigation for better clinical management of the patient.
A quality project for radiation reduction in the cath lab

Abstract The radiation exposure in the cath lab of patients, cardiologists, and nurses was measured during three consecutive periods of 8 weeks. The first 8 weeks the baseline radiation exposure was obtained. In the second period standard incidences for coronarography and frame rate were changed, without compromising the image quality of the examination. In the third period, a pelvic shield covered the lower part of the patient. This pilot quality project demonstrates that further significant reduction in radiation exposure of 37% is possible for patients. A significant reduction in radiation exposure of 53 and 62% was obtained among cardiologists and nurses working in the cath lab, even with the already diminished radiation exposure over the last years by better equipment and general radioprotection measures.
Rectal cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.

Department of Radiotherapy, Mount Vernon Centre for Cancer Treatment, Northwood, London, UK; Department of Gastrointestinal Cancer, Maria SklodowskaCurie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland; Department of Surgery, Sorbonne Universités, UPMC Univ Paris 06, Paris; APHP, Hôpital Saint-Antoine, Paris, France; Department of Radiology, The Imperial College and Royal Marsden Hospital, Sutton, Surrey, UK; Department of Radiotherapy and Oncology, University of Frankfurt, Frankfurt, Germany; CIBERONC, Medical Oncology Department, INCLIVA University of Valencia, Valencia, Spain; Instituto CUF de Oncologia (I.C.O.), Lisbon, Portugal
Dietary patterns and whole grain cereals in the Scandinavian countries – differences and similarities. The HELGA project

Abstract Objective To identify dietary patterns with whole grains as a main focus to see if there is a similar whole grain pattern in the three Scandinavian countries; Denmark, Sweden and Norway. Another objective is to see if items suggested for a Nordic Food Index will form a typical Nordic pattern when using factor analysis. Setting The HELGA study population is based on samples of existing cohorts: the Norwegian Women and Cancer Study, the Swedish Västerbotten cohort and the Danish Diet, Cancer and Health study. The HELGA study aims to generate knowledge about the health effects of whole grain foods. Subjects The study included a total of 119 913 participants. Design The associations among food variables from FFQ were investigated by principal component analysis. Only food groups common for all three cohorts were included. High factor loading of a food item shows high correlation of the item to the specific diet pattern. Results The main whole grain for Denmark and Sweden was rye, while Norway had highest consumption of wheat. Three similar patterns were found: a cereal pattern, a meat pattern and a bread pattern. However, even if the patterns look similar, the food items belonging to the patterns differ between countries. Conclusions High loadings on breakfast cereals and whole grain oat were common in the cereal patterns for all three countries. Thus, the cereal pattern may be considered a common Scandinavian whole grain pattern. Food items belonging to a Nordic Food Index were distributed between different patterns.
In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

Currently, genome sequences of a total of 19 Porphyromonas gingivalis strains are available, including eight completed genomes (strains W83, ATCC 33277, TDC60, HG66, A7436, AJW4, 381, and A7A1-28) and 11 high-coverage draft sequences (JCVI SC001, F0185, F0566, F0568, F0569, F0570, SJD2, W4087, W50, Ando, and MP4-504) that are assembled into fewer than 300 contigs. The objective was to compare these genomes at both nucleotide and protein sequence levels in order to understand their phylogenetic and functional relatedness. Four copies of 16S rRNA gene sequences were identified in each of the eight complete genomes and one in the other 11 unfinished genomes. These 43 16S rRNA sequences represent only 24 unique sequences and the derived phylogenetic tree suggests a possible evolutionary history for these strains. Phylogenomic comparison based on shared proteins and whole genome nucleotide sequences consistently showed two groups with closely related members: one consisted of ATCC 33277, 381, and HG66, another of W83, W50, and A7436. At least 1,037 core/shared proteins were identified in the 19 P. gingivalis genomes based on the most stringent detecting parameters. Comparative functional genomics based on genome-wide comparisons between NCBI and RAST annotations, as well as additional approaches, revealed functions that are unique or missing in individual P. gingivalis strains, or species-specific in all P. gingivalis strains, when compared to a neighboring species P. asaccharolytica. All the comparative results of this study are available online for download at ftp://www.homd. org/publication_data/20160425/.
Coverage-Based Greybox Fuzzing as Markov Chain

Coverage-based Greybox Fuzzing (CGF) is a random testing approach that requires no program analysis. A new test is generated by slightly mutating a seed input. If the test exercises a new and interesting path, it is added to the set of seeds; otherwise, it is discarded. We observe that most tests exercise the same few “high-frequency” paths and develop strategies to explore significantly more paths with the same number of tests by gravitating towards low-frequency paths. We explain the challenges and opportunities of CGF using a Markov chain model which specifies the probability that fuzzing the seed that exercises path $i$ i generates an input that exercises path $j$ j . Each state (i.e., seed) has an energy that specifies the number of inputs to be generated from that seed. We show that CGF is considerably more efficient if energy is inversely proportional to the density of the stationary distribution and increases monotonically every time that seed is chosen. Energy is controlled with a power schedule. We implemented several schedules by extending AFL. In 24 hours, AFLFast exposes 3 previously unreported CVEs that are not exposed by AFL and exposes 6 previously unreported CVEs 7x faster than AFL. AFLFast produces at least an order of magnitude more unique crashes than AFL. We compared AFLFast to the symbolic executor Klee. In terms of vulnerability detection, AFLFast is significantly more effective than Klee on the same subject programs that were discussed in the original Klee paper. In terms of code coverage, AFLFast only slightly outperforms Klee while a combination of both tools achieves best results by mitigating the individual weaknesses.
T E C H N I C a L a D V a N C E Open Access

Novel methods for microCT-based analyses of vasculature in the renal cortex reveal a loss of perfusable arterioles and glomeruli in eNOS-/-mice Abstract Background: Two-dimensional measures of vascular architecture provide incomplete information about vascular structure. This study applied a novel rigorous method for 3D microCT-based analysis of total and cortical renal vasculature combined with a novel method to isolate and quantify the number of perfused glomeruli to assess vascular changes in eNOS-/-mice. Methods: Two month old male wildtype and eNOS-/-mice were perfused with heparinized saline followed by radiopaque Microfil. The Microfil-perfused vasculature of excised kidneys was imaged by μCT with an isotropic voxel-size of 5.0 μm. For analysis of renal cortical vasculature, a custom algorithm was created to define the cortical volume of interest (VOI) as the entire volume within 600 μm of the renal surface. Vessel thickness in the whole kidney or renal cortex was analyzed by plotting the distribution of vascular volume at each measured thickness and examining differences between the genotypes at individual thicknesses. A second image processing algorithm was created to isolate, identify, and extract contrast perfused glomeruli from the cortical vessels.
A prospective observational study of catheter-related bacteraemia and thrombosis in a haemodialysis cohort : univariate and multivariate analyses of risk association

Background.Central venous catheterization is a fundamental component in delivering haemodialysis yet is associated with significantly higher complication rates than other methods of vascular access. In this study, we report results of univariate and multivariate analyses designed to identify and quantify independent risk association for catheterization type, clinical variables and laboratory variables with regard to the development of catheter-related bacteraemia (CRB) and catheter failure due to poor haemodialysis flow. Methods. A2-year prospective study of all incident haemodialysis vascular access catheter insertions was conducted. Laboratory and clinical variables were recorded at catheter insertion, and the clinical course was followed up to the point of catheter removal. CRB and catheter failure due to poor flow were recorded as outcome events. Univariate and multivariate analyses were used to test for association between clinical and laboratory variables and outcome. Results. Forty-four thousand five hundred seventy-six catheter days were accumulated over the study period. Multivariate analysis demonstrated an independent association between non-tunnelled catheterization procedures and adverse outcomes compared with tunnelled central venous catheter insertions. Elevated modified Charlson comorbidity score was independently associated with the development of CRBc. Elevated C-reactive protein and low haemodialysis blood pump flow were independently associated with catheter failure due to poor flow. Conclusions. The data demonstrate that tunnelled central venous catheter insertions have an association with lower complication rates than non-tunnelled central venous catheter insertions that is independent of whether patients have acute or chronic renal failure, or high levels of comorbidity.
Inhibition of semicarbazide‐sensitive amine oxidase/vascular adhesion protein‐1 reduces lipopolysaccharide‐induced neuroinflammation

Neuroinflammation is initiated by a variety of stimuli including infections, sepsis, neurodegenerative diseases or traumatic brain injury and, if not adequately controlled, can lead to various degrees of neuronal damage and behavioural impairment. A critical event in the initial steps of inflammation is neutrophil extravasation. Semicarbazide‐sensitive amine oxidase (SSAO, also known as vascular adhesion protein 1 or VAP‐1) regulates neutrophil adhesion and extravasation. Here, we elucidate the role of SSAO/VAP‐1 in the early stage inflammatory response after LPS insult in the brain.
DBC1 (Deleted in Breast Cancer 1) modulates the stability and function of the nuclear receptor Rev-erbα

The nuclear receptor Rev-erbα has been implicated as a major regulator of the circadian clock and integrates circadian rhythm and metabolism. Rev-erbα controls circadian oscillations of several clock genes and Rev-erbα protein degradation is important for maintenance of the circadian oscillations and also for adipocyte differentiation. Elucidating the mechanisms that regulate Rev-erbα stability is essential for our understanding of these processes. In the present paper, we report that the protein DBC1 (Deleted in Breast Cancer 1) is a novel regulator of Rev-erbα. Rev-erbα and DBC1 interact in cells and in vivo, and DBC1 modulates the Rev-erbα repressor function. Depletion of DBC1 by siRNA (small interfering RNA) in cells or in DBC1-KO (knockout) mice produced a marked decrease in Rev-erbα protein levels, but not in mRNA levels. In contrast, DBC1 overexpression significantly enhanced Rev-erbα protein stability by preventing its ubiquitination and degradation. The regulation of Rev-erbα protein levels and function by DBC1 depends on both the N-terminal and C-terminal domains of DBC1. More importantly, in cells depleted of DBC1, there was a dramatic decrease in circadian oscillations of both Rev-erbα and BMAL1. In summary, our data identify DBC1 as an important regulator of the circadian receptor Rev-erbα and proposes that Rev-erbα could be involved in mediating some of the physiological effects of DBC1.
Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method

Intertidal mudflats are land–sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences. Multiple environmental factors were also measured and analyzed in conjunction with the prokaryotic composition profiles. A prokaryotic diversity analysis based on the metatranscriptome datasets revealed two or threefold higher diversity indices (associated with potentially active microbes participating in biogeochemical processes in Dongtan) compared with the diversity indices based on 16S rRNA gene amplicons. Bacteria were numerically dominant relative to archaea, and the potentially active prokaryotic taxa were mostly assigned to the bacterial phyla Chloroflexi, Acidobacteria, and Bacteroidetes and the classes Delta- and Gamma-proteobacteria, along with the archaeal lineages phylum Bathyarchaeota and the order Thermoplasmatales. The total nitrogen and carbon content of the sediment samples were environmental factors that significantly affected the depth-wise distributions of both bacterial and archaeal communities. Furthermore, the activity of potentially active taxa (including the prevalent order Desulfobacterales and family Anaerolineaceae) appeared to be significantly underestimated by PCR-based methods, notably at the DNA level, and indicates that using normal PCR amplification of DNA limits the study of potential microbial activity. This is the first study of potentially active microbial communities in depth-wise sediments from Dongtan. The improved knowledge of microbial communities in Dongtan provides a foundation for exploring biogeochemical cycling and microbial functions.