Miracle-dz/UniFAR-FTUs huggingface dataset:
Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity

ABSTRACT We investigated the prevalence, distribution, and structure of espP in Shiga toxin-producing Escherichia coli (STEC) and assessed the secretion and proteolytic activity of the encoded autotransporter protein EspP (extracellular serine protease, plasmid encoded). espP was identified in 56 of 107 different STEC serotypes. Sequencing of a 3,747-bp region of the 3,900-bp espP gene distinguished four alleles (espPα, espPβ, espPγ, and espPδ), with 99.9%, 99.2%, 95.3%, and 95.1% homology, respectively, to espP of E. coli O157:H7 strain EDL933. The espPβ, espPγ, and espPδ genes contained unique insertions and/or clustered point mutations that enabled allele-specific PCRs; these demonstrated the presence of espPα, espPβ, espPγ, and espPδ in STEC isolates belonging to 17, 16, 15, and 8 serotypes, respectively. Among four subtypes of EspP encoded by these alleles, EspPα (produced by enterohemorrhagic E. coli [EHEC] O157:H7 and the major non-O157 EHEC serotypes) and EspPγ cleaved pepsin A, human coagulation factor V, and an oligopeptide alanine-alanine-proline-leucine-para-nitroaniline, whereas EspPβ and EspPδ either were not secreted or were proteolytically inactive. The lack of proteolysis correlated with point mutations near the active serine protease site. We conclude that espP is widely distributed among STEC strains and displays genetic heterogeneity, which can be used for subtyping and which affects EspP activity. The presence of proteolytically active EspP in EHEC serogroups O157, O26, O111, and O145, which are bona fide human pathogens, suggests that EspP might play a role as an EHEC virulence factor.
Cloning and sequencing of potato virus Y coat protein gene from an Indian isolate and development of transgenic tobacco for PVY resistance

Potato virus Y (PVY) coat protein gene has been cloned from an Indian isolate of PVY°. The coat protein gene from this isolate showed 93.2% nucleic acid sequence homology and more than 94% amino acid sequence homology compared to an American isolate. The coat protein gene has been sub-cloned into plant expression vector pBINPLUS and tobacco leaf discs were transformed using Agrobacterium tumefaciens. The transgenic tobacco plants analysed through PCR and Southern hybridization, confirmed the integration of coat protein gene into tobacco genome. The transgenic plants were hardened in the greenhouse and were mechanically infected with crude viral extract. The virus titre was analysed through ELISA and the transgenic plants showed less virus titre compared to non-transformed control plants. The cloned coat protein gene of PVY will be useful for imparting resistance against that virus in Indian potato cultivars.
Stability of FDG-PET Radiomics features: An integrated analysis of test-retest and inter-observer variability

Abstract Purpose. Besides basic measurements as maximum standardized uptake value (SUV)max or SUVmean derived from 18F-FDG positron emission tomography (PET) scans, more advanced quantitative imaging features (i.e. “Radiomics” features) are increasingly investigated for treatment monitoring, outcome prediction, or as potential biomarkers. With these prospected applications of Radiomics features, it is a requisite that they provide robust and reliable measurements. The aim of our study was therefore to perform an integrated stability analysis of a large number of PET-derived features in non-small cell lung carcinoma (NSCLC), based on both a test-retest and an inter-observer setup. Methods. Eleven NSCLC patients were included in the test-retest cohort. Patients underwent repeated PET imaging within a one day interval, before any treatment was delivered. Lesions were delineated by applying a threshold of 50% of the maximum uptake value within the tumor. Twenty-three NSCLC patients were included in the inter-observer cohort. Patients underwent a diagnostic whole body PET-computed tomography (CT). Lesions were manually delineated based on fused PET-CT, using a standardized clinical delineation protocol. Delineation was performed independently by five observers, blinded to each other. Fifteen first order statistics, 39 descriptors of intensity volume histograms, eight geometric features and 44 textural features were extracted. For every feature, test-retest and inter-observer stability was assessed with the intra-class correlation coefficient (ICC) and the coefficient of variability, normalized to mean and range. Similarity between test-retest and inter-observer stability rankings of features was assessed with Spearman's rank correlation coefficient. Results. Results showed that the majority of assessed features had both a high test-retest (71%) and inter-observer (91%) stability in terms of their ICC. Overall, features more stable in repeated PET imaging were also found to be more robust against inter-observer variability. Conclusion. Results suggest that further research of quantitative imaging features is warranted with respect to more advanced applications of PET imaging as being used for treatment monitoring, outcome prediction or imaging biomarkers.
Contrast-enhanced ultrasonographic imaging diagnosis on assessment of vascularity in liver metastatic lesions.

AIM To investigate the vasculature of rabbit liver metastatic lesions by color Doppler imaging and power Doppler imaging (PDI) techniques. METHODS Eight New Zealand rabbits with implanted VX2 liver tumors were used. All ultrasound examinations were performed with a HP 5500 color Doppler ultrasound scanner. Before and after the injection of contrast agent, the changes of gray scale and the periphery and intralesional blood flow of the liver metastatic lesion were carefully observed by B mode ultrasound, color Doppler flow imaging (CDFI) and PDI. RESULTS Twelve lesions were found in the eight rabbits with implanted VX2 liver tumors, whose diameter ranged from 1.6 to 4.8 cm. Echoes of these lesions were not characterized and has lack of specificity. After the injection of contrast agent, the numbers of dot or strip-like flow messages increased both at the periphery and inside of these lesions under the mode of CDFI and PDI, and were more pronounced under PDI. Morphology of intralesional vessels extended, even branched and some signals were clearly found encircling the lesion. And some vessels were found penetrating into the center of the lesion. CONCLUSION PDI after injection of self-made echo contrast agent can show a pronounced sensitivity than that of B mode ultrasound and CDFI in diagnosis of vascularity of a metastatic lesion.
The framework of a geospatial semantic web-based spatial decision support system for Digital Earth

Abstract While significant progress has been made to implement the Digital Earth vision, current implementation only makes it easy to integrate and share spatial data from distributed sources and has limited capabilities to integrate data and models for simulating social and physical processes. To achieve effectiveness of decision-making using Digital Earth for understanding the Earth and its systems, new infrastructures that provide capabilities of computational simulation are needed. This paper proposed a framework of geospatial semantic web-based interoperable spatial decision support systems (SDSSs) to expand capabilities of the currently implemented infrastructure of Digital Earth. Main technologies applied in the framework such as heterogeneous ontology integration, ontology-based catalog service, and web service composition were introduced. We proposed a partition-refinement algorithm for ontology matching and integration, and an algorithm for web service discovery and composition. The proposed interoperable SDSS enables decision-makers to reuse and integrate geospatial data and geoprocessing resources from heterogeneous sources across the Internet. Based on the proposed framework, a prototype to assist in protective boundary delimitation for Lunan Stone Forest conservation was implemented to demonstrate how ontology-based web services and the services-oriented architecture can contribute to the development of interoperable SDSSs in support of Digital Earth for decision-making.
MR Imaging detection of cerebral metastases with a single injection of high‐dose gadoteridol

The utility of a single high‐dose (0.3 mmol/kg) injection of gadoteridol, a gadolinium chelate, in the detection of brain metastases on magnetic resonance images was studied. Patients (n = 29) with a high suspicion for brain metastases at clinical examination and by history were imaged on two occasions–separated by more than 24 hours and less than 7 days–with a 0.1 mmol/kg contrast agent dose used for the first study and a 0.3 mmol/kg dose for the second. In patients (n = 15) with confirmed brain metastases by clinical, radiologic, and/or histologic criteria, 40 lesions were detected at the 0.3 mmol/kg dose by a single reader blinded to contrast agent dose, compared with 33 lesions at 0.1 mmol/kg, a 21% increase. Three of 15 patients (20%) demonstrated an increase in the number of lesions detected at the higher dose. Region‐of‐interest analysis of signal intensity measurements showed that lesion contrast (relative to normal brain) improved from 54% at 0.1 mmol/kg to 92% at 0.3 mmol/kg. A 0.3 mmol/kg dose of gadoteridol, administered in a single injection, permits identification of brain metastases not detected at 0.1 mmol/kg. Such information can influence the choice of therapy.
Utilisabilité d'un Espace Personnel d'Information Modifiable par les Utilisateurs

Cet article présente une étude sur l'utilisabilité d'un nouveau prototype de système de gestion des informations personnelles sur Internet (PIMI). Les objectifs sont d'évaluer sa facilité d'utilisation, et d'évaluer la modification utilisateur comme technique d'évaluation. Trente utilisateurs ont participé à l'expérience : une première partie consistait en un test utilisateur classique (TUC) et une seconde partie était un test d'utilisabilité avec modifications utilisateur (TUM). Un total de 51 problèmes d'utilisabilité a été diagnostiqué. Parmi eux, 32 avec TUC, et 19 avec TUM. Une partie de ces derniers (11) s'ajoute à ceux identifiés avec TUC, et à ceux diagnostiqués précédemment lors d'une inspection de l'utilisabilité (IU avec Critères Ergonomiques). La participation active des utilisateurs au travers de scénarios de personnalisation semble fournir des indices supplémentaires pour l'évaluation de l'utilisabilité et pour la conception (nouvelles recommandations génériques d'utilisabilité).
Experimental airborne transmission of Salmonella Agona and Salmonella Typhimurium in weaned pigs

SUMMARY This study tested the hypothesis of airborne transmission of Salmonella Agona (Trial I) and Salmonella Typhimurium (Trial II) in weaned pigs. The trials were performed using stainless-steel/glass isolation cabinets connected by air ducts to permit an unidirectional airflow from cabinet 1 (two control pigs) to cabinet 3 (two sentinel pigs), passing through cabinet 2 (two inoculated pigs). Air samples, pooled faecal samples from the floor and rectal swabs were collected daily and assessed by culture and PCR. A fumigation chamber and rubber gloves coupled to the cabinets allowed sampling without opening the system. Trials I and II lasted 15 and 19 days respectively. The recovery of S. Agona and S. Typhimurium and detection of seroconversion in sentinel pigs indicate that airborne Salmonella transmission in weaned pigs over short distances is possible. Further studies on the role of aerosols in the epidemiology of Salmonella in intensive pig production should be performed.
Noise-Induced Coherence in Neural Networks.

We investigate numerically the dynamics of large networks of $N$ globally pulse-coupled integrate and fire neurons in a noise-induced synchronized state. The powerspectrum of an individual element within the network is shown to exhibit in the thermodynamic limit ($N\to \infty$) a broadband peak and an additional delta-function peak that is absent from the powerspectrum of an isolated element. The powerspectrum of the mean output signal only exhibits the delta-function peak. These results are explained analytically in an exactly soluble oscillator model with global phase coupling.
Effects of low-pass filtering on the perception of word-final plurality markers in children and adults with normal hearing.

PURPOSE The purpose of this study was to evaluate the effect of low-pass filtering on the detection of word-final /s/ and /z/ for children and adults with normal hearing. METHOD Stimuli were nouns from the University of Western Ontario Plurals Test (Glista & Scollie, 2012), low-pass filtered with 5 different cutoff frequencies: 8000 Hz, 5000 Hz, 4000 Hz, 3000 Hz, and 2000 Hz. Listeners were children (age range = 7-13 years) and adults with normal hearing. The task was a 2-alternative forced-choice task with a picture-pointing response. RESULTS Performance was worse for lower than for higher low-pass filter cutoff frequencies, but the effect of low-pass filtering was similar for children and adults. Nearly all listeners achieved 100% correct performance when stimuli were low-pass filtered with cutoff frequencies of 8000 Hz or 5000 Hz. Performance remained well above chance even for the most severe filtering condition (2000 Hz). Restricting high-frequency audibility influenced performance for plural items to a greater extent than for singular items. CONCLUSION The results indicate that children and adults with normal hearing can use acoustic information below the spectral range of frication noise typically associated with /s/ and /z/ to discriminate between singular and plural forms of nouns in the context of the University of Western Ontario Plurals Test.
Failure analysis of thermally and mechanically stressed plastic core solder balls

Plastic Core Solder Balls (PCSB) offer improved mechanical compliance compared to traditional solder balls in assemblies where materials with significantly different coefficient of thermal expansion are present. However, failure mechanisms for systems with lead free PCSB have not been studied sufficiently to allow direct replacement in applications for harsh environments. An assembly of a ceramic carrier onto an organic circuit board intended for application in a harsh environment subsea has been studied with regard to replacement of traditional lead free solder balls with lead free PCSB. Assembled test vehicles were exposed to mechanical and thermal environmental stress testing and failure analysis performed. Degradation of the PCSBs was observed in electrical measurements and in studies of cross sectioned test vehicles. Cracks were observed in relation to formation of intermetallic compounds and a suggestion is made with regard to improvement of the metal system of the PCSBs.
Big data analytics in prevention, preparedness, response and recovery in crisis and disaster management

— The scientific area of crisis management has been in the center of attention for multiple disciplines especially the computer science. In the information centered and computer driven world, a major aim of computer scientists is to manage and analyze Big Data, extract information from heterogeneous sources and store it in unified structure formats that allow further processing. In this paper, Big Data analytics techniques and tools that are useful in all phases of crisis management are presented. Furthermore, a system-engineering approach of a big data management system will be analyzed that comprises of four phases; data generation, data acquisition, data storage, and data analytics. Benefits of the usage of Big Data for crisis management are analyzed. An innovative view of open problems concerning Big Data in crisis management is introduced.
‘Ere Be Dragons: heartfelt gaming

Abstract A new pervasive digital game is discussed, relating technical and conceptual innovation. A combination of sensor technologies enables a responsive visual and auditory environment to be overlaid on the real world. This allows processes within the player's body to be mapped to the environment through which the player passes, externalising the internal. Rather than using technology to replicate the rigid goals and structures of many conventional games, this game explores the concept of ‘open play’, a form of personal exploration. The work is an interdisciplinary collaboration between digital artists and health scientists with an agenda to alter players’attitudes to the body and health as well as to break new ground artistically.
Diversity of Bacteria and Glycosyl Hydrolase Family 48 Genes in Cellulolytic Consortia Enriched from Thermophilic Biocompost

ABSTRACT The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. In this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. Community structure based on 16S rRNA gene clone libraries featured extensive representation of clostridia from cluster III, with minor representation of clostridial clusters I and XIV and a novel Lutispora species cluster. Our studies reveal different levels of 16S rRNA gene diversity, ranging from 3 to 18 operational taxonomic units (OTUs), as well as variability in community membership across the three enrichment cultures. By comparison, glycosyl hydrolase family 48 (GHF48) diversity analyses revealed a narrower breadth of novel clostridial genes associated with cultured and uncultured cellulose degraders. The novel GHF48 genes identified in this study were related to the novel clostridia Clostridium straminisolvens and Clostridium clariflavum, with one cluster sharing as little as 73% sequence similarity with the closest known relative. In all, 14 new GHF48 gene sequences were added to the known diversity of 35 genes from cultured species.
Myocardial Injury After Noncardiac Surgery (MINS) in Vascular Surgical Patients: A Prospective Observational Cohort Study

Objective: To determine the prognostic relevance, clinical characteristics, and 30-day outcomes associated with myocardial injury after noncardiac surgery (MINS) in vascular surgical patients. Background: MINS has been independently associated with 30-day mortality after noncardiac surgery. The characteristics and prognostic importance of MINS in vascular surgery patients are poorly described. Methods: This was an international prospective cohort study of 15,102 noncardiac surgery patients 45 years or older, of whom 502 patients underwent vascular surgery. All patients had fourth-generation plasma troponin T (TnT) concentrations measured during the first 3 postoperative days. MINS was defined as a TnT of 0.03 ng/mL of higher secondary to ischemia. The objectives of the present study were to determine (i) if MINS is prognostically important in vascular surgical patients, (ii) the clinical characteristics of vascular surgery patients with and without MINS, (iii) the 30-day outcomes for vascular surgery patients with and without MINS, and (iv) the proportion of MINS that probably would have gone undetected without routine troponin monitoring. Results: The incidence of MINS in the vascular surgery patients was 19.1% (95% confidence interval (CI), 15.7%–22.6%). 30-day all-cause mortality in the vascular cohort was 12.5% (95% CI 7.3%–20.6%) in patients with MINS compared with 1.5% (95% CI 0.7%–3.2%) in patients without MINS (P < 0.001). MINS was independently associated with 30-day mortality in vascular patients (odds ratio, 9.48; 95% CI, 3.46–25.96). The 30-day mortality was similar in MINS patients with (15.0%; 95% CI, 7.1–29.1) and without an ischemic feature (12.2%; 95% CI, 5.3–25.5, P = 0.76). The proportion of vascular surgery patients who suffered MINS without overt evidence of myocardial ischemia was 74.1% (95% CI, 63.6–82.4). Conclusions: Approximately 1 in 5 patients experienced MINS after vascular surgery. MINS was independently associated with 30-day mortality. The majority of patients with MINS were asymptomatic and would have gone undetected without routine postoperative troponin measurement.
Stage-specific mortality and survival trends of prostate cancer patients in Finland before and after introduction of PSA

Abstract Background: The early diagnosis and right treatment strategy of localized prostate cancer (PCa) remains problematic. In order to characterize the survival of PCa patients, we compared patients’ all-cause and cancer-specific mortalities between pre- and post-PSA periods by stage in Finland. Material and methods: All PCa cases diagnosed in Finland between 1985 and 2013 (N = 91,329) were identified from the Finnish Cancer Registry (FCR). PCa stage at diagnosis was defined as localized, local node positive or metastasized. Standardized mortality ratios (SMRs), and relative and cause-specific survival were assessed by stage and introduction of PSA testing. The main limitation was the high proportion of men with unknown stage (28%). Results: A clear decreasing trend in the SMR of PCa patients was evident when pre- and post-PSA eras were compared: for localized PCa, the SMR was 1.43 (95%CI 1.38–1.48) in 1985–1989 and 0.98 (95%CI 0.95–1.01) in 2000–2004, and for metastasized PCa, the SMRs were 4.51 (95%CI 4.30–4.72) and 3.01 (95%CI 2.89–3.12), respectively. Difference between cause-specific and relative survival was pronounced in localized PCa in post-PSA period: 10-year relative survival was 94.6% (95%CI 91.4–97.8) and cause-specific 84.2% (95%CI 82.9–85.5%). In metastasized PCa the difference was not that significant. Conclusions: From 1985 to 2009, the SMR among men diagnosed with PCa decreased significantly in Finland. Among men with localized PCa, the SMR decreased even below that of the Finnish male population. This and the increased difference between relative and cause-specific survival reflects most likely selection of men to opportunistic PSA testing. The results highlight the importance of caution in the use of PSA testing in healthy men.
Analysis of the peptidoglycan structure of Bacillus subtilis endospores

Peptidoglycan was prepared from purified Bacillus subtilis spores of wild-type and several mutant strains. Digestion with muramidase resulted in cleavage of the glycosidic bonds adjacent to muramic acid replaced by peptide or alanine side chains but not the bonds adjacent to muramic lactam. Reduction of the resulting muropeptides allowed their separation by reversed-phase high-pressure liquid chromatography. The structures of 20 muropeptides were determined by amino acid and amino sugar analysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In wild-type spores, 50% of the muramic acid had been converted to the lactam and 75% of these lactam residues were spaced regularly at every second muramic acid position in the glycan chains. Single L-alanine side chains were found on 25% of the muramic acid residues. The remaining 25% of the muramic acid had tetrapeptide or tripeptide side chains, and 11% of the diaminopimelic acid in these side chains was involved in peptide cross-links. Analysis of spore peptidoglycan produced by a number of mutants lacking proteins involved in cell wall metabolism revealed structural changes. The most significant changes were in the spores of a dacB mutant which lacks the sporulation-specific penicillin-binding protein 5*. In these spores, only 46% of the muramic acid was in the lactam form, 12% had L-alanine side chains, and 42% had peptide side chains containing diaminopimelic acid, 29% of which was involved in cross-links.