Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenesis of experimental cholera: biologic ativities of purified procholeragen A.

Procholeragen A, a choleragenic moiety elaborated by Vibrio cholerae 569 B Inaba, has been concentrated and partially purified by gel filtration with Sephadex G-200. Purified Procholeragen A, which is essentially free of cholera endotoxin but still not pure, gives a single zone of precipitation with rabbit anti-choleragen antibody adsorbed with live vibrios and causes experimental cholera when amounts as little as 6.0-µg are administered, with Procholeragen B, per os in infant rabbits. When inoculated intradermally in adult rabbits in 0.1 to 0.2-µg amounts, it causes a delayed but sustained local erythematous edematous induration which fixes intravenous Evans blue dye. Procholeragen B, which was formerly considered to be essential for the activity of Procholeragen A, simply serves to protect the latter against destruction under acid conditions in the stomach and can be replaced by a variety of buffers. Procholeragen A causes experimental cholera when inoculated, by itself, into the small bowel of infant rabbits. On the basis of the experimental observations, it is suggested, as an operational concept, that an increase of villus capillary permeability, as a consequence of the direct action of a Procholeragen A-like factor elaborated by cholera vibrios in the small intestines, is a major factor in the pathogenesis of cholera.
Supporting UPA and restriction on an extension of XML Schema

We describe an extension of regular expresions using arbitrary all-groups and numeric exponents (as in W3C XML Schema). We are able to provide polynomial-time algorithms for testing UPA and content model subsumption for these extended regular expressions. The algorithm handles numeric exponents (as opposed to the Kleene operators of traditional regular expressions), but comparisons of exponents are exponential in the depth of exponent nesting. The algorithm for UPA testing with all groups in USCM is polynomial in the size of the expression, but uses push-down automata — much more complex machinery than used here for that purpose, and current known algorithms for subsumption involve unrolling the numeric exponents. This is exponential in the size of the exponents — in other words, large exponent values are much more onerous than small ones. As XML Schema uses numeric exponents this is a significant issue for validators. We also show how to extend these algorithms to handle XML Schema’s wildcards and substitution groups. Supporting UPA and restriction on an extension of XML Schema Table of
Transmission dynamics: critical questions and challenges

This article overviews the dynamics of disease transmission in one-host–one-parasite systems. Transmission is the result of interacting host and pathogen processes, encapsulated with the environment in a ‘transmission triangle’. Multiple transmission modes and their epidemiological consequences are often not understood because the direct measurement of transmission is difficult. However, its different components can be analysed using nonlinear transmission functions, contact matrices and networks. A particular challenge is to develop such functions for spatially extended systems. This is illustrated for vector transmission where a ‘perception kernel’ approach is developed that incorporates vector behaviour in response to host spacing. A major challenge is understanding the relative merits of the large number of approaches to quantifying transmission. The evolution of transmission mode itself has been a rather neglected topic, but is important in the context of understanding disease emergence and genetic variation in pathogens. Disease impacts many biological processes such as community stability, the evolution of sex and speciation, yet the importance of different transmission modes in these processes is not understood. Broader approaches and ideas to disease transmission are important in the public health realm for combating newly emerging infections. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Practical Point-to-Point Multiple-Goal Task Realization in a Robot Arm with a Rotating Table

This study presents a multiple-goal task realization in a system composed of a 6-d.o. f. robot arm and a one-axis rotating table. The problem is complex due to the existence of multiple goals and the kinematic redundancy of the system. We propose a design approach integrating the base placement, task sequencing and motion coordination methods. We show that this approach reduces the task completion time of the robot arm; the motion planning is realized through straight-line paths in the configuration space despite collision occurrences. Furthermore, we introduce a hybrid graph-search method combining the greedy nearest-neighbor method and the Dijkstra method to solve the motion coordination of the robot arm and the table. We show the effectiveness of the design approach and the search method through a time-constrained simulation-based optimization.
Digital Signal Processing for Coherent Transceivers Employing Multilevel Formats

Digital coherent transceivers have revolutionized optical fiber communications due to their superior performance offered compared to intensity modulation and direct detection based alternatives. As systems employing digital coherent transceivers seek to approach their information theoretic capacity, the use of multilevel modulation formats combined with appropriate forward error correction becomes essential. Given this context, in this tutorial paper, we, therefore, explore the digital signal processing (DSP) utilized in a coherent transceiver with a focus on multilevel modulation formats. By way of an introduction, we open by discussing the photonic technology required to realize a coherent transceiver. After discussing this interface between the analog optical channel and the digital domain, the rest of the paper is focused on DSP. We begin by discussing algorithms that correct for imperfections in the optical to digital conversion, including IQ imbalance and timing skew. Next, we discuss channel equalization including means for their realization for both quasi-static and dynamic channel impairments. Synchronization algorithms that correct for the difference between the transmitter and receiver oscillators both optical and electrical are then discussed and issues associated with symbol decoding highlighted. For most of the cases, we start with polarization division multiplexed quadrature phase-shift keying format as a basis and then discuss the extension to allow for high-order multilevel formats. Finally, we conclude by discussing some of the open research challenges in the field.
Clinical and Cost-effectiveness of a Comprehensive geriatric assessment and management for Canadian elders with Cancer—the 5C study: a study protocol for a randomised controlled phase III trial

Introduction Geriatric assessment and management is recommended for older adults with cancer referred for chemotherapy but no randomised controlled trial has been completed of this intervention in the oncology setting. Trial design A two-group parallel single blind multi-centre randomised trial with a companion trial-based economic evaluation from both payer and societal perspectives with process evaluation. Participants A total of 350 participants aged 70+, diagnosed with a solid tumour, lymphoma or myeloma, referred for first/second line chemotherapy, who speak English/French, have an Eastern Collaborative Oncology Group Performance Status 0–2 will be recruited. All participants will be followed for 12 months. Intervention Geriatric assessment and management for 6 months. The control group will receive usual oncologic care. All participants will receive a monthly healthy ageing booklet for 6 months. Objective To study the clinical and cost-effectiveness of geriatric assessment and management in optimising outcomes compared with usual oncology care. Randomisation Participants will be allocated to one of the two arms in a 1:1 ratio. The randomisation will be stratified by centre and treatment intent (palliative vs other). Outcome Quality of life. Secondary outcomes (1) Cost-effectiveness, (2) functional status, (3) number of geriatric issues successfully addressed, (4) grades3–5 treatment toxicity, (5) healthcare use, (6) satisfaction, (7) cancer treatment plan modification and (8) overall survival. Planned analysis For the primary outcome we will use a pattern mixture model using an intent-to-treat approach (at 3, 6 and12 months). We will conduct a cost-utility analysis alongside this clinical trial. For secondary outcomes 2–4, we will use a variety of methods. Ethics and dissemination Our study has been approved by all required REBs. We will disseminate our findings to stakeholders locally, nationally and internationally and by publishing the findings. Trial registration number NCT03154671.
Callisto: A Configurable Annotation Workbench

In order to support a range of textual annotation tasks, we have developed a new annotation tool called Callisto. To promote taskspecific specialization of the interface and associated constraint checking, Callisto provides a facility for the independent development, compilation and installation of task module plug-ins (in the form of Java Archive jar files). The common Callisto backend provides a set of annotation services to which all separate GUI components can subscribe, enabling a common framework through which annotation updates are propagated to all components. A number of annotation task models have already been defined, and those that are of very general applicability have been made easily re-configurable for small changes in task definition. Callisto is implemented in Java to make use of Java s considerable support for Unicode-encoded multilingual data. Callisto is freely available for downloading
Removal of uncontrollable phase distortions in synthetic aperture radar signals

This paper presents a new method for removing distortions in the phase spectrum of synthetic aperture radar (SAR) images by using the properties of multidimensional finite signals. The quality of the restored images and the time of reconstruction are examined. Results of the reconstruction process are demonstrated on a digital model of a radar image.
PSYCHOMETRIC HEPATIC ENCEPHALOPATHY SCORE FOR THE DIAGNOSIS OF MINIMAL HEPATIC ENCEPHALOPATHY IN ROMANIAN CIRRHOTIC PATIENTS--PARTIAL RESULTS.

UNLABELLED In Romania, minimal hepatic encephalopathy (MHE) is underdiagnosed and undertreated in patients with liver cirrhosis. The psychometric hepatic encephalopathy score (PHES) is recommended as the first-line tool for the diagnosis of MHE. AIM To use PHES in a group of Romanian cirrhotic patients and highlight the relationships between demographic and biological factors and tests results. MATERIALS AND METHODS Of the 148 patients with liver cirrhosis admitted to the Iaşi Institute of Gastroenterology and Hepatology between August 2014 and February 2015 only 80 who met the eligibility criteria were enrolled and completed the study. Blood samples for routine tests and serum ammonia were collected from all patients on the day of PHES evaluation. RESULTS In the study group (n = 80) mean age was 57.7 ± 8.5 years, and the average number of years of education was 11.2 ± 2.7. The main causes of cirrhosis were alcohol consumption (31 patients--38.8%), hepatitis C virus infection (29 patients--36.3%) and hepatitis B virus infection (17 patients--21.3%). Age, number of years of education, severity of liver disease (measured by using Child-Pugh and MELD scores) and some biological constants (albumin, bilirubin, International Normalized Ratio-INR) were significantly correlated (p < 0.05) with most psychometric tests. CONCLUSIONS PHES is a practical, objective and useful method for the diagnosis of MHE. Demographic and biological factors correlated with the results of the psychometric test. The PHES requires standardization before applying it in Romanian cirrhotic patients.
Conjugative Transfer by the Virulence System of Agrobacterium tumefaciens

Agrobacterium tumefaciens transfers part of its Ti plasmid, the transferred DNA (T-DNA), to plant cells during tumor induction. Expression of this T-DNA in plant cells results in their transformation into tumor cells. There are similarities between the process of T-DNA transfer to plants and the process of bacterial conjugation. Here, the T-DNA transfer machinery mediated conjugation between bacteria. Thus, products of the Vir region of the Ti plasmid of Agrobacterium tumefaciens, normally involved in transfer of DNA from bacteria to plants, can direct the conjugative transfer of an IncQ plasmid between agrobacteria.
Research Commentary - Information in Digital, Economic, and Social Networks

Digital technologies have made networks ubiquitous. A growing body of research is examining these networks to gain a better understanding of how firms interact with their consumers, how people interact with each other, and how current and future digital artifacts will continue to alter business and society. The increasing availability of massive networked data has led to several streams of inquiry across fields as diverse as computer science, economics, information systems, marketing, physics, and sociology. Each of these research streams asks questions that at their core involve “information in networks”---its distribution, its diffusion, its inferential value, and its influence on social and economic outcomes. We suggest a broad direction for research into social and economic networks. Our analysis describes four kinds of investigation that seem most promising. The first studies how information technologies create and reveal networks whose connections represent social and economic relationships. The second examines the content that flows through networks and its economic, social, and organizational implications. A third develops theories and methods to understand and utilize the rich predictive information contained in networked data. A final area of inquiry focuses on network dynamics and how information technology affects network evolution. We conclude by discussing several important cross-cutting issues with implications for all four research streams, which must be addressed if the ensuing research is to be both rigorous and relevant. We also describe how these directions of inquiry are interconnected: results and ideas will pollinate across them, leading to a new cumulative research tradition.
Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages

Significance Macrophages are immune cells equipped with multiple double-stranded RNA (dsRNA) sensors designed to detect viral infection and amplify innate antiviral immunity. However, many coronaviruses can infect and propagate in macrophages without activating dsRNA sensors. Here we present a function of murine coronavirus nonstructural protein 15 in preventing detection of viral dsRNA by host sensors. We show that coronaviruses expressing a mutant form of nonstructural protein 15 allow for activation of dsRNA sensors, resulting in an early induction of interferon, rapid apoptosis of macrophages, and a protective immune response in mice. Identifying the strategies used by viruses to evade detection provides us with new approaches for generating vaccines that elicit robust innate immune responses and protective immunity. Coronaviruses are positive-sense RNA viruses that generate double-stranded RNA (dsRNA) intermediates during replication, yet evade detection by host innate immune sensors. Here we report that coronavirus nonstructural protein 15 (nsp15), an endoribonuclease, is required for evasion of dsRNA sensors. We evaluated two independent nsp15 mutant mouse coronaviruses, designated N15m1 and N15m3, and found that these viruses replicated poorly and induced rapid cell death in mouse bone marrow-derived macrophages. Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3, which expresses a catalysis-deficient nsp15, activated MDA5, PKR, and the OAS/RNase L system, resulting in an early, robust induction of type I IFN, PKR-mediated apoptosis, and RNA degradation. Immunofluorescence imaging of nsp15 mutant virus-infected macrophages revealed significant dispersal of dsRNA early during infection, whereas in WT virus-infected cells, the majority of the dsRNA was associated with replication complexes. The loss of nsp15 activity also resulted in greatly attenuated disease in mice and stimulated a protective immune response. Taken together, our findings demonstrate that coronavirus nsp15 is critical for evasion of host dsRNA sensors in macrophages and reveal that modulating nsp15 stability and activity is a strategy for generating live-attenuated vaccines.
Albumin and Hyaluronic Acid-Coated Superparamagnetic Iron Oxide Nanoparticles Loaded with Paclitaxel for Biomedical Applications

Super paramagnetic iron oxide nanoparticles (SPION) were augmented by both hyaluronic acid (HA) and bovine serum albumin (BSA), each covalently conjugated to dopamine (DA) enabling their anchoring to the SPION. HA and BSA were found to simultaneously serve as stabilizing polymers of Fe3O4·DA-BSA/HA in water. Fe3O4·DA-BSA/HA efficiently entrapped and released the hydrophobic cytotoxic drug paclitaxel (PTX). The relative amount of HA and BSA modulates not only the total solubility but also the paramagnetic relaxation properties of the preparation. The entrapping of PTX did not influence the paramagnetic relaxation properties of Fe3O4·DA-BSA. Thus, by tuning the surface structure and loading, we can tune the theranostic properties of the system.
Fault-induced transient detection based on real-time analysis of the wavelet coefficient energy

In the last years, wavelet-based methodologies have been proposed as a good alternative for real-time fault detection. However, these methodologies usually fail to detect faults with overdamped transients and they are highly influenced by the choice of the mother wavelet, presenting time delay in the real-time analysis. By using the discrete wavelet transform (DWT) or the maximal overlap discrete wavelet transform (MODWT), the wavelet coefficient energy has been also used for fault analysis and presents the same drawbacks of the wavelet coefficient analysis. However, this paper presents a novel wavelet-based methodology for real-time detection of fault-induced transients in transmission lines, where the wavelet coefficient energy takes into account the border effects of the sliding windows. As a consequence, the performance of the proposed energy analysis is not affected by the choice of the mother wavelet, presenting no time delay in real-time fault detection, and the fault detection is scarcely influenced to the fault inception angle, fault resistance, and fault location, even if in critical situations where there are no fault-induced transients. The performance of the proposed methodology was assessed by using actual and simulated data. Some records were reproduced to be analyzed in real-time with a digital signal processor (DSP).
Complete sequence and gene organization of the mitochondrial genome of Asio flammeus (Strigiformes, strigidae)

Abstract The complete sequence of the mitochondrial genome was determined for Asio flammeus, which is distributed widely in geography. The length of the complete mitochondrial genome was 18,966 bp, containing 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and 1 non-coding region (D-loop). All the genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The D-loop of A. flammeus contained many tandem repeats of varying lengths and repeat numbers. The molecular-based phylogeny showed that our species acted as the sister group to A. capensis and the supported Asio was the monophyletic group.
Enabling objects for participatory design of socio-technical systems

The aim of this paper is to identify and explore the role of objects in participatory ergonomics design processes. The question in focus is: What characterizes objects in PE processes? First the concept of boundary objects is introduced as a starting point for investigating the role of objects. Second, findings of a search to identify objects in PE processes are reported. Third, objects fulfilling the requirements for boundary objects are placed in one of five categories. Fourth, empirical findings from two PE case studies in which objects played an important role are presented. Finally, based on a grounded theory approach, a characterization of objects in PE design processes is developed and a framework for how the use of objects in PE processes could be conceptualized is proposed. In conclusion, the concept of objects in PE processes is contextual, and the ergonomist or other design actor needs to actively consider their selection and the stage at which they are to be used.
Efficacy of a Negative Conversion Trial and Subsequent Living Donor Kidney Transplant Outcome in Recipients with a Positive Lymphocyte Crossmatch

Background: Patients with a positive lymphocyte crossmatch (LCX) do not undergo kidney transplantation. In such patients, a negative conversion protocol consisting of intravenous immunoglobulin (IVIG), plasmapheresis, and potent immunosuppressant is one of the options for transplantation. Methods: 14 patients who showed a positive LCX with living donors underwent a trial of negative conversion between January 2002 and July 2007. Plasmapheresis was performed every other day, up to 6 times maximum. IVIG was infused after plasmapheresis, with a total dose of 500 mg/kg divided over 6 days. Kidney transplantation was performed immediately after negative conversion. Anti-thymocyte globulin (ATG) or OKT3 induction therapy was used with the combination of tacrolimus, mycophenolate mofetil, and prednisone in the perioperative period. Results: Negative conversion of LCX was achieved in 13 of 14 patients (92.9%). Transplantations were performed successfully in these 13 patients without hyperacute rejection. Four recipients developed acute rejection, which was well controlled by steroid pulse therapy. During the follow-up periods of 45.4 ± 22.0 months, all recipients except 1 showed excellent graft function. Conclusion: Selected patients with a positive LCX can undergo successful transplantation using plasmapheresis, IVIG, and potent immunosuppressants. Recipients with negative conversion of LCX showed acceptable posttransplant results.
A chip‐based amide‐HILIC LC/MS platform for glycosaminoglycan glycomics profiling

A key challenge to investigations into the functional roles of glycosaminoglycans (GAGs) in biological systems is the difficulty in achieving sensitive, stable, and reproducible mass spectrometric analysis. GAGs are linear carbohydrates with domains that vary in the extent of sulfation, acetylation, and uronic acid epimerization. It is of particular importance to determine spatial and temporal variations of GAG domain structures in biological tissues. In order to analyze GAGs from tissue, it is useful to couple MS with an on‐line separation system. The purposes of the separation system are both to remove components that inhibit GAG ionization and to enable the analysis of very complex mixtures. This contribution presents amide–silica hydrophilic interaction chromatography (HILIC) in a chip‐based format for LC/MS of heparin, heparan sulfate (HS) GAGs. The chip interface yields robust performance in the negative ion mode that is essential for GAGs and other acidic glycan classes while the built‐in trapping cartridge reduces background from the biological tissue matrix. The HILIC chromatographic separation is based on a combination of the glycan chain lengths and the numbers of hydrophobic acetate (Ac) groups and acidic sulfate groups. In summary, chip based amide‐HILIC LC/MS is an enabling technology for GAG glycomics profiling.