Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Binding of Respiratory Syncytial Virus to Pneumococci: A Phenomenon That Enhances Both Pneumococcal Adherence to Human Epithelial Cells and Pneumococcal Invasiveness in a Murine Model

In a previous study we showed that pneumococcal adherence to epithelial cells was enhanced by a preceding respiratory syncytial virus (RSV) infection. RSV-glycoproteins, expressed on the infected cell surface, may play a role in this enhanced pneumococcal binding, by acting as bacterial receptors. In the current study, it was attempted to analyze the capacity of pneumococci to interact directly with RSV virions. By flow-cytometry, a direct interaction between RSV and pneumococci could be detected. Heparin, an inhibitor of RSV infectivity that interacts with RSV protein-G, blocked RSV-pneumococcal binding, indicating that the latter interaction is indeed mediated by protein-G. RSV-pneumococcal complexes showed enhanced adherence to uninfected human epithelial cells, compared with pneumococcal adherence without bound RSV, and this enhancement was also blocked by heparin. In addition, the significance of these findings in vitro was explored in vivo in a murine model. Both mice that were pretreated with RSV at day 4 before pneumococcal challenge and mice infected with both agents simultaneously showed significantly higher levels of bacteraemia than controls. Simultaneous infection with both agents enhanced the development of pneumococcal bacteraemia most strongly. It was hypothesized that direct viral binding is another mechanism by which RSV can induce enhanced pneumococcal binding to epithelial cells, a phenomenon that is translated in vivo by a higher invasiveness of pneumococci when administered simultaneously with RSV to mice. Apparently, RSV acts in this process as a direct coupling particle between bacteria and uninfected epithelial cells, thereby increasing colonization by and enhancing invasiveness of pneumococci.
A new 5-alkylresorcinol glucoside derivative from Cybianthus magnus

One new 5-alkylresorcinol glucoside (1) was isolated from leaves of Cybianthus magnus, along with 12 known compounds, isolated from four plants belonging to Myrsinaceae family (2, 3 isolated from C. magnus; 4–7, 10 and 11 isolated from Myrsine latifolia; 4, 8 and 9 isolated from Myrsine sessiflora; 6, 7, 10, 12 and 13 isolated from Myrsine congesta). Their structures were determined on the basis of spectroscopic analysis and by comparison of their spectral data with those reported in the literature. So far, only nine 5-alkylresorcinol glucosides were isolated from leaves of Grevillea robusta. Since resorcinols are known to exhibit strong cytotoxic activity, compounds 1 and 2 were tested against cell lines 3T3, H460, DU145 and MCF-7 for cytotoxicity in vitro and compounds 3–13 were tested for their antileishmanial activity. Compound 2 displayed a strong cytotoxic activity with IC50 values ranging between 22 and 100 μM for all tested cell lines. Compounds 3–13 were not active against Leishmania amazonensis amastigotes. One new 5-alkylresorcinol glucoside (1) was isolated from leaves of Cybianthus magnus, along with 12 known compounds (2–13), isolated from four plants belonging to Myrsinaceae family. Their structures were determined on the basis of spectroscopic analysis and by comparison of their spectral data with those reported in the literature. Among the tested molecules, only compound 2 displayed a strong cytotoxic activity with IC50 values ranging between 22 and 100 μM for all cell lines tested.
Student input — A case of an extended flipped classroom

The idea from Socrates about the knowledge being a part of the students' knowledge base or ability of combining accessible knowledge forms the backdrop for how the most recent course in Knowledge Management (spring of 2017) was conducted. The course is 7,5 ECTS and the students are primarily adults in a worklife. The course is net and seminar based, with three seminars per semester. During the seminars the concept of Flipped Classroom is used. This means that the students are provided with a recorded lecture in beforehand and only highlights are presented. The rest of the time during the seminar is used to activate the students through tasks and problem solving. However, the tasks are not predefined and prefabricated. The way this course is structured, the students themselves are giving the input to the tasks and assignments. This is based on the idea that the students themselves, coming from a worklife where knowledge management is a part of their every day worklife, should reflect upon their own practice. Also, it is important to share knowledge and by utilizing each students own experiences it is possible to enrich the “database” of cases or tasks for the students to solve and work with in order to incorporate the new theory from the course curriculum. Basing the problem solving on student input provide the lecturer AND the students with a richer knowledge base and case portfolio. This does, however, require some effort from the lecturers side. The input from the students are generally key words and fragments. The session is facilitated by the lecturer, encouraging the students to bring forward own experiences or situations they would like resolved, either real or fiction. The key words and fragments are discussed amongst the students and the lecturer makes notes on a blackboard or on a digital canvas (MS PowerPoint or similar). The students are given a break and the lecturer collects the key words and synthesizes this into a case. Upon the return of the students, they solve the cases in groups and discuss possible solutions and what theory that apply to the different aspects of the case. Then a plenary session is facilitated where a suggested solution is developed. During a one-day seminar three to four cases are developed as a “joint venture” amongst the students and the lecturer. The feedback from the students is very positive. They claim that this way of working strongly contributes to an enhanced learning outcome. Some students also report on utilizing knowledge acquired at these seminars back at their workplace. These are some results from the survey and interviews. This research will be presented in detail in the paper. We will also elaborate on how this way of flipping the classroom can be utilized in different courses and areas.
Multi-shot Person Re-Identification Using Part Appearance Mixture

Appearance based person re-identification in real-world video surveillance systems is a challenging problem for many reasons, including ineptness of existing low level features under significant viewpoint, illumination, or camera characteristic changes to robustly describe a person's appearance. One approach to handle appearance variability is to learn similarity metrics or ranking functions to implicitly model appearance transformation between cameras for each camera pair, or group, in the system. The alternative, that this paper follows, is the more fundamental approach of improving appearance descriptors, called signatures, to cater for high appearance variance and occlusions. The novel signature representation for multi-shot person reidentification presented in this paper uses multiple appearance models, each describing appearance as a probability distribution of a low-level feature for a certain portion of individual's body. Combined with metric learning, rank-1 recognition rates of 92:5% and 79:5% are achieved on PRID2011 [12] and iLIDS-VID [34] datasets, respectively.
An approach to ontologies integration

Ontology, as a representation of shared conceptualization of specific domain, is a key technology for the Semantic Web. In recent years, many ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies we need a flexible mechanism to integrate ontologies. In this paper we present an approach to ontology integration which combines ontology integration algorithm and ontology similarity measures. After integrating, we perform ontology pruning and consistency check of the integrated ontology. Furthermore, we develop running prototype and conduct experiments for ontology integration and we evaluate the method in terms of ontology alignment quality.
Guidance for Occupational Health Services in Medical Centers.

INTRODUCTION Guidance for Occupational Health Services in Medical Centers is dedicated to the memory of Dr. Geoff Kelafant who was tragically killed in a diving accident in March 2004. Geoff was the original author of a set of guidelines for the practice of occupational health in medical centers; his work established a format and content upon which we continue to expand with the current guidance document. Geoff’s enduring legacy is the profound impact he made upon medical center occupational health care in the United States and Canada.
A criteria for selecting background knowledge for domain specific semantic matching

Ontology matching is a problem that is rapidly reaching maturity especially in the context of the emergent semantic web. Semantic matching is the detection of specific correspondences between concepts in two ontologies including but not limited to ≡, ⊑ and ⊒. Many semantic matching approaches today use some form of background knowledge to aid them in discovering correspondences. This paper presents criteria that can be used when selecting a background knowledge source.
Prevention of Osteoporosis and Hypogonadism by Allogeneic Ovarian Transplantation in Conjunction With Intra-Bone Marrow–Bone Marrow Transplantation

Background. We investigated the effects of ovarian allograft in conjunction with intra-bone marrow–bone marrow transplantation (IBM-BMT) on estrogen deficiency in mice. Methods. Female C57BL/6 mice underwent ovariectomy (OvX). After 3 months, the mice were irradiated at 9.5 Gy, and the bone marrow cells (BMCs) of female BALB/c mice (8 weeks old) were then injected into the bone cavity of the B6 mice. Simultaneously, allogeneic ovaries from BALB/c mice were transplanted under the renal capsules of the B6 mice. Results. Three months after the transplantation, the hematolymphoid cells were found to be completely reconstituted with donor-derived cells. The transplanted ovary tissues under the renal capsules were accepted without using immunosuppressants; there were a large number of growing follicles at different stages of development. Atrophic endometrium and its glands were also recovered by ovarian transplantation (OT). The transplanted allogeneic ovaries secreted estrogen at normal levels. Furthermore, bone loss was prevented to a certain extent. Conclusions. These findings suggest that IBM-BMT+OT will become a valuable strategy for young women with malignant tumors to prevent premature senescence, including hypogonadism and osteoporosis, after radiochemotherapy.
Quality of life of adults with chronic illness: a psychometric study.

Reliability and validity of the Flanagan Quality of Life Scale (QOLS) were tested in four chronic illness groups. Open-ended questions and four instruments, the QOLS, Duke-UNC Health Profile (DUHP), Life Satisfaction Index (LSI-Z), and either the Arthritis Impact Measurement Scales (AIMS) or the Ostomy Adjustment Scale (OAS) were administered by telephone interview and mailed questionnaires to 227 adults three times over 6 weeks. Subjects generated verbal responses that substantiated the content validity of the QOLS. Stability reliability estimates for all instruments ranged from . 53 to . 90. Cronbach's alpha coefficients averaged . 87 for the QOLS. Appropriate validity coefficients indicated both convergent and discriminant construct validity.
Tenascin-C Hexabrachion Assembly Is a Sequential Two-step Process Initiated by Coiled-coil α-Helices*

We have investigated the oligomerization process of tenascin-C using a variety of recombinant wild-type and mutant polypeptide chain fragments produced by heterologous gene expression inEscherichia coli. Biochemical and biophysical analyses of the structures and assemblies of these fragments indicated a sequential two-step oligomerization mechanism of tenascin-C involving the concerted interaction of two distinct domains and cysteines 64, 111, and 113. First, the sequence between alanine 114 and glutamine 139 initiates hexabrachion formation via a parallel three-stranded coiled coil. Subsequently, the tenascin assembly domain, which is unique to the tenascins, is responsible for the connection of two triplets to a hexamer. The oligomerization of the tenascin assembly domains by the three-stranded coiled coil increases their homophilic binding affinity and is an important prerequisite for tenascin-C hexamerization. Although formation of the characteristic hexabrachion structure involves the covalent linkage of the six subunits by cysteine residues, mutational analysis indicates that hexamer formation is not dependent on intermolecular disulfide bonds. Most interestingly, substitution of glutamate 130 within the coiled-coil domain by leucine or alanine resulted in the formation of parallel four-stranded helix structures, which further associated to dodecamers. Aside from supporting a sequential process of tenascin-C assembly, this finding provides experimental evidence that non-core residues can have profound effects on the oligomerization states of coiled coils.
16S rRNA-based detection of oral pathogens in coronary atherosclerotic plaque.

BACKGROUND Atherosclerosis develops as a response of the vessel wall to injury. Chronic bacterial infections have been associated with an increased risk for atherosclerosis and coronary artery disease. The ability of oral pathogens to colonize in coronary atheromatous plaque is well known. AIM The aim of this study was to detect the presence of Treponema denticola, Porphyromonas gingivalis and Campylobacter rectus in the subgingival and atherosclerotic plaques of patients with coronary artery disease. MATERIALS AND METHODS Fifty-one patients in the age group of 40-80 years with coronary artery disease were selected for the study. DNA was extracted from the plaque samples. The specific primers for T. denticola, C. rectus and P. gingivalis were used to amplify a part of the 16S rRNA gene by polymerase chain reaction. STATISTICAL ANALYSIS USED Chi-square analysis, correlation coefficient and prevalence percentage of the microorganisms were carried out for the analysis. RESULTS Of the 51 patients, T. denticola, C. rectus and P. gingivalis were detected in 49.01%, 21.51% and 45.10% of the atherosclerotic plaque samples. CONCLUSIONS Our study revealed the presence of bacterial DNA of the oral pathogenic microorganisms in coronary atherosclerotic plaques. The presence of the bacterial DNA in the coronary atherosclerotic plaques in significant proportion may suggest the possible relationship between periodontal bacterial infection and genesis of coronary atherosclerosis.
A MEMS Based DNA Computer for Solving SAT Problems

This paper presents a novel MEMS-based DNA computer for solving SAT problems. A modified back-side exposure process and a low-cost fluorescent microscope system for image acquisition are used for the computing experiment such that no time-consuming alignment procedures and delicate sample applying equipment are required for the proposed microarray-based DNA computing. Moreover, experimental results show the bound DNA sequences can sustain the chemical solutions and multiple UV exposures during computing processes such that the proposed method shall be useful in dealing with large scale problems. An algorithm based on a modified sticker model accompanied with a state-of-the-art MEMS-based microarray experiment is demonstrated to solve SAT problem which has long served as a benchmark in DNA computing. Unlike conventional DNA computing algorithms need an initial data pool to cover all correct and incorrect answers and further execute a series of separation procedures to destroy the unwanted ones, we built solutions in parts to satisfy one clause in one step, and eventually solve the entire Boolean formula through steps. Accordingly this algorithm greatly reduces the formation of unnecessary candidate solutions and shall be very practical as problem size grows
Evaluating Movement Quality Through Intrapersonal Synchronization

We present a method to measure intrapersonal synchronization of movement from motion capture data, and we show that our method is effective in classifying the level of skills of athletes performing karate kata. Our method is based on detecting relevant peaks of acceleration of limbs (arms and legs) and measuring their synchronization. We run a multiscale analysis, based on topological persistence, to rank the importance of peaks of acceleration. The resulting impulse signals are processed next with a multievent class synchronization algorithm, in order to define an <italic>overall synchronization index</italic> that scores the level of intrapersonal synchronization with a single scalar value. We build a basic multiclass classifier, which uses just the means of indexes computed on the different classes in the training set. We make a statistical analysis and a cross validation of the classifier on real data. Performances by athletes from three levels of skill have been recorded, classified by experts, and used to test our method. Cross validation of the classifier is performed by leave-one-out and bootstrap resampling. Results show that our method can classify correctly with very high probability (beyond <inline-formula><tex-math notation="LaTeX">$\text{99}\%$</tex-math></inline-formula>), while it succeeds on <inline-formula><tex-math notation="LaTeX">$\text{100}\%$</tex-math></inline-formula> of the data used in cross validation.
End-to-End Audiovisual Fusion with LSTMs

Several end-to-end deep learning approaches have been recently presented which simultaneously extract visual features from the input images and perform visual speech classification. However, research on jointly extracting audio and visual features and performing classification is very limited. In this work, we present an end-to-end audiovisual model based on Bidirectional Long Short-Term Memory (BLSTM) networks. To the best of our knowledge, this is the first audiovisual fusion model which simultaneously learns to extract features directly from the pixels and spectrograms and perform classification of speech and nonlinguistic vocalisations. The model consists of multiple identical streams, one for each modality, which extract features directly from mouth regions and spectrograms. The temporal dynamics in each stream/modality are modeled by a BLSTM and the fusion of multiple streams/modalities takes place via another BLSTM. An absolute improvement of 1.9% in the mean F1 of 4 nonlingusitic vocalisations over audio-only classification is reported on the AVIC database. At the same time, the proposed end-to-end audiovisual fusion system improves the state-of-the-art performance on the AVIC database leading to a 9.7% absolute increase in the mean F1 measure. We also perform audiovisual speech recognition experiments on the OuluVS2 database using different views of the mouth, frontal to profile. The proposed audiovisual system significantly outperforms the audio-only model for all views when the acoustic noise is high.
New Assays to Characterise Growth-Related Phenotypes of Plasmodium falciparum Reveal Variation in Density-Dependent Growth Inhibition between Parasite Lines

The growth phenotype of asexual blood stage malaria parasites can influence their virulence and also their ability to survive and achieve transmission to the next host, but there are few methods available to characterise parasite growth parameters in detail. We developed a new assay to measure growth rates at different starting parasitaemias in a 96-well format and applied it to characterise the growth of Plasmodium falciparum lines 3D7-A and 3D7-B, previously shown to have different invasion rates and to use different invasion pathways. Using this simple and accurate assay we found that 3D7-B is more sensitive to high initial parasitaemia than 3D7-A. This result indicates that different parasite lines show variation in their levels of density-dependent growth inhibition. We also developed a new assay to compare the duration of the asexual blood cycle between different parasite lines. The assay is based on the tight synchronisation of cultures to a 1 h parasite age window and the subsequent monitoring of schizont bursting and formation of new rings by flow cytometry. Using this assay we observed differences in the duration of the asexual blood cycle between parasite lines 3D7 and HB3. These two new assays will be useful to characterise variation in growth-related parameters and to identify growth phenotypes associated with the targeted deletion of specific genes or with particular genomic, transcriptomic or proteomic patterns. Furthermore, the identification of density-dependent growth inhibition as an intrinsic parasite property that varies between parasite lines expands the repertoire of measurable growth-related phenotypic traits that have the potential to influence the outcome of a malarial blood infection.
Characteristics, impact, and tolerance of partial disk failures

Hard-disk failures are one of the primary causes of data loss. Most disk failures are partial failures, where only some sectors are unavailable due to a latent sector error or some blocks are silently corrupted. This dissertation focuses on all aspects of such partial disk failures—their characteristics, their impact on different systems, and techniques that can be used tolerate them. We perform the first large-scale study of partial disk failures, involving 1.53 million disks. We find that partial disk failures affect a large percentage of disks. We also find that (i) SATA drives have a higher probability of developing partial disk failures and (ii) failures are not independent; failures within the same disk have high spatial and temporal locality. We examine the impact of partial disk failures on a variety of systems. We use model checking to examine data protection in RAID systems, and find that most schemes do not protect against one or more failures, leading to data loss. We apply type-aware fault injection to examine the impact of partial disk failures on the virtual-memory systems of Linux, FreeBSD, and Windows XP. We find that these systems use simplistic or inconsistent failure-handling policies. We analyze the impact of corrupt on-disk pointers on file systems NTFS and ext3. We find that these systems do not use fault-tolerance techniques effectively, resulting in data loss. We have built an N-version file system to tolerate partial disk failures. This system stores data in N different file systems, thereby eliminating the reliance on a single complex file system. Our system uses existing file systems, such as ext3 and JFS, thus avoiding the development costs of building different versions. Our experiments show that an N-version file system significantly reduces the probability of data loss.
Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits*

eIF3k, the smallest subunit of eukaryotic initiation factor 3 (eIF3), interacts with several other subunits of eIF3 and the 40 S ribosomal subunit. eIF3k is conserved among high eukaryotes, including mammals, insects, and plants, and it is ubiquitously expressed in human tissues. Interestingly, eIF3k does not exist in some species of yeast. Thus, eIF3k may play a unique regulatory role in higher organisms. Here we report the crystal structure of human eIF3k, the first high-resolution structure of an eIF3 component. This novel structure contains two distinct domains, a HEAT (named for Huntington, elongation factor 3, A subunit of protein phosphatase 2A, target of rapamycin) repeat-like HAM (HEAT analogous motif) domain and a winged-helix-like WH domain. Through structural comparison and sequence conservation analysis, we show that eIF3k has three putative protein-binding surfaces and has potential RNA binding activity. The structure provides key information for understanding the structure and function of the eIF3 complex.