Miracle-dz/UniFAR-FTUs huggingface dataset:
Infection with Conditionally Virulent Streptococcus pneumoniae Δpab Strains Induces Antibody to Conserved Protein Antigens but Does Not Protect against Systemic Infection with Heterologous Strains

ABSTRACT Avirulent strains of a bacterial pathogen could be useful tools for investigating immunological responses to infection and potentially effective vaccines. We have therefore constructed an auxotrophic TIGR4 Δpab strain of Streptococcus pneumoniae by deleting the pabB gene Sp_0665. The TIGR4 Δpab strain grew well in complete medium but was unable to grow in serum unless it was supplemented with para-aminobenzoic acid (PABA). The TIGR4 Δpab strain was markedly attenuated in virulence in mouse models of S. pneumoniae nasopharyngeal colonization, pneumonia, and sepsis. Supplementing mouse drinking water with PABA largely restored the virulence of TIGR4 Δpab. An additional Δpab strain constructed in the D39 capsular serotype 2 background was also avirulent in a sepsis model. Systemic inoculation of mice with TIGR4 Δpab induced antibody responses to S. pneumoniae protein antigens, including PpmA, PsaA, pneumolysin, and CbpD, but not capsular polysaccharide. Flow cytometry demonstrated that IgG in sera from TIGR4 Δpab-vaccinated mice bound to the surface of TIGR4 and D39 bacteria but not to a capsular serotype 3 strain, strain 0100993. Mice vaccinated with the TIGR4 Δpab or D39 Δpab strain by intraperitoneal inoculation were protected from developing septicemia when challenged with the homologous S. pneumoniae strain. Vaccination with the TIGR4 Δpab strain provided only weak or no protection against heterologous challenge with the D39 or 0100993 strain but did strongly protect against a TIGR4 capsular-switch strain expressing a serotype 2 capsule. The failure of cross-protection after systemic vaccination with Δpab bacteria suggests that parenteral administration of a live attenuated vaccine is not an attractive approach for preventing S. pneumoniae infection.
AmphiBMP2/4, an amphioxus bone morphogenetic protein closely related to Drosophila decapentaplegic and vertebrate BMP2 and BMP4: Insights into evolution of dorsoventral axis specification

Amphioxus AmphiBMP2/4 appears to be a single gene closely related to vertebrate BMP2and BMP4. In amphioxus embryos, the expression patterns of AmphiBMP2/4 suggest patterning roles in the ectodermal dorsoventral axis (comparable to dorsoventral axis establishment in the ectoderm by Drosophila decapentaplegic and vertebrate BMP4). In addition AmphiBMP2/4 may be involved in somite evagination, tail bud growth, pharyngeal differentiation (resulting in club‐shaped gland morphogenesis), hindgut regionalization, differentiation of olfactory epithelium, patterning of the anterior central nervous system, and establishment of the heart primordium. One difference between the developmental role of amphioxus AmphiBMP2/4 and vertebrate BMP4is that the former does not appear to be involved in the initial establishment of the dorsoventral polarity of the mesoderm. Dev. Dyn. 1998;213:130–139. © 1998 Wiley‐Liss, Inc.
Factors Inﬂuencing the Chance of Dropout or Being at Risk of Dropout in Higher Education

: The purpose of this paper is to establish what sociodemographic and institutional factors cause students to drop out, become uncertain about their intentions to obtain a degree, or conﬁdently advance towards the fulﬁlment of their ambitions. Our analysis is based on the combined databases of large-sample questionnaire surveys carried out among former students who dropped out from higher education institutions in an eastern region of Hungary as well as those carried out among current students. In addition to bivariate methods, we conduct multinomial logistic regression analysis to explore how students’ gender, social background, the funding of their training, willingness to do paid work alongside their studies, and relationships with academic staff and fellow students affect the chance of dropout, the risk of dropout, and persistence. In contrast to previous studies, which have mostly identiﬁed those at risk of dropping out of higher education and have primarily focused on the deﬁciencies of institutional integration, our novel results show that the actual dropout rate is at least as inﬂuenced by students’ unfavourable social background as it is by institutional factors.
On the complexity of wireless uplink scheduling with successive interference cancellation

In this paper, we study the problem of uplink scheduling in wireless networks with successive interference cancellation (SIC). With SIC, concurrent transmissions, if properly scheduled, can be successfully decoded at a receiver. The scheduler decides: (i) in which time-slot, and (ii) in what order in a time-slot to decode each transmission in order to maximize the system utility. These two scheduling decisions effectively determine the rates allocated to concurrent transmissions, which in turn determine the throughput and fairness of the system. We consider two scheduling problems, namely Maximum Throughput Scheduling and Proportional Fair Scheduling. We prove the first problem is NP-hard, while the second seemingly harder problem can be solved in polynomial time.
Pediatric tectal plate gliomas: clinical and radiological progression, MR imaging characteristics, and management of hydrocephalus.

OBJECT Tectal plate gliomas are generally low-grade astrocytomas with favorable prognosis, and observation of the lesion and management of hydrocephalus remain the mainstay of treatment. METHODS A cohort of patients with tectal plate gliomas at 2 academic institutions was retrospectively reviewed. RESULTS Forty-four patients with a mean age of 10.2 years who harbored tectal plate gliomas were included in the study. The mean clinical and radiological follow-up was 7.6 ± 3.3 years (median 7.9 years, range 1.5-14.7 years) and 6.5 ± 3.1 years (median 6.5 years, range 1.1-14.7 years), respectively. The most frequent intervention was CSF diversion (81.8% of patients) followed by biopsy (11.4%), radiotherapy (4.5%), chemotherapy (4.5%), and resection (2.3%). On MR imaging tectal plate gliomas most commonly showed T1-weighted isointensity (71.4%), T2-weighted hyperintensity (88.1%), and rarely enhanced (19%). The initial mean volume was 1.6 ± 2.2 cm(3) and it increased to 2.0 ± 4.4 cm(3) (p = 0.628) at the last follow-up. Frontal and occipital horn ratio (FOHR) and third ventricular width statistically decreased over time (p < 0.001 and p < 0.05, respectively). CONCLUSIONS The authors' results support existing evidence that tectal plate gliomas frequently follow a benign clinical and radiographic course and rarely require any intervention beyond management of associated hydrocephalus.
Smith ScholarWorks Smith

The regulation of pyelonephritis-associated pill (pap) pflin gene transcription has been examined using two operons (pap-17 and pap-21) isolated from the pyelonephritogenic Escherichia coli strain C1212. DNA sequence analysis and E.coli minicell analysis were used to map two genes (papB and papl) within the pilin regulatory regions of both pap-17 and pap-21, and the protein products of these genes were identified. Pilin transcription, initiated at the papBA promoter, was monitored by constructing single copy operon fusions with lacZYA in E.coli K-12. Inoculation of E.coli (pap'-lac) strains onto solid M9 minimal medium containing glycerol and the Lac indicator X-gal (M9-Glycerol) yielded both Lac' and Lac-colony phenotypes. The Lac' ('phase on') and Lac-('phase off') phenotypes were heritable since reinoculation of M9-Glycerol with bacteria picked from Lac' colonies gave rise to a much higher fraction of Lac' colonies than reinoculation of M9-Glycerol with bacteria picked from Lac-colonies. Measurement of phase transition rates for E.coli (pap17'-lac) inoculated onto M9-Gly-cerol showed that the Lac - -Lac+ transition frequency (1.57 x 10-4/cell/generation) was reduced 35-fold when cells were inoculated onto minimal medium containing glucose (M9-Glucose). However, the Lac+-Lac- transition frequency obtained using M9-Glycerol (2.60 x 10-2/cell/generation) was 1.4-fold lower compared to results obtained with M9-Glucose. In contrast, lowering the incubation temperature of E.coli (pap17'-lac) cultures from 37°C to 23'C caused all cells to shift to the Lac-state. Together, our results strongly indicate that pap pfli phase-variation is transcriptionally regulated and show that phase-variation is responsive to changes in the bacterial environment.
Reachability Games and Game Semantics: Comparing Nondeterministic Programs

We investigate the notions of may- and must-approximation in Erratic Idealized Algol (a nondeterministic extension of Idealized Algol), and give explicit characterizations of both using its game model. Notably, must-approximation is captured by a novel preorder on nondeterministic strategies, whose definition is formulated in terms of winning regions in a reachability game. The game is played on traces of one of the strategies and its objective is reaching a complete position without encountering any divergences. The concrete accounts of may- and must-approximation make it possible to derive tight complexity bounds for the corresponding decision problems in the finitary (finite datatypes) variant EIAf of Erratic Idealized Algol. In fact we give a complete classification of the complexity of may- and must-approximation for fragments of EIAf of bounded type order (for terms in beta-normal form). The complexity of the decidable cases ranges from PSPACE to 2-EXPTIME for may-approximation and from EXPSPACE to 3-EXPTIME for must-approximation. Our decidability results rely on a representation theorem for nondeterministic strategies which, for a given term, yields a single (finite or visibly pushdown) automaton capturing both traces and divergences of the corresponding strategy with two distinct sets of final states. The decision procedures producing optimal bounds incorporate numerous automata-theoretic techniques: complementation, determinization, computation of winning regions in reachability games over finite and pushdown graphs as well as product constructions. We see our work as a starting point of research that relates game semantics with other game-based theories.
ø29 DNA Polymerase Residue Ser122, a Single-stranded DNA Ligand for 3′-5′ Exonucleolysis, Is Required to Interact with the Terminal Protein*

Three amino acid residues highly conserved in most proofreading DNA polymerases, a phenylalanine contained in the Exo II motif and a serine and a leucine belonging to the S/TLx2 h motif, were recently shown to be critical for 3′-5′ exonucleolysis by acting as single-stranded DNA ligands (de Vega, M., Lázaro, J.M., Salas, M. and Blanco, L. (1998) J. Mol. Biol. 279, 807–822). In this paper, site-directed mutants at these three residues were used to analyze their functional importance for the synthetic activities of ø29 DNA polymerase, an enzyme able to start linear ø29 DNA replication using a terminal protein (TP) as primer. Mutations introduced at Phe65, Ser122, and Leu123 residues of ø29 DNA polymerase severely affected the replication capacity of the enzyme. Three mutants, F65S, S122T, and S122N, were strongly affected in their capacity to interact with a DNA primer/template structure, suggesting a dual role during both polymerization and proofreading. Interestingly, mutant S122N was not able to maintain a stable interaction with the TP primer, thus impeding the firsts steps (initiation and transition) of ø29 DNA replication. The involvement of Ser122 in the consecutive binding of TP and DNA is compatible with the finding that the TP/DNA polymerase heterodimer was not able to use a DNA primer/template structure. Assuming a structural conservation among the eukaryotic-type DNA polymerases, a model for the interactions of ø29 DNA polymerase with both TP and DNA primers is presented.
Real-time sensor-fusion based indoor localization for mobile Augmented Reality

In this paper we propose a sensor fusion based indoor localization method for mobile Augmented Reality (MAR). The aim of this research is to provide fine-tuning of the line feature based localization to accuracy of centimeter-level by exploring multi-modality of a mobile device. In order to match with line features from the captured scene and the given floor map, a line-based indoor scene analysis is proposed with Manhattan world assumption. An efficient pairwise line matching method using corresponding compass sensor data is presented to yield accurate localization and registration for MAR. Experimental results demonstrated that the proposed method is able to provide real-time performance and robustness in indoor environment.
NAP Enhances Neurodevelopment of Newborn Apolipoprotein E-Deficient Mice Subjected to Hypoxia

Perinatal hypoxic injury is associated with significant neonatal morbidity and long-term neurodevelopmental complications. NAP, a peptide derived from ADNP (activity-dependent neuroprotective protein), has previously shown neuroprotective abilities in various adult animal models. To evaluate its neuroprotective role in neonatal hypoxic-ischemic injury, we evaluated the neurodevelopmental outcome in apolipoprotein E (ApoE)-deficient (knockout) mice (a breed prone to brain damage during hypoxic insult) exposed to postnatal global hypoxic damage with and without treatment with NAP. ApoE-deficient (n = 80) and control (C57B6) mice pups (n = 81) were exposed to postnatal global hypoxia (35 min of 8% O2 within 24 h of birth) or room air with or without subsequent subcutaneous NAP treatment during postnatal days 1 to 14. Pups were then evaluated for neonatal motor reflex attainment, spatial learning ability in the Morris water maze, and locomotor open-field activity. The C57B6 and ApoE-deficient anoxic groups showed significantly slower achievement of neonatal reflexes, diminished locomotor activity, and diminished spatial learning ability compared with their control groups. This was more pronounced in the anoxic ApoE-deficient pups. NAP treatment had a pronounced effect on neurodevelopmental outcome in both breeds, particularly in the ApoE-deficient mice. ApoE-deficient and control mouse pups exposed to postnatal hypoxia and treated with NAP showed improvement in neurodevelopmental outcome compared with nontreated mice pups. ApoE-deficient mice show a greater susceptibility to hypoxic damage and better response to NAP treatment.
Auto-calibrated MIMO-OFDM channel sounder for 3D spatial channel characterization

This paper presents an improved test-bed designed for analyzing the spatial behaviour of wideband indoor channels using MIMO-OFDM systems. A 3D antenna positioning system (3-DAPS) is specifically designed for obtaining 3D spatial data. Also, it allows carrying out some measurements in the range of correlation distance where fading of the radio channel link is significant for indoor scenarios. Special emphasize is made on the RF calibration module, which is designed to track the frequency response of all RF chain of transmitter and receiver and apply those responses to the channel measurements. The average of the pseudo-spectrum MUSIC over all frequencies improves the resolution of the spatial spectrum giving clear peaks where a signal source is and smoothing fake peaks coming from scatters.
Expanded view of the local-regional richness relationship by incorporating functional richness and time: a large-scale perspective

Aim: We investigate the relationship between local and regional richness in marine fouling assemblages using an expanded and globally replicated approach by incorporating two dimensions of diversity (taxonomic and functional) and different successional stages. Location: Global. Methods: In eight different biogeographic regions (Australia, Brazil, Chile, England, Italy, Japan, Portugal and Sweden) 68 polyvinylchloride (PVC) panels (15 × 15 × 0.3 cm) were deployed for colonization. Communities colonizing panels were analysed by measuring percentage cover at each of four different successional ages: 2, 4, 6 and 8 months. Local richness was assessed as the average number of species and functional groups (FGs) per panel and regional richness was evaluated as the estimated (Jack2) asymptote of the sample-accumulation curves for species and FG on experimental panels. Results: We found that the shape of the relationship between local and regional richness depended on successional stage and the type of richness considered, i.e. taxonomic or functional richness. Hardly any relationship was detectable between local taxonomic richness and regional taxonomic richness at any successional stage. In contrast, the relation between local functional and regional functional richness shows a unimodal pattern of change during succession, passing through the stages ‘independent’, ‘unsaturated rising’, ‘saturated rising’ and once again ‘independent’. Main conclusions: The relationship between local and regional richness, whether taxonomic or functional, frequently displays independence of the two scales, particularly in early and late phases of the successional process.
The Influence of Green Intellectual Capital on Sustainable SMEs

Environmental degradation is a global issue that invites attention from various groups, including small and medium enterprises (SMEs). To preserve the environment and build a sustainable business, it is necessary to optimize environmentally friendly resources. Green intellectual capital, which includes green human capital, green structural capital, and green relational capital, can be practiced by SMEs in maintaining sustainable business. The research aims to empirically prove the influence of green intellectual capital on sustainable SMEs. The research adopted a quantitative method with a self-administered survey. The research sample consisted of 157 respondents who were SMEs in Madiun of Indonesia. Furthermore, the data were analyzed using Smart-PLS 3.0 to prove the hypothesis. The results show that green human capital and green relational capital do not have a significant influence on sustainable SMEs. Meanwhile, green structural capital has a significant influence on sustainable SMEs. This implies that SMEs must pay attention to the internal organizational management system in practicing environmentally businesses.
DELIVERABLE SUBMISSION SHEET

FP7-ICT Strategic Targeted Research Project PHEME (No. 611233) Deliverable D2.2 (WP 2) In this deliverable we report on work done in the context of task 2.2 “Ontological modelling” and task 2.3 “Multilingual Pre-processing” of WP2 “Ontologies, Multilinguality, and Spatio-Temporal Grounding” of the Pheme project. The aim of those taks was 1) to build ontological models of veracity, misinformation, social and information diffusion networks, rumours, disputed claims, temporal validity of statements, and user online behavior; and 2) to compare adopt and adapt the necessary linguistic pre-processing tools for Bulgarian, English and German, including language identification, POS tagging, chunking, dependency parsing, entity and relation recognition, and LOD-based entity disambiguation. These adapted tools will be used to generate linguistic and semantic features for the methods to be deployed in WP3 “Contextual Interpretation“ and WP4 “Detecting Rumours and Veracity“. Keyword list: ontologies, text pre-processing, social media, rumours Nature: Prototype Dissemination: PU Contractual date of delivery: 31 Dec 2014 Actual date of delivery: 08 Jan 2015 Reviewed By: Kalina Bontcheva Web links: http://www.pheme. eu/software-downloads/ D2.2 / Linguistic Pre-processing Tools and Ontological Models of Rumours and Phemes
Differential hydrophobicity drives self-assembly in Huntington's disease

Identifying the driving forces and the mechanism of association of huntingtin-exon1, a close marker for the progress of Huntington's disease, is an important prerequisite to finding potential drug targets and, ultimately, a cure. We introduce here a modeling framework based on a key analogy of the physicochemical properties of the exon1 fragment to block copolymers. We use a systematic mesoscale methodology, based on dissipative particle dynamics, which is capable of overcoming kinetic barriers, thus capturing the dynamics of significantly larger systems over longer times than considered before. Our results reveal that the relative hydrophobicity of the poly(glutamine) block as compared with the rest of the (proline-based) exon1 fragment, ignored to date, constitutes a major factor in the initiation of the self-assembly process. We find that the assembly is governed by both the concentration of exon1 and the length of the poly(glutamine) stretch, with a low-length threshold for association, even at the lowest volume fractions we considered. Moreover, this self-association occurs irrespective of whether the glutamine stretch is in random-coil or hairpin configuration, leading to spherical or cylindrical assemblies, respectively. We discuss the implications of these results for reinterpretation of existing research within this context, including that the routes toward aggregation of exon1 may be distinct from those of the widely studied homopolymeric poly(glutamine) peptides.
A Multicriteria Model Applied in the Diagnosis of Alzheimer's Disease: A Bayesian Network

This study considers the construction of a multicriteria model to assist in the diagnosis of Alzheimerpsilas disease. Alzheimerpsilas disease is considered the most frequent of the dementias and it is responsible for about 50% of the cases. Due to this fact and the therapeutical limitations in the most advanced stage of the disease, diagnosis of Alzheimerpsilas disease is extremely important and it can provide better life conditions to patients and their families. The main focus of this work is to develop a multicriteria model for aiding in decision making for the diagnosis of Alzheimerpsilas disease, using Bayesian networks as a modeling tool. In this work, the modeling and evaluation processes have been conducted with the aid of a medical expert, bibliographic sources and battery of standardized assessments. The construction of cardinal value scales was implemented through Hiview and Macbeth.
Contribution in analyzing directional propagation flow in EEG recordings investigating entropic methods and realistic physiological models

Our objective is to analyze EEG signals recorded with depth electrodes during seizures in patients with drug-resistant epilepsy. Usually, different phases are observed during the seizure process, including a fast onset activity (FOA). We aim to determine how cerebral structures get involved during this FOA, in particular whether some structures can “drive” some other structures. We compare a transfer entropy based measure with a measure related to linear Granger causality index to detect causal interdependences in multivariate signals generated either by a linear autoregressive model or by a physiology-based model of coupled neuronal populations. Experimental simulation results support the relevance of the new measure for characterizing the information flow for direct and indirect relations.