jimnoneill/paper-to-field-training huggingface dataset:
Identification of a conserved Moraxella catarrhalis haemoglobin-utilization protein, MhuA

Moraxella catarrhalis is a leading cause of acute otitis media in children and is a cause of respiratory disease in adults with underlying lung disease. This organism is a strict human pathogen that has an absolute requirement for iron in order to grow and cause disease. Previous studies identified transferrin and lactoferrin receptors used by M. catarrhalis to obtain iron from the human host, yet other iron-acquisition systems remain undefined. In this study, it is demonstrated that this strict mucosal pathogen can utilize haemoglobin (Hb) as a sole source of iron for growth. A novel 107 kDa outer-membrane protein involved in Hb utilization by this pathogen was also identified. An isogenic mutant defective in this Moraxella Hb-utilization protein (MhuA), 7169 : : mhuA, showed a significant lag during growth in the presence of Hb as the sole iron source. This protein appears to be expressed constitutively, regardless of growth conditions, and a mAb directed to MhuA demonstrated that this protein contains highly conserved, surface-exposed epitopes. Data demonstrating that expression of MhuA may be highly specific to isolates of M. catarrhalis are also presented, suggesting a potential role as a diagnostic marker. To our knowledge, this is the first report demonstrating that M. catarrhalis expresses an Hb-binding protein and that this bacterium can utilize Hb as a sole iron source for growth.

Topic: Pneumonia and Respiratory Infections
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Reliabilities of χ<sup>2</sup>- and F Tests in Gauss-Markov Model

Power and level breakdown points are used in robust statistics to determine the global reliability of a test. A method for calculating the finite-sample versions of these for tests such as χ2 or F is given here when observations have the Gauss-Markov model. Outliers are compared with the generating model using a coordinate transformation and simulated samples. Outliers are considered in two groups, namely, "doubtful" and "clear." The reliability of a χ2- or F test changes with the magnitude, number, and kind of outliers (i.e., random outliers or influential outliers), and also with the level of significance, α. The χ2- and F tests are generally insensitive to both doubtful and clear outliers. The χ2 test can reliably reject the null hypothesis at α = 0.05, when the observations contain multiple clear random outliers, only if the magnitude of one of them is at least greater than 5σ. Also, the F test can reliably reject the null hypothesis at α = 0.05, when the observations contain multiple clear random outliers, only if the magnitude of one of them is at least greater than 6σ. The greater the magnitude and number of clear outliers that are contained in the observations, the more successful is the χ2- or F test in rejecting the null hypothesis. The reliabilities of the χ2- and F tests decrease as the number of unknowns increases. For this case, the power and level finite-sample breakdown points of the χ2- and F tests are estimated here to be approximately 1/2.

Topic: Advanced Statistical Methods and Models
Subfield: Statistics and Probability
Field: Mathematics
Domain: Physical Sciences
Please Your Self: Social Identity Effects on Selective Exposure to News About In- and Out-Groups

Journal Article Please Your Self: Social Identity Effects on Selective Exposure to News About in- and Out-Groups Get access Silvia Knobloch-Westerwick, Silvia Knobloch-Westerwick 1School of Communication, The Ohio State University, Columbus, OH 43210, USA Search for other works by this author on: Oxford Academic Google Scholar Matthias R. Hastall Matthias R. Hastall 2Department of Communication, Zeppelin University Friedrichshafen, Friedrichshafen, Germany Search for other works by this author on: Oxford Academic Google Scholar Journal of Communication, Volume 60, Issue 3, September 2010, Pages 515–535, https://doi.org/10.1111/j.1460-2466.2010.01495.x Published: 19 August 2010

Topic: Social Media and Politics
Subfield: Communication
Field: Social Sciences
Domain: Social Sciences
Comparison of some listening test methods : a case study

Abstract: The goal of this study was to compare various listening test methods in the particular case of nine in-car ventilation noises. Six listening tests were conducted:- absolute evaluation of noise pleasantness;- evaluation of pleasantness, during which the subject could hear all noises as often as necessary;- paired comparisons (forced choice procedure);- paired comparisons (five levels scale);- paired comparisons (continuous scale);- similarity ratings, analysed with a multidimensional scaling method (Indscal). These six tests were realised by 64 subjects. Different items were examined for each test: its perceived and real duration, its estimated difficulty, the accuracy of merit scores attributed to noises, the perceptual spaces which could be built and the accuracy of a pleasantness indicator computed from the results. It appeared that:- the second procedure can propose a good compromise between the accuracy of the results and the time needed for subjects to realise the test. Thus, it can be recommended for many industrial purposes;- however, the not-forced choice paired comparisons enable a greater discrimination between stimuli;- perceptual spaces built from the paired comparison tests and the similarity rating one were similar, indicating a great stability of sound features used by listeners, whatever their task. 1

Topic: Acoustic Wave Phenomena Research
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
CA trust management for the Web PKI

The steadily growing number of certification authorities (CAs) assigned to the Web Public Key Infrastructure (Web PKI) and trusted by current browsers imposes severe security issues.Apart from being impossible for relying entities to assess whom they actually trust, the current binary trust model implemented with the Web PKI makes each CA a single point of failure and creates an enormous attack surface.In this article, we present CA-TMS, a user-centric CA trust management system based on trust views.CA-TMS can be used by relying entities to individually reduce the attack surface.CA-TMS works by restricting the trust placed in CAs of the Web PKI to trusting in exactly those CAs actually required by a relying entity.This restriction is based on locally collected information and does not require the alteration of the existing Web PKI.CA-TMS is complemented by an optional reputation system that allows to utilize the knowledge of other entities while maintaining the minimal set of trusted CAs.Our evaluation of CA-TMS with real world data shows that an attack surface reduction by more than 95% is achievable.

Topic: Access Control and Trust
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Shareholder vs. stakeholder governance index and performance: evidence from the Tunisian quoted banks

In this study, we investigate the association between bank performance and governance index of the Tunisian quoted banks. On the one hand, we estimate two types of banking governance index, such as the shareholder governance index and the stakeholder governance index using the data envelopment analysis (DEA) method. Then, we elaborate a classification of the Tunisian banks according to their governance practices and we classify the governance indexes relating to the bank ownership structure. Our results show that the private banks present the best shareholder governance index, whereas the privatised banks hold the best stakeholder governance index. On the other hand, we explore the impact of the governance index on the bank performance. We find evidence that the shareholder governance index is positively related to the shareholder performance and that the stakeholder governance index positively influences the stakeholder performance.

Topic: Efficiency Analysis Using DEA
Subfield: Management Science and Operations Research
Field: Decision Sciences
Domain: Social Sciences
SM3-Text-to-Query: Synthetic Multi-Model Medical Text-to-Query Benchmark

Electronic health records (EHRs) are stored in various database systems with different database models on heterogeneous storage architectures, such as relational databases, document stores, or graph databases. These different database models have a big impact on query complexity and performance. While this has been a known fact in database research, its implications for the growing number of Text-to-Query systems have surprisingly not been investigated so far. In this paper, we present SM3-Text-to-Query, the first multi-model medical Text-to-Query benchmark based on synthetic patient data from Synthea, following the SNOMED-CT taxonomy -- a widely used knowledge graph ontology covering medical terminology. SM3-Text-to-Query provides data representations for relational databases (PostgreSQL), document stores (MongoDB), and graph databases (Neo4j and GraphDB (RDF)), allowing the evaluation across four popular query languages, namely SQL, MQL, Cypher, and SPARQL. We systematically and manually develop 408 template questions, which we augment to construct a benchmark of 10K diverse natural language question/query pairs for these four query languages (40K pairs overall). On our dataset, we evaluate several common in-context-learning (ICL) approaches for a set of representative closed and open-source LLMs. Our evaluation sheds light on the trade-offs between database models and query languages for different ICL strategies and LLMs. Last, SM3-Text-to-Query is easily extendable to additional query languages or real, standard-based patient databases.

Topic: Scientific Computing and Data Management
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
The GPI sidechain of <i>Toxoplasma gondii</i> inhibits parasite pathogenesis

ABSTRACT Glycosylphosphatidylinositols (GPIs) are highly conserved anchors for eukaryotic cell surface proteins. The apicomplexan parasite, Toxoplasma gondii , is a widespread intracellular parasite of warm-blooded animals whose plasma membrane is covered with GPI-anchored proteins, and free GPIs called GIPLs. While the glycan portion is conserved, species differ in sidechains added to the triple mannose core. The functional significance of the Glcα1,4GalNAcβ1- sidechain reported in Toxoplasma gondii has remained largely unknown without understanding its biosynthesis. Here we identify and disrupt two glycosyltransferase genes and confirm their respective roles by serology and mass spectrometry. Parasites lacking the sidechain on account of deletion of the first glycosyltransferase, PIGJ, exhibit increased virulence during primary and secondary infections, suggesting it is an important pathogenesis factor. Cytokine responses, antibody recognition of GPI-anchored SAGs, and complement binding to PIGJ mutants are intact. By contrast, the scavenger receptor CD36 shows enhanced binding to PIGJ mutants, potentially explaining a subtle tropism for macrophages detected early in infection. Galectin-3, which binds GIPLs, exhibits an enhancement of binding to PIGJ mutants, and the protection of galectin-3 knockout mice from lethality suggests that Δ pigj parasite virulence in this context is sidechain dependent. Parasite numbers are not affected by Δ pigj early in the infection in wild-type mice, suggesting a breakdown of tolerance. However, increased tissue cysts in the brains of mice infected with Δ pigj parasites indicate an advantage over wild-type strains. Thus, the GPI sidechain of T. gondii plays a crucial and diverse role in regulating disease outcomes in the infected host. IMPORTANCE The functional significance of sidechain modifications to the glycosylphosphatidylinositol (GPI) anchor in parasites has yet to be determined because the glycosyltransferases responsible for these modifications have not been identified. Here we present identification and characterization of both Toxoplasmsa gondii GPI sidechain-modifying glycosyltransferases. Removal of the glycosyltransferase that adds the first GalNAc to the sidechain results in parasites without a sidechain on the GPI, and increased host susceptibility to infection. Loss of the second glycosyltransferase results in a sidechain with GalNAc alone, and no glucose added, and has negligible effect on disease outcomes. This indicates GPI sidechains are fundamental to host-parasite interactions.

Topic: Toxoplasma gondii Research Studies
Subfield: Parasitology
Field: Immunology and Microbiology
Domain: Life Sciences
Nutrient Balance Analysis for Finishing Hog Production: High-Rise Hog vs. Conventional Deep Pit Systems

This report describes the design and objectives of a study to compare the High Rise hog building(HRHB) to conventional deep-pit systems. Manure properties as well as estimated nitrogen, water and drymatter losses for a HRHB, both before and after composting, are compared to published values for adeep-pit finishing system. Results showed that 517 kg/pig (57 kg dry/pig) of manure was produced duringa hog grow-finishing cycle of 120 days. From 167 to 171 kg/pig of manure, including added bedding, wasremoved from the HRHB while 413 kg/pig was estimated to be removed from a deep-pit system. Asubstantial amount of N was lost (72-75% of the excreted N) during its accumulation while only 17% ofthe nitrogen from a deep-pit system was reportedly lost. Deep-pit manure has a moisture content of 89%and a nitrogen content of 8%, while the HRHB manure had a near optimal moisture content (62-67%moisture) for composting. Full scale windrow composting of the HRHB manure showed that thecumulative dry matter loss was 37-39% as compared to the excreted manure. Cumulative water and Nlosses after composting were 90-94% and 81-87% respectively. The amount of manure/beddingremaining after composting was 60-83 kg/pig for the HRHB and 413 kg/pig for the deep-pit system. TheHRHB coupled with composting reduced the weight of manure by 84-88% and the volume by 62-63% ascompared to the deep-pit system, however, after composting, only 0.59 to 0.88 kg N/pig was left of the4.6 kg N excreted per pig during finishing. In summary, the HRHB manure management systemsubstantially reduced the moisture content, dry and wet weight of swine manure as compared to literaturevalues for a conventional deep-pit system.

Topic: Metallurgy and Material Science
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Sirenomelia - A case report

Mermaid baby also known as sirenomelia is a rare and usually lethal congenital abnormality with multisystem involvement. Characteristic feature consists of varying degrees of lower limb fusion which in severe form results in single lower limb with nondiscernible limb bones. We herein report a case of sirenomelia with variable malformation.

Topic: Congenital gastrointestinal and neural anomalies
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Functionalised Oligoenes with Unusual Topologies: Synthesis, Electrochemistry and Structural Studies on Redox-Active [3]- and [4]-Dendralenes

New [3]- and [4]-dendralenes bearing electron-donor 1,3-dithiole and ferrocene substituents have been synthesised. Compounds 8, 15 and 17 have been characterised by single-crystal X-ray diffraction. Two of the dithiole rings of 8 are conjugated (dihedral angle 9°), while the third dithiole ring is almost orthogonal to this plane, and hence its π-electron system is isolated. For the dendralene precursor molecule 15, the substituted cyclopentadienyl ring, two C=C bonds and fused dithiole and dithiine rings comprise an extended π-conjugated system. In molecule 17 the potential conjugation path C(6)C(3)C(4)C(5)-C5H5 is distorted by an 8° twist around the C(3)−C(4) bond and a 7° twist around the C(5)−C(21) bond, and the delocalisation along the chain is insignificant. Solution electrochemical data demonstrate that the dendralenes are strong π-electron donors, which give rise to dication, radical trication or tetracation species. Spectroelectrochemical studies on compounds 7 and 10 suggest that the radical species are situated within the linear 1,2-ethylenediylidene moieties and that a conformational change may occur at the dication redox stage. UV/Vis spectroscopic data are consistent with poor cross-conjugation in these systems.

Topic: Molecular Junctions and Nanostructures
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Big DNA datasets analysis under push down automata

Consensus is a significant part that supports the identification of unknown information about animals, plants and insects around the globe. It represents a small part of Deoxyribonucleic acid (DNA) known as the DNA segment that carries all the information for investigation and verification. However, excessive datasets are the major challenges to mine the accurate meaning of the experiments. The datasets are increasing exponentially in ever seconds. In the present article, a memory saving consensus finding approach is organized. The principal component analysis (PCA) and independent component (ICA) are used to pre-process the training datasets. A comparison is carried out between these approaches with the Apriori algorithm. Furthermore, the push down automat (PDA) is applied for superior memory utilization. It iteratively frees the memory for storing targeted consensus by removing all the datasets that are not matched with the consensus. Afterward, the Apriori algorithm selects the desired consensus from limited values that are stored by the PDA. Finally, the Gauss-Seidel method is used to verify the consensus mathematically.

Topic: Advanced biosensing and bioanalysis techniques
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
SH3317827.08FU

UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.

Topic: Seaweed-derived Bioactive Compounds
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
© Springer-Verlag Berlin Heidelberg 2009 A Desynchronization Resilient Watermarking Scheme

Abstract. This paper presents a content-based desynchronization resistant digi-tal image watermarking scheme. The image content is represented by strong important feature points obtained by our robust and improved Harris corner de-tector. These feature points are more resistant to geometric attacks and are therefore used by the Delaunay triangle matching and image restoration method to reduce synchronization errors. The spread-spectrum-based blind watermark embedding and retrieval scheme is applied in the Fourier domain of each per-ceptually highly textured subimage. The multiplicative scheme is then used to embed the same copy of the watermark at highly secure mid-frequency posi-tions generated by one-way hash functions with different secret keys. The wa-termark detection decision is based on the number of matched bits between the recovered and embedded watermarks in embedding subimages. Experimental results demonstrate that our scheme is more robust to desynchronization attacks (i.e., geometric and common image processing attacks) than other peer feature-based approaches.

Topic: Advanced Steganography and Watermarking Techniques
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
Effect of chemical composition on the response of zwitterionic glucose sensitive hydrogels studied by design of experiments

ABSTRACT A stimuli‐responsive hydrogel that contains the anionic monomer 3‐acrylamidophenylboronic acid and the cationic monomer N ‐[3‐(dimethylamino)propyl]acrylamide binds with cis‐diol groups of glucose molecules selectively and reversibly. Even though such hydrogels have good selectivity for glucose, there are still remaining thresholds that should be overcome to enhance the sensitivity (swelling pressure response magnitude) and to reduce the response time (inverse of 1st order rate constant). In this study, the sensitivity and response time of zwitterionic glucose sensitive hydrogels (GSHs) were studied with three factor DOE analysis. The DOE results show that the molar ratio of 3‐acrylamidophenylboronic acid/ N ‐[3‐(dimethylamino)propyl]acrylamide and the wt % of monomer in the pregel solution are the most important factors for enhancing the hydrogel sensitivity. In addition, fast response times can best be achieved by decreasing the molar ratio of cross‐linker. The results of this study will be useful as guidelines for the optimal synthesis of glucose sensitive hydrogels. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 40667.

Topic: Hydrogels: synthesis, properties, applications
Subfield: Molecular Medicine
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Some properties of the continuous latitude distributions of the brightness of the K and F coronas as deduced from the LASCO data

Using two new methods for separating the K and F coronas and the LASCO C2 and C3 coronagraph data, continuous latitude distributions of the brightness of the K and F coronas have been obtained and examined as a function of the distance for different solar activity phases.

Topic: Solar and Space Plasma Dynamics
Subfield: Astronomy and Astrophysics
Field: Physics and Astronomy
Domain: Physical Sciences
Relative Importance of Lexical Features in Word Processing During L2 English Reading

Word processing during reading is known to be influenced by lexical features, especially word length, frequency, and predictability. This study examined the relative importance of these features in word processing during L2 English reading. We used data from an eye-tracking corpus and applied a machine-learning approach to model word-level eye-tracking measures and identify key predictors. Predictors comprised several lexical features, including length, frequency, and predictability (e.g., surprisal). Additionally, sentence, passage, and reader characteristics were considered for comparison. The analysis found that word length was the most important variable across several eye-tracking measures. However, for certain measures, word frequency and predictability were more important than length, and in some cases, reader characteristics such as proficiency were more significant than lexical features. These findings highlight the complexity of word processing during reading, the shared processes between L1 and L2 reading, and their potential to refine models of eye-movement control.

Topic: Reading and Literacy Development
Subfield: Developmental and Educational Psychology
Field: Psychology
Domain: Social Sciences