Miracle-dz/UniFAR-FTUs huggingface dataset:
Transformation of a plasmid-free, genital tract isolate of Chlamydia trachomatis with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype

The development of a plasmid-based genetic transformation protocol for Chlamydia trachomatis provides the basis for the detailed investigation of the function of the chlamydial plasmid and its individual genes or coding sequences (CDS). In this study we constructed a plasmid vector with CDS6 deleted (pCDS6KO) from the original Escherichia coli/C. trachomatis shuttle vector pGFP::SW2. pCDS6KO was transformed into a clinical isolate of C. trachomatis from Sweden that is plasmid-free (C. trachomatis SWFP–). Penicillin-resistant transformants expressing the green fluorescent protein were selected. These transformants did not stain with iodine, indicating that this property is regulated by CDS6 or its gene product. In addition, mature inclusions of C. trachomatis SWFP– transformed by pCDS6KO displayed an identical morphological phenotype to the untransformed plasmid-free recipient host. In this phenotype the morphology of inclusions was altered with the chlamydiae lining the periphery of the inclusion leaving a ‘hole’ in the centre. These green fluorescent inclusions appear ‘doughnut-shaped’ with an empty centre when examined under blue light, giving rise to a characteristic ‘black hole’ phenotype. Our study demonstrates the power of the new genetic system for investigating chlamydial gene function using gene deletion technology.
Outer membrane-like vesicles secreted by Actinobacillus actinomycetemcomitans are enriched in leukotoxin.

Actinobacillus actinomycetemcomitans is associated with early onset periodontal diseases and secretes membranous vesicles that appear to contain several virulence-associated proteins. However, the composition of these vesicles and the process leading to their secretion are not well defined. Electron micrographs of thin sectioned bacterial cells and purified vesicle preparations showed that vesicles are spherical lipid bilayers, 50-100 nm in diameter, that appear to form by budding from the outer membrane of the bacterium. Thin layer chromatography identified the predominant lipid components of vesicles as lipopolysaccharide, phosphatidylethanolamine and cardiolipin, similar to the main lipid constituents of the outer membrane. However, vesicles also contained minor lipids that were not detected in outer membrane samples. The major protein constituents of vesicles co-migrated with proteins in outer membrane extracts of A. actinomycetemcomitans, but the outer membrane preparations possessed polypeptides that were not detected in vesicles. Three vesicle proteins were identified; the heat-modifiable OmpA homologue of A. actinomycetemcomitans, a 28 kDa lipoprotein related to the major outer membrane lipoprotein of Mannheimia haemolytica and leukotoxin. Incubation of leukotoxin-sensitive human HL60 cells with vesicles from A. actinomycetemcomitans strains JP2 and 652 resulted in cell lysis, indicating that vesicle-associated leukotoxin is biologically active. Vesicles from the highly leukotoxic strain JP2 were five- to 10-fold more toxic than vesicles from the minimally leukotoxic 652 strain. Furthermore, the specific leukotoxic activity of JP2 vesicles was approximately four- to five-fold higher than isolated outer membrane preparations from JP2, suggesting that vesicles are enriched in leukotoxin. Together, these results suggest that the formation of A. actinomycetemcomitans vesicles occurs by a process that results in the enrichment of leukotoxin.
A title I teacher's beliefs, decision‐making, and instruction at the third and seventh grade levels

Abstract The purpose of this study was to compare previous research findings (Mitchell, Konopak, & Readence, 1991) that examined the consistency between a Title I teacher's beliefs about reading and her instructional practices at the third and seventh grade levels. The researchers selected a pull‐out class to observe during five separate instructional sessions. All data were qualitatively analyzed by a research team that searched for meaningful patterns and trends. There was some variation between the Title I teacher's belief about reading and her instructional practices at the third and seventh grade levels, a result of the complex nature of the two schools. Results support (a) the need for teacher improvement programs to focus on the identification of constraints/opportunities that influence instructional decision‐making, ways to sort through dilemmas, and weigh alternatives, (b) the need to coordinate Title I instruction with regular classroom instruction, and (c) the importance of the study of teacher.
Driver behaviours on rural highways with and without curbs – a driving simulator based study

The speed limit of 55 mph (88 km/h) is used typically on rural highways in the U.S. When curbs are installed, a lower speed limit is suggested because running into curbs at high speeds may cause significant vehicular damage and severe injuries. However, it has been argued that lowering the speed limit may cause confusion in drivers, who do not perceive the risk and tend to operate their vehicles at the same speed as before. To better understand driver behaviour on two-lane rural highways before and after curb installation, the authors conducted a series of experiments on a high-fidelity driving simulator in different posted speed limit, curb installation, lateral curb clearance, weather, visibility, and traffic conditions. Results of the study suggest that driver behaviours are influenced by the various factors in a complex and interrelated manner. It is likely that curbs have no influence on a driver's selection of speed. Drivers do perceive the risk from the curb or the opposing traffic when selecting their lane positions. The available space between the curb and the opposing traffic is crucial and has significant effects on driving behaviours. The subjective effects of drivers are found to be influential to driving behaviours.
Neisseria meningitidis PorB, a TLR2 Ligand, Induces an Antigen-Specific Eosinophil Recall Response: Potential Adjuvant for Helminth Vaccines?1

Efficacious adjuvants are important components of new vaccines. The neisserial outer membrane protein, PorB, is a TLR2 ligand with unique adjuvant activity. We demonstrate that PorB promotes Th2-skewed cellular immune response to the model Ag, OVA, in mice, including Ag-specific recall eosinophil recruitment to the peritoneum. PorB induces chemokine secretion by myeloid cells using both TLR2-dependent and -independent mechanisms, suggesting that anatomical distribution of TLR2+ cells may not be a limiting factor for potential vaccine strategies. The results from this study suggest that PorB, and other TLR2 ligands, may be ideal for use against pathogens where eosinophilia may be protective, such as parasitic helminths.
Tumor Suppressor Cylindromatosis (CYLD) Controls HIV Transcription in an NF-κB-Dependent Manner

ABSTRACT Characterizing the cellular factors that play a role in the HIV replication cycle is fundamental to fully understanding mechanisms of viral replication and pathogenesis. Whole-genome small interfering RNA (siRNA) screens have identified positive and negative regulators of HIV replication, providing starting points for investigating new cellular factors. We report here that silencing of the deubiquitinase cylindromatosis protein (CYLD), increases HIV infection by enhancing HIV long terminal repeat (LTR)-driven transcription via the NF-κB pathway. CYLD is highly expressed in CD4+ T lymphocytes, monocyte-derived macrophages, and dendritic cells. We found that CYLD silencing increases HIV replication in T cell lines. We confirmed the positive role of CYLD silencing in HIV infection in primary human CD4+ T cells, in which CYLD protein was partially processed upon activation. Lastly, Jurkat T cells latently infected with HIV (JLat cells) were more responsive to phorbol 12-myristate 13-acetate (PMA) reactivation in the absence of CYLD, indicating that CYLD activity could play a role in HIV reactivation from latency. In summary, we show that CYLD acts as a potent negative regulator of HIV mRNA expression by specifically inhibiting NF-κB-driven transcription. These findings suggest a function for this protein in modulating productive viral replication as well as in viral reactivation. IMPORTANCE HIV transcription is regulated by a number of host cell factors. Here we report that silencing of the lysine 63 deubiquitinase CYLD increases HIV transcription in an NF-κB-dependent manner. We show that CYLD is expressed in HIV target cells and that its silencing increases HIV infection in transformed T cell lines as well as primary CD4+ T cells. Similarly, reactivation of latent provirus was facilitated in the absence of CYLD. These data suggest that CYLD, which is highly expressed in CD4+ T cells, can control HIV transcription in productive infection as well as during reactivation from latency.
Calvatia oblongispora sp. nov. from Brazil, with close affinities to C. sporocristata from Costa Rica

A new species of Calvatia from Manaus in Amazonas State, Brazil, is proposed, which is very close to Calvatia sporocristata, recently described from Costa Rica. The two species have been compared macroscopically and examined using light and scanning electron microscopy. The proposed new species, C. oblongispora, possesses a distinctly two-layered exoperidium consisting of a hyphal outer layer and an inner pseudoparenchymatous layer. This contrasts to the single pseudoparenchymatous exoperidium possessed by C. sporocristata. A table comparing the main exoperidial, basidiospore, and capillitial differences between both species is provided.
Partial preprocessing C code for variability analysis

The C preprocessor is commonly used to implement variability. Given a feature selection, code fragments can be excluded from compilation with #ifdef and similar directives. However, the token-based nature of the C preprocessor makes variability implementation difficult and error-prone. Additionally, variability mechanisms are intertwined with macro definitions, macro expansion, and file inclusion. To determine whether a code fragment is compiled, the entire file must be preprocessed. We present a partial preprocessor that preprocesses file inclusion and macro expansion, but retains variability information for further analysis. We describe the mechanisms of the partial preprocessor, provide a full implementation, and present some initial experimental results. The partial preprocessor is part of a larger endeavor in the TypeChef project to check variability implementations (syntactic correctness, type correctness) in C projects such as the Linux kernel.
Characteristics of Patients With Work-Related Asthma Seen in the New York State Occupational Health Clinics

Objective: The objective of this study was to characterize the work-related asthma population seen by the New York State Occupational Health Clinic Network (OHCN) to determine which industries, occupations, and causal agents are associated with work-related asthma in New York State (NYS). Methods: The OHCN patient database was analyzed to identify those patients with a diagnosis of work-related asthma and medical charts were then abstracted for data on demographics, clinical history, disease severity, industry, occupation, and putative agent. Results: The OHCN patients with work-related asthma were most commonly employed in the service and manufacturing industries. Common occupations included teachers, farm operators/managers, and construction trades. The most frequently reported putative agents associated with work-related asthma were dust, indoor air, mold, and solvents. Conclusions: Our findings suggest the potential importance of prevention of workplace exposure in reducing adult asthma in NYS.
RECOGNIZING THE SETTING BEFORE REPORTING THE ACTION: INVESTIGATING HOW VISUAL EVENTS ARE MENTALLY CONSTRUCTED FROM SCENE IMAGES

While watching a film, the viewer begins to construct mental representations of it, which are called events. During the opening scene of a film, the viewer is presented with two distinct pieces of information that can be used to construct the event, namely the setting and an action by the main character. But, which of these two constructs are first cognitively represented by the viewer? Experiment 1 examined the time-course of basic level action categorization with superordinate and basic level scene categorization using masking. The results indicated that categorization occurred in a course-to-fine manner, inconsistent with Rosch et al.’s (1976) basic level theory. Interestingly, basic level action categorization performance did not reach ceiling when it was processed for a 367 ms SOA, suggesting that additional scene information and processing time were required. Thus, Experiment 2 examined scene and action categorization performance over multiple fixations, and the scene information that was fixated for each categorization task. Both superordinate and basic level scene categorization required only a single fixation to reach ceiling performance, inconsistent with basic level primacy, whereas basic level action categorization took two to three fixations, and led to more object fixations than in either scene categorization task. Eye movements showed evidence of a person bias across all three categorization tasks. Additionally, the categorization task did produce differences in the scene information that was fixated (Yarbus, 1967). However, could basic level theory still be correct when subjects are given a different task? When the same scene images were named, basic level action terms were used more often than basic level scene category terms, while superordinate level action terms were used relatively less often, and superordinate level scene category terms were hardly ever used. This shows that linguistic categorization (naming) is sensitive to informative, middle-level categories, whereas early perceptual categorization makes use of coarse high level distinctions. Additionally, the early perceptual advantage for scene categorization over basic level action categorization suggests that the scene category is the first construct that is used to represent events in scene images, and maybe even events in visual narratives like film. RECOGNIZING THE SETTING BEFORE REPORTING THE ACTION: INVESTIGATING HOW VISUAL EVENTS ARE MENTALLY CONSTRUCTED FROM SCENE IMAGES by
Gender Difference in Timing of Nocturnal Rise of Subjective Sleepiness

Abstract. Experimental research of diurnal variations in body temperature and melatonin secretion consistently revealed an earlier entrained circadian phase in women than in men. Since it is well documented that daily fluctuations in self-reported level of sleepiness closely follow the circadian rhythms of melatonin and body temperature, one can predict that gender differences in phase characteristics of the 24-hour fluctuations of subjective sleepiness resemble the differences revealed by research of physiological and hormonal rhythms. Analysis of sleepiness self-scored by 46 male and 54 female participants of sleep deprivation experiments showed that female participants scored significantly higher their midnight sleepiness level. The model-based simulations of sleepiness curves confirmed the prediction of a relatively earlier phase of 24-hour oscillations of sleepiness in women. Such gender differences persisted after accounting for individual variation in habitual sleep times and morning-evening prefer.
Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill

During the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria. Colwellia eventually supplanted Oceanospirillales, which dominated the plume early in the spill. These successional changes may have resulted, in part, from the changing composition and abundance of hydrocarbons over time. Colwellia abundance peaked when gaseous and simple aromatic hydrocarbons increased, yet the metabolic pathway used by Colwellia in hydrocarbon disposition is unknown. Here we used single-cell genomics to gain insights into the genome properties of a Colwellia enriched during the DWH deep-sea plume. A single amplified genome (SAG) of a Colwellia cell isolated from a DWH plume, closely related (avg. 98% 16S rRNA gene similarity) to other plume Colwellia, was sequenced and annotated. The SAG was similar to the sequenced isolate Colwellia psychrerythraea 34H (84% avg. nucleotide identity). Both had genes for denitrification, chemotaxis, and motility, adaptations to cold environments and a suite of nutrient acquisition genes. The Colwellia SAG may be capable of gaseous and aromatic hydrocarbon degradation, which contrasts with a DWH plume Oceanospirillales SAG which encoded non-gaseous n-alkane and cycloalkane degradation pathways. The disparate hydrocarbon degradation pathways are consistent with hydrocarbons that were abundant at different times in the deep-sea plume; first, non-gaseous n-alkanes and cycloalkanes that could be degraded by Oceanospirillales, followed by gaseous, and simple aromatic hydrocarbons that may have been degraded by Colwellia. These insights into the genomic properties of a Colwellia species, which were supported by existing metagenomic sequence data from the plume and DWH contaminated sediments, help further our understanding of the successional changes in the dominant microbial players in the plume over the course of the DWH spill.
Psychological Capital and Organisational Commitment: Nature, Structure and Relationship in an Indian Sample

Nowadays, researchers are expressing more concern regarding the use of scales which were not validated or standardised in the Indian context. Direct application of such scales to the Indian population is sometimes not practical due to differences in culture, belief, language and lifestyle. In order to get accurate validation and applicability, we should verify the nature and structure of original scales in the Indian context through factor analyses. Based on this need, the authors carried out factor analyses involving both exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) on psychological capital questionnaire by Luthans, Avolio, Avey and Norman (2007) and CFA for organisational commitment scale by Mowday, Steers and Porter (1979). The study involves a sample of 276 employees (150 male, 126 female) from three manufacturing units in India. The EFA of psychological capital suggested a three factors model instead of a four factors model. When it was estimated with CFA, the three factors measurement model was more well fitted than single factor as well as four factors models. The series of CFAs conducted for the organisational commitment scale through the measurement model reported that two factors structure is good enough to measure commitment behaviour. Internal consistencies through Cronbach’s alpha have also been checked. Structural equation modelling (SEM) analysis reports that psychological capital contributes significantly to organisational commitment. The researchers conclude this article with implications and directions for future research.
Youths’ Entrepreneurial Behaviour and Intentions. Empirical Study on Students with Entrepreneurship Education

The research aimed to identify the psychological and behavioural characteristics as potential triggers of youths’ entrepreneurial intentions within the context of rational action and planned behaviour theory. The empirical study proposed nine antecedents of entrepreneurial intentions for Romanian students with entrepreneurial higher education background. The results emphasized that behavioural variables (favourable subjective norms and attitude development, perceived behavioural control) influence entrepreneurial intentions in a higher degree than the psychological ones (propensity to risk-taking, self-confidence, need for achievement, innovativeness). Moreover, some psychological variables (locus of control and tolerance of ambiguity) have been identified as having insignificant influence on entrepreneurial intentions of the respondent students.
Measuring Corporate Governance: Lessons from the 'Bundles Approach'

This paper reviews recent studies that analyse and criticise existing academic and commercial corporate governance (CG) indices. Most of these ‘rating the ratings’ papers reach the conclusion that encompassing composite measures of CG are ineffective and suggest therefore to return to simpler measures. This paper draws on the 'configurational' - or 'bundles approach' to CG and argues that, while the criticisms made by the 'rating the ratings' papers are justified, their recommendations are misguided. Based on four central insights derived from the 'bundles approach', the paper shows that reverting to simpler measures of firm-level CG practices is a step in the wrong direction, in that it eliminates information about interactions between different corporate governance mechanisms. This is particularly consequential for comparative CG research that aims to identify differences in country-specific CG systems. Alternative solutions are developed to improve corporate governance measures, which take into account insights from the 'bundles approach'.
Des-Aspartate-Angiotensin I Attenuates Mortality of Mice Exposed to Gamma Radiation via a Novel Mechanism of Action

ACE inhibitors and ARBs (angiotensin receptor blockers) have been shown to attenuate radiation injuries in animal models of lethal gamma irradiation. These two classes of drug act by curtailing the actions of angiotensin II-linked inflammatory pathways that are up-regulated during gamma radiation in organ systems such as the brain, lung, kidney, and bone marrow. ACE inhibitors inhibit ACE and attenuate the formation of angiotensin II from angiotensin I; ARBs block the angiotensin AT1 receptor and attenuate the actions of angiotensin II that are elicited through the receptor. DAA-I (des-aspartate-angiotensin I), an orally active angiotensin peptide, also attenuates the deleterious actions of angiotensin II. It acts as an agonist on the angiotensin AT1 receptor and elicits responses that oppose those of angiotensn II. Thus, DAA-I was investigated for its anticipated radioprotection in gamma irradiated mice. DAA-I administered orally at 800 nmole/kg/day for 30 days post exposure (6.4 Gy) attenuated the death of mice during the 30-day period. The attenuation was blocked by losartan (50 nmole/kg/day, i.p.) that was administered sequential to DAA-I administration. This shows that the radioprotection was mediated via the angiotensin AT1 receptor. Furthermore, the radioprotection correlated to an increase in circulating PGE2 of surviving animals, and this suggests that PGE2 is involved in the radioprotection in DAA-I-treated mice. At the hematopoietic level, DAA-I significantly improved two syndromes of myelosuppression (leucopenia and lymphocytopenia), and mice pre-treated with DAA-I prior to gamma irradiation showed significant improvement in the four myelodysplastic syndromes that were investigated, namely leucopenia, lymphocytopenia, monocytopenia and thrombocytopenia. Based on the known ability of PGE2 to attenuate the loss of functional hematopoietic stem and progenitor cells in radiation injury, we hypothesize that PGE2 mediated the action of DAA-I. DAA-I completely attenuated the increase in circulating level of two inflammatory cytokines, TNFα and IL-6, in irradiated mice; and this shows that DAA-I exerted additional anti-inflammatory actions, which could also have contributed to its radioprotection. These findings show that DAA-I acts via a novel mechanism of action on the angiotensin AT1 receptor to specifically release PGE2, which mediates radioprotection in the gamma irradiated mice.