Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclic-di-GMP levels affect Pseudomonas aeruginosa fitness in the presence of imipenem.

A large number of genes coding for enzymes predicted to synthesize and degrade 3'-5'-cyclic diguanylic acid (c-di-GMP) is found in most bacterial genomes and this dinucleotide emerged as an intracellular signal-controlling bacterial behaviour. An association between high levels of c-di-GMP and antibiotic resistance may be expected because c-di-GMP regulates biofilm formation and this mode of growth leads to enhanced antibiotic resistance. However, a clear understanding of this correlation has not been established. We found that increased levels of c-di-GMP in Pseudomonas aeruginosa improve fitness in the presence of imipenem, even when grown as planktonic cells. P. aeruginosa post-transcriptionally regulates the amounts of five porins in response to c-di-GMP, including OprD, responsible for imipenem uptake. Cells with low c-di-GMP levels are consequently more sensitive to this antibiotic. Main efflux pumps or β-lactamase genes did not show altered mRNA levels in P. aeruginosa strains with modified different c-di-GMP concentrations. Together, our findings show that c-di-GMP levels modulate fitness of planktonic cultures in the presence of imipenem.
Fate of arsenate following arsenite oxidation in Agrobacterium tumefaciens GW4.

The fate of arsenate (As(V) ) generated by microbial arsenite (As(III) ) oxidation is poorly understood. Agrobacterium tumefaciens wild-type strain (GW4) was studied to determine how the cell copes with As(V) generated in batch culture. GW4 grown heterotrophically with mannitol used As(III) as a supplemental energy supply as reflected by enhanced growth and increased cellular levels of NADH and ATP. Under low phosphate (Pi) conditions and presence of As(III) oxidation, up to ∼ 50% of the resulting As(V) was taken up and found associated with the periplasm, membrane or cytoplasm fractions of the cells. Arsenic was found associated with proteins and polar lipids, but not in nucleic acids or sugars. Thin-layer chromatography and gas chromatography-mass spectrometry analysis suggested the presence of arsenolipids in membranes, presumably as part of the bilayer structure of the cell membrane and replacing Pi under Pi-limiting conditions. The potential role of a Pi-binding protein (PstS) for As(V) uptake was assessed with the His-tag purified protein. Intrinsic tryptophan fluorescence spectra analysis suggests that PstS can bind As(V) , but with lower affinity as compared with Pi. In early stationary phase cells, the As(V) : Pi ratio was approximately 4.3 and accompanied by an altered cell ultrastructure.
The design of a smokefree home leaflet and home pack: a Guernsey case study

Purpose – This paper aims to explore the beliefs and attitudes of young mothers in relation to smokefree homes and passive smoke in Guernsey, and to encourage them to contribute to the designing of a smokefree home leaflet and pack aimed at young mothers.Design/methodology/approach – Semi‐structured interviews were conducted with 11 participants (aged 17‐23 years). Findings – Most participants were smokers, however, they all knew what passive smoke was and asserted that their homes were smokefree. Even if they were unable to list specific impacts of second hand smoke on children, they all agreed that children should be protected. A few of them described the difficulties in telling people not to smoke around their children in other people's homes and in cars. Moreover, some young mothers said that they found it hard to persuade their partners not to smoke around the children.Originality/value – This paper presents the respondents ideas for promoting and supporting smokefree homes for young mothers and infor.
Validação da escala motora funcional EK para a língua portuguesa

OBJECTIVE: To validate a Portuguese version of the EK scale (Egen Klassifikation), that was developed in Denmark for patients with Duchenne muscular dystrophy, and spinal muscular atrophy. METHODS: An English version of the EK scale was translated into the Portuguese language as spoken in Brazil. This scale was applied to 26 male patients (mean age = 12.7 ± 4.0 years) with Duchenne muscular dystrophy. Patients also answered questions of a Portuguese version of the Barthel index questionnaire, and had their right and left hand grip forces measured with a dynamometer. RESULTS: The mean total EK scale score was 8.1 ± 7.3 and the Barthel index 54.0 ± 26.2. The mean hand grip force was 12.7 ± 17.2 % predicted for the right hand, and 14.6 ± 19.8 % predicted for the left hand. The EK scale scores showed highly significant statistical correlations with age (r= 0.596, p= 0.0013), right hand grip force (r= -0.556, p= 0.0032), left hand grip force (r= -0.623, p=0.0007), and Barthel index (r= -0.928, p < 0.0001). CONCLUSION: This translated Portuguese version of the EK scale is an adequate tool to be used for Brazilian Duchenne muscular dystrophy patients.
FgSKN7 and FgATF1 have overlapping functions in ascosporogenesis, pathogenesis and stress responses in Fusarium graminearum.

Fusarium head blight caused by Fusarium graminearum is one of the most destructive diseases of wheat and barley. Deoxynivalenol (DON) produced by the pathogen is an important mycotoxins and virulence factor. Because oxidative burst is a common defense response and reactive oxygen species (ROS) induces DON production, in this study, we characterized functional relationships of three stress-related transcription factor genes FgAP1, FgATF1 and FgSKN7. Although all of them played a role in tolerance to oxidative stress, deletion of FgAP1 or FgATF1 had no significant effect on DON production. In contrast, Fgskn7 mutants were reduced in DON production and defective in H2 O2 -induced TRI gene expression. The Fgap1 mutant had no detectable phenotype other than increased sensitivity to H2 O2 and Fgap1 Fgatf1 and Fgap1 Fgskn7 mutants lacked additional or more severe phenotypes than the single mutants. The Fgatf1, but not Fgskn7, mutant was significantly reduced in virulence and delayed in ascospore release. The Fgskn7 Fgatf1 double mutant had more severe defects in growth, conidiation and virulence than the Fgatf1 or Fgskn7 mutant. Instead of producing four-celled ascospores, it formed eight small, single-celled ascospores in each ascus. Therefore, FgSKN7 and FgATF1 must have overlapping functions in intracellular ROS signalling for growth, development and pathogenesis in F. graminearum.
"Galveston Orientation and Amnesia Test": tradução e validação

OBJETIVO: Traduzir e validar o Galveston Orientation and Amnesia Test para uso em nosso meio. METODOS: Esse teste foi traduzido para o portugues e retro-traduzido para o ingles por diferentes especialistas na lingua e por fim, feita a avaliacao da equivalencia entre o instrumento original e a versao retro-traduzida. Sua aplicacao em 73 vitimas de trauma crânio-encefalico contuso e a indicacao da gravidade dessa lesao, estabelecida pela Escala de Coma de Glasgow, permitiram verificar as propriedades de medida do instrumento. RESULTADOS: A confiabilidade verificada pelo Alfa de Cronbach resultou em 0,76. Houve indicacao de validade convergente e discriminante do instrumento quando os resultados de aplicacao do Galveston Orientation and Amnesia Test foram analisados perante a gravidade do trauma crânio-encefalico. CONCLUSAO: Os resultados observados dao suporte para a aplicacao do Galveston Orientation and Amnesia Test em nosso meio como indicador do termino da amnesia pos-traumatica.
Enzymes of the benzoyl-coenzyme A degradation pathway in the hyperthermophilic archaeon Ferroglobus placidus.

The Fe(III)-respiring Ferroglobus placidus is the only known archaeon and hyperthermophile for which a complete degradation of aromatic substrates to CO2 has been reported. Recent genome and transcriptome analyses proposed a benzoyl-coenzyme A (CoA) degradation pathway similar to that found in the phototrophic Rhodopseudomonas palustris, which involves a cyclohex-1-ene-1-carboxyl-CoA (1-enoyl-CoA) forming, ATP-dependent key enzyme benzoyl-CoA reductase (BCR). In this work, we demonstrate, by first in vitro studies, that benzoyl-CoA is ATP-dependently reduced by two electrons to cyclohexa-1,5-dienoyl-CoA (1,5-dienoyl-CoA), which is further degraded by hydration to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA (6-OH-1-enoyl-CoA); upon addition of NAD(+) , the latter was subsequently converted to β-oxidation intermediates. The four candidate genes of BCR were heterologously expressed, and the enriched, oxygen-sensitive enzyme catalysed the two-electron reduction of benzoyl-CoA to 1,5-dienoyl-CoA. A gene previously assigned to a 2,3-didehydropimeloyl-CoA hydratase was heterologously expressed and shown to act as a typical 1,5-dienoyl-CoA hydratase that does not accept 1-enoyl-CoA. A gene previously assigned to a 1-enoyl-CoA hydratase was heterologously expressed and identified to code for a bifunctional crotonase/3-OH-butyryl-CoA dehydrogenase. In summary, the results consistently provide biochemical evidence that F. placidus and probably other archaea predominantly degrade aromatics via the Thauera/Azoarcus type and not or only to a minor extent via the predicted R. palustris-type benzoyl-CoA degradation pathway.
Morphological Compensation for the Enhancement of Compressed Image

This paper describes a morphological compensation algorithm for the enhancement of grayscale image compression under the standard of JPEG and JPEG2000, which is more effective for remote sense image than for natural image. Morphological reconstruction is a nonlinear filter. When used for image enhancement it dilates some pixels while preserving the edge information. The algorithm has a close relationship with morphological reconstruction. When this compensation algorithm is applied to images, among which there are images compressed by standard JPEG2000 and JPEG, it can improve the quality of decompressed image.
Diagnostic accuracy of clinical tests for subacromial impingement syndrome (SIS): A systematic review and meta-analysis

Background Shoulder complaints are the third most common cause of musculoskeletal problems. Subacromial impingement syndrome (SIS) is the most frequent cause of shoulder pain. SIS is a clinical syndrome that indicates pain and pathology relating to the subacromial bursa and rotator cuff tendons within the subacromial space. Objective The aim of this systematic review and meta-analysis is to examine the diagnostic accuracy of clinical tests for diagnosing SIS. Methods A systematic literature search was conducted to identify all studies that examined the diagnostic accuracy of clinical tests for SIS test with surgery as the reference standard. The methodological quality of selected studies was assessed using the quality assessment of diagnostic accuracy studies (QUADAS) tool. Studies were combined using a bivariate random effects model. Heterogeneity was assessed using the variance of logit transformed sensitivity and specificity. Results Our systematic literature search yielded 16 articles. Ten studies with 1684 patients are included in the meta-analysis. The Hawkins-Kennedy test, Neer's sign, empty can test are shown to be useful for ruling out rather than ruling in SIS, with greater pooled sensitivity estimates (range 0.69–0.78) than specificity (range 0.57–0.62). A negative Neer's sign reduces the probability of SIS from 45% to 14%. The drop arm test and lift off test have higher pooled specificities (range 0.92–0.97) than sensitivities (range 0.21–0.42) indicating that they are useful for ruling in SIS if the test is positive. The methodological quality of the studies included ranges from moderate to good. However, the time delay between the clinical test and the reference test is not optimal in some studies and it is unclear if the assessors were blinded to outcome of index and reference tests. Discussion This is the first systematic review to examine the diagnostic accuracy of these common clinical tests, with a surgical diagnosis as the reference standard. However, there is a need for future high quality prospective cohort studies in primary care settings to investigate the diagnostic utility of these clinical tests. Conclusion This systematic review quantifies the diagnostic accuracy of three clinical tests for SIS. Application of these tests as diagnostic tools may serve to improve appropriate diagnosis and management of individuals with shoulder complaints.
Engulfing Darkness: The Impact of HIV/AIDS on the Family

A qualitative study undertaken in Mumbai, India, explored the family experience of HIV/AIDS. Seven nuclear households (4 with concordant couples in which both spouses in the marriage were seropositive, and 3 with discordant couples in which only one spouse was seropositive) included in the study reported devastating impacts in various spheres of family life, following the onset and the progress of HIV-related illness, and the knowledge of the seropositive diagnosis. Complex changes were observed in family composition, spousal relationships, family formation, family roles and responsibilities, family economy, quality of life, and family aspirations. The findings have direct implications for policy formulation, program planning, and service delivery in the field of HIV/AIDS.
Land cover analysis at a regional scale exploiting low and medium resolution ENVISAT ASAR Data: Application to Poyang Lake Area (Jianxi Province, P.R. China)

Located in Jiangxi Province, Poyang Lake is the largest freshwater lake in China and constitutes a major hydrological subsystem of the middle Yangtze river (Changjiang) basin in central China. An impressive amount of low to medium resolution ENVISAT data covering the Poyang Lake's 2004 and 2005 hydrologic years were acquired and analysed within the framework of the flood DRAGON project. Land cover mapping was realized synergistically using: 1) a land cover map derived from a colour composition containing seasonal ENVISAT ASAR Global Monitoring Mode image sums, and; 2) a land cover map derived from a colour composition containing filtered, seasonal ENVISAT ASAR wide swath mode image sums. Confronted and validated with the hydrodynamic characterization derived from Landsat reference data, these preliminary classifications lead to a land cover map with 13 classes covering 20,000 km2 (170 km from north to south and 120 km from East to West) and was realized at a 1/200 000 scale, but can be used from 1/150 000 to 1/500 000. The results highlight the great potential of ASAR medium and low resolution products for wide-area mapping. Worldwide, large archives of such data already exist which should enable access to the prerequisite amount of data required for such large-scale, land cover characterization.
Microbial community composition but not diversity changes along succession in arctic sand dunes

The generality of increasing diversity of fungi and bacteria across arctic sand dune succession was tested. Microbial communities were examined by high-throughput sequencing of 16S rRNA genes (bacteria) and internal transcribed spacer (ITS) regions (fungi). We studied four microbial compartments (inside leaf, inside root, rhizosphere and bulk soil) and characterized microbes associated with a single plant species (Deschampsia flexuosa) across two sand dune successional stages (early and late). Bacterial richness increased across succession in bulk soil and leaf endosphere. In contrast, soil fungal richness remained constant while root endosphere fungal richness increased across succession. There was, however, no significant difference in Shannon diversity indices between early and late successional stage in any compartment. There was a significant difference in the composition of microbial communities between early and late successional stage in all compartments, although the major microbial OTUs were shared between early and late successional stage. Co-occurrence network analysis revealed successional stage-specific microbial groups. There were more co-occurring modules in early successional stage than in late stage. Altogether, these results emphasize that succession strongly affects distribution of microbial species, but not microbial diversity in arctic sand dune ecosystem and that fungi and bacteria may not follow the same successional trajectories.
Composition and diversity of mucosa‐associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences

Mucosa-associated microbial populations of the gastrointestinal tract are in intimate contact with the outer mucus layer. This proximity offers these populations a higher potential, than lumenal microbiota, in exerting effects on the host. Functional characteristics of the microbiota and influences of host-physiology shape the composition and activity of the mucosa-associated bacterial community. We have shown previously that inclusion of an artificial sweetener, SUCRAM, included in the diet of weaning piglets modulates the composition of lumenal-residing gut microbiota and reduces weaning-related gastrointestinal disorders. In this study, using Illumina sequencing we characterised the mucosa-associated microbiota along the length of the intestine of piglets, and determined the effect of SUCRAM supplementation on mucosa-associated populations. There were clear distinctions in the composition of mucosa-associated microbiota, between small and large intestine, concordant with differences in regional oxygen distribution and nutrient provision by the host. There were significant differences in the composition of mucosa-associated compared with lumenal microbiota in pig caecum. Dietary supplementation with SUCRAM affected mucosa-associated bacterial community structure along the length of the intestinal tract. Most notably, there was a substantial reduction in predominant Campylobacter populations proposing that SUCRAM supplementation of swine diet has potential for reducing meat contamination and promoting food safety.
Impact of Exercise Frequency on Hand Strength of the Elderly

ABSTRACT Purpose: To determine if an every other day exercise program achieves comparable results to an everyday program, and to compare participants’ adherence to each program. Study Design: Randomized controlled trial. Methods: Thirty-six independent living individuals age 55 and older were randomly assigned to one of two groups. Group A performed grip and pinch therapy putty exercises daily. Group B performed the same exercises every other day. Participants were also assessed for program adherence. Results: There was no significant difference (p = 0.05) in grip strength change scores between the low- and high-frequency groups over the 8-week training period. Six out of eight pinch strength change scores indicated no significant difference between groups. Adherence data were better for the low-frequency group. Conclusion: For the most part, results indicated no significant difference between the hand-strengthening protocols when measuring hand strength over an 8-week period. Level of Evidence: 1b.
Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation

A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.
National early warning score (NEWS) is not suitable for all patients

McGinlay and Pearse worry about the use of the national early warning score (NEWS) in people recovering from brain injury,1 2 but its insensitivity in people developing acute brain insults is also worrying. In the assessment of brain dysfunction, NEWS depends solely on the “alert, verbal, pain, unresponsive (AVPU)” system. Although useful in initial triage, such simplicity is inadequate in monitoring hospital patients at risk of neurological deterioration. Crucially, AVPU findings are compressed to only …
Exploring HIV-Related Stigma in Kerala, India

The purpose of this qualitative study was to understand whether HIV-positive persons experience stigma in relation to HIV/AIDS and how it has impacted their lives and that of their families. Ethnographic techniques were used to collect data from Kerala, India. The findings were organized into three themes: (a) physical appearance and HIV-related stigma; (b) the “informed” and the “ignorant”: knowledge and ignorance in the context of HIV/AIDS; and (c) immorality as a perceived cause of HIV infection and the family context. The study highlighted the need to develop a more nuanced understanding of HIV-related stigma that extends beyond the current conceptualization of stigma
The buffer gas beam: an intense, cold, and slow source for atoms and molecules.

Beams of atoms and molecules are stalwart tools for spectroscopy and studies of collisional processes. The supersonic expansion technique can create cold beams of many species of atoms and molecules. However, the resulting beam is typically moving at a speed of 300−600 m s^(−1) in the laboratory frame and, for a large class of species, has insufficient flux (i.e., brightness) for important applications. In contrast, buffer gas beams can be a superior method in many cases, producing cold and relatively slow atoms and molecules (see Figure 1) in the laboratory frame with high brightness and great versatility. There are basic differences between supersonic and buffer gas cooled beams regarding particular technological advantages and constraints. At present, it is clear that not all of the possible variations on the buffer gas method have been studied. In this review, we will present a survey of the current state of the art in buffer gas beams, and explore some of the possible future directions that these new methods might take.