Miracle-dz/UniFAR-FTUs huggingface dataset:
Managing Change and Role Enactment in the Professionalized Organization

The Aims of this research are to examine how clinical directors and service managers from non-clinical backgrounds interpret and enact their roles and use them to implement effective service change. We recognise that the assessment of ? effective? change will require assessment on multiple criteria. As a secondary research question, we therefore seek to identify what additional factors account for individual or organisational differences in the effectiveness of change implementation. The approach, which we propose is a qualitative, inductive one, comparing and contrasting case studies of ten sites which have been purposefully selected. This design will facilitate the construction of a large-scale database with both internal and external validity. The ten sites consist of four primary care sites and six acute sector sites in London and the W.Midlands. In each site, the case focuses on a selected area of care and our design includes three clinical areas of care, namely, cancer care; maternity care and diabetes care (in primary care). These care groups have been chosen in relation to the priorities set out in the National Plan. Case study sites have been purposefully selected using a two stage process, to assess case contexts as of ? higher? and ? lower? complexity. The rationale for this selection is to enable the researchers to examine the extent to which complex, contextual pressures affect the interpretation and enactment of roles and relationships. Case studies will be constructed by gathering data on the context; the roles; the interpretation of the roles and the activities undertaken. Data collection methods will include archival data; interviews and observations of meetings, but with interviews as a prime data source. Interviews will be semi-structured and approximately 200 interviews are targeted. All interviews will be recorded and transcribed. Analysis will be an iterative process and will occur in stages. Initially, there will be a first scan of the transcripts, based on a pre-formulated analytic frame built on the interview questions. As a preliminary validation, pairs of transcripts will be exchanged between Researchers who will work in pairs and code ? blind? against the pre-formulated framework, to improve rater reliability. Two further analytic stages will include iterative cycles of comparisons between cases in care groups and across care groups. The final stages of the methods consist of local/regional workshops, run collaboratively with professional organisations and user/advocacy organisations, to debate and action plan on the basis of the findings. The research will lead to specific improvements in the way change is implemented in various settings. We anticipate that the recommendations will cover staff selection; training and development; roles and organisation structures and the processes of performance management.
Shiga toxin-producing Escherichia coli in British Columbia, 2011-2017: Analysis to inform exclusion guidelines.

Background Shiga toxin-producing Escherichia coli (STEC) can cause severe illness including bloody diarrhea and hemolytic-uremic syndrome (HUS) through the production of Shiga toxins 1 (Stx1) and 2 (Stx2). E. coli O157:H7 was the most common serotype detected in the 1980s to 1990s, but improvements in laboratory methods have led to increased detection of non-O157 STEC. Non-O157 STEC producing only Stx1 tend to cause milder clinical illness. Exclusion guidelines restrict return to high-risk work or settings for STEC cases, but most do not differentiate between STEC serogroups and Stx type. Objective To analyze British Columbia (BC) laboratory and surveillance data to inform the BC STEC exclusion guideline. Methods For all STEC cases reported in BC in 2011-2017, laboratory and epidemiological data were obtained through provincial laboratory and reportable disease electronic systems, respectively. Incidence was measured for all STEC combined as well as by serogroup. Associations were measured between serogroups, Stx types and clinical outcomes. Results Over the seven year period, 984 cases of STEC were reported. A decrease in O157 incidence was observed, while non-O157 rates increased. The O157 serogroup was significantly associated with Stx2. Significant associations were observed between Stx2 and bloody diarrhea, hospitalization and HUS. Conclusion The epidemiology of STEC has changed in BC as laboratories increasingly distinguish between O157 and non-O157 cases and identify Stx type. It appears that non-O157 cases with Stx1 are less severe than O157 cases with Stx2. The BC STEC exclusion guidelines were updated as a result of this analysis.
Effect of water and nitrogen levels on yield attributes, water productivity and economics of cluster bean (Cyamopsis tetragonoloba) in hot arid region

A field experiment was conducted at research farm, Agricultural Research Sub-Station, Hanumangarh, Swami Keshwanand Rajasthan Agricultural University, Bikaner, Rajasthan during Kharif, 2016 to study the effect of water and nitrogen levels on yield attributes, water productivity and economics of cluster bean [Cyamopsis tetragonoloba (L.) Taub. ]. Cluster bean variety RGC-1055 with seed rate of 16 kg/ha was planted using 3 levels of irrigation (100, 200 and 300 mm) and 4 level of nitrogen (0, 20, 40 and 60 kg/ha) and analyzed in split plot design with three replication. Results showed that irrigation at 200 mm significantly increased number of pods/plant (44.7), number of seeds/pod (7.8), test weight (28.7g), net returns (Rs 31179/ha) and B:C ratio (2.1) over 100 mm irrigation level.However, water productivity (0.25 kg m-3) was highest at 100 mm irrigation level. Nitrogen level at 40 kg/ha significantly increased number of pods/plant (48.3), number of seeds/pod (8.4), test weight (32.2 g), net returns (Rs.32273/ha), B:C ratio (2.12) and water productivity (0.27 kg m-3) over no application of N.
In vitro production of the biological control agent Heterorhabditis indica SL0708 in different agar media

ABSTRACT Heterorhabditis indica SL0708 is an entomopathogenic nematode isolated from Valle del Cauca-Colombia, whose bacterial symbiont, Photorhabdus luminescens subsp. akhurstii SL0708, has potential to control pests of economic importance in Colombia. Since in vivo production does not supply its demand, this investigation evaluated H. indica SL0708 production on different agar media. Five culture media (I, II, III, IV and V) were evaluated for productivity and pathogenicity of infective juveniles (IJs). IJs emerged between 11 and 16 days after inoculation in all media, with a total of 2.7 × 104 and 4.7 × 106 IJs produced during 15 days after IJs emergence, with maximum productivity at day five and high variability. Pathogenicity to Galleria mellonella larvae was not significantly different between in vitro and in vivo produced IJs on all media tested. Media IV and V were selected for their higher productivity. Subsequently, nematode inoculum size was evaluated in selected media at 2000, 4000 and 6000 IJs ml−1, but significant differences were not observed in productivity and pathogenicity. Lastly, lipid source influence was evaluated in medium IV comparing canola, olive and soy oils. None of the plant-based oils had a significant effect on IJs production and pathogenicity. A medium was selected for H. indica SL0708 IJs production which was suitable in terms of productivity, culture time and pathogenicity of IJs produced. The medium and parameters selected in this study could be applied as an alternative for mass production of this entomopathogenic nematodes.
Locus Coeruleus Engagement Drives Network Connectivity Dynamics In Humans And Rats

The locus coeruleus (LC) projects broadly throughout the brain, serving as the main source of norepinephrine and consequently driving arousal, attention and task performance. However, the arousal-performance relationship is non-monotonic, with low and high LC engagement associated with poorer task performance than intermediate LC activity. Signs of this “YerkesDodson” LC-performance curve have been observed in both humans and animals, but its underlying computational mechanisms remain poorly understood. We hypothesized that LC’s role in driving performance is due largely to its effect on neural noise, i.e. variability in innervated network activity. As a preliminary test, using two existing fMRI datasets we examined how LC engagement impacted BOLD and functional connectivity variability and dynamics in resting state and attentional networks in humans and rats. LC engagement changed (a) BOLD variability in a network-specific manner (humans), and (b) dynamic functional connectivity state switching speed between LC and thalamus (rats). These results provide preliminary cross-species evidence suggesting that LC’s computational role in regulating performance may rest largely on its role in regulating
Bacterial Diversity in the Metal-Rich Terrestrial Deep Subsurface Sediments of Krishna Godavari Basin, India

Abstract Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. ‘Abundant’ and ‘rare’ sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region.
INHIBITORY EFFECT OF MEDIATIONAL BOTANICAL EXTRACTS AGAINST ROOT ROT OF MUSKMELON CAUSED BY PHYTOPHTHORA DRECHSLERI (TUCKER): Department of Plant Pathology, University College of Agriculture, University of Sargodha, Pakistan

Phytophthora drechsleri (Tucker) causing root rot of muskmelon is a threatening pathogen in Pakistan. Non-chemical control based on the use of plant extracts are considered the best alternatives of noxious chemical pesticides as they are considered to be eco-friendly with no or minimal residual effects. The results of all tested botanicals suppressed the mycelial growth of pathogen. Extract of garlic (Allium sativum) showed maximum (86.5%) mycelial growth inhibition of root rot pathogen, followed by parthenium (Parthenium hysterophorus) (82.8%) and datura (Datura stramonium) (82%) at 30% concentration, while minimum inhibition was shown by Aak (Calatropis procera) (42.8%). These results suggested that plant extracts can be used as an alternative to chemicals for the management of root rot of muskmelon.
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes

When bacterial symbionts become associated with their hosts, their genomes are thought to decay inexorably towards an organelle-like fate due to decreased recombination and inefficient selection. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine endosymbionts that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts recombination rates, and that exceedingly low recombination rates are associated with genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable intermediate symbiont genome sizes that maintain substantial functional genetic variation. One-sentence summary Bacterial symbiont genomes maintain functional diversity through high rates of horizontal transmission and recombination.
Robustness and applicability of functional genomics tools on scRNA-seq data

Many tools have been developed to extract functional and mechanistic insight from bulk transcriptome profiling data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events, low library sizes and a comparatively large number of samples/cells. It is thus not clear if functional genomics tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. To address this question, we performed benchmark studies on in silico and in vitro single-cell RNA-seq data. We included the bulk-RNA tools PROGENy, GO enrichment and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compared them against the tools AUCell and metaVIPER, designed for scRNA-seq. For the in silico study we simulated single cells from TF/pathway perturbation bulk RNA-seq experiments. Our simulation strategy guarantees that the information of the original perturbation is preserved while resembling the characteristics of scRNA-seq data. We complemented the in silico data with in vitro scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on both the simulated and real data revealed comparable performance to the original bulk data. Additionally, we showed that the TF and pathway activities preserve cell-type specific variability by analysing a mixture sample sequenced with 13 scRNA-seq different protocols. Our analyses suggest that bulk functional genomics tools can be applied to scRNA-seq data, outperforming dedicated single cell tools. Furthermore we provide a benchmark for further methods development by the community.
Interspecific variation in organ position in hydrophiine snakes is explained by modifications to the vertebral column

Interspecific disparities in the position of the internal organs of snakes have been associated with evolutionary history and cardiovascular performance, as influenced by habitat use. For snakes, the positions of internal organs are typically determined as a linear measurement relative to body length. Therefore, interspecific variation in organ position could be explained either as heterotopic shifts in organ position or by modifications to the vertebral column. Using vertebral counts from radiographs, I determined the positions of the atria and pyloric sphincter relative to the cloaca in hydrophiine sea snakes. I found interspecific variation in the number of pre-atrial vertebrae to be labile, whereas the number of vertebrae in the atria to pyloric sphincter region and in the pyloric sphincter to cloaca region was relatively constrained. Furthermore, the number of pre-atrial vertebrae was dissociated from the number of vertebrae between the atria and cloaca, indicating that these two regions of the vertebral column can evolve independently. I conclude that variation in organ position among hydrophiine sea snake species is attributable, in part, to differences in the number of vertebrae among regions of the vertebral column rather than to heterotopic shifts in the positions of the internal organs.
Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis

Abstract HORMA domain-containing proteins such as Hop1 play crucial regulatory roles in various chromosomal functions. Here, we investigated roles of the fission yeast Hop1 in the formation of recombination-initiating meiotic DNA double strand breaks (DSBs). Meiotic DSB formation in fission yeast relies on multiple protein-protein interactions such as the one between the chromosome axial protein Rec10 and the DSB-forming complex subunit Rec15. Chromatin immunoprecipitation sequencing demonstrated that Hop1 is colocalized with both Rec10 and Rec15, and we observed physical interactions of Hop1 to Rec15 and Rec10. These results suggest that Hop1 promotes DSB formation by interacting with both axis components and the DSB-forming complex. We also show that Hop1 binding to DSB hotspots requires Rec15 and Rec10, while Hop1 axis binding requires Rec10 only, suggesting that Hop1 is recruited to the axis via Rec10, and to hotspots by hotspot-bound Rec15. Furthermore, we introduced separation-of-function Rec10 mutations, deficient for interaction with either Rec15 or Hop1. These single mutations and hop1Δ conferred only partial defects in meiotic recombination, while the combining the Rec15-binding-deficient rec10 mutation with hop1Δ synergistically reduced meiotic recombination, at least at a model hotspot. Taken together, Hop1 likely functions as a stabilizer for Rec15–Rec10 interaction to promote DSB formation.
Unravelling how the biosynthesis of sphingolipids impacts stress responses in Aspergillus nidulans

v General Index . vii Figure Index . ix Table Index . xi List of Acronyms . xiii CHAPTER 1 – Introduction . 1 1.1 The Fungal Kingdom . 2 1.2 Fungal Taxonomy . 3 1.3 Aspergillus nidulans . 5 1.4 Antifungal Drugs . 6 1.5 Sphingolipid Biosynthesis . 8 1.6 Ionic Liquids . 10 1.7 Objectives . 12 CHAPTER 2 – Materials and Methods . 13 2.1 Chemicals . 14 2.2 Strains and storage conditions . 15 2.3 Culture mediums . 15 2.4 Generation of deletion strains . 16 2.4. 1 Construction of deletion cassettes. 16 2.4. 2 Generation of transformable protoplasts and their transformation. 19 2.4. 3 Selection and confirmation . 20 2.5 Determination of minimal inhibitory concentrations of ionic liquids . 20 2.6 Determination of radial growth in solid medium supplemented with ionic liquids . 21 2.7 Lipid content assessment . 21
The Health and Health Care Use of Manitoba''s Seniors: Have They Changed Over Time

Catalyst for purifying exhaust gas comprises manganese oxide as a main catalytic component, calcium aluminate as a binder, and heat-resistant aggregate, wherein the manganese oxide is bonded and solidified onto the aggregate by calcium aluminate(mAl2O3, nCaO), and has an excellent ability to purify the exhaust gas from petroleum combustors or automobiles and a long catalytic life owing to its high heat resistance.
RhlR-Regulated Acyl-Homoserine Lactone Quorum Sensing in a Cystic Fibrosis Isolate of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a prominent cystic fibrosis (CF) pathogen that uses quorum sensing (QS) to regulate virulence. In laboratory strains, the key QS regulator is LasR. Many isolates from patients with chronic CF infections appear to use an alternate QS circuitry in which another transcriptional regulator, RhlR, mediates QS. We show that a LasR-null CF clinical isolate engages in QS through RhlR and remains capable of inducing cell death in an in vivo-like lung epithelium cell model. Our findings support the notion that LasR-null clinical isolates can engage in RhlR QS and highlight the centrality of RhlR in chronic P. aeruginosa infections. ABSTRACT The opportunistic pathogen Pseudomonas aeruginosa is a leading cause of airway infection in cystic fibrosis (CF) patients. P. aeruginosa employs several hierarchically arranged and interconnected quorum sensing (QS) regulatory circuits to produce a battery of virulence factors such as elastase, phenazines, and rhamnolipids. The QS transcription factor LasR sits atop this hierarchy and activates the transcription of dozens of genes, including that encoding the QS regulator RhlR. Paradoxically, inactivating lasR mutations are frequently observed in isolates from CF patients with chronic P. aeruginosa infections. In contrast, mutations in rhlR are rare. We have recently shown that in CF isolates, the QS circuitry is often rewired such that RhlR acts in a LasR-independent manner. To begin understanding how QS activity differs in this rewired background, we characterized QS activation and RhlR-regulated gene expression in P. aeruginosa E90, a LasR-null, RhlR-active chronic infection isolate. In this isolate, RhlR activates the expression of 53 genes in response to increasing cell density. The genes regulated by RhlR include several that encode virulence factors. Some, but not all, of these genes are present in the QS regulon described in the well-studied laboratory strain PAO1. We also demonstrate that E90 produces virulence factors at similar concentrations as PAO1, and in E90, RhlR plays a significant role in mediating cytotoxicity in a three-dimensional lung epithelium cell model. These data illuminate a rewired LasR-independent RhlR regulon in chronic infection isolates and suggest further investigation of RhlR as a possible target for therapeutic development in chronic infections. IMPORTANCE Pseudomonas aeruginosa is a prominent cystic fibrosis (CF) pathogen that uses quorum sensing (QS) to regulate virulence. In laboratory strains, the key QS regulator is LasR. Many isolates from patients with chronic CF infections appear to use an alternate QS circuitry in which another transcriptional regulator, RhlR, mediates QS. We show that a LasR-null CF clinical isolate engages in QS through RhlR and remains capable of inducing cell death in an in vivo-like lung epithelium cell model. Our findings support the notion that LasR-null clinical isolates can engage in RhlR QS and highlight the centrality of RhlR in chronic P. aeruginosa infections.
COMMENSAL SMALL MAMMAL SPECIES AND BAIT PREFERENCES IN URBAN AREAS OF PENANG ISLAND

Physical trapping is an important first step in controlling pest populations and species identification; and bait preferences are crucial information for effective management. This study was conducted to explore species diversity and bait preferences of commensal species in urban areas on Penang Island. Live trapping was carried out in eight sampling sites on Penang Island in commercial and residential areas. Eight different type of baits were used; apple and peanut butter (APB), white bread and peanut butter (BPB), salted fish (SF), salted fish and peanut butter (SFPB), white bread and fish extract (BFE), fried chicken leftover (FCL), vegetables and peanut butter (VPB) and sausages (S). The most successful bait was the high protein bait, fried chicken leftover (FCL), with a capture success rate of 35.56%. We also analysed the bait preferences for the different species of small mammals captured in our study. Five species of small mammals were captured in our study sites: Rattus norvegicus, Rattus rattus, Mus musculus, Bandicota bengalensis and Suncus murinus. Norway rats, R. norvegicus was the most trapped species in commercial areas whereas lesser bandicoot rats, B. bengalensis was the most captured species in residential areas.