bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chlorophyll Fluorescence Analysis of Cyanobacterial Photosynthesis and Acclimation
Authors: Campbell Douglas , Hurry Vaughan , Clarke Adrian K. , Gustafsson Petter , Öquist Gunnar 
Published: December 2019

SUMMARY

Cyanobacteria are ecologically important photosynthetic prokaryotes that also serve as popular model organisms for studies of photosynthesis and gene regulation. Both molecular and ecological studies of cyanobacteria benefit from real-time information on photosynthesis and acclimation. Monitoring in vivo chlorophyll fluorescence can provide noninvasive measures of photosynthetic physiology in a wide range of cyanobacteria and cyanolichens and requires only small samples. Cyanobacterial fluorescence patterns are distinct from those of plants, because of key structural and functional properties of cyanobacteria. These include significant fluorescence emission from the light-harvesting phycobiliproteins; large and rapid changes in fluorescence yield (state transitions) which depend on metabolic and environmental conditions; and flexible, overlapping respiratory and photosynthetic electron transport chains. The fluorescence parameters F
V
/F
M
, F
V
′/F
M
′,q
p
,q
N
, NPQ, and φPS II were originally developed to extract information from the fluorescence signals of higher plants. In this review, we consider how the special properties of cyanobacteria can be accommodated and used to extract biologically useful information from cyanobacterial
in vivo
chlorophyll fluorescence signals. We describe how the pattern of fluorescence yield versus light intensity can be used to predict the acclimated light level for a cyanobacterial population, giving information valuable for both laboratory and field studies of acclimation processes. The size of the change in fluorescence yield during dark-to-light transitions can provide information on respiration and the iron status of the cyanobacteria. Finally, fluorescence parameters can be used to estimate the electron transport rate at the acclimated growth light intensity.
Linkage Map of
Escherichia coli
K-12, Edition 10: The Physical Map
Authors: Rudd Kenneth E. 
Published: December 2019

SUMMARY
A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter “y” by using a systematic nomenclature.
Regulation of Cdc28 Cyclin-Dependent Protein Kinase Activity during the Cell Cycle of the Yeast
Saccharomyces cerevisiae
Authors: Mendenhall Michael D. , Hodge Amy E. 
Published: December 2019

SUMMARY
The cyclin-dependent protein kinase (CDK) encoded by CDC28 is the master regulator of cell division in the budding yeast Saccharomyces cerevisiae. By mechanisms that, for the most part, remain to be delineated, Cdc28 activity controls the timing of mitotic commitment, bud initiation, DNA replication, spindle formation, and chromosome separation. Environmental stimuli and progress through the cell cycle are monitored through checkpoint mechanisms that influence Cdc28 activity at key cell cycle stages. A vast body of information concerning how Cdc28 activity is timed and coordinated with various mitotic events has accrued. This article reviews that literature. Following an introduction to the properties of CDKs common to many eukaryotic species, the key influences on Cdc28 activity—cyclin-CKI binding and phosphorylation-dephosphorylation events—are examined. The processes controlling the abundance and activity of key Cdc28 regulators, especially transcriptional and proteolytic mechanisms, are then discussed in detail. Finally, the mechanisms by which environmental stimuli influence Cdc28 activity are summarized.
Antisense RNA: Function and Fate of Duplex RNA in Cells of Higher Eukaryotes
Authors: Kumar Madhur , Carmichael Gordon G. 
Published: December 2019

SUMMARY
There is ample evidence that cells of higher eukaryotes express double-stranded RNA molecules (dsRNAs) either naturally or as the result of viral infection or aberrant, bidirectional transcriptional readthrough. These duplex molecules can exist in either the cytoplasmic or nuclear compartments. Cells have evolved distinct ways of responding to dsRNAs, depending on the nature and location of the duplexes. Since dsRNA molecules are not thought to exist naturally within the cytoplasm, dsRNA in this compartment is most often associated with viral infections. Cells have evolved defensive strategies against such molecules, primarily involving the interferon response pathway. Nuclear dsRNA, however, does not induce interferons and may play an important posttranscriptional regulatory role. Nuclear dsRNA appears to be the substrate for enzymes which deaminate adenosine residues to inosine residues within the polynucleotide structure, resulting in partial or full unwinding. Extensively modified RNAs are either rapidly degraded or retained within the nucleus, whereas transcripts with few modifications may be transported to the cytoplasm, where they serve to produce altered proteins. This review summarizes our current knowledge about the function and fate of dsRNA in cells of higher eukaryotes and its potential manipulation as a research and therapeutic tool.
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes
Authors: Gupta Radhey S. 
Published: December 2019

SUMMARYThe presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.
Bacillus subtilis
Spore Coat
Authors: Driks Adam 
Published: December 2019

SUMMARY
In response to starvation, bacilli and clostridia undergo a specialized program of development that results in the production of a highly resistant dormant cell type known as the spore. A proteinacious shell, called the coat, encases the spore and plays a major role in spore survival. The coat is composed of over 25 polypeptide species, organized into several morphologically distinct layers. The mechanisms that guide coat assembly have been largely unknown until recently. We now know that proper formation of the coat relies on the genetic program that guides the synthesis of spore components during development as well as on morphogenetic proteins dedicated to coat assembly. Over 20 structural and morphogenetic genes have been cloned. In this review, we consider the contributions of the known coat and morphogenetic proteins to coat function and assembly. We present a model that describes how morphogenetic proteins direct coat assembly to the specific subcellular site of the nascent spore surface and how they establish the coat layers. We also discuss the importance of posttranslational processing of coat proteins in coat morphogenesis. Finally, we review some of the major outstanding questions in the field.
Surface Proteins of Gram-Positive Bacteria and Mechanisms of Their Targeting to the Cell Wall Envelope
Authors: Navarre William Wiley , Schneewind Olaf 
Published: December 2019

SUMMARYThe cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialized binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections. In this review we describe the mechanisms for both sorting and targeting of proteins to the envelope of gram-positive bacteria and review the functions of known surface proteins.
Transposon Tn21, Flagship of the Floating Genome
Authors: Liebert Cynthia A. , Hall Ruth M. , Summers Anne O. 
Published: December 2019

SUMMARYThe transposon Tn21 and a group of closely related transposons (the Tn21 family) are involved in the global dissemination of antibiotic resistance determinants in gram-negative facultative bacteria. The molecular basis for their involvement is carriage by the Tn21 family of a mobile DNA element (the integron) encoding a site-specific system for the acquisition of multiple antibiotic resistance genes. The paradigm example, Tn21, also carries genes for its own transposition and a mercury resistance (mer) operon. We have compiled the entire 19,671-bp sequence of Tn21 and assessed the possible origins and functions of the genes it contains. Our assessment adds molecular detail to previous models of the evolution of Tn21 and is consistent with the insertion of the integron In2 into an ancestral Tn501-like mer transposon. Codon usage analysis indicates distinct host origins for the ancestral mer operon, the integron, and the gene cassette and two insertion sequences which lie within the integron. The sole gene of unknown function in the integron, orf5, resembles a puromycin-modifying enzyme from an antibiotic producing bacterium. A possible seventh gene in the mer operon (merE), perhaps with a role in Hg(II) transport, lies in the junction between the integron and the mer operon. Analysis of the region interrupted by insertion of the integron suggests that the putative transposition regulator, tnpM, is the C-terminal vestige of a tyrosine kinase sensor present in the ancestral mer transposon. The extensive dissemination of the Tn21 family may have resulted from the fortuitous association of a genetic element for accumulating multiple antibiotic resistances (the integron) with one conferring resistance to a toxic metal at a time when clinical, agricultural, and industrial practices were rapidly increasing the exposure to both types of selective agents. The compendium offered here will provide a reference point for ongoing observations of related elements in multiply resistant strains emerging worldwide.
More than 50% of hip replacements seem to last 25 years
Authors: Cook Rob , Davidson Peter , Martin Rosie 
Published: December 2019

The studyHow long does a hip replacement last? A systematic review and meta-analysis of case series and national registry reports with more than 15 years of follow-upEvans JT, Evans JP, Walker R, Blom AW, Whitehouse MR, Sayers APublished on 16 February 2019 Lancet 2019;393:647-54This study was supported by the NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol. To read the full NIHR Signal, go to: https://discover.dc.nihr.ac.uk/content/signal-000781/more-than-50-of-hip-replacements-appear-to-last-25-years
Diagnostic property of direct referral from general practitioners to contrast-enhanced thoracoabdominal CT in patients with serious but non-specific symptoms or signs of cancer: a retrospective cohort study on cancer prevalence after 12 months
Authors: Møller Marie , Juvik Bue , Olesen Stine Chabert , Sandstrøm Hanne , Laxafoss Erling , Reuter Simon Bertram , Bodtger Uffe 
Published: December 2019

ObjectivesTo describe the diagnostic properties of thoracoabdominal contrast-enhanced CT (ceCT), when general practitioners (GPs) managed referral to ceCT through the non-specific symptoms or signs of cancer-cancer patient pathway (NSSC-CPP).DesignRetrospective cohort study including patients from a part of Denmark.SettingDepartment of Internal Medicine at a university hospital.ParticipantsIn total, 529 patients underwent ceCT.Primary and secondary outcomesOur primary objective was to estimate the negative and positive likelihood ratios for being diagnosed with cancer within 1 year after ceCT. Our secondary outcomes were prevalence and final diagnoses of malignancy (including temporal trends since implementation of NSSC-CPP in 2012), the prevalence of revision of CT scans and referral patterns based on ceCT results.ResultsIn total, 529 subjects underwent ceCT and malignancy was identified in 104 (19.7%) patients; 101 (97.1%) during initial workup and 3 patients during the subsequent 12 months follow-up.Eleven patients had a false-negative ceCT, and revision classified the ceCT as ‘probable/possible malignancy’ in eight (73%) patients. The negative predictive value was 98% and positive predictive value 63%. Negative and positive likelihood ratios for malignancy was 0.1 and 7.9, respectively.ConclusionOur study shows that ceCT as part of GP-coordinated workup has a low negative likelihood ratio for identifying malignancy; this is important since identifying patients for further workup is vital.
Providing care to refugees through mainstream general practice in the southern health region of New Zealand: a qualitative study of primary healthcare professionals’ perspectives
Authors: Richard Lauralie , Richardson Georgia , Jaye Chrystal , Stokes Tim 
Published: December 2019

ObjectiveTo explore the perspectives of primary healthcare (PHC) professionals providing care to refugees through mainstream general practice.DesignQualitative exploratory design with semistructured interviews subjected to inductive thematic analysis.Setting and participantsNine general practices enrolled in the Dunedin Refugee Resettlement Programme, in New Zealand (NZ)’s southern health region. Participants included nine general practitioners and six practice nurses.ResultsThree analytical constructs were identified: relational engagement with refugees, refugee healthcare delivery and providers’ professional role shaped by complexity. Building meaningful relational connections involved acknowledging refugees’ journeys by getting to know them as people. This was instrumental for the development of an empathetic understanding of the complex human trajectories that characterise refugees’ journeys to NZ. Participants encountered challenges in providing care to refugees with respect to time-limited consultations, variable use of interpreter services, fragmentation of care between agencies and need for improved health infrastructure to ensure a fluid interface between PHC, secondary care and community support services. The current business model of NZ general practice was perceived to interfere with value-driven care and discouraged tailoring of care to specific patient groups, raising concerns about the ‘fit’ of mainstream general practice to address the complex healthcare needs of refugees. Meeting the needs of refugees across the social determinants of health involved a lot of ‘behind the scenes work’ particularly in the absence of shared information systems and the lack of well-established referral pathways to connect refugees to services beyond the health sector. This led to providers feeling overwhelmed and uncertain about their ability to provide appropriate care to refugees.ConclusionsThis study provides rich context-specific findings that enhance PHC responsiveness to the needs of refugees in NZ.
Directed intervention to improve the rate of admission medication reconciliation in an acute care hospital
Authors: Kyi Htay Htay , Sundus Saira , Marcus Huda , Sotzen Jason , Suit Parker , Cranford James , Bachuwa Ghassan , McDonald Philip J 
Published: December 2019

IntroductionElectronic medication reconciliation systems are known to reduce medication errors. We hypothesised that refinement of the electronic medical record (EMR) and provider education could improve adherence to completion of admission medication reconciliation, thereby potentially limiting prescribing errors. Our goal was to improve the percentage of patients with medication reconciliation completed within 24 hours of admission to at least 90%.MethodsA prospective interventional study was conducted at a university-affiliated community hospital between 1 January 2017 and 30 September 2018. We determined the baseline percentage of medication reconciliations performed within 24 hours of admission, and those completed at any time prior to discharge from the hospital. Three plan-do-study-act cycles were then performed, with interventions including live and email reminders to complete medication reconciliation and addition of a column to EMR patient lists indicating whether reconciliation had been completed.ResultsThe percentage of medication reconciliations completed within 24 hours of admission was lowest for the pre-intervention cycle (62.4%) and was highest for Cycle 3 (80.9%). The percentage of reconciliations completed any time prior to discharge was higher and increased in a similar stepwise fashion from 71.1% to 88.4% through Cycle 3. There was a post-intervention trend toward a higher rate of reconciliation completion for patients aged 18–40. Male patients were also more likely to have their admission medication reconciliations completed prior to discharge.ConclusionOur interventions resulted in a statistically significant 18.5% increase in the rate of admission reconciliation completion. Though this increase fell short of our goal, this study demonstrates that provider education and optimisation of the EMR can sustainably improve adherence with medication reconciliation, thereby fostering improved patient care. Further improvement could be achieved by focusing on the medication lists of our older patients and female patients.
Sleep in elite swimmers: prevalence of sleepiness, obstructive sleep apnoea and poor sleep quality
Authors: Surda Pavol , Putala Matus , Siarnik Pavel , Walker Abigail , De Rome Katherine , Amin Nikul , Sangha Miljyot Singh , Fokkens Wytske 
Published: December 2019

ObjectivesLimited data suggest that swimmers might be affected by poor quality of sleep significantly. The aim was to explore the prevalence of sleep disturbances in swimmers and possible link between rhinitis and sleep disturbance.MethodsStudy 1 was an observational case–control, questionnaire-based study involving 157 elite and non-elite swimmers, 36 non-swimming athletes and 50 controls. In study 2, we measured sleep quality and duration using actigraphy in 20 elite swimmers. We also looked for presence of sleep-disordered breathing using overnight pulse oximetry monitor.ResultsIn study 1, we observed a significant difference in prevalence of excessive daytime sleepiness between groups of elite swimmers and controls. Pittsburgh Sleep Quality Index (PSQI) scores do not suggest that quality of sleep in group of swimmers is impaired. In study 2, we found that prevalence of obstructive sleep apnoea (OSA) in elite swimmers defined as oxygen desaturation index ≥5 was 30%. Analysis of actigraphy data revealed that on nights prior to training days, ‘going to’ bed time was significantly earlier and total sleep time was significantly reduced.ConclusionSwimmers and non-swimming athletes suffer significantly more with excessive daytime sleepiness than healthy controls. In elite swimmers, this is likely linked to high prevalence of OSA. PSQI scores do not suggest that quality of sleep in group of swimmers is impaired, but actigraphy shows great variations between sleep pattern preceding training and rest day. This seems to be associated with early-morning sessions which can be a disruptive element of weekly sleep patterns.