bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution
Authors: Lang Daniel , Ullrich Kristian K. , Murat Florent , Fuchs Jörg , Jenkins Jerry , Haas Fabian B. , Piednoel Mathieu , Gundlach Heidrun , Van Bel Michiel , Meyberg Rabea , Vives Cristina , Morata Jordi , Symeonidi Aikaterini , Hiss Manuel , Muchero Wellington , Kamisugi Yasuko , Saleh Omar , Blanc Guillaume , Decker Eva L. , van Gessel Nico , Grimwood Jane , Hayes Richard D. , Graham Sean W. , Gunter Lee E. , McDaniel Stuart F. , Hoernstein Sebastian N.W. , Larsson Anders , Li Fay‐Wei , Perroud Pierre‐François , Phillips Jeremy , Ranjan Priya , Rokshar Daniel S. , Rothfels Carl J. , Schneider Lucas , Shu Shengqiang , Stevenson Dennis W. , Thümmler Fritz , Tillich Michael , Villarreal Aguilar Juan C. , Widiez Thomas , Wong Gane Ka‐Shu , Wymore Ann , Zhang Yong , Zimmer Andreas D. , Quatrano Ralph S. , Mayer Klaus F.X. , Goodstein David , Casacuberta Josep M. , Vandepoele Klaas , Reski Ralf , Cuming Andrew C. , Tuskan Gerald A. , Maumus Florian , Salse Jérome , Schmutz Jeremy , Rensing Stefan A. 
Published: December 2017

SummaryThe draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome‐scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene‐ and TE‐rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono‐centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein‐coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure‐based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant‐specific cell growth and tissue organization. The P. patens genome lacks the TE‐rich pericentromeric and gene‐rich distal regions typical for most flowering plant genomes. More non‐seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
Draft Genome Sequence of Loktanella cinnabarina Strain XM1 Isolated from Coastal Surface Water
Authors: Ma Ruijie , Wang Jianjun , Wang Qiong , Ma Zhaofeng , Li Jia , Chen Liqi 
Published: December 2017

ABSTRACT

We report here the draft genome sequence of
Loktanella cinnabarina
strain XM1, which was isolated from coastal surface water and shared 99.43% 16S rRNA gene sequence identity with the deep-sea bacterium
L. cinnabarina
LL-001
T
. The estimated genome size of strain XM1 is 3,782,785 bp, with a G+C content of 67.9%.
Stable Signal Peptides and the Response to Secretion Stress in
Staphylococcus aureus
Authors: Craney Arryn , Romesberg Floyd E. 
Published: December 2017

ABSTRACT

Protein secretion is essential, but how it is managed is poorly understood. In bacteria, most secreted proteins require release from the outer surface of the cytoplasmic membrane by type I signal peptidase (SPase), which cleaves the mature protein from its membrane-bound N-terminal signal peptide. As the first step that occurs outside the protected cytoplasmic environment and because insufficient activity can rapidly result in the toxic accumulation of preproteins, the activity of SPase is expected to be closely monitored and perhaps supplemented when insufficient. Indeed, we previously demonstrated that inhibition of SPase in
Staphylococcus aureus
results in derepression of the
ayrRABC
operon, which encodes an alternate mechanism to release proteins. However, in this case, the proteins are released with partially intact signal peptides, with the exception of IsaA, which is released with a virtually intact signal peptide. Here we show that mutation of AyrA [
ayrA
(R233K)] results in constitutive derepression of
ayrRABC
and that mutation of IsaA’s signal peptide [
isaA
(K2Q)] results in hyperderepression upon SPase inhibition, which also requires AyrA. Further studies demonstrate that the inducing signal for
ayrRABC
derepression is accumulation of a subset of preproteins with signal peptides that are stable toward further processing and that the signal is critically amplified by the K2Q mutation and relayed to AyrR by AyrA. These results elucidate the mechanism by which
S. aureus
monitors and responds to secretion stress. The presence of
ayrRA
in other bacteria suggests that it may represent a general strategy linking membrane stress to appropriate transcriptional responses.

IMPORTANCE
Bacteria interact with their environment by secreting proteins that perform a myriad of functions, and the final step is the release of the mature protein from the cell surface via the activity of type I signal peptidase (SPase). While the bacterial response to many stresses is understood in some detail, almost nothing is known about how cells respond to secretion stress, such as insufficient SPase activity, which would eventually result in cell death. We previously demonstrated that the inhibition of SPase in
Staphylococcus aureus
results in the derepression of the
ayrRABC
operon, which can functionally replace SPase, but which is normally repressed by AyrR. We now demonstrate that the inducing signal for derepression is accumulation of a subset of preproteins with signal peptides that are stable to further processing and that the signal is relayed to AyrR via AyrA.
South Korea’s Claim to Dokdo
Authors: Lee Hee Eun 
Published: December 2017

Abstract
Dokdo are tiny islets located in the East Sea (Sea of Japan) that have been the source of a longstanding conflict between Korea and Japan. Japan argues that the islets, referred to as Takeshima by Japan, were terra nullius when it incorporated them in 1905 during the Russo-Japanese War. However, South Korea claims that previous Korean kingdoms had sovereignty over the islets as evidenced through numerous historical records and maps. South Korea asserts original title over Dokdo noting that Japan’s incorporation of the islets and eventual annexation of the entire Korean peninsula was illegal. This article summarizes the major points South Korea has publicly raised in asserting its claim to Dokdo noting that South Korea’s claim to Dokdo is framed from the perspective of the historical injustice of Japanese imperialism and that Dokdo was the first Korean territory taken by Japan in its expansion into Asia in the early 20th century.
Esophageal Dysmotility in Patients following Total Laryngectomy
Authors: Zhang Teng , Maclean Julia , Szczesniak Michal , Bertrand Paul P. , Quon Harry , Tsang Raymond K. , Wu Peter I. , Graham Peter , Cook Ian J. 
Published: December 2017

ObjectivesDysphagia is common in total laryngectomees, with some symptoms suggesting esophageal dysmotility. Tracheoesophageal (TE) phonation requires effective esophagopharyngeal air passage. Hence, esophageal dysmotility may affect deglutition or TE phonation. This study aimed to determine (1) the characteristics of esophageal dysmotility in laryngectomees, (2) whether clinical history is sensitive in detecting esophageal dysmotility, and (3) the relationship between esophageal dysmotility and TE prosthesis dysfunction.Study DesignMultidisciplinary cross‐sectional study.SettingTertiary academic hospital.Subjects and MethodsFor 31 participants undergone total laryngectomy 1 to 12 years prior, clinical histories were taken by a gastroenterologist and a speech pathologist experienced in managing dysphagia. Esophageal high‐resolution manometry was performed and analyzed using Chicago Classification v3.0.ResultsInterpretable manometric studies were obtained in 23 (1 normal manometry). Esophageal dysmotility patterns included achalasia, esophagogastric junction outflow obstruction, diffuse esophageal spasm, and other major (30%) and minor (50%) peristaltic disorders. The sensitivity of predicting any esophageal dysmotility was 28%, but it is noteworthy that patients with achalasia and diffuse esophageal spasm (DES) were predicted. Two of 4 participants with TE puncture leakage had poor esophageal clearance. Of 20 TE speakers, 12 had voice problems, no correlation between poor voice, and any dysmotility pattern.ConclusionsPeristaltic and lower esophageal sphincter dysfunction are common in laryngectomees. Clinical history, while not predictive of minor motor abnormalities, predicted correctly cases with treatable spastic motor disorders. Dysmotility was not associated with poor phonation, although TE puncture leakage might be linked to poor esophageal clearance. Esophageal dysmotility should be considered in the laryngectomees with persisting dysphagia or leaking TE puncture.
How is palliative care understood in the context of dementia? Results from a massive open online course
Authors: McInerney Fran , Doherty Kathleen , Bindoff Aidan , Robinson Andrew , Vickers James 
Published: December 2017

Background: A palliative approach to the care of people with dementia has been advocated, albeit from an emergent evidence base. The person-centred philosophy of palliative care resonates with the often lengthy trajectory and heavy symptom burden of this terminal condition. Aim: To explore participants’ understanding of the concept of palliative care in the context of dementia. The participant population took an online course in dementia. Design: The participant population took a massive open online course on ‘Understanding Dementia’ and posted answers to the question: ‘palliative care means …’ We extracted these postings and analysed them via the dual methods of topic modelling analysis and thematic analysis. Setting/participants: A total of 1330 participants from three recent iterations of the Understanding Dementia Massive Open Online Course consented to their posts being used. Participants included those caring formally or informally for someone living with dementia as well as those with a general interest in dementia Results: Participants were found to have a general awareness of palliative care, but saw it primarily as terminal care, focused around the event of death and specialist in nature. Comfort was equated with pain management only. Respondents rarely overtly linked palliative care to dementia. Conclusions: A general lack of palliative care literacy, particularly with respect to dementia, was demonstrated by participants. Implications for dementia care consumers seeking palliative care and support include recognition of the likely lack of awareness of the relevance of palliative care to dementia. Future research could access online participants more directly about their understandings/experiences of the relationship between palliative care and dementia.
Association between vitamin D, oestradiol and interferon-gamma in female patients with inactive systemic lupus erythematosus: A cross-sectional study
Authors: Kokic Visnja , Martinovic Kaliterna Dusanka , Radic Mislav , Tandara Leida , Perkovic Dijana 
Published: December 2017

Objectives To investigate possible associations between 25-hydroxyvitamin D3 (25(OH)D3), oestradiol (E2) and IFN-gamma (IFNγ) in female patients with inactive systemic lupus erythematosus (SLE). Methods Female patients with inactive SLE and age-matched healthy controls were recruited into this cross-sectional study. Serum concentrations of 25(OH)D3, E2 and IFNγ were measured by radioimmunoassay with gamma-counters and enzyme-linked immunosorbent assay. Results 36 patients and 37 controls were enrolled. In patients with SLE, the concentration of 25(OH)D3 was lower and E2 was higher compared with controls. In vitamin D deficient (i.e., 25(OH)D3≤20 ng/ml) patients, IFNγ was 150% higher compared with patients with 25(OH)D3>20 ng/ml and controls. The concentration of E2 was higher in all patients compared with controls independently of the vitamin D level. A difference was found between patients and controls in the correlation of 25(OH)D3 with E2 and a positive correlation was found between E2 and IFNγ in all participants. Conclusions Our results suggest that E2 may have a strong modulating effect on vitamin D function which is significant only at low concentration of E2.
Non-invasive vagus nerve stimulation for the acute treatment of episodic and chronic cluster headache: A randomized, double-blind, sham-controlled ACT2 study
Authors: Goadsby Peter J , de Coo Ilse F , Silver Nicholas , Tyagi Alok , Ahmed Fayyaz , Gaul Charly , Jensen Rigmor H , Diener Hans-Christoph , Solbach Kasia , Straube Andreas , Liebler Eric , Marin Juana CA , Ferrari Michel D 
Published: December 2017

Background Clinical observations and results from recent studies support the use of non-invasive vagus nerve stimulation (nVNS) for treating cluster headache (CH) attacks. This study compared nVNS with a sham device for acute treatment in patients with episodic or chronic CH (eCH, cCH). Methods After completing a 1-week run-in period, subjects were randomly assigned (1:1) to receive nVNS or sham therapy during a 2-week double-blind period. The primary efficacy endpoint was the proportion of all treated attacks that achieved pain-free status within 15 minutes after treatment initiation, without rescue treatment. Results The Full Analysis Set comprised 48 nVNS-treated (14 eCH, 34 cCH) and 44 sham-treated (13 eCH, 31 cCH) subjects. For the primary endpoint, nVNS (14%) and sham (12%) treatments were not significantly different for the total cohort. In the eCH subgroup, nVNS (48%) was superior to sham (6%; p < 0.01). No significant differences between nVNS (5%) and sham (13%) were seen in the cCH subgroup. Conclusions Combing both eCH and cCH patients, nVNS was no different to sham. For the treatment of CH attacks, nVNS was superior to sham therapy in eCH but not in cCH. These results confirm and extend previous findings regarding the efficacy, safety, and tolerability of nVNS for the acute treatment of eCH.
Computer-assisted detection of tardus parvus waveforms on Doppler ultrasound
Authors: Gunabushanam Gowthaman , Millet John D , Stilp Erik , Crawford Forrest W , McNamara Robert L , Scoutt Leslie M 
Published: December 2017

Objective To determine if a novel computer-generated metric, effective acceleration time, improves accuracy for detecting tardus parvus waveforms on spectral Doppler ultrasound. Methods Patients with echocardiography-confirmed aortic valve stenosis ( n = 132; 60 mild, 44 moderate, 28 severe) and matched controls ( n = 48) who underwent carotid Doppler ultrasound were identified through an imaging database search at a single medical center. A custom-built spectral analysis computer program generated effective acceleration time values for spectral Doppler waveforms in the carotid arteries and a receiver operating characteristic analysis was performed to determine the optimal median effective acceleration time cutoff value to detect tardus parvus waveforms. Two radiologists, blinded to subject disease status, reviewed and rated all carotid sonograms for presence of tardus parvus waveforms. Inter-rater variability was measured, and the accuracy of aortic valve stenosis detection with and without use of the effective acceleration time cutoff was calculated. Results Receiver operating characteristic analysis revealed an optimal effective acceleration time cutoff of ≥ 48 ms with a corresponding area under the curve of 0.77 (95% CI: 0.70–0.84). Use of the effAT cutoff demonstrated an accuracy of 74%. Accuracy of visual waveform interpretation by raters ranged from 43% to 61%. Inter-rater agreement in detection of tardus parvus waveforms was 76% (136/180 cases, K = 0.44, p < 0.001). Conclusions Detection of tardus parvus waveforms through visual interpretation of spectral Doppler waveform morphology is limited by low accuracy and moderate inter-rater variability. Use of a computer-generated median effective acceleration time cutoff value markedly improves diagnostic accuracy and avoids observer variability.
Energy envelope maintenance among patients with myalgic encephalomyelitis and chronic fatigue syndrome: Implications of limited energy reserves
Authors: O’connor Kelly , Sunnquist Madison , Nicholson Laura , Jason Leonard A , Newton Julia L , Strand Elin B 
Published: December 2017

Objective The Energy Envelope Theory of myalgic encephalomyelitis and chronic fatigue syndrome postulates that individuals with myalgic encephalomyelitis and chronic fatigue syndrome may experience some increase in functioning if their level of exertion consistently remains within the limits of their available energy. Findings of several studies support this theory; however, the current study is the first to explore how an individual’s initial level of available energy may influence the relation between energy envelope maintenance and level of functioning. Method The functioning, activity, and symptomatology of six groups of individuals with myalgic encephalomyelitis and chronic fatigue syndrome were compared. Groups were created based upon level of available energy (higher or lower) and energy envelope adherence (underextended, within, overextended). Results Results indicate that, as expected, individuals with myalgic encephalomyelitis and chronic fatigue syndrome who had higher available energy also had better functioning than individuals with lower available energy; however, this relation was less pronounced for individuals who were overexerting themselves. Discussion These results are consistent with the Energy Envelope Theory, and they suggest that overexertion was particularly impactful for individuals with higher levels of available energy.
Would you Speak up if the Consultant Got it Wrong? …And Would you Listen if Someone Said You'd Got it Wrong?
Authors: Bromiley Martin , Mitchell Lucy 
Published: December 2017

In 2005 my late wife died during an attempted operation. I'm an airline pilot and I recognised early on that the factors that lead to Elaine's death mirrored those commonly found in many aviation accidents. In this article I'll ask you to reflect on the culture within healthcare around human error and ‘teamwork’. I will ask you to reflect on your own personal responsibilities about safety. I will also argue that technical competence is not a guarantee of safe outcomes; alongside it you must have competence in ‘non-technical’ skills.
Surgical Gowning and Gloving
Authors: Pirie Susan 
Published: December 2017

Surgical gowning and gloving is an essential element of perioperative practice and is undertaken by the members of the anaesthetic and surgical teams involved in a perioperative intervention or procedure. Gowning and gloving will take place immediately after surgical hand antisepsis and the whole process is often referred to as scrubbing, gowning and gloving. Surgical hand antisepsis is defined as ‘an extension of hand washing’ (AfPP 2007), and ‘the antiseptic surgical scrub or antiseptic hand rubs performed before donning sterile attire preoperatively’” (AORN 2008). The aim of these processes is to improve the perioperative outcome of interventions and procedures by enhancing and further promoting aseptic techniques (ACORN 2006, AfPP 2007).
Evaluating the Effect of Music on Patient Anxiety during Minor Plastic Surgery
Authors: Mcleod Roddy 
Published: December 2017

Aim The study sought to assess the effectiveness of music on patient anxiety levels during minor surgery. Methods Eighty patients attending a minor plastic surgery out-patient department were assessed using the Spielberger State-Trait Anxiety Inventory Questionnaire. Forty participants in the experimental group listened to music which was self selected and played during their operation. Forty participants in the control group received the standard care during their operation but with no music. The questionnaire was used to collect data pre and post-operatively. During the recovery period all participants were asked to reflect on their level of anxiety during surgery while completing the questionnaire. Analysis was carried out using Statistical Package for Social Sciences (SPSS) version 12. Results The postoperative mean anxiety score of the control group was 33.5 (SD 10.6). The mean anxiety score for the experimental group was 30.52 (SD 9.82). Statistical analysis revealed that there was no significant difference among those who did and did not listen to music during their procedure. Conclusion Although the researcher did not find statistically significant differences in the selected outcome measures, the intervention seemed to be enjoyed by the patients in the experimental group. Minimising anxiety prior to and during a minor operation may help promote relaxation and enhance patient comfort.
The efficacy of oral analgesia for postoperative pain
Authors: O'neill Olga 
Published: December 2017

The aims of this study were to assess the efficacy of acute pain management for the postoperative patient, identify analgesic requirements and to ascertain the incidences of side effects, if any. One important observation noted from the study was that there were quite a significant number of patients that were receiving more that one analgesic on a regular basis. The implications of multi-prescription without strict controls could have a profound negative effect on patient health. Although side effects were noted to be higher in the group of patients that received multiple analgesics, no patient suffered any detrimental or long term effects, and in general patients did appear to be satisfied with their analgesic regime.
Patient care in the operating department (1)
Authors: Taylor Marion , Campbell Claire 
Published: December 2017

Judging by the positive feedback I have received about this series it is a timely reminder – or introduction – to the perioperative area. It has been suggested that universities and colleges should be made aware of the existence of this series in order that students may benefit prior to the theatre placement. So why don't you recommend it to your tutors, universities and colleges? This article will introduce three aspects of patient care, undertaken in the operating department. These are prevention of errors in surgical procedures, patient positioning and pressure area care. Dina Plowes, series editor