bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of and Evolutionary Relationships between Extant Vaccinia Virus Strains
Authors: Qin Li , Favis Nicole , Famulski Jakub , Evans David H. 
Published: November 2014

ABSTRACT
Although vaccinia virus (VACV) was once used as a vaccine to eradicate smallpox on a worldwide scale, the biological origins of VACV are uncertain, as are the historical relationships between the different strains once used as smallpox vaccines. Here, we sequenced additional VACV strains that either represent relatively pristine examples of old vaccines (e.g., Dryvax, Lister, and Tashkent) or have been subjected to additional laboratory passage (e.g., IHD-W and WR). These genome sequences were compared with those previously reported for other VACVs as well as other orthopoxviruses. These extant VACVs do not always cluster in simple phylogenetic trees that are aligned with the known historical relationships between these strains. Rather, the pattern of deletions suggests that all existing strains likely come from a complex stock of viruses that has been passaged, distributed, and randomly sampled over time, thus obscuring simple historical or geographic links. We examined surviving nonclonal vaccine stocks, like Dryvax, which continue to harbor larger and now rare variants, including one that we have designated “clone DPP25.” DPP25 encodes genes not found in most VACV strains, including an ankyrin-F-box protein, a homolog of the variola virus (Bangladesh) B18R gene which we show can be deleted without affecting virulence in mice. We propose a simple common mechanism by which recombination of a larger and hypothetical DPP25-like ancestral strain, combined with selection for retention of critically important genes near the terminal inverted repeat boundaries (vaccinia virus growth factor gene and an interferon alpha/beta receptor homolog), could produce all known VACV variants.

IMPORTANCE
Smallpox was eradicated by using a combination of intensive disease surveillance and vaccination using vaccinia virus (VACV). Interestingly, little is known about the historical relationships between different strains of VACV and how these viruses may have evolved from a common ancestral strain. To understand these relationships, additional strains were sequenced and compared to existing strains of VACV as well as other orthopoxviruses by using whole-genome sequence alignments. Extant strains of VACV did not always cluster in simple phylogenetic trees based on known historical relationships between these strains. Based on these findings, it is possible that all existing strains of VACV are derived from a single complex stock of viruses that has been passaged, distributed, and sampled over time.
A case–control study comparing the incidence of early symptoms in pancreatic and biliary tract cancer
Authors: Keane M G , Horsfall L , Rait G , Pereira S P 
Published: November 2014

ObjectivesPancreatic ductal adenocarcinoma (PDAC) and biliary tract cancers (BTC) are often diagnosed late and at an advanced stage. Population-based screening programmes do not exist and diagnosis is primarily dependent on symptom recognition. Recently symptom-based cancer decision support tools (CDSTs) have been introduced into primary care practices throughout the UK to support general practitioners (GPs) in identifying patients with suspected PDAC. However, future refinement of these tools to improve their diagnostic accuracy is likely to be necessary.SettingThe Health Improvement Network (THIN) is a primary care database, which includes more than 11 million electronic patient records, from 562 GP practices in the UK.ParticipantsAll patients with a diagnosis of PDAC or BTC between 2000 and 2010 were included in the study along with six matched controls; 2773 patients with PDAC, 848 patients with BTC and 15 395 controls.Primary and secondary outcome measuresThe primary aim of this study was to determine the early symptom profiles of PDAC and BTC. Secondary aims included comparing early symptom trends between BTC and PDAC, defining symptom onset in PDAC and evaluating trends in routine blood tests nearest to the time of diagnosis.ResultsIn the year prior to diagnosis, patients with PDAC visited their GP on a median of 18 (IQR 11–27) occasions. PDAC was associated with 11 alarm symptoms and BTC with 8. Back pain (OR 1.33 (95% CI 1.18 to 1.49) p<0.001), lethargy (1.42 (95% CI 1.25 to 1.62) p<0.001) and new onset diabetes (OR 2.46 (95% CI 2.16 to 2.80)) were identified as unique features of PDAC.ConclusionsPDAC and BTC are associated with numerous early alarm symptoms. CDSTs are therefore likely to be useful in identifying these tumours at an early stage. Inclusion of unique symptoms, symptoms with an early onset and routinely performed blood tests is likely to further improve the sensitivity of these tools.
Does a fall prevention educational programme improve knowledge and change exercise prescribing behaviour in health and exercise professionals? A study protocol for a randomised controlled trial
Authors: Tiedemann A , Sturnieks D L , Hill A-M , Lovitt L , Clemson L , Lord S R , Harvey L , Sherrington C 
Published: November 2014

IntroductionFalling in older age is a serious and costly problem. At least one in three older people fall annually. Although exercise is recognised as an effective fall prevention intervention, low numbers of older people engage in suitable programmes. Health and exercise professionals play a crucial role in addressing fall risk in older adults. This trial aims to evaluate the effect of participation in a fall prevention educational programme, compared with a wait-list control group, on health and exercise professionals’ knowledge about fall prevention and the effect on fall prevention exercise prescription behaviour and confidence to prescribe the exercises to older people.Methods and analysisA randomised controlled trial involving 220 consenting health and exercise professionals will be conducted. Participants will be individually randomised to an intervention group (n=110) to receive an educational workshop plus access to internet-based support resources, or a wait-list control group (n=110). The two primary outcomes, measured 3 months after randomisation, are: (1) knowledge about fall prevention and (2) self-perceived change in fall prevention exercise prescription behaviour. Secondary outcomes include: (1) participants’ confidence to prescribe fall prevention exercises; (2) the proportion of people aged 60+ years seen by trial participants in the past month who were prescribed fall prevention exercise; and (3) the proportion of fall prevention exercises prescribed by participants to older people in the past month that comply with evidence-based guidelines. Outcomes will be measured with a self-report questionnaire designed specifically for the trial.Ethics and disseminationThe trial protocol was approved by the Human Research Ethics Committee, The University of Sydney, Australia. Trial results will be disseminated via peer reviewed journals, presentations at international conferences and participants’ newsletters.Trial registration numberTrial protocol was registered with the Australian and New Zealand Clinical Trials Registry (Number ACTRN12614000224628) on 3 March 2014.
A comparison of magnetic susceptibility measurement techniques and ferrimagnetic component analysis from recent sediments in Lake Pepin (USA)
Authors: Blumentritt Dylan J. , Lascu Ioan 
Published: November 2014

Abstract

Magnetic susceptibility (MS) is commonly measured on lake sediments and used as a proxy for clastic input and soil erosion, for correlating among cores in the same lake basin and aligning successive overlapping drives of the same core. There are several common techniques for measuring MS, each with its own advantages. Here we compare three such techniques measured on a sediment core from Lake Pepin: (a) loop-sensor MS logging on wet sediment of the intact core; (b) point-sensor MS logging on wet sediment of a split (lengthwise) core; and (c) discrete MS measurements of dried subsamples using a susceptibility bridge. To obtain further information about the origin of downcore MS variability, additional magnetic measurements were performed on discrete samples to model ferrimagnetic sedimentary components. Overall trends and individual features in MS curves agree reasonably well between techniques; however, the amplitude of local minima and maxima varies according to the technique used. All three MS techniques captured distinct events
c.
1900 and 1940, attributed to increases in allochthonous ferrimagnetic components. The ferrimagnetic particle flux has declined over the past half-century despite increasing sediment accumulation in Lake Pepin, suggesting a possible shift in sediment sources from fields to stream banks.
Peritoneal Dialysis as a First versus Second Option after Previous Haemodialysis: A Very Long-Term Assessment
Authors: Barone Roberto José , Cámpora María Inés , Gimenez Nélida Susana , Ramirez Liliana , Panese Sergio Alberto , Santopietro Mónica 
Published: November 2014

For renal replacement therapy, overall survival is more important than the choice of currently available individual therapy.Objectives. To compare patients and technique survival on peritoneal dialysis as first treatment (PDF) versus after previous haemodialysis (HDPD) and other indicators of follow-up.Methods. We prospectively studied 110 incident patients, during the period from August 4, 1993, to June 30, 2012, for patients and technique survival (Kaplan-Meier) (log rankP< 0.05).Results. Groups: (A) PDF: 37 patients, 24 females, age: 52.2 ± 14.9 years old, time at risk: 2123 patient-months (p/m), mean: 57 ± 42 months; (B) HDPD: 73 patients, 42 females, age: 52.45 ± 14.7 years old, time in haemodialysis: 3569.2 (p/m), range: 3–216 months, mean: 49 ± 45 months, time at risk in PD: 3700 (p/m), mean: 51 ± 49 months. Patients’ survival: (A) PDF: 100%, 76.6%, 65.6%, and 19.7%; (B) HDPD: 95.4%, 65.6%, 43%, and 43% at 12, 60, 120, and 144 months, respectively,P=0.34. Technique: (A) PDF: 100%, 90%, 59.8%, and 24%; (B) HDPD: 94%, 75%, 32%, and 32% at 12, 60, 120, and 144 months, respectively,P=0.40.Conclusions. Comparable patient and technique survival were observed. Peritoneal dialysis enables a greater extension of renal replacement therapy for patients with serious difficulties continuing with haemodialysis.
Antarctic Ocean and Sea Ice Response to Ozone Depletion: A Two-Time-Scale Problem
Authors: Ferreira David , Marshall John , Bitz Cecilia M. , Solomon Susan , Plumb Alan 
Published: November 2014

Abstract
The response of the Southern Ocean to a repeating seasonal cycle of ozone loss is studied in two coupled climate models and is found to comprise both fast and slow processes. The fast response is similar to the interannual signature of the southern annular mode (SAM) on sea surface temperature (SST), onto which the ozone hole forcing projects in the summer. It comprises enhanced northward Ekman drift, inducing negative summertime SST anomalies around Antarctica, earlier sea ice freeze-up the following winter, and northward expansion of the sea ice edge year-round. The enhanced northward Ekman drift, however, results in upwelling of warm waters from below the mixed layer in the region of seasonal sea ice. With sustained bursts of westerly winds induced by ozone hole depletion, this warming from below eventually dominates over the cooling from anomalous Ekman drift. The resulting slow time-scale response (years to decades) leads to warming of SSTs around Antarctica and ultimately a reduction in sea ice cover year-round. This two-time-scale behavior—rapid cooling followed by slow but persistent warming—is found in the two coupled models analyzed: one with an idealized geometry and the other with a complex global climate model with realistic geometry. Processes that control the time scale of the transition from cooling to warming and their uncertainties are described. Finally the implications of these results are discussed for rationalizing previous studies of the effect of the ozone hole on SST and sea ice extent.
Fluoroscopic-guided insertion of self-expanding metal stents for malignant gastroduodenal outlet obstruction: immediate results and clinical outcomes
Authors: Diamantopoulos Athanasios , Sabharwal Tarun , Katsanos Konstantinos , Krokidis Miltiadis , Adam Andreas 
Published: November 2014

Background Application of self-expanding metal stents (SEMS) to treat patients suffering from malignant gastroduodenal outlet obstruction (GDOO) is today considered a well-recognized palliative treatment. Use of SEMS has emerged as an attractive alternative to surgical treatment of such patients. Purpose To report the immediate and the mid-term clinical outcomes from a series of consecutive patients treated with exclusively fluoroscopic-guided insertion of SEMS. Material and Methods This was a retrospective study including patients suffering from GDOO that were either ineligible for or unwilling to undergo surgery. Patients with potentially curable disease, uncorrectable coagulopathy, gastrointestinal perforation, sepsis, presence of distal small bowel obstruction, and bowel ischemia were excluded. Technical success, clinical success, and major complications were calculated. In addition, stent migration, stent re-obstruction, restenosis, and overall re-interventions due to recurrent symptoms were considered. Kaplan-Meier survival analysis was used for patient survival estimation while both bivariable and multivariable analysis were performed to identify any independent predictors of outcomes. Results Fifty-one patients, (mean age, 63.73 ± 15.62 years) met the study’s criteria and were included in the final analysis. Technical and clinical success were 90.19% ( n = 46/51) and 91.30% ( n = 42/46), respectively. Major complications rate was 3.92%. Stent migration was noted in four cases. Restenosis and re-obstruction rates were 19.57% and 10.87%, respectively. No cases of peri-procedural mortality were noted, while Kaplan-Meier estimates for 1- and 2-year survival were 16.8% and 7.2%, respectively. Clinically successful cases and patients with primary GI tumor were related with more favorable survival compared to unsuccessful and patients suffering from GDOO due to extrinsic compression by neoplastic or lymph node disease. Conclusion Exclusively fluoroscopically inserted SEMS for GDOO is safe and highly effective method for palliative treatment.
Plasma-soluble urokinase-type plasminogen activator receptor levels are associated with clinical and pathological activities in lupus nephritis: a large cohort study from China
Authors: Qin D D , Song D , Huang J , Yu F , Zhao M H 
Published: November 2014

Background In this study, we detected plasma urokinase plasminogen activator (uPA) and soluble urokinase-type plasminogen activator receptor (uPAR) levels in Chinese lupus nephritis patients from a large cohort. The associations between plasma uPA and soluble uPAR and clinico-pathological characteristics were further analyzed. Methods The levels of plasma uPA and soluble uPAR were detected by ELISA in 202 patients with active lupus nephritis, 17 systemic lupus erythematosus (SLE) patients without renal involvement and 21 normal controls. Results There were no significant differences in the levels of the average plasma uPA among the lupus nephritis group, non-renal SLE group and normal control group ( p = 0.129). The plasma-soluble uPAR level in the lupus nephritis group was significantly higher than that in the non-renal involvement SLE group ( p = 0.004) and that in normal controls ( p < 0.001). The plasma uPAR levels were positively associated with SLEDAI scores ( r = 0.215, p = 0.007). In renal pathological data, there was significant difference of plasma-soluble uPAR levels among various pathological classes, which was the highest in the class IV group ( p = 0.012). The level of plasma-soluble uPAR was found to be a risk factor for long-term renal outcomes in lupus nephritis by univariate survival analysis ( p = 0.013, HR = 6.326, 95% CI: 1.466–27.298). Conclusions Our study showed that the significantly increased plasma levels of soluble uPAR could be found in active lupus nephritis, and they were associated with some clinico-pathological features. Its involvement in the pathogenesis of lupus nephritis warrants further study.
Outcome of prolonged QRS interval in dilated cardiomyopathy: role of implantable cardioverter-defibrillators on mortality
Authors: Shuaib Waqas , Shahid Hassan , Khan Muhammad Shahzeb , Alweis Richard , Sanchez Laura Rosemary 
Published: November 2014

Aim: The main objectives of this study were to investigate the relationship between prolonged QRS interval and its prognosis in patients with dilated cardiomyopathy (DCM), and to determine the effects of cardiac pacing with an implantable cardioverter-defibrillator (ICD) on mortality in patients with a QRS width > 150 ms. Methods: We retrospectively queried the healthcare enterprise data warehouse and the patient medical records from January 2007 to December 2012 for 1453 cases of DCM at a university- affiliated hospital. Of the 1453 cases, 989 patients were included in the final analyses. Primary outcome variable was all-cause mortality. Results: Of the 989 patients, 20% ( n = 198) of the patients had a QRS width > 150 ms. Compared with patients who had a QRS < 120 ms, patients with a QRS > 150 ms had significantly higher rates of death ( p < 0.001). Among the subgroup of 198 patients who had a QRS width > 150 ms, survival (84.3%, n = 75) was significantly higher ( p < 0.001) in patients with a pacemaker inserted compared with those (45.0%, n = 49) who had not been paced. Conclusions: Prolonged QRS interval is significantly associated with a higher rate of mortality. However, we believe that cardiac pacing with an ICD in such patients can significantly improve outcomes.
The Five-Box Method: The “Four-Box Method” for the Catholic Physician
Authors: Marugg Lindsey , Atkinson Marie-Noelle , Fernandes Ashley 
Published: November 2014

Background/Hypothesis The traditional ethical model of the “Four-Box Method” can be adapted to integrate the perspective of a Catholic physician. In an increasingly secularist environment, medical students and physicians are often asked to “leave religious beliefs at the door” and not consider the care and stewardship of our own morality and involvement as a provider. We reject this view. A patient's own religious and moral beliefs should be respected to the extent that they do not destroy our own; for us, the Catholic viewpoint can shine a light into dark corners and aid us in translating true things to patients of any religion. Methods We analyzed a sample case in five different categories: medical indications, patient preferences, quality of life, contextual features, and the Catholic context. We explored how to methodically integrate the perspective of a Catholic physician into the analysis of this case to make the best decision for the patients. Results/Discussion We felt that we were successfully able to integrate this perspective and create a “fifth box” based on the principles of Catholic social teaching. There were also points during the analysis that the perspective of the Catholic physician was integrated into the discussion of medical indications, proving to us that the “Catholic perspective” cannot be just put in one box either. Lay Summary The traditional ethical model of the “four-box method” can be adapted to integrate the perspective of a Catholic physician. In an increasingly secularist environment, medical students and physicians are often asked to “leave religious beliefs at the door” and not consider the care and stewardship of our own morality and involvement as a provider. We reject this view. A patient's own religious and moral beliefs should be respected to the extent that they do not destroy our own; for us, the Catholic viewpoint can shine a light into dark corners and aid us in translating true things to patients of any religion. By expanding to a “fifth box” of Catholic social teaching, the Catholic physician finds a way to methodically analyze an ethical scenario. This case study is an example of this type of “five-box” analysis.
Microtubule sliding drives proplatelet elongation and is dependent on cytoplasmic dynein
Authors: Bender Markus , Thon Jonathan N. , Ehrlicher Allen J. , Wu Stephen , Mazutis Linas , Deschmann Emoke , Sola-Visner Martha , Italiano Joseph E. , Hartwig John H. 
Published: November 2014

Key PointsDynein-dependent microtubule sliding drives proplatelet elongation under static and physiological shear stress conditions. Proplatelet formation is a process that can be divided into repetitive phases: extension, pause, and retraction.
Interactions of antiparasitic sterols with sterol 14α-demethylase (CYP51) of human pathogens
Authors: Warfield Jasmine , Setzer William N , Ogungbe Ifedayo Victor 
Published: November 2014

Abstract
Sterol 14α-demethylase is a validated and an attractive drug target in human protozoan parasites. Pharmacological inactivation of this important enzyme has proven very effective against fungal infections, and it is a target that is being exploited for new antitrypanosomal and antileishmanial chemotherapy. We have used in silico calculations to identify previously reported antiparasitic sterol-like compounds and their structural congeners that have preferential and high docking affinity for CYP51. The sterol 14α-demethylase from Trypanosoma cruzi and Leishmania infantum, in particular, preferentially dock to taraxerol, epi-oleanolic acid, and α/β-amyrim structural scaffolds. These structural information and predicted interactions can be exploited for fragment/structure-based antiprotozoal drug design.
Ventilator-associated tracheobronchitis: pre-emptive, appropriate antibiotic therapy recommended
Authors: Craven Donald E , Hudcova Jana , Lei Yuxiu 
Published: November 2014

AbstractNseir and colleagues presented data from a large multicenter study of patients with ventilator-associated tracheobronchitis (VAT), demonstrating that appropriate antibiotic therapy for VAT was an independent predictor for reducing transition to pneumonia (ventilator-associated pneumonia, or VAP). These data added to the growing evidence supporting the use of appropriate antibiotic therapy for VAT as a standard of care to prevent VAP and improve patient outcomes.
Stopping outbreaks with real-time genomic epidemiology
Authors: Tang Patrick , Gardy Jennifer L 
Published: November 2014

AbstractOne of the most successful public health applications of next-generation sequencing is whole-genome sequencing of pathogens to not only detect and characterize outbreaks, but also to inform outbreak management. Using genomics, infection control teams can now track, with extraordinarily high resolution, the transmission events within outbreaks, opening up possibilities for targeted interventions. These successes are positioning the emerging field of genomic epidemiology to replace traditional molecular epidemiology, and increasing our ability to limit the spread of multidrug-resistant organisms.
Kinetic and Stereochemical Analyses of Amine-Additive Effects on the Hydrogenation of α-Phenylcinnamic Acid over Cinchonidine-Modified Pd/C
Authors: Nakai Kengo , Misaki Tomonori , Okamoto Yasuaki , Sugimura Takashi 
Published: November 2014

Abstract
Asymmetric hydrogenation of α-phenylcinnamic acid catalyzed by cinchonidine (CD)-modified palladium has been performed. Without benzylamine (BA), a modification inconsistency was observed: the rate diminished when a small amount of CD was used, whereas the product enantiomeric excess (ee) increased when substantially more CD was used. By altering the amount of amine additive, we deduced that this inconsistency was caused by the amine effect of CD itself. With a 1,8-diazabicyclo[5.4.0]undec-7-ene additive, the catalytic amount was sufficient to result in the highest ee of 81%.