bluuebunny/crossref_metadata_2025_split huggingface dataset:
A general goodness-of-fit test for survival analysis
Authors: Price Michael Holton , Jones James Holland 
Published: February 2017

AbstractExisting goodness-of-fit tests for survival data are either exclusively graphical in nature or only test specific model assumptions, such as the proportional hazards assumption. We describe a flexible, parameter-free goodness-of-fit test that provides a simple numerical assessment of a model’s suitability regardless of the structure of the underlying model. Intuitively, the goodness-of-fit test utilizes the fact that for a good model early event occurrence is predicted to be just as likely as late event occurrence, whereas a bad model has a bias towards early or late events. Formally, the goodness-of-fit test is based on a novel generalized Martingale residual which we call the martingale survival residual. The martingale survival residual has a uniform probability density function defined on the interval −0.5 to +0.5 if censoring is either absent or accounted for as one outcome in a competing hazards framework. For a good model, the set of calculated residuals is statistically indistinguishable from the uniform distribution, which is tested using the Kolmogorov-Smirnov statistic.
Co-adaption of tRNA Gene Copy Number and Amino Acid Usage Influences Translation Rates in Three Life Domains
Authors: Du Meng-Ze , Wei Wen , Qin Lei , Liu Shuo , Zhang An-Ying , Zhang Yong , Zhou Hong , Guo Feng-Biao 
Published: February 2017

AbstractThe cellular translation process should obey the principle of maximizing efficiency and minimizing resource and energy costs. Here, we validated this principle by focusing on the basic translation components of tRNAs and amino acids. To most efficiently utilize these components, we reasoned that the quantities of the 20 tRNAs and their corresponding amino acids would be consistent in an organism. The two values should match at both the organismal and protein scales. For the former, they co-vary to meet the need to translate more proteins in fast-growing or larger cells. For the latter, they are consistent to different extents for various proteins in an organism to comply with different needs of translation speed. In this work, 310 out of 410 genomes in three domains had significant co-adaptions between the tRNA gene copy number and amino acid composition, and thus validating the principle at the organism scale. Furthermore, fast-growing bacteria co-adapt better than slow-growing ones. Highly expressed proteins and those connected to acute responses have better co-adaption, illustrating the principle at the individual protein scale. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set ofEscherichia coliindeed lifted the translation rate (speed). Our results also contribute to revealing a translation rate-associated factor with universal and global effects. From a practical perspective, our findings suggest a strategy to increase the expression of target proteins and have implications for designing chassis cells in the field of synthetic biology field.
Phylogenetic analyses reveal an increase in the speciation rate of raphid pennate diatoms in the Cretaceous
Authors: Castro-Bugallo Alexandra , Rojas Danny , Rocha Sara , Cermeño Pedro 
Published: February 2017

AbstractThe raphid pennates (order Bacillariales) are a diverse group of diatoms easily recognized by having a slit in the siliceous cell wall, called the raphe, with functions in cell motility. It has been hypothesized that this morphological innovation contributed to the evolutionary success of this relatively young but species-rich group of diatoms. However, owing to the incompleteness of the fossil record this hypothesis remains untested. Using the 18S ribosomal RNA gene, fossil calibrations, and Bayesian phylogenetic and diversification frameworks, we detect a shift in the speciation rate of marine raphid pennate diatoms in the Cretaceous, not detected in other diatom lineages nor previously recognized in the microfossil record. Our results suggest a positive link between the speciation of raphid pennate diatoms and the benefits derived from evolving motility skills, which could account for their outstanding present-day global diversity. The coincidence between the advent of the raphe and the increase in the speciation rate of raphid pennates supports the idea that simple morphological novelties can have important consequences on the evolutionary history of eukaryotic microorganisms.
Identifying the abundant and active microorganisms common to full-scale anaerobic digesters
Authors: Kirkegaard Rasmus H. , McIlroy Simon J. , Kristensen Jannie M. , Nierychlo Marta , Karst Søren M. , Dueholm Morten S. , Albertsen Mads , Nielsen Per H. 
Published: February 2017

AbstractAnaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. To this end, we investigated the microbial community composition of thirty-two full-scale digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the active microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of individual plants surveyed were remarkably similar – with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as likely inactive immigrating microbes. By identifying the abundant and active taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process important organisms towards an in-depth understanding of the microbial ecology of these biotechnologically important systems.
A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms
Authors: Jiang Wen , Guo Zhanyong , Lages Nuno , Jim Zheng W. , Feliers Denis , Zhang Fangyuan , Wang Degeng 
Published: February 2017

AbstractTo understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured transcription rate (TR), mRNA abundance (RA) and translation activity (TA). This revealed multiple quantitative insights. First, the genomic profiles of the three parameters are systematically different in key statistical features. Sequentially more genes exhibit extreme low or high expression values from TR to RA, then to TA. That is, because of cellular coordination of these regulatory mechanisms, sequentially higher levels of gene expression selectivity are achieved as genetic information flow from the genome to the proteome. Second, the contribution of the stabilization-by-translation regulatory mechanism to the cellular coordination process was assessed. The data enabled an estimation of mRNA stability, revealing a moderate but significant positive correlation between the estimated mRNA stability and translation activity. Third, the proportion of a mRNA occupied by un-translated regions (UTR) exhibits a negative relationship with the level of this correlation, and is thus a major determinant of the mode of regulation of the mRNA. High-UTR-proportion mRNAs tend to defy the stabilization-by-translation regulatory mechanism, staying out of the polysome but remaining stable; mRNAs with little UTRs largely follow this regulation. In summary, we quantitatively delineated the relationship among multiple transcriptome regulation parameters, i.e., cellular coordination of corresponding regulatory mechanisms.
Many places called home: the adaptive value of seasonal adjustments in range fidelity
Authors: Lafontaine Alexandre , Drapeau Pierre , Fortin Daniel , St‐Laurent Martin‐Hugues 
Published: February 2017

Summary

The vast majority of animal species display range fidelity, a space‐use behaviour enhancing familiarity with local habitat features. While the fitness benefits of this behaviour have been demonstrated in a variety of taxa, some species or populations rather display infidelity, displacing their home range over time. Others, such as many ungulate species, show seasonal adjustments in their range fidelity to accommodate changes in the dominance of limiting factors or in the distribution of resources.

Few empirical studies have explored the adaptive value of seasonal adjustments in range fidelity. Using boreal populations of woodland caribou (Rangifer tarandus caribou) as a biological model, we evaluated how range fidelity impacted individual performance during two seasons where juvenile and adult survival are limited by different predation pressures.

Between 2004 and 2013, we monitored the survival, reproductive success, habitat selection and range fidelity of female caribou in the boreal forest of eastern Canada. Using resource selection functions, we assessed how seasonal range fidelity was linked to two fitness correlates: calf survival in summer and adult female survival in winter.

Females displayed season‐specific space use tactics: they selected previously used areas during calving and summer, but tended to shift their winter range from 1 year to the next. During calving and summer, range fidelity yielded relatively high fitness benefits, as females that did not lose their calf displayed stronger fidelity than females that did. In winter, however, adult survival was negatively linked to range fidelity, as females that survived selected areas further away from their seasonal range of the previous year than females that died.

We provide one of the first evidences that making seasonal adjustments in range fidelity can be an adaptive behaviour influencing the spatial distribution of a threatened species. Assessing the seasonal nature of range fidelity tactics may improve our predictions of space use and associated fitness implications for species displaying this behaviour.
Multiple myeloma: routes to diagnosis, clinical characteristics and survival – findings from a UK population‐based study
Authors: Howell Debra , Smith Alexandra , Appleton Simon , Bagguley Timothy , Macleod Una , Cook Gordon , Patmore Russell , Roman Eve 
Published: February 2017

SummaryPrompt cancer diagnosis may align UK survival with European averages. We examined the impact of route to diagnosis on survival for multiple myeloma patients diagnosed 2012–2013 using data from our population‐based patient cohort that links to national death notifications and collects details on treatment and response (n = 441). Emergency presentation was associated with advanced disease and poorer outcomes, and was the commonest route to diagnosis (28·1%) followed by General Practitioner urgent (19·0%) and two‐week wait (17·2%) referrals. CRAB (elevated Calcium, Renal failure, Anaemia, Bone lesions) distribution varied by route (P < 0·001), with patients with emergency presentations most likely to have ≥2 features and significantly worse survival (log‐rank test χ2 = 13·8, P = 0·0002).
Urban climate and physical geography: A response to Ashmore and Dodson
Authors: Brazel Anthony J. 
Published: February 2017

Key Messages

Physical geographers are focusing on urban areas through the expanding field of urban climatology.
Physical geographers in Canada have a long legacy of urban climate studies, one which is evident world‐wide.
Urban climatologists and affiliated organizations study urban place and contexts by definition and have also turned towards creating tools to span scales from global to local.
Influence of health locus of control and fear of hypoglycaemia on glycaemic control and treatment satisfaction in people with Type 1 diabetes on insulin pump therapy
Authors: Indelicato L. , Mariano V. , Galasso S. , Boscari F. , Cipponeri E. , Negri C. , Frigo A. , Avogaro A. , Bonora E. , Trombetta M. , Bruttomesso D. 
Published: February 2017

AbstractAimTo assess the influence of health locus of control and fear of hypoglycaemia on metabolic control and treatment satisfaction in people with Type 1 diabetes mellitus on continuous subcutaneous insulin infusion.MethodsPeople with Type 1 diabetes on continuous subcutaneous insulin infusion for at least 1 year, sub‐classified as an ‘acceptable glucose control’ group [HbA1c ≤ 58 mmol/mol (7.5%)] and a ‘suboptimum glucose control’ group [HbA1c > 58 mmol/mol (7.5%)], were consecutively enrolled in a multicentre cross‐sectional study. Questionnaires were administered to assess health locus of control [Multidimensional Health Locus of Control (MHLC) scale, with internal and external subscales], fear of hypoglycaemia [Hypoglycaemia Fear Survey II (HFS‐II)] and treatment satisfaction [Diabetes Treatment Satisfaction Questionnaire (DTSQ)].ResultsWe enrolled 214 participants (mean ± sd age 43.4 ± 12.1 years). The suboptimum glucose control group (n = 127) had lower mean ± sd internal MHLC and DTSQ scores than the acceptable glucose control group (19.6 ± 5.2 vs 21.0 ± 5.0, P = 0.04 and 28.8 ± 4.8 vs 30.9 ± 4.5, P < 0.001). HFS‐II scores did not differ between the two groups. Internal MHLC score was negatively associated with HbA1c (r = −0.15, P < 0.05) and positively associated with the number of mild and severe hypoglycaemic episodes (r = 0.16, P < 0.05 and r = 0.18, P < 0.001, respectively) and with DTSQ score (r = 0.17, P < 0.05).HFS‐II score was negatively associated with DTSQ score (r = −0.18, P < 0.05) and positively with number of severe hypoglycaemic episodes (r = 0.16, P < 0.5).ConclusionsIn adults with Type 1 diabetes receiving continuous subcutaneous insulin infusion, high internal locus represents the most important locus of control pattern for achieving good metabolic control.
A Narrative Based Model of Differentiating Rioters
Authors: WILLMOTT DOMINIC , IOANNOU MARIA 
Published: February 2017

AbstractThe present study applied a narrative analysis upon rioter accounts of their motivations during the August 2011 England riots. To the authors’ knowledge, this piece of research was the first to utilise narrative theory to explore the phenomenon of rioting. Narrative accounts of 20 rioters were compiled from media, online, and published sources. Content analysis of the cases produced a set of 47 variables relating to offenders’ motivations given when describing their criminality. Data were subjected to Smallest Space Analysis (SSA), a non‐metric multidimensional scaling procedure, and results revealed four distinct themes: the Professional Rioter; the Revenger Rioter; the Victim Rioter; and the Adventurer Rioter, in line with previous research conducted on differing crime types (Canter, Kaouri and Ioannou 2003; Youngs and Canter 2011b). The four narrative themes are consistent with motivations identified in previous theories.
Effect of Delayed Digital Hypothermia on Lamellar Inflammatory Signaling in the Oligofructose Laminitis Model
Authors: Dern K. , Watts M. , Werle B. , van Eps A. , Pollitt C. , Belknap J. 
Published: February 2017

BackgroundIn the oligofructose (OF) model of sepsis‐related laminitis (SRL), digital hypothermia (“cryotherapy”) initiated before the onset of clinical signs is reported not only to limit lamellar injury, but also to cause marked inhibition of lamellar inflammatory signaling.Hypothesis/ObjectivesBecause hypothermia also has been reported to be protective when not initiated until the onset of lameness in the OF model of SRL, we hypothesized that the lamellar protection conferred by hypothermia is caused by local lamellar inhibition of inflammatory signaling as described when hypothermia was initiated earlier in the disease process.AnimalsEight Standardbred geldings aged 3–11 years with no lameness and no abnormalities of the feet detectable by gross or radiographic examination.MethodsUsing the OF model of SRL, lamellar mRNA concentrations of proinflammatory cytokines, chemokines, and endothelial adhesion proteins were compared between samples from treated limbs (CRYO, submerged in ice water for 36 hour starting at the onset of lameness), untreated limbs (NON‐CRYO, opposite limb from CRYO limbs maintained at ambient temperature), and untreated limbs from normal horses in which laminitis was not induced (CON).ResultsAlthough OF administration resulted in increases in lamellar mRNA concentrations of several inflammatory mediators in NON‐CRYO limbs (vs CON), digital hypothermia had no significant effect on these increases.Conclusions and Clinical ImportanceThe lack of inflammatory inhibition in lamellar tissue samples in our study indicates that the protective effects of digital hypothermia instituted at the onset of clinical signs of laminitis do not arise from inhibition of inflammatory pathways.
Unique clinical courses of transfusion‐transmitted hepatitis E in patients with immunosuppression
Authors: Satake Masahiro , Matsubayashi Keiji , Hoshi Yuji , Taira Rikizo , Furui Yasumi , Kokudo Norihiro , Akamatsu Nobuhisa , Yoshizumi Tomoharu , Ohkohchi Nobuhiro , Okamoto Hiroaki , Miyoshi Masato , Tamura Akinori , Fuse Kyoko , Tadokoro Kenji 
Published: February 2017

BACKGROUNDThe high prevalence of specific immunoglobulin G for hepatitis E virus (HEV) in Japanese people raises the possibility of a high incidence of HEV‐viremic blood donors and therefore frequent transfusion‐transmitted HEV (TT‐HEV).STUDY DESIGN AND METHODSTT‐HEV cases established in Japan through hemovigilance and those published in the literature were collected. Infectivity of HEV‐contaminated blood components and disease severity in relation to immunosuppression were investigated.RESULTSTwenty established TT‐HEV cases were recorded over the past 17 years. A lookback study verified that five of 10 patients transfused with known HEV‐contaminated blood components acquired HEV infection. The minimal infectious dose of HEV through transfusion was 3.6 × 104 IU. Nine of the 19 TT‐HEV cases analyzed had hematologic diseases. Only two cases showed the maximal alanine aminotransferase level of more than 1000 U/L. Two patients with hematologic malignancy and two liver transplant recipients had chronic liver injury of moderate severity.CONCLUSIONThe infectivity of HEV‐contaminated components was 50%. Immunosuppression likely causes the moderate illness of TT‐HEV, but it may lead to the establishment of chronic sequelae. Transfusion recipients, a population that is variably immunosuppressed, are more vulnerable to chronic liver injury as a result of TT‐HEV than the general population is as a result of food‐borne infection.
Evaluation of the optic nerve using strain and shear wave elastography in patients with multiple sclerosis and healthy subjects
Authors: İnal Mikail , Tan Sinan , Yumusak Erhan M. , Şahan Mehmet Hamdi , Alpua Murat , Örnek Kemal 
Published: February 2017

Aims: Our aim was to evaluate the elasticity features of the optic nerve using strain (SE) and shear wave elastography (SWE) in multiple sclerosis (MS) patients in comparison with healthy subjects. Material and methods: One hundred and seven optic nerves from 54 MS patients and 118 optic nerves from 59 healthy subjects were examined prospectively by SE and SWE. Optic nerves were divided into three types in accordance to the elasticity designs, as follows: type 1 predominantly blue (hardest tissue); type 2 predominantly blue/green (hard tissue); and type 3 predominantly green (intermediate tissue). Quantitative measurements of optic nerve hardness with SWE were analyzed in kilopascals. Results: Elastographic images from healthy volunteers showed mostly type 3 optic nerves (61.9%); type 2 was also found (38.1%), but type 1 was not observed. Elastographic examination of MS patients showed mostly type 2 optic nerves (88%), while some type 1 (4.6%) and type 3 optic nerves (6.5%) were rarely observed. There was a statistically significant difference in terms of elasticity patterns between patients and healthy volunteers (p<0.001). Statistically significant differences were observed between patients and healthy volunteers in the analysis of SWE values (10.381±3.48 kPa and 33.87±11.64 p<0.001). The receiver operating characteristic curve analysis was perfect (0.993; 95% confidence interval [CI]=0.971–0.999), and a cut-off value of 18.3 kPa shear had very high sensitivity and specificity for the patient group. No significant differences were observed between patients with and without previous optic neuritis. Conclusion: SE and SWE examination findings concerning the optic nerve in MS patients demonstrated remarkable differences according to the healthy group.
Early Detection of Ovarian Cancer using the Risk of Ovarian Cancer Algorithm with Frequent CA125 Testing in Women at Increased Familial Risk – Combined Results from Two Screening Trials
Authors: Skates Steven J. , Greene Mark H. , Buys Saundra S. , Mai Phuong L. , Brown Powel , Piedmonte Marion , Rodriguez Gustavo , Schorge John O. , Sherman Mark , Daly Mary B. , Rutherford Thomas , Brewster Wendy R. , O'Malley David M. , Partridge Edward , Boggess John , Drescher Charles W. , Isaacs Claudine , Berchuck Andrew , Domchek Susan , Davidson Susan A. , Edwards Robert , Elg Steven A. , Wakeley Katie , Phillips Kelly-Anne , Armstrong Deborah , Horowitz Ira , Fabian Carol J. , Walker Joan , Sluss Patrick M. , Welch William , Minasian Lori , Horick Nora K. , Kasten Carol H. , Nayfield Susan , Alberts David , Finkelstein Dianne M. , Lu Karen H. 
Published: February 2017

AbstractPurpose: Women at familial/genetic ovarian cancer risk often undergo screening despite unproven efficacy. Research suggests each woman has her own CA125 baseline; significant increases above this level may identify cancers earlier than standard 6- to 12-monthly CA125 &gt; 35 U/mL.Experimental Design: Data from prospective Cancer Genetics Network and Gynecologic Oncology Group trials, which screened 3,692 women (13,080 woman-screening years) with a strong breast/ovarian cancer family history or BRCA1/2 mutations, were combined to assess a novel screening strategy. Specifically, serum CA125 q3 months, evaluated using a risk of ovarian cancer algorithm (ROCA), detected significant increases above each subject's baseline, which triggered transvaginal ultrasound. Specificity and positive predictive value (PPV) were compared with levels derived from general population screening (specificity 90%, PPV 10%), and stage-at-detection was compared with historical high-risk controls.Results: Specificity for ultrasound referral was 92% versus 90% (P = 0.0001), and PPV was 4.6% versus 10% (P &gt; 0.10). Eighteen of 19 malignant ovarian neoplasms [prevalent = 4, incident = 6, risk-reducing salpingo-oophorectomy (RRSO) = 9] were detected via screening or RRSO. Among incident cases (which best reflect long-term screening performance), three of six invasive cancers were early-stage (I/II; 50% vs. 10% historical BRCA1 controls; P = 0.016). Six of nine RRSO-related cases were stage I. ROCA flagged three of six (50%) incident cases before CA125 exceeded 35 U/mL. Eight of nine patients with stages 0/I/II ovarian cancer were alive at last follow-up (median 6 years).Conclusions: For screened women at familial/genetic ovarian cancer risk, ROCA q3 months had better early-stage sensitivity at high specificity, and low yet possibly acceptable PPV compared with CA125 &gt; 35 U/mL q6/q12 months, warranting further larger cohort evaluation. Clin Cancer Res; 23(14); 3628–37. ©2017 AACR.