bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Agreement Measures Based on Survival Processes
Authors: Guo Ying , Li Ruosha , Peng Limin , Manatunga Amita K. 
Published: July 2013

Summary
The need to assess agreement arises in many scenarios in biomedical sciences when measurements were taken by different methods on the same subjects. When the endpoints are survival outcomes, the study of agreement becomes more challenging given the special characteristics of time-to-event data. In this article, we propose a new framework for assessing agreement based on survival processes that can be viewed as a natural representation of time-to-event outcomes. Our new agreement measure is formulated as the chance-corrected concordance between survival processes. It provides a new perspective for studying the relationship between correlated survival outcomes and offers an appealing interpretation as the agreement between survival times on the absolute distance scale. We provide a multivariate extension of the proposed agreement measure for multiple methods. Furthermore, the new framework enables a natural extension to evaluate time-dependent agreement structure. We develop nonparametric estimation of the proposed new agreement measures. Our estimators are shown to be strongly consistent and asymptotically normal. We evaluate the performance of the proposed estimators through simulation studies and then illustrate the methods using a prostate cancer data example.
Ultra‐mini percutaneous nephrolithotomy (UMP): one more armamentarium
Authors: Desai Janak , Solanki Ronak 
Published: July 2013

ObjectiveTo describe our newly developed technique for the removal of renal stones, which we have called ultra‐mini percutaneous nephrolithotomy (UMP).MethodsUMPwas performed in 62 patients using a 3.5‐Fultra‐thin telescope and specially designed inner and outer sheaths. A standard puncture was made and the tract was dilated up to 13F.The outer sheath was introduced into the pelvicalyceal system and the stone was disintegrated with a 365‐μ holmium laser fibre, introduced through the inner sheath.Stone fragments were evacuated using the specially designed sheath by creating an eddy current of saline; the fragments then came out automatically.ResultsThe mean calculus size was 16.8 mm. Four of the 62 patients were children, three had a solitary kidney and two were obese.UMPwas feasible in all cases with a mean (sd) 1.4 (1.0) gm/dL haemoglobin decrease and a mean hospital stay of 1.2 (0.8) days. The stone‐free rate at 1 month was 86.66%.In two patients intraoperative bleeding obscured vision, requiring conversion to mini‐percutaneous nephrolithotomy. There was one postoperative complication of hydrothorax, but there were no other postoperative complications and no auxiliary procedures were required.ConclusionsUMPis a very safe and effective method of removing renal calculi up to 20 mm. The use of consumables and disposables is minimal and the patient recovery was fast.Further clinical studies and direct comparison with other available techniques are required to define the place ofUMPin the treatment of low‐bulk and medium‐bulk renal urolithiasis. It may be particularly useful for lower calyx calculi and paediatric cases.
Vegetable‐based dietary pattern and liver cancer risk: Results from the Shanghai Women's and Men's Health Studies
Authors: Zhang Wei , Xiang Yong‐Bing , Li Hong‐Lan , Yang Gong , Cai Hui , Ji Bu‐Tian , Gao Yu‐Tang , Zheng Wei , Shu Xiao‐Ou 
Published: July 2013

Although dietary patterns, specific foods, and their constituents have been linked to cancer risk, the role of dietary patterns and specific food groups in liver cancer risk has not been investigated. In the Shanghai Women's Health Study (SWHS) and Shanghai Men's Health Study (SMHS), two cohort studies of 132 837 Chinese women and men, we evaluated the relationship between dietary patterns, food groups, and liver cancer risk. Through in‐person interviews, dietary information intake over the preceding year was collected by using a validated food‐frequency questionnaire. Cox regression model was used to estimate hazard ratios and 95% confidence intervals with adjustment for potential confounders. During an average follow‐up of 10.9 (SWHS) or 5.5 (SMHS) years, 267 incident liver cancer cases were identified after the first 2 years of study enrolment. Three dietary patterns were derived by factor analysis. A vegetable‐based dietary pattern was inversely associated with liver cancer; hazard ratios (95% confidence intervals) for the lowest to highest quartiles were: 1.00; 0.98 (0.71–1.35); 0.93 (0.67–1.29); and 0.58 (0.40–0.84); Ptrend = 0.01. The association was stronger among participants with a history of chronic liver disease. Further analyses showed high intakes of celery, mushrooms, allium vegetables, composite vegetables (including asparagus lettuce and garland chrysanthemum), legumes and legume products were associated with reduced liver cancer risk (all Ptrend < 0.05). Fruit‐ and meat‐based dietary patterns were not associated with liver cancer risk. Our study suggests that a vegetable‐based dietary pattern is associated with reduced liver cancer risk.
The United Kingdom Primary Immune Deficiency (UKPID) Registry: report of the first 4 years' activity 2008–2012
Authors: Edgar J D M , Buckland M , Guzman D , Conlon N P , Knerr V , Bangs C , Reiser V , Panahloo Z , Workman S , Slatter M , Gennery A R , Davies E G , Allwood Z , Arkwright P D , Helbert M , Longhurst H J , Grigoriadou S , Devlin L A , Huissoon A , Krishna M T , Hackett S , Kumararatne D S , Condliffe A M , Baxendale H , Henderson K , Bethune C , Symons C , Wood P , Ford K , Patel S , Jain R , Jolles S , El-Shanawany T , Alachkar H , Herwadkar A , Sargur R , Shrimpton A , Hayman G , Abuzakouk M , Spickett G , Darroch C J , Paulus S , Marshall S E , McDermott E M , Heath P T , Herriot R , Noorani S , Turner M , Khan S , Grimbacher B 
Published: July 2013

Summary
This report summarizes the establishment of the first national online registry of primary immune deficency in the United Kingdom, the United Kingdom Primary Immunodeficiency (UKPID Registry). This UKPID Registry is based on the European Society for Immune Deficiency (ESID) registry platform, hosted on servers at the Royal Free site of University College, London. It is accessible to users through the website of the United Kingdom Primary Immunodeficiency Network (http://www.ukpin.org.uk). Twenty-seven centres in the United Kingdom are actively contributing data, with an additional nine centres completing their ethical and governance approvals to participate. This indicates that 36 of 38 (95%) of recognized centres in the United Kingdom have engaged with this project. To date, 2229 patients have been enrolled, with a notable increasing rate of recruitment in the past 12 months. Data are presented on the range of diagnoses recorded, estimated minimum disease prevalence, geographical distribution of patients across the United Kingdom, age at presentation, diagnostic delay, treatment modalities used and evidence of their monitoring and effectiveness.
Increased long‐term remission after adequate medical cortisol suppression therapy as presurgical treatment in Cushing's disease
Authors: van den Bosch O. F. C. , Stades A. M. E. , Zelissen P. M. J. 
Published: July 2013

SummaryObjectiveIn the last decade, pre‐operative medical cortisol suppression therapy has frequently been used in Cushing's disease to normalize cortisol concentrations pre‐operatively. Our aim was to assess the efficacy of presurgical medical cortisol suppression therapy in Cushing's disease.Design and MethodsWe retrospectively assessed the medical files of all patients with Cushing's disease that received presurgical cortisol suppression therapy with ketoconazole or metyrapone and underwent subsequent transsphenoidal surgery between 1990 and 2010 at our centre. We retrieved the pretreatment regimen, adequacy of pretreatment, early postoperative serum cortisol levels, adverse effects and long‐term remission status.ResultsNineteen of 33 patients (58%) obtained long‐term remission after pituitary surgery without additional postoperative therapy. Thirteen of 16 patients with adequate presurgical cortisol suppression therapy had postoperative cortisol concentrations <50 nmol/l. The 16 patients with adequate presurgical cortisol suppression had a higher long‐term remission rate after primary surgery compared with the 13 patients with borderline or inadequate pretreatment (81% vs 38%; P < 0·05).ConclusionsAdequate presurgical cortisol suppression treatment with ketoconazole or metyrapone in Cushing's disease seems to be associated with suppressed postoperative cortisol concentrations and an increased long‐term remission rate.
Thinking about Health‐Related Outcomes: What Do We Need Evidence about?
Authors: Glasgow Russell E. , Brownson Ross C. , Kessler Rodger S. 
Published: July 2013

AbstractBackgroundThere is an urgent need for efficient, equitable interventions across the disease spectrum from prevention to palliative care. To identify and prioritize such interventions, evidence of effectiveness important to potential constituents is needed on outcomes relevant to them.MethodsTo inform practice and policy, evidence is needed on actionable, harmonized outcomes which are feasible to collect in most settings and relevant to citizens, practitioners, and decision makers. We propose that increased priority should be given to certain outcomes that are infrequently collected across multiple domains.ResultsA modification of a logic model of health outcomes by Proctor et al. is used to propose key domains and measures of implementation, service delivery, biomarkers, and health and functioning outcomes. Recommendations are made to give increased priority to implementation (especially reach, resource requirements/costs; and fidelity/adaptation); Institute of Medicine service delivery categories of equity and safety; and patient reported health and functioning outcomes.ConclusionsImplications of this outcomes framework include that biomarkers are not always the most important or relevant outcomes; that harmonized, pragmatic, and actionable measures are needed for each of these types of outcomes, and that significant changes in training and review of grants and publications are needed.
The significance of possible selves in patients of an early intervention programme for psychotic disorders
Authors: Norman Ross M.G. , Windell Deborah , Lynch Jill , Manchanda Rahul 
Published: July 2013

AbstractAimsTo assess the possible importance of patients' perceptions of possible future selves in determining self‐esteem and mood.MethodsOne hundred and two patients of an early intervention programme for psychotic disorders completed measures of perceived positive and negative current and possible future selves, as well as indices of self‐esteem and mood.ResultsMeasures of current and possible selves generally showed bivariate correlations with self‐esteem, depression and anger/hostility. Perceived negative possible self was the most important independent predictor of self‐esteem, depression and anger/hostility.ConclusionsPerceptions of possible negative future selves may be a particularly important determinant of self‐esteem and negative mood states. Addressing fears about possible future self is likely to be an important aspect of recovery from psychotic disorders.
The role of dopamine in the perceptual modulation of nociceptive stimuli by monetary wins or losses
Authors: Becker Susanne , Gandhi Wiebke , Elfassy Nathaniel M. , Schweinhardt Petra 
Published: July 2013

AbstractDopamine has been suggested to have direct antinociceptive effects. However, effects on the motivation to endure or to avoid nociceptive stimulation would be more in line with dopamine's well‐established role in the motivation to obtain reward. Thus, dopamine might either inhibit or facilitate the perception of nociceptive stimuli to bias an organism towards endurance or avoidance depending on the relative importance of the nociceptive input. To test this hypothesis, we conducted two psychophysical experiments in human volunteers. In Experiment 1, the respective antinociceptive and pro‐nociceptive effects of monetary wins and losses were assessed by administering thermal stimuli (three intensities, within‐subject factor) while participants simultaneously won, lost, or neither won nor lost (neutral condition) money (within‐subject factor) in a wheel‐of‐fortune task. In Experiment 2, we tested the effect of low‐dose sulpiride (a centrally‐acting D2‐receptor antagonist increasing the synaptic availability of dopamine via predominant pre‐synaptic blockade) on the same task as in Experiment 1 using a placebo‐controlled, cross‐over design. Monetary wins decreased and losses enhanced the perception of nociceptive stimuli, which was highly reproducible. Sulpiride augmented perceptual modulation by monetary outcomes. This augmentation was driven by increased effects of monetary losses on the perception of nociceptive stimuli. The perception of nociceptive stimuli in the absence of monetary wins and losses was not affected by sulpiride. Based on these findings, we propose a new role of dopamine in the context of nociception: biasing the organism towards a decision in situations with conflicting motivations, depending on the relative importance of the nociceptive input.
Plumbagin inhibits cytokinesis in Bacillus subtilis by inhibiting FtsZ assembly – a mechanistic study of its antibacterial activity
Authors: Bhattacharya Anusri , Jindal Bhavya , Singh Parminder , Datta Anindya , Panda Dulal 
Published: July 2013

The assembly of FtsZ plays a central role in construction of the cytokinetic Z‐ring that orchestrates bacterial cell division. A naturally occurring naphthoquinone, plumbagin, is known to exhibit antibacterial properties against several types of bacteria. In this study, plumbagin was found to perturb formation of the Z‐ring in Bacillus subtilis 168 cells and to cause elongation of these cells without an apparent effect on nucleoid segregation, indicating that it may inhibit FtsZ assembly. Furthermore, it bound to purified B. subtilis FtsZ (BsFtsZ) with a dissociation constant of 20.7 ± 5.6 μm, and inhibited the assembly and GTPase activity of BsFtsZ in vitro. Interestingly, plumbagin did not inhibit either the assembly or GTPase activity of Escherichia coli FtsZ (EcFtsZ) in vitro. Using docking analysis, a putative plumbagin‐binding site on BsFtsZ was identified, and the analysis indicated that hydrophobic interactions and hydrogen bonds predominate. Based on the in silico analysis, two variants of BsFtsZ, namely D199A and V307R, were constructed to explore the binding interaction of plumbagin and BsFtsZ. The effects of plumbagin on the assembly and GTPase activity of the variant BsFtsZ proteins in vitro indicated that the residues D199 and V307 may be involved in the binding of plumbagin to BsFtsZ. The results suggest that plumbagin inhibits bacterial proliferation by inhibiting the assembly of FtsZ, and provide insight into the binding site of plumbagin on BsFtsZ, which may help in the design of potent FtsZ‐targeted antibacterial agents.
Characterization of an alpine tree line using airborne LiDAR data and physiological modeling
Authors: Coops Nicholas C. , Morsdorf Felix , Schaepman Michael E. , Zimmermann Niklaus E. 
Published: July 2013

AbstractUnderstanding what environmental drivers control the position of the alpine tree line is important for refining our understanding of plant stress and tree development, as well as for climate change studies. However, monitoring the location of the tree line position and potential movement is difficult due to cost and technical challenges, as well as a lack of a clear boundary. Advanced remote sensing technologies such as Light Detection and Ranging (LiDAR) offer significant potential to map short individual tree crowns within the transition zone despite the lack of predictive capacity. Process‐based forest growth models offer a complementary approach by quantifying the environmental stresses trees experience at the tree line, allowing transition zones to be defined and ultimately mapped. In this study, we investigate the role remote sensing and physiological, ecosystem‐based modeling can play in the delineation of the alpine tree line. To do so, we utilize airborne LiDAR data to map tree height and stand density across a series of altitudinal gradients from below to above the tree line within the Swiss National Park (SNP), Switzerland. We then utilize a simple process‐based model to assess the importance of seasonal variations on four climatically related variables that impose non‐linear constraints on photosynthesis. Our results indicate that all methods predict the tree line to within a 50 m altitudinal zone and indicate that aspect is not a driver of significant variations in tree line position in the region. Tree cover, rather than tree height is the main discriminator of the tree line at higher elevations. Temperatures in fall and spring are responsible for the major differences along altitudinal zones, however, changes in evaporative demand also control plant growth at lower altitudes. Our results indicate that the two methods provide complementary information on tree line location and, when combined, provide additional insights into potentially endangered forest/grassland transition zones.
Leaf and fine root carbon stocks and turnover are coupled across Arctic ecosystems
Authors: Sloan Victoria L. , Fletcher Benjamin J. , Press Malcolm C. , Williams Mathew , Phoenix Gareth K. 
Published: July 2013

AbstractEstimates of vegetation carbon pools and their turnover rates are central to understanding and modelling ecosystem responses to climate change and their feedbacks to climate. In the Arctic, a region containing globally important stores of soil carbon, and where the most rapid climate change is expected over the coming century, plant communities have on average sixfold more biomass below ground than above ground, but knowledge of the root carbon pool sizes and turnover rates is limited. Here, we show that across eight plant communities, there is a significant positive relationship between leaf and fine root turnover rates (r2 = 0.68, P < 0.05), and that the turnover rates of both leaf (r2 = 0.63, P < 0.05) and fine root (r2 = 0.55, P < 0.05) pools are strongly correlated with leaf area index (LAI, leaf area per unit ground area). This coupling of root and leaf dynamics supports the theory of a whole‐plant economics spectrum. We also show that the size of the fine root carbon pool initially increases linearly with increasing LAI, and then levels off at LAI = 1 m2 m−2, suggesting a functional balance between investment in leaves and fine roots at the whole community scale. These ecological relationships not only demonstrate close links between above and below‐ground plant carbon dynamics but also allow plant carbon pool sizes and their turnover rates to be predicted from the single readily quantifiable (and remotely sensed) parameter of LAI, including the possibility of estimating root data from satellites.
Self‐perceived quality of sleep and mortality in Norwegian dialysis patients
Authors: Brekke Fredrik B. , Waldum Bård , Amro Amin , Østhus Tone B. H. , Dammen Toril , Gudmundsdottir Helga , Os Ingrid 
Published: July 2013

AbstractSleep complaints are prevalent and associated with poor health‐related quality of life (HRQoL), depression and possibly mortality in dialysis patients. This study aimed to explore possible associations between sleep quality, daytime sleepiness and mortality in dialysis patients. In this study, 301 dialysis patients were followed up to 4.3 years. HRQoL was evaluated at baseline with the Kidney Disease and Quality of Life—Short Form (KDQoL‐SF), depression with Beck Depression Inventory (BDI), sleep quality with Pittsburgh Sleep Quality Index and daytime sleepiness with Epworth Sleepiness Scale. The single item “on a scale from 0–10, how would you evaluate your sleep?” in the sleep subscale in KDQoL‐SF was used to identify poor (0–5) and good sleepers (6–10). A total of 160 patients (53.3%) were characterized as poor sleepers. They were younger (r = 0.241, P < 0.001), had more depression (BDI: 8.72 ± 6.79 vs. 13.60 ± 8.04, P < 0.001), a higher consumption of hypnotics and antidepressants and reduced HRQoL (Mental Component Summary score: 45.4 ± 11.0 vs. 50.0 ± 10.4, P < 0.001. Physical Component Summary score: 35.0 ± 9.9 vs. 38.5 ± 10.5, P = 0.004). In multivariate analyses, poor sleepers had nearly a twofold increase in mortality risk (hazard ratio [HR] 1.92, confidence interval [CI] 1.10‐3.35, P = 0.022). Daytime sleepiness was not related to mortality (HR 1.01, CI 0.95‐1.08, P = 0.751). Sleep complaints predicted increased mortality risk in dialysis patients and should therefore be routinely assessed. Further studies are needed to find suitable treatment options for poor sleep in dialysis patients as it may affect both HRQoL and survival.
Spontaneous clearance of serum hepatitis C virus RNA during the clinical course of hepatocellular carcinoma in patients with chronic hepatitis C
Authors: Minami Tatsuya , Tateishi Ryosuke , Shiina Shuichiro , Fujiwara Naoto , Mikami Shintaro , Sato Masaya , Uchino Koji , Enooku Kenichiro , Asaoka Yoshinari , Kondo Yuji , Yoshida Haruhiko , Koike Kazuhiko 
Published: July 2013

AimSpontaneous clearance of serum hepatitis C virus (HCV) RNA in chronic HCV carriers is assumed to be rare especially after development of hepatocellular carcinoma (HCC). We analyzed patients with chronic hepatitis C who spontaneously resolved serum HCV RNA after the treatment for HCC.MethodsA database search was performed to identify patients with HCC in whom serum HCV RNA was positive before the treatment for HCC and became negative during the clinical course. Those who received interferon therapy were excluded.ResultsA total of 1145 patients with HCC who had not received interferon therapy were positive for HCV RNA before the treatment. Among them, five patients (M/F = 4/1) spontaneously resolved viremia during the clinical course, with the incidence rate of at least 0.11%/person‐year (95% confidence interval: 0.05%–0.26%). The mean age at the time of negative test for HCV RNA was 77 (range: 52–84). Three and two were infected with HCV genotype 1 and 2, respectively. The mean initial viral load was 9.0 K IU/mL (range: 1.6–31.6). The alanine aminotransferase level decreased to within the normal range in all patients after the clearance of serum HCV RNA. Fibrosis grade of background liver, evaluated according to METAVIR classification, was F1 in 1, F2 in 1, F4 in 2, and unknown in 1. All patients survived more than 7 years after the initial treatment for HCC.ConclusionSpontaneous clearance of serum HCV RNA after HCC development possibly occurs even in elderly patients. The prognosis was good probably due to improved inflammation in the liver.