bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smoking and survival after breast cancer diagnosis in Japanese women: A prospective cohort study
Authors: Kakugawa Yoichiro , Kawai Masaaki , Nishino Yoshikazu , Fukamachi Kayoko , Ishida Takanori , Ohuchi Noriaki , Minami Yuko 
Published: June 2015

The results of previous studies investigating whether there is an association between active smoking and risk of death among breast cancer patients have been inconsistent. We investigated the association between active and passive smoking and risk of all‐cause and breast cancer‐specific death among female breast cancer patients in relation to menopausal and tumor estrogen/progesterone receptor (ER/PR) status. The present study included 848 patients admitted to a single hospital in Japan from 1997 to 2007. Active or passive smoking status was assessed using a self‐administered questionnaire. The patients were followed until 31 December 2010. We used a Cox proportional‐hazard model to estimate hazard ratios (HR). During a median follow‐up period of 6.7 years, 170 all‐cause and 132 breast cancer‐specific deaths were observed. Among premenopausal patients, current smokers showed a non‐significant higher risk of all‐cause and breast cancer‐specific death. A duration of smoking >21.5 years was positively associated with all‐cause (HR = 3.09, 95% confidence interval [CI], 1.17–8.20) and breast cancer‐specific death (HR = 3.35, 95%CI: 1.22–9.23,Ptrend = 0.035) among premenopausal patients. In premenopausal patients withER+ orPR+ tumors, there was some suggestion that a longer duration of smoking was associated with higher risk of all‐cause and breast cancer‐specific death. Passive smoking demonstrated no significant risk. Our results suggest that a longer duration of active smoking is associated with an increased risk of all‐cause and breast cancer‐specific death among premenopausal patients, possibly with hormonal receptor‐positive tumors. Breast cancer patients should be informed about the importance of smoking cessation.
Caregiver daily impression could reflect illness latency and severity in frail elderly residents in long‐term care facilities: A pilot study
Authors: Ae Ryusuke , Kojo Takao , Okayama Masanobu , Tsuboi Satoshi , Makino Nobuko , Kotani Kazuhiko , Aoyama Yasuko , Nakamura Yosikazu 
Published: June 2015

AimsTo propose a caregiver daily impression (CDI) rating instrument for personal caregivers of residents living in long‐term care facilities (LTCF) to comprehensively evaluate residents' daily health condition, and to investigate whether the CDI reflects illness latency and severity in residents transferred emergently.MethodsWe carried out a retrospective review of facility care records from 20 LTCF in Hyogo, Japan. The participants were 169 LTCF residents with episodes of transfer to emergency hospitalization facilities during a 3‐month period. We determined specific CDI variables by interviewing experienced LTCF caregivers, and then carried out a principal component analysis to determine the major parameter set. The generated components were incorporated into a regression model to investigate the association with hospitalization.ResultsThe mean age was 87.9 ± 6.5 years, 68% were women and 28% of transfers resulted in hospitalization. The interview procedure identified 12 specific CDI variables, and the principal component analysis generated five distinct components: “change in feeding,” “change in emotion,” “disengaged or listless gaze,” “decrease in eye reactivity” and “change in movement.” By multivariate logistic regression, hospitalization was associated with “decrease in eye reactivity” (adjusted OR 1.78, 95% CI 1.07–2.97) and poor vital signs (adjusted OR 2.84, 95% CI 1.15–6.98), but not with body temperature (adjusted OR 1.29, 95% CI 0.52–3.21).ConclusionsThe CDI might reflect underlying illness severity beyond quantitative physical findings. Once the CDI can be appropriately validated, quantified and linked to physical findings, it could be used by caregivers for daily resident assessments and as a practical triage tool in emergency situations. Geriatr Gerontol Int 2016; 16: 612–617.
Intra‐ and trans‐generational effects of larval diet on susceptibility to an entomopathogenic fungus, Beauveria bassiana, in the greater wax moth, Galleria mellonella
Authors: Kangassalo K. , Valtonen T. M. , Roff D. , Pölkki M. , Dubovskiy I. M. , Sorvari J. , Rantala M. J. 
Published: June 2015

AbstractIn addition to nutritional conditions experienced by individuals themselves, those experienced by their parents can affect their immune function. Here, we studied the intra‐ and trans‐generational effects of larval diet on susceptibility to an entomopathogenic fungus, Beauveria bassiana, in the greater wax moth, Galleria mellonella. In the first part of the study, a split‐brood design was used to compare the susceptibility of full sibs raised either on low‐ or on high‐nutrition larval diet. In the second part of the study, a similar experimental design was employed to investigate the effects of maternal and paternal diet as well as their interaction on offspring's susceptibility. In the first part of the study, we found that individuals fed with high‐nutrition diet had higher mortality from infection than individuals fed with low‐nutrition diet. However, diet did not affect post‐infection survival time. Conversely, in the second part of the study, maternal diet was found to have no significant effect on final mortality rate of offspring, but it affected survival time: larvae with high‐nutrition maternal diet survived fewer days after infection than larvae with low‐nutrition maternal diet. Paternal diet had no significant effect on offspring's susceptibility to the fungus, indicating that paternal effects are not as important as maternal effects in influencing immune function in this species. Our findings provide further indication that maternal nutrition affects immune function in insects, and suggest that the direct effects of nutrition on immunity may be different, yet parallel, to those caused by parental nutrition.
Empirical gradient threshold technique for automated segmentation across image modalities and cell lines
Authors: CHALFOUN J. , MAJURSKI M. , PESKIN A. , BREEN C. , BAJCSY P. , BRADY M. 
Published: June 2015

SummaryNew microscopy technologies are enabling image acquisition of terabyte‐sized data sets consisting of hundreds of thousands of images. In order to retrieve and analyze the biological information in these large data sets, segmentation is needed to detect the regions containing cells or cell colonies. Our work with hundreds of large images (each 21 000×21 000 pixels) requires a segmentation method that: (1) yields high segmentation accuracy, (2) is applicable to multiple cell lines with various densities of cells and cell colonies, and several imaging modalities, (3) can process large data sets in a timely manner, (4) has a low memory footprint and (5) has a small number of user‐set parameters that do not require adjustment during the segmentation of large image sets. None of the currently available segmentation methods meet all these requirements. Segmentation based on image gradient thresholding is fast and has a low memory footprint. However, existing techniques that automate the selection of the gradient image threshold do not work across image modalities, multiple cell lines, and a wide range of foreground/background densities (requirement 2) and all failed the requirement for robust parameters that do not require re‐adjustment with time (requirement 5).We present a novel and empirically derived image gradient threshold selection method for separating foreground and background pixels in an image that meets all the requirements listed above. We quantify the difference between our approach and existing ones in terms of accuracy, execution speed, memory usage and number of adjustable parameters on a reference data set. This reference data set consists of 501 validation images with manually determined segmentations and image sizes ranging from 0.36 Megapixels to 850 Megapixels. It includes four different cell lines and two image modalities: phase contrast and fluorescent. Our new technique, called Empirical Gradient Threshold (EGT), is derived from this reference data set with a 10‐fold cross‐validation method. EGT segments cells or colonies with resulting Dice accuracy index measurements above 0.92 for all cross‐validation data sets. EGT results has also been visually verified on a much larger data set that includes bright field and Differential Interference Contrast (DIC) images, 16 cell lines and 61 time‐sequence data sets, for a total of 17 479 images. This method is implemented as an open‐source plugin to ImageJ as well as a standalone executable that can be downloaded from the following link:https://isg.nist.gov/.
Programmed death 1 and its ligands do not limit experimental foreign antigen‐induced immune complex glomerulonephritis
Authors: Ooi Joshua D , Li Ming , Kourkoutzelos Katerina , Yagita Hideo , Azuma Miyuki , Holdsworth Stephen R , Kitching A Richard 
Published: June 2015

AbstractAimInteractions between the co‐stimulatory molecule programmed death 1 (PD‐1) and its ligands, PD‐L1 and PD‐L2, constrain T‐cell responses and help maintain peripheral tolerance. Glomerulonephritis can result from a variety of antigens, both self and foreign, and from humoural and cellular effector responses. These studies aimed to define the role of PD1 and its ligands in circulating immune complex glomerulonephritis induced by immunity to a foreign antigen.MethodsImmune complex glomerulonephritis was initiated by injecting BALB/c mice with horse spleen apoferritin intraperitoneally daily for 14 days. Inhibitory anti‐mouse PD‐1, anti‐PD‐L1 or anti‐PD‐L2 antibodies were administered every other day. Renal disease and immune responses were studied.ResultsDaily injection of horse spleen apoferritin‐induced proliferative immune complex glomerulonephritis in control antibody‐treated mice, but inhibiting PD‐1 did not augment renal injury. Specifically, blocking PD‐1 did not increase serum antigen‐specific antibodies or increase glomerular immunoglobulin G deposition, the hallmark of injury in this model. Furthermore, C3 deposition was unaffected and glomerular macrophages were reduced after anti‐PD‐1 antibodies. However, anti‐PD‐1 administration did increase splenocyte proliferation and cytokine production including interferon‐γ, interleukin (IL)‐4, and IL‐17, but not IL‐10. Neutralizing either PD‐L1 or PD‐L2 alone did not result in major alterations in renal injury.ConclusionThe endogenous PD‐1/PD‐L pathway does not limit acute experimental foreign antigen‐induced circulating immune complex glomerulonephritis.
Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity
Authors: Koenen Erik J. M. , Clarkson James J. , Pennington Terence D. , Chatrou Lars W. 
Published: June 2015

Summary

Tropical rainforest hyperdiversity is often suggested to have evolved over a long time‐span (the ‘museum’ model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world‐wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved.

We inferred the largest time‐calibrated phylogeny for the family to date, reconstructed ancestral states for habitat and deciduousness, estimated diversification rates and modeled potential shifts in macro‐evolutionary processes using a recently developed Bayesian method.

The ancestral Meliaceae is reconstructed as a deciduous species that inhabited seasonal habitats. Rainforest clades have diversified from the Late Oligocene or Early Miocene onwards. Two contemporaneous Amazonian clades have converged on similar ecologies and high speciation rates.

Most species‐level diversity of Meliaceae in rainforest is recent. Other studies have found steady accumulation of lineages, but the large majority of plant species diversity in rainforests is recent, suggesting (episodic) species turnover. Rainforest hyperdiversity may best be explained by recent radiations from a large stock of higher level taxa.
Plant contributions to our understanding of sex chromosome evolution
Authors: Charlesworth Deborah 
Published: June 2015

SummaryA minority of angiosperms have male and female flowers separated in distinct individuals (dioecy), and most dioecious plants do not have cytologically different (heteromorphic) sex chromosomes. Plants nevertheless have several advantages for the study of sex chromosome evolution, as genetic sex determination has evolved repeatedly and is often absent in close relatives. I review sex‐determining regions in non‐model plant species, which may help us to understand when and how (and, potentially, test hypotheses about why) recombination suppression evolves within young sex chromosomes. I emphasize high‐throughput sequencing approaches that are increasingly being applied to plants to test for non‐recombining regions. These data are particularly illuminating when combined with sequence data that allow phylogenetic analyses, and estimates of when these regions evolved. Together with comparative genetic mapping, this has revealed that sex‐determining loci and sex‐linked regions evolved independently in many plant lineages, sometimes in closely related dioecious species, and often within the past few million years. In reviewing recent progress, I suggest areas for future work, such as the use of phylogenies to allow the informed choice of outgroup species suitable for inferring the directions of changes, including testing whether Y chromosome‐like regions are undergoing genetic degeneration, a predicted consequence of losing recombination.

Contents

Summary
52

I.
Introduction: advantages of plants for the study of sex chromosome evolution
53

II.
Sex chromosomes and estimation of their ages from sequence divergence
53

III.
Which plants have sex chromosomes?
54

IV.
Haploid plants
55

V.
Plants with very small, or no, non‐recombining regions
55

VI.
Comparative genetic mapping
56

VII.
Why does suppressed recombination evolve?
57

VIII.
Recombination suppression: mechanisms
58

IX.
Old established sex chromosome systems
59

X.
Genetic degeneration: the need for empirical data in a phylogenetic setting
59

XI.
Plant sex‐determining loci
61

XII.
Conclusions
62

Acknowledgements
62

References
62
Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora
Authors: Sánchez Miguel A. , Cid Pablo , Navarrete Humberto , Aguirre Carlos , Chacón Gustavo , Salazar Erika , Prieto Humberto 
Published: June 2015

SummaryThe potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen‐mediated gene flow from GM crops and non‐GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national‐scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from ‘very low’ (1) to ‘very high’ (5)] was developed, showing medium OPs (3) for GM–native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape‐Vitis vinifera GM–introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile.
Taste dysfunction in patients undergoing hematopoietic stem cell transplantation: Clinical evaluation in children
Authors: Majorana Alessandra , Amadori Francesca , Bardellini Elena , Campus Guglielmo , Conti Giulio , Strohmenger Laura , Schumacher Richard Fabian , Polimeni Antonella 
Published: June 2015

AbstractThe aim of this study was to determine the variability of TD in children undergoing HSCT. Cases were identified as consecutively enrolled children in the period January 2011–January 2013 among patients attending the Paediatric Department of Spedali Civili of Brescia and all candidates to HSCT. The TST was conducted in two phases: identification of threshold values and identification of perceived stimulus intensity. Sixteen sapid solutions with four flavors (sucrose, sodium chloride, citric acid, and quinine hydrochloride) at four different concentrations were administered in a random sequence. The same protocol was administered at different time intervals: before starting the conditioning therapy (T0), during the conditioning therapy (T1) (two times), and every three months (two times) after engraftment post‐HSCT (T2). A p‐value < 0.05 was considered statistically significant. Fifty‐one children (29 female and 22 male, mean age 5.2 ± 0.7 yr) were enrolled. Threshold value means for the four flavors increased during HSCT conditioning therapy (T1) (p < 0.01); intensity of perceived stimulus decreased during HSCT conditioning therapy (p < 0.01). At six months after engraftment (T2), both parameters had returned to starting values (T0). Changes in taste perception in children undergoing HSCT seem to occur especially during the conditioning therapy and resolve in about six months after engraftment post‐HSCT.
Vaccination‐Related Side Effects, Humoral Immunity, and Adverse Events during the Civilian Smallpox Vaccination Campaign, Arkansas, 2003
Authors: Haselow Dirk 
Published: June 2015

AbstractObjectiveSmallpox vaccination has been associated with notable side effects and adverse events. This study assessed the frequency of each among public health workers immunized during the 2003 Arkansas civilian smallpox vaccination campaign to allow individuals and policymakers to make informed decisions whether repeat vaccination, as recommended in 10‐year intervals, should be considered.Design and SampleThis descriptive study summarizes postvaccination surveillance data for all civilians receiving smallpox vaccine (Dryvax) in Arkansas in 2003.MeasuresRates of side effects and adverse events were determined. Vaccinia‐specific antibody titers among a subset of public health response team members were also assessed.ResultsOf the 1,124 vaccine recipients, 87% had a major take response. Substantial symptomatology, a 2% adverse event rate, a 0.5% hospitalization rate, and zero inadvertent transmission following vaccination were observed. Vaccinia‐specific antibody titers increased on average 9‐fold from 2.21*102 to 2.16*103 one month after vaccination. We found no association of age, sex, or racial subgroups with adverse events, hospitalizations, a lower take response rate, or lower postvaccination antibody titers.ConclusionsProminent side effect profiles and adverse events among study participants seem to support individual and institutional reluctance to vaccinate civilians in the absence of smallpox reemergence.
Gestational Weight Gain Trend and Population Attributable Risks of Adverse Fetal Growth Outcomes in Ohio
Authors: Chen Aimin , Xu Fan , Xie Changchun , Wu Tianying , Vuong Ann M. , Miao Maohua , Yuan Wei , DeFranco Emily A. 
Published: June 2015

AbstractBackgroundThe trend of gestational weight gain (GWG) in relation to the Institute of Medicine (IOM) guidelines and the population attributable risks (PARs) of GWG on fetal growth outcomes remain unclear.MethodsWe analysed Ohio birth certificates from 2006 to 2012 to examine GWG trend by prepregnancy body mass index, to calculate the risk of small‐ and large‐for‐gestational age (SGA and LGA), and macrosomia (birthweight >4000 g or >4500 g) infants, and to estimate the PARs of GWG below or above the guidelines.ResultsOf 869 531 women who delivered singleton live births at 22–44 weeks of gestation, 4.5% were underweight, 48.9% were normal weight, 23.9% were overweight, and 22.7% were obese before pregnancy. About 36.5% of underweight, 52.6% of normal weight, 72.5% of overweight, and 62.4% of obese women gained weight above the guidelines, with only slight changes from 2006 to 2012. Also, 34.9% of underweight, 20.1% of normal weight, 16.3% of overweight, and 27.0% of obese women gained weight below the guidelines. The PAR of GWG below or above the guidelines was −13% for SGA, 32.6% for LGA, 28.1% for macrosomia >4000 g, and 48.3% for macrosomia >4500 g, mostly driven by currently GWG above the guidelines in normal weight, overweight, and obese women.ConclusionsA high percentage of pregnant women gained weight outside of the current IOM GWG guidelines; however, changes from 2006 to 2012 were small. GWG above the IOM guidelines significantly contributed to a large proportion of LGA and macrosomic infants in the general population.
A Proportional Hazards Regression Model for the Subdistribution with Covariates‐adjusted Censoring Weight for Competing Risks Data
Authors: He Peng , Eriksson Frank , Scheike Thomas H. , Zhang Mei‐Jie 
Published: June 2015

AbstractWith competing risks data, one often needs to assess the treatment and covariate effects on the cumulative incidence function. Fine and Gray proposed a proportional hazards regression model for the subdistribution of a competing risk with the assumption that the censoring distribution and the covariates are independent. Covariate‐dependent censoring sometimes occurs in medical studies. In this paper, we study the proportional hazards regression model for the subdistribution of a competing risk with proper adjustments for covariate‐dependent censoring. We consider a covariate‐adjusted weight function by fitting the Cox model for the censoring distribution and using the predictive probability for each individual. Our simulation study shows that the covariate‐adjusted weight estimator is basically unbiased when the censoring time depends on the covariates, and the covariate‐adjusted weight approach works well for the variance estimator as well. We illustrate our methods with bone marrow transplant data from the Center for International Blood and Marrow Transplant Research. Here, cancer relapse and death in complete remission are two competing risks.