bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isotopic turnover of carbon and nitrogen in bovine blood fractions and inner organs
Authors: Bahar Bojlul , Harrison Sabine M. , Moloney Aidan P. , Monahan Frank J. , Schmidt Olaf 
Published: March 2014

RATIONALEIsotope ratio analysis of bovine tissues is a tool for inferring aspects of the dietary history of cattle. The objective of this experiment was to quantify the carbon (C) and nitrogen (N) isotopic turnover in blood (serum and residue) and inner organs (liver, kidney, heart and brain) of beef cattle.METHODSGrowing beef cattle (n = 70 in total) were either switched from a control diet containing barley and urea to an experimental diet containing maize and 15N‐enriched urea, for various intervals prior to slaughter or maintained on the control diet for 168 days pre‐slaughter. Samples of blood, liver, kidney, heart and brain were collected at 0, 14, 28, 56, 112 and 168 days and analysed using Isotope Ratio Mass Spectrometry.RESULTSAfter 168 days, C‐ and N‐isotopic equilibrium was reached in the blood serum, liver and kidney, approached in the heart and brain, but not reached in the non‐serum component of blood. The estimated C and N half‐lives were 16.5 and 20.7 days for liver, 19.2 and 25.5 days for kidney, 29.2 and 35.6 days for blood serum, 37.6 and 49.9 days for heart, 53.3 and 52.2 days for brain and 113.3 and 115.0 days for the non‐serum blood residue, respectively. Modelling the C and N turnover in the different tissue combinations revealed that a combined analysis of liver and heart as well as brain and kidney can provide the most accurate estimation of the timing of the diet switch.CONCLUSIONSBased on the difference in turnover rates, bovine soft tissues can provide isotopic information on short‐ and long‐term dietary changes, which in turn may be linked to the geographic or production origin of beef cattle. This study also provides basic biological data on organ C and N turnover in a large herbivorous mammal. Copyright © 2014 John Wiley & Sons, Ltd.
Improved isobaric tandem mass tag quantification by ion mobility mass spectrometry
Authors: Sturm Robert M. , Lietz Christopher B. , Li Lingjun 
Published: March 2014

RATIONALEIsobaric tandem mass tags are an attractive alternative to mass difference tags and label‐free approaches for quantitative proteomics due to the high degree of multiplexing that can be performed with their implementation. A drawback of tandem mass tags are that the co‐isolation and co‐fragmentation of labeled peptide precursors can result in chimeric tandem mass (MS/MS) spectra that can underestimate the fold‐change expression of each peptide. Ion mobility (IM) separations coupled to quadrupole time‐of‐flight (Q‐TOF) instruments have the potential to mitigate MS/MS spectra chimeracy since IM‐MS has the ability to separate ions based on charge, m/z, and collision cross section (CCS).METHODSTwo complex protein mixtures, labeled with DiLeu isobaric tandem mass tags in opposite ratios, were mixed together and analyzed by data‐dependent LC/IM‐MS/MS. The accuracy of reporters from interfering pairs was compared with and without IM separation.RESULTSIM separation was able to mitigate isobaric interference from differentially charged interfering ion pairs, as well as pairs of the same charge. Of the eight example precursors shown, only one had reporters that remained compressed below the significance threshold after IM separation.CONCLUSIONSThe results of this investigation demonstrate proof‐of‐principle that IM separation of tagged precursors prior to MS/MS fragmentation can help mitigate quantitative inaccuracies caused by isobaric interference. Future improvements of the method would include software for automated correction and use of higher resolution IM instrumentations. Copyright © 2014 John Wiley & Sons, Ltd.
Combined 13C and 15N isotope analysis on small samples using a near‐conventional elemental analyzer/isotope ratio mass spectrometer setup
Authors: Langel Reinhard , Dyckmans Jens 
Published: March 2014

RATIONALEA high sensitivity elemental analyzer/isotope ratio mass spectrometer setup was developed to allow analysis of 13C and 15N isotopic composition on microgram amounts of C and N, respectively.METHODSIncreased sensitivity of a conventional elemental analyzer equipped with a low blank autosampler was obtained by decreased carrier gas flow of 35 mL/min. The diameters of the oxidation and reduction reactors and water trap were reduced to 7.8, 7.8 and 4 mm i.d., respectively, to obtain sharp sample peaks in the mass spectrometer. To increase the lifetime of the reduction reactor, a 1:1 He/O2 mixture was used as oxidizing agent in the elemental analyzer.RESULTSSample amounts of 0.6 µg N and 1 µg C were sufficient for accurate isotopic analysis with <1 ‰ standard error after blank correction. One major advantage of the setup is the easy switching between conventional EA and μEA as only consumable parts need to be exchanged.CONCLUSIONSThe proposed setup proved to be suitable to analyze minute amounts of C and N in one analytical run simultaneously. Copyright © 2014 John Wiley & Sons, Ltd.
Joint modeling of two longitudinal outcomes and competing risk data
Authors: Andrinopoulou Eleni‐Rosalina , Rizopoulos Dimitris , Takkenberg Johanna J. M. , Lesaffre Emmanuel 
Published: March 2014

AbstractAortic gradient and aortic regurgitation are echocardiographic markers of aortic valve function. Both are biomarkers repeatedly measured in patients with valve abnormalities, and thus, it is expected that they are biologically interrelated. Loss of follow‐up could be caused by multiple reasons, including valve progression related, such as an intervention or even the death of the patient. In that case, it would be of interest and appropriate to analyze these outcomes jointly. Joint models have recently received much attention because they cover a wide range of clinical applications and have promising results. We propose a joint model consisting of two longitudinal outcomes, one continuous (aortic gradient) and one ordinal (aortic regurgitation), and two time‐to‐events (death and reoperation). Moreover, we allow for more flexibility for the average evolution and the subject‐specific profiles of the continuous repeated outcome by using B‐splines. A disadvantage, however, is that when adopting a non‐linear structure for the model, we may have difficulties when interpreting the results. To overcome this problem, we propose a graphical approach. In this paper, we apply the proposed joint models under the Bayesian framework, using a data set including serial echocardiographic measurements of aortic gradient and aortic regurgitation and measurements of the occurrence of death and reoperation in patients who received a human tissue valve in the aortic position. The interpretation of the results will be discussed. Copyright © 2014 John Wiley & Sons, Ltd.
Active surveillance for men with low‐risk prostate cancer
Authors: Sturch Paul , Kirby Roger , Challacombe Ben 
Published: March 2014

AbstractActive surveillance is often advised as an initial management strategy for men with low‐risk localised prostate cancer. In this review the authors examine popular strategies for patient selection, and question whether a more holistic approach could further enhance quality of life and life expectancy. Copyright © 2014 John Wiley & Sons
Genetic Counselors’ Views and Experiences with the Clinical Integration of Genome Sequencing
Authors: Machini Kalotina , Douglas Jessica , Braxton Alicia , Tsipis Judith , Kramer Kate 
Published: March 2014

AbstractIn recent years, new sequencing technologies known as next generation sequencing (NGS) have provided scientists the ability to rapidly sequence all known coding as well as non‐coding sequences in the human genome. As the two emerging approaches, whole exome (WES) and whole genome (WGS) sequencing, have started to be integrated in the clinical arena, we sought to survey health care professionals who are likely to be involved in the implementation process now and/or in the future (e.g., genetic counselors, geneticists and nurse practitioners). Two hundred twenty‐one genetic counselors— one third of whom currently offer WES/WGS—participated in an anonymous online survey. The aims of the survey were first, to identify barriers to the implementation of WES/WGS, as perceived by survey participants; second, to provide the first systematic report of current practices regarding the integration of WES/WGS in clinic and/or research across the US and Canada and to illuminate the roles and challenges of genetic counselors participating in this process; and third to evaluate the impact of WES/WGS on patient care. Our results showed that genetic counseling practices with respect to WES/WGS are consistent with the criteria set forth in the ACMG 2012 policy statement, which highlights indications for testing, reporting, and pre/post test considerations. Our respondents described challenges related to offering WES/WGS, which included billing issues, the duration and content of the consent process, result interpretation and disclosure of incidental findings and variants of unknown significance. In addition, respondents indicated that specialty area (i.e., prenatal and cancer), lack of clinical utility of WES/WGS and concerns about interpretation of test results were factors that prevented them from offering this technology to patients. Finally, study participants identified the aspects of their professional training which have been most beneficial in aiding with the integration of WES/WGS into the clinical setting (molecular/clinical genetics, counseling and bioethics) and suggested that counseling aids (to assist them when explaining aspects of these tests to patients) and webinars focused on WES/WGS (for genetic counselors and other health care professionals) would be useful educational tools. Future research should permit us to further enhance our knowledge of pitfalls and benefits associated with the introduction of these powerful technologies in patient care and to further explore the roles and opportunities for genetic counselors in this rapidly evolving field.
The trans‐10,cis‐15 18:2: a Missing Intermediate of trans‐10 Shifted Rumen Biohydrogenation Pathway?
Authors: Alves Susana P. , Bessa Rui J. B. 
Published: March 2014

AbstractThe “trans‐10 shifted” biohydrogenation pathway is frequently established in the rumen when high starch diets are fed to ruminants, resulting in the accumulation of trans‐10 18:1 in ruminant products. It has been proposed that the “trans‐10 shifted” biohydrogenation pathway of α‐linolenic acid generates two intermediates, the trans‐10,cis‐15 18:2 and trans‐10,cis‐12,cis‐15 18:3, although none of these have been found in the rumen. We analyzed digestive contents and meat samples from two trials, where animals were fed: a compound feed diet supplemented with 8 % oil blend containing linseed oil (samples A); and a forage based diet supplemented with 6 % linseed oil (samples B). The use of the new SLB‐IL111 chromatographic column allowed the detection of two different 18:2 isomers in each sample trial, which could not be resolved when the CP‐Sil 88 column is used. The two 18:2 isomers were characterized by mass spectrometry using 4,4‐dimethyloxazoline derivatives. However, because they were subject to higher temperatures and present different chromatographic properties compared with the fatty acid methyl esters, we also used the “covalent adduct chemical ionization” technique to confirm the identity of both 18:2 isomers. We detected and identified the 10,15‐18:2 in samples A and the 11,15‐18:2 in samples B. The geometry of both isomers was tentatively assigned as trans,cis taking in account their elution order and biologic plausibility. As far as we know, this is the first time that the trans‐10,cis‐15 18:2 has been found in ruminant digestive contents and meat samples associated with the “trans‐10 shifted” biohydrogenation pathway of α‐linolenic acid.
Evaluation of Groundwater Vulnerability in the Lower Varuna Catchment Area, Uttar Pradesh, India using AVI Concept
Authors: Raju N. Janardhana , Ram Prahlad , Gossel Wolfgang 
Published: March 2014

Abstract
Groundwater vulnerability assessments calculate the sensitivity of quality of groundwater to an imposed contaminant load which is essential element of the aquifer management plans. Seventy five groundwater samples have been analyzed for different chemical parameters to understand the groundwater quality of the lower Varuna river basin, Uttar Pradesh, India. The intrinsic groundwater vulnerability map of the lower Varuna catchment area in the north of the city of Varanasi (India) shows a high dependency on the depth to groundwater. The topmost layer of alluvial silty clay, protects the groundwater against contamination in this urban area, but the retention time in the unsaturated zone can be estimated to several months only. The input dataset is very sparse i.e. groundwater levels were measured twice (pre- and post-monsoon 2009) and the geological map shows only alluvium as the outcrop. Several boreholes in this area show, that the alluvium has a thickness of about 4 m and below that are fine grained sands. The surface information does not allow the development of a risk map since land use changes very fast and contamination areas can not be identified accurately. The vulnerability maps developed in this study have become important tools for environmental planning and predictive management of the groundwater resources in the fast urbanizing region in the Varanasi area.
Delineation of Fresh Aquifers in Tannery Belt for Sustainable Development – A Case Study from Southern India
Authors: Sonkamble Sahebrao , Kumar V. Satish , Amarender B. , Dhunde, P.M. , Sethurama S. , Kumar K. Raj 
Published: March 2014

Abstract
The tannery effluents discharged by the existing units on either side of the Palar river at Ambur town (known for tannery industry), has resulted in vertical and lateral spread of pollution. The study area of 55.3 km2 is situated on a granitic terrain of Archaean age with undulating topography and hillocks. The shallow aquifers, in flood plain and valley fills of the river are highly polluted (with EC: 15340 μS/cm) by tannery effluents making groundwater unfit for any use, hence the local population (20000) face health hazards and shortage of potable water. Hydrogeological, geophysical and in-situ groundwater quality measurement were carried out to demarcate fresh groundwater zones and to delineate lateral and vertical extent of pollution. The results show, brackish aquifer was characterized by low order of resistivity (&lt;20 Ω-m) with a thickness of 8.5 to 28 m located in the flood plains, valley fills, and partially in hard rock formations, whereas the fresh water aquifer resistivity varying from 23 to 216 Ω-m in hard rock. Further, these results were correlated with the water quality data and Ground Penetrating Radar (GPR) signals. The integrated studies revealed that pollution due to tannery effluents has spread over an area of 33.4 km2 (60.4 %) on either side of the river and only a small area of 21.9 km2 (39.6 %) was identified as fresh groundwater zone, which has to be conserved and exploited in sustainable manner for future generations.
Carbonate Diagenesis of the Upper Jurassic Successions in the West of Binalud - Eastern Alborz (NE Iran)
Authors: Aghaei Ali , Mahboubi Asadollah , Harami Reza Moussavi , Nadjafi Mahdi , Chakrapani Govind Joseph 
Published: March 2014

Abstract
The upper Jurassic carbonate settings in Iran are widely exposed in north and northeastern parts. Five stratigraphic columns were selected in the north eastern Iran. Their thickness ranges from 330 to 500 m. The various diagenetic processes identified include, micritization, cementation, compaction (physical and chemical), dissolution, neomorphism, pyritization, hematitization, silicification and dolomitization, which affected these carbonates. Elemental and stable isotopes analysis indicated that these deposits have undergone both meteoric and burial diagenesis in a relatively open system with moderate water-rock interaction. The positive trend between trace elements and oxygen isotope depletion also support these burial conditions. Lighter δl8O values of the dolomite samples may be related to an increase in temperature during the burial, which correspond to coarser euhedral crystals. Relatively higher δ18O values in finer dolomite crystals indicate their formation at lower burial depths relative to coarser crystals. Petrographic evidences such as coarse euhedral crystals with bright and dull zonation prove this interpretation. Chert nodules also have lighter 18O values relative to carbonate host rock, thus indicating the influence of burial diagenetic processes in their formation. The average environmental palaeotemperature was estimated to be 26°C on the basis of oxygen isotope values of less altered lime-mudstones.
RELATIVE PRODUCTIVITY, PROFITABILITY AND WATER USE EFFICIENCY OF CROPPING SYSTEMS IN HOT ARID INDIA
Authors: RATHORE V. S. , NATHAWAT N. S. , MEEL B. , YADAV B. M. , SINGH J. P. 
Published: March 2014

SUMMARYThe choice of an appropriate cropping system is critical to maintaining or enhancing agricultural sustainability. Yield, profitability and water use efficiency are important factors for determining suitability of cropping systems in hot arid region. In a two-year field experiment (2009/10–2010/11) on loam sandy soils of Bikaner, India, the production potential, profitability and water use efficiency (WUE) of five cropping systems (groundnut–wheat, groundnut–isabgol, groundnut–chickpea, cluster bean–wheat and mung bean–wheat) each at six nutrient application rate (NAR) i.e. 0, 25, 50, 75, 100% recommended dose of N and P (NP) and 100% NP + S were evaluated. The cropping systems varied significantly in terms of productivity, profitability and WUEs. Averaged across nutrient application regimes, groundnut–wheat rotation gave 300–1620 kg ha−1and 957–3365 kg ha−1higher grain and biomass yields, respectively, than other cropping systems. The mean annual net returns were highest for the mung bean–wheat system, which returned 32–57% higher net return than other cropping systems. The mung bean–wheat and cluster bean–wheat systems had higher WUE in terms of yields than other cropping systems. The mung bean–wheat system recorded 35–63% higher WUE in monetary terms compared with other systems. Nutrients application improved yields, profit and WUEs of cropping systems. Averaged across years and cropping systems, the application of 100% NP improved grain yields, returns and WUE by 1.7, 3.9 and 1.6 times than no application of nutrients. The results suggest that the profitability and WUEs of crop production in this hot arid environment can be improved, compared with groundnut–wheat cropping, by substituting groundnut by mung bean and nutrients application.
The causal nature of the association between neighborhood deprivation and drug abuse: a prospective national Swedish co-relative control study
Authors: Kendler K. S. , Ohlsson H. , Sundquist K. , Sundquist J. 
Published: March 2014

BackgroundRisk for drug abuse (DA) is strongly associated with neighborhood social deprivation (SD). However, the causal nature of this relationship is unclear.MethodThree Swedish population-based cohorts were followed up over 5 years for incident registration of DA in medical, legal or pharmacy records. In each cohort, we examined the SD–DA association, controlling carefully for individual socio-economic status (SES) with multiple measures, in the entire sample and among pairs of first cousins, paternal and maternal half-siblings, full siblings and monozygotic (MZ) twins discordant for SD exposure. The number of informative relative pairs ranged from 6366 to 166 208.ResultsIn all cohorts, SD was prospectively related to risk for incident DA. In relative pairs discordant for SD exposure, the SD–DA association was similar to that seen in the entire population in cousins, half-siblings, full siblings and MZ twins. Eliminating subjects who were residentially unstable or had DA in the first two follow-up years did not alter this pattern. When divided by age, in the youngest groups, the SD–DA association was weaker in siblings than in the entire population.ConclusionsAcross three cohorts, controlling for individual SES and confounding familial factors, SD prospectively predicted risk for incident DA registration. These results support the hypothesis that the SD–DA association is in part causal and unlikely to result entirely from personal attributes, which both increase risk for DA and cause selection into high SD environments. At least part of the SD–DA association arises because exposure to SD causes an increased risk of DA.
The Distribution of Household Income in China: Inequality, Poverty and Policies
Authors: Li Shi , Sicular Terry 
Published: March 2014

AbstractThis article examines recent trends in inequality and poverty and the effects of distributional policies in China. After a discussion of data and measurement issues, we present evidence on national, as well as rural and urban, inequality and poverty. We critically examine a selection of policies pursued during the Hu–Wen decade that had explicit distributional objectives: the individual income tax, the elimination of agricultural taxes and fees, minimum wage policies, the relaxation of restrictions on rural–urban migration, the minimum living standard guarantee programme, the “open up the west” development strategy, and the development-oriented rural poverty reduction programme. Despite these policies, income inequality in China increased substantially from the mid-1990s through to 2008. Although inequality stabilized after 2008, the level of inequality remained moderately high by international standards. The ongoing urban–rural income gap and rapid growth in income from private assets and wealth have contributed to these trends in inequality. Policies relaxing restrictions on rural–urban migration have moderated inequality. Our review of selected distributional policies suggests that not all policy measures have been equally effective in ameliorating inequality and poverty.