bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silage Fermentation of PM‐ and AM‐Cut Alfalfa Wilted in Wide and Narrow Swaths
Authors: Tremblay Gaëtan F. , Morin Chantale , Bélanger Gilles , Bertrand Annick , Castonguay Yves , Berthiaume Robert , Allard Guy 
Published: December 2013

ABSTRACTNonstructural carbohydrate (NSC) concentration in alfalfa (Medicago sativa L.) increases by cutting in the afternoon (PM) and wilting in wide swaths but the impact of this greater concentration during silage fermentation is not well known. We determined if increased NSC concentration associated with PM‐cutting and wide swathing is maintained during fermentation and whether it affects conservation attributes of wilted alfalfa silages. The cutting time effect was measured in spring growth and summer regrowth of 2007 and 2008 (Experiment 1) while the combined effect of cutting time and swathing type was measured in spring growth and summer regrowth of 2008 (Experiment 2). Alfalfa was field wilted [≈390 g dry matter (DM) kg−1 fresh matter] and ensiled in mini‐silos. Differences in alfalfa NSC concentration at ensiling (10 to 36 g kg−1 DM) due to PM‐cutting combined or not with wide swaths were reduced during silage fermentation to between 0 and 15 g kg−1 DM mostly through a reduction in soluble carbohydrate concentration. When NSC concentration differences at ensiling were > 10 g kg−1 DM, silage conservation attributes were improved with lower pH (−0.2 to −0.4), greater concentrations of lactate (+8 to +20 g kg−1 DM), and lower concentrations of volatile fatty acids (−8 to −11 g kg−1 DM) and NH3–N (−6 to −11 g kg−1 total N). Improved silage conservation attributes along with a greater residual starch concentration from NSC‐enriched alfalfa has the potential to improve milk production.
Haplotype Classification Using Copy Number Variation and Principal
Components Analysis
Authors: Blighe Kevin 
Published: December 2013

Elaborate downstream methods are required to analyze large microarray data-sets. At times, where the end goal
is to look for relationships between (or patterns within) different subgroups or even just individual samples, large data-sets
must first be filtered using statistical thresholds in order to reduce their overall volume. As an example, in anthropological
microarray studies, such ‘dimension reduction’ techniques are essential to elucidate any links between polymorphisms and
phenotypes for given populations. In such large data-sets, a subset can first be taken to represent the larger data-set. For
example, polling results taken during elections are used to infer the opinions of the population at large. However, what is
the best and easiest method of capturing a sub-set of variation in a data-set that can represent the overall portrait of
variation?
In this article, principal components analysis (PCA) is discussed in detail, including its history, the mathematics behind
the process, and in which ways it can be applied to modern large-scale biological datasets. New methods of analysis using
PCA are also suggested, with tentative results outlined.
Normal dimensions of the posterior pituitary bright spot on magnetic resonance imaging
Authors: Côté Martin , Salzman Karen L. , Sorour Mohammad , Couldwell William T. 
Published: December 2013

Object
The normal pituitary bright spot seen on unenhanced T1-weighted MRI is thought to result from the T1-shortening effect of the vasopressin stored in the posterior pituitary. Individual variations in its size may be difficult to differentiate from pathological conditions resulting in either absence of the pituitary bright spot or in T1-hyperintense lesions of the sella. The objective of this paper was to define a range of normal dimensions of the pituitary bright spot and to illustrate some of the most commonly encountered pathologies that result in absence or enlargement of the pituitary bright spot.

Methods
The authors selected normal pituitary MRI studies from 106 patients with no pituitary abnormality. The size of each pituitary bright spot was measured in the longest axis and in the dimension perpendicular to this axis to describe the typical dimensions. The authors also present cases of patients with pituitary abnormalities to highlight the differences and potential overlap between normal and pathological pituitary imaging.

Results
All of the studies evaluated were found to have pituitary bright spots, and the mean dimensions were 4.8 mm in the long axis and 2.4 mm in the short axis. The dimension of the pituitary bright spot in the long axis decreased with patient age. The distribution of dimensions of the pituitary bright spot was normal, indicating that 99.7% of patients should have a pituitary bright spot measuring between 1.2 and 8.5 mm in its long axis and between 0.4 and 4.4 mm in its short axis, an interval corresponding to 3 standard deviations below and above the mean. In cases where the dimension of the pituitary bright spot is outside this range, pathological conditions should be considered.

Conclusions
The pituitary bright spot should always be demonstrated on T1-weighted MRI, and its dimensions should be within the identified normal range in most patients. Outside of this range, pathological conditions affecting the pituitary bright spot should be considered.
Cerebrospinal fluid white blood cell counts in infants with myelomeningoceles
Authors: Albright A. Leland , Ferson Susan S. , Okechi Humphrey 
Published: December 2013

Object
The authors undertook this study to determine white blood cell (WBC) counts in CSF obtained from lateral ventricles and myelomeningoceles (MMCs) in infants in a developing country at the time of their initial presentation for medical evaluation.

Methods
CSF was aspirated from the lateral ventricles and from MMC sacs of 100 consecutive infants at Kijabe Hospital, Kijabe, Kenya. Peripheral blood WBC counts and CSF WBC counts were determined in the laboratory. CSF with WBC counts of 5 cells/mm3 or greater was cultured.

Results
The mean WBC count in ventricular CSF was 16 cells/mm3, with a median and mode of 0 cells/mm3. The mean WBC count of CSF in MMC sacs was 141 cells/mm3 (median 15 cells/mm3). No child had both a positive culture from ventricular CSF and a negative culture from MMC CSF. There was no correlation between age at presentation and WBC counts in the MMCs. Infants younger than 8 days old were as likely to have high WBC counts in CSF from their MMC sacs as were older children; 7 of 12 infants with 500 WBCs or more in CSF from their MMCs were younger than 8 days old. Only 5 of 58 CSF specimens from MMC sacs with 5 or more WBCs/mm3 had positive bacterial cultures, which may be a reflection of CSF specimen processing rather than of true culture negativity.

Conclusions
CSF from ventricular fluid of infants presenting with MMCs infrequently has high WBC counts, so infrequently that it does not need to be evaluated routinely. CSF in MMC sacs often has high WBC counts that suggest the presence of bacterial infection. In developing countries where culture reliability is questionable, intravenous administration of antibiotics before MMC closure for infants with high MMC WBC counts may diminish postoperative meningitis/ventriculitis.
Slave Trade, Commercial Organization and Industrial Growth in Eighteenth-Century Nantes
Authors: Boulle Pierre H. 
Published: December 2013

The slave trade was one of the important motors of economic concentration in the eighteenth century. One thesis would even have it that, in England, this commerce was closely tied to the Industrial Revolution. Gaston Martin has suggested a similar pattern in the case of Nantes, the first slave-trading port of France, around which a true industrial revolution is supposed to have taken place, thanks to the armateurs' economic concentration. Hence, the case of Nantes may reveal something about French economie transformation and its limits in the eighteenth century.
Such a concentration, based on a rational organization of commerce, took place within Nantes' slave-trading oligarchy between 1730 and 1755. There, unlike in other ports, the effect of this concentration was not dissipated through heavy non-commercial investments. Rather, accumulated capital was used to expand the trade's impact, especially through investments in local industries (mostly textiles), the character of which was remarkably modem (quantity replaced quality ; a modem financial structure was adopted ; labor problems and competition arose). However, the Seven Years' War interrupted the Atlantic trade. Nantes, over-specialized, suffered more than other ports. Traditional investments having regained their the postwar period saw the old slave-trading families replaced by more cautious and less specialized armateurs. Furthermore, the era being characterized by lower profits, less risk capital was available to industry. The port's industrial growth was stopped and modernization not pursued.
Thus, the Seven Years' War is a turning point for Nantes' economy. The fragility and isolation of the latter may be fundamental causes of the city's failure to industrialize, but these weaknesses had been overcome earlier. Therefore, the French fleet's powerlessness to protect the merchant navy was an important factor in the French eighteenth-century failure to keep up with England in the industrial realm.
18F, 11C and 68Ga in small animal PET imaging
Authors: Muellauer J. , Willimayer R. , Goertzen A. L. , Wanek T. , Langer O. , Birkfellner W. , Kuntner C. 
Published: December 2013

Summary
Aim: The partial volume effect (PVE) significantly affects quantitative accuracy in PET. In this study we used a micro-hollow sphere phantom filled with 18F, 11C or 68Ga to evaluate different partial volume correction methods (PVC). Additionally, phantom data were applied on rat brain scans to evaluate PVC methods on in vivo datasets. Methods: The four spheres (7.81, 6.17, 5.02, 3.90 mm inner diameter) and the background region were filled to give sphere-to-background (sph/bg) activity ratios of 20 : 1, 10 : 1, 5 : 1 and 2 : 1. Two different acquisition and reconstruction protocols and three radionuclides were evaluated using a small animal PET scanner. From the obtained images the recovery coefficients (RC) and contrast recovery coefficients (CRC) for the different sph/bg ratios were calculated. Three methods for PVC were evaluated: a RC based, a CRC based and a volume of interest (VOI) based method. The most suitable PVC methods were applied to in vivo rat brain data. Results: RCs were shown to be dependent on the radionuclide used, with the highest values for 18F, followed by 11C and 68Ga. The calculated mean CRCs were generally lower than the corresponding mean RCs. Application of the different PVC methods to rat brain data led to a strong increase in time-activity curves for the smallest brain region (entorhinal cortex), whereas the lowest increase was obtained for the largest brain region (cerebellum). Conclusion: This study was able to show the importance and impact of PVE and the limitations of several PVC methods when performing quantitative measurements in small structures.
Longitudinal Changes in Health-Related Quality of Life Scores in Brazilian Incident Peritoneal Dialysis Patients (Brazpd): Socio-Economic Status Not a Barrier
Authors: Grincenkov Fabiane Rossi dos Santos , Fernandes Natália , Chaoubah Alfredo , da Silva Fernandes Neimar , Bastos Kleyton , Lopes Antonio Alberto , Qureshi Abdul Rashid , Finkelstein Fredric O. , Pecoits–Filho Roberto , Divino–Filho José Carolino , Bastos Marcus Gomes 
Published: December 2013

Background and Objectives A large proportion of the patients on peritoneal dialysis (PD) in Brazil have low levels of education and family income. The present study assessed whether education level and family income are associated with baseline and longitudinal changes in health-related quality of life (HRQOL) scores during the first year of PD therapy. Methods We evaluated 1624 incident patients from the Brazilian Peritoneal Dialysis Multicenter Study (BRAZPD) at baseline, and 486 of them after 12 months. The SF-36 was used to determine HRQOL and the Karnofsky index (KI), physical performance. Results At baseline, patients received high KI scores compared with scores on the SF-36. The means of the mental and physical components at baseline and after 12 months were 39.9 ± 10.5 compared with 38.7 ± 11.7 and 41.8 ± 9.6 compared with 40.7 ± 9.8 respectively, which were not statistically different. A multivariate regression analysis showed that age, sex, diabetes, and cardiovascular disease were predictors of the mental component (respectively, β = 0.12, p < 0.001; β = 0.11, p < 0.001; β = –0.08, β = 0.007; and β = –0.07, p = 0.007) and that age, sex, diabetes, cardiovascular disease, hemoglobin, glucose, and creatinine were predictors of the physical component (respectively, β = –0.28, p < 0.001; β = 0.06, p = 0.009; β = –0.09, p = 0.002; β = –0.09, p = 0.001; β = 0.07, p = 0.004; β = –0.05, p = 0.040; and β = 0.05, p = 0.040). Education level and family income were not significantly associated with HRQOL (mental and physical components) in the multivariate regression. Conclusions The results indicate that, as predictors, family income and education level have no impact on HRQOL, supporting the idea that socio-economic status should not be a barrier to the selection of PD as a treatment modality in Brazil.
Metabolic Implications of Peritoneal Dialysis in Patients with Acute Kidney Injury
Authors: Góes Cassiana Regina , Berbel Marina Nogueira , Balbi Andre Luis , Ponce Daniela 
Published: December 2013

Background Peritoneal dialysis (PD) is a treatment for selected acute kidney injury patients (AKI), but little is known about its metabolic implications. The aim of the present study was to evaluate the metabolic implications of glucose absorption, sodium removal, protein loss into the dialysate, and catabolism in AKI patients undergoing high-volume PD and to identify risk factors associated with those metabolic effects. Methods A prospective cohort study over 18 consecutive months evaluated 208 sessions of high-volume PD performed in 31 AKI patients. One session of high-volume PD lasted 24 hours. Repeated-measures analysis was performed, and correlations were calculated using the Spearman test for continuous variables and generalized linear models for categorical variables. Results Glucose absorption remained at approximately 35.3% ± 10.5% per session. Protein loss measured 4.2 ± 6.1 g daily, with higher values initially, which declined significantly after 2 sessions. Nitrogen balance (NB) was initially negative, but stabilized at approximately zero after 3 sessions. Glucose uptake was positively correlated with the Acute Tubular Necrosis Individual Severity Score [ATNISS ( r = 0.21, p = 0.0036)], C-reactive protein ( r = 0.26, p = 0.0167), protein loss ( r = 0.36, p < 0.0001), and sodium removal ( r = 0.24, p = 0.002). Protein loss was positively correlated with sodium removal ( r = 0.22, p = 0.0085) and gastrointestinal disease ( p = 0.0004). Sodium removal was positively correlated with serum sodium ( r = 0.21, p = 0.0064), ATNISS ( r = 0.15, p = 0.0411), urea nitrogen appearance [UNA ( r = 0.24, p = 0.0019)], and fluid overload as an indication for dialysis ( p < 0.0001). Urea nitrogen appearance was positively correlated with the indication for dialysis (electrolyte disturbances: p = 0.0287) and negatively correlated with nephrotoxic AKI ( p < 0.0001). Nitrogen balance was negatively correlated with UNA ( r = –0.389, p < 0.0001) and ischemic AKI ( p = 0.0047). Conclusions High-volume PD did not increase hypercatabolism in AKI patients, and protein loss and glucose uptake remained constant during treatment. Those parameters were influenced by the clinical condition of the patients, including the cause of AKI, inflammation, and comorbidities—factors that should be known before the prescription of dialysis and nutrition, thus avoiding metabolic complications such as hyperglycemia, hypernatremia, and worsening catabolism.
Let's Use Haptics!
Authors: Quintas Manuel Rodrigues , Restivo Maria Teresa , Rodrigues José , Ubaldo Pedro 
Published: December 2013

The concept and the use of haptic devices need to be disseminated and they should become familiar among young people. At present haptics are used in many everyday tasks in different fields.
Additionally, their use in interaction with virtual reality applications simulating real systems sense of touch will increase the usersâ?? realism and immersion and, consequently, they will contribute to improve the intrinsic knowledge to the simulationsâ?? goals.
However, haptics are associated with expensive equipment and usually they offer several degrees of freedom. The objective of this work is to make their cost not much more expensive than a â??specialâ? mouse by offering a low cost solution with just one degree of freedom (1DOF) useful in many simple cases.
Additionally, it is also an objective of this work the development of simple virtual reality systems requiring interactions only requiring one degree of freedom.
A low cost, single-axis force-feedback haptic device of 1 degree of freedom has been developed. For evaluating the interest of this prototype a â??Spring Constantâ? application was built and used as a demonstrator. The complete system - the haptic interacting with the â??Spring Constantâ? - will be described in the present work.
STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post‐Translational Modifications
Authors: Spencer Jean L. , Bhatia Vivek N. , Whelan Stephen A. , Costello Catherine E. , McComb Mark E. 
Published: December 2013

AbstractThe identification of protein post‐translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography–tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post‐Translational Modification edition) is a program that was developed to facilitate the characterization of PTMs using spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs from complex data sets. The software facilitates multi‐sample comparison by collating, scoring, and ranking PTMs, and by summarizing data visually. The freely available software (beta release) installs on a PC and processes data in protXML format obtained from files parsed through the Trans‐Proteomic Pipeline. The easy‐to‐use interface allows examination of results at protein, peptide, and PTM levels, and the overall design offers tremendous flexibility that provides proteomics insight beyond simple assignment and counting. Curr. Protoc. Bioinform. 44:13.22.1‐13.22.36. © 2013 by John Wiley & Sons, Inc.
Land‐atmosphere coupling manifested in warm‐season observations on the U.S. southern great plains
Authors: Phillips Thomas J. , Klein Stephen A. 
Published: December 2013

AbstractThis study examines several observational aspects of land‐atmosphere coupling on daily average time scales during warm seasons of the years 1997 to 2008 at the Department of Energy Atmospheric Radiation Measurement Program's Southern Great Plains (SGP) Central Facility site near Lamont, Oklahoma. Characteristics of the local land‐atmosphere coupling are inferred by analyzing the covariability of selected land and atmospheric variables that include precipitation and soil moisture, surface air temperature, relative humidity, radiant and turbulent fluxes, as well as low‐level cloud base height and fractional coverage. For both the energetic and hydrological aspects of this coupling, it is found that large‐scale atmospheric forcings predominate, with local feedbacks of the land on the atmosphere being comparatively small much of the time. The relatively weak land feedbacks are manifested especially by (1) the inability of soil moisture to comprehensively impact the coupled land‐atmosphere energetics and (2) the limited recycling of local surface moisture under conditions where most of the rainfall derives from convective cells that originate at remote locations. There is some evidence, nevertheless, that the local land feedback becomes stronger as the soil dries out in the aftermath of precipitation events, or on days when the local boundary layer clouds are influenced by thermal updrafts associated with convection that originates at the surface. Potential implications of these results for climate‐model representation of regional land‐atmosphere coupling also are discussed.
Adaptive air–fuel ratio control scheme and its experimental validations for port‐injected spark ignition engines
Authors: Jiao Xiaohong , Zhang Jiangyan , Shen Tielong , Kako Junichi 
Published: December 2013

SUMMARYTo maintain the stoichiometric air–fuel ratio (AFR), this paper presents a model‐based adaptive AFR control scheme for port‐injected spark ignition engines. The utilized mean‐value model in control design accounts for the impingement and the evaporation process of the injected fuel on the walls and calculates on the uncertainties in the dynamics of the intake manifold and crankshaft rotation. A fueling controller with adaptive update laws is derived for estimating the uncertain parameters related to inaccuracies in air flow and fuel delivery into the cylinders and engine torque production, which is implemented by utilizing engine speed, manifold pressure and temperature, air mass flow rate at the throttle, and the universal exhaust gas oxygen (UEGO) sensor information, without knowledge of the fuel flow mass. Theoretical analysis shows that the proposed strategy is able to regulate the AFR against the parameter uncertainties. Moreover, both simulation and experiment on an engine test bench demonstrate the capability of the adaptive controller to recover the performance and robustness properties of the control system in the presence of various operating conditions and uncertainties including air path and fuel path perturbations and load torque disturbance as well. Copyright © 2013 John Wiley & Sons, Ltd.
Potocki–shaffer deletion encompassing ALX4 in a patient with frontonasal dysplasia phenotype
Authors: Ferrarini Alessandra , Gaillard Muriel , Guerry Frederic , Ramelli Gianpaolo , Heidi Fodstad , Keddache Caroline Verley , Wieland Ilse , Beckmann Jacques S. , Jaquemont Sébastien , Martinet Danielle 
Published: December 2013

ABSTRACTFrontonasal dysplasia (FND) is a genetically heterogeneous malformation spectrum with marked hypertelorism, broad nasal tip and bifid nose. Only a small number of genes have been associated with FND phenotypes until now, the first gene being EFNB1, related to craniofrontonasal syndrome (CFNS) with craniosynostosis in addition, and more recently the aristaless‐like homeobox genes ALX3, ALX4, and ALX1, which have been related with distinct phenotypes named FND1, FND2, and FND3 respectively. We here report on a female patient presenting with severe FND features along with partial alopecia, hypogonadism and intellectual disability. While molecular investigations did not reveal mutations in any of the known genes, ALX4, ALX3, ALX1 and EFNB1, comparative genomic hybridization (array CGH) techniques showed a large heterozygous de novo deletion at 11p11.12p12, encompassing the ALX4 gene. Deletions in this region have been described in patients with Potocki–Shaffer syndrome (PSS), characterized by biparietal foramina, multiple exostoses, and intellectual disability. Although the patient reported herein manifests some overlapping features of FND and PPS, it is likely that the observed phenotype maybe due to a second unidentified mutation in the ALX4 gene. The phenotype will be discussed in view of the deleted region encompassing the ALX4 gene. © 2013 Wiley Periodicals, Inc.