bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioseparation in Antibody Manufacturing: The Good, The Bad and The Ugly
Authors: Gottschalk Uwe 
Published: April 2008

AbstractImprovements in upstream production have boosted productivity in the biomanufacturing industry, but this is leading to bottlenecks in downstream processing as current technology platforms reach their limits of throughput and scalability. Although chromatography remains an indispensible component of downstream processing due to its simplicity and high resolving power (The Good), there is virtually no economy of scale effect so more product translates almost linearly into greater production costs. Bind‐and‐elute processes (such as the initial capture step in antibody manufacturing) are volume‐driven and therefore have knock‐on effects that impact on the entire production facility since the space required for preparation, storage, and cleaning steps has to be similarly adapted (The Bad). During long‐term operations with multiple cycles, thorough cleaning is necessary to prevent progressive fouling and microbial contamination (The Ugly). Innovative solutions are required, which may include revisiting simpler and less expensive separation technologies, the use of disposable modules, and the integration of improved processes that are scalable to cope with increased demands. Among the alternatives that have been put forward, membrane adsorbers are beginning to make a real impact on the industry, particularly for flow‐through applications such as polishing and viral clearance.
LAVH for large uteri by various strategies
Authors: CHANG WEN‐CHUN , HUANG SU‐CHENG , SHEU BOR‐CHING , TORNG PAO‐LING , HSU WEN‐CHIUNG , CHEN SZU‐YU , CHANG DAW‐YUAN 
Published: April 2008

AbstractBackground. To study if there are specific problems in laparoscopically assisted vaginal hysterectomy (LAVH) for a certain weight of bulky uteri and the strategies to overcome such problems. Methods. One hundred and eighty‐one women with myoma or adenomyosis, weighing 350‐1,590 g, underwent LAVH between August 2002 and December 2005. Key surgical strategies were special sites for trocar insertion, uterine artery or adnexal collateral pre‐ligation, laparoscopic and transvaginal volume reduction technique. The basic clinical and operative parameters were recorded for analysis. Results. Based on significant differences in the operative time and estimated blood loss, the patients were divided into medium uteri weighing 350–749 g, n = 138 (76%), and large uteri weighing ≥750 g, n = 43 (24%). There was no significant difference in terms of age, body mass index, preoperative diagnoses, complications and duration of hospital stay among groups. The operative time and estimated blood loss increased with larger uterine size (p<0.001). The operative time (196±53, 115–395 min), estimated blood loss (234±200, 50–1,000 ml) and frequency of excessive bleeding (14%) or transfusion (5%) were significantly greater, but in acceptable ranges, for those with large uteri. Conversion to laparotomy was required in a patient (2%) with a large uterus, and the overall conversion rate was 0.6%. There was no re‐operation or surgical mortality. Conclusion. Using various combinations of special strategies, most experienced gynecologic surgeons can conduct LAVH for most large uteri with minimal rates of complications and conversion to laparotomy.
Relationship between perceptual ratings of nasality and nasometry in children/adolescents with cleft palate and/or velopharyngeal dysfunction
Authors: Sweeney Triona , Sell Debbie 
Published: April 2008

Background: Nasometry has supplemented perceptual assessments of nasality, using speech stimuli, which are devoid of nasal consonants. However, such speech stimuli are not representative of conversational speech. A weak relationship has been found in previous studies between perceptual ratings of hypernasality and nasalance scores for passages containing nasal consonants.Aims: This study aimed to evaluate the relationship between perceptual assessment and acoustic measurements of nasality using controlled speech stimuli.Methods & Procedure: A perceptual scale (the Temple Street Scale) describing nasality was devised for this study. Fifty children presenting with nasality were assessed using the Temple Street Scale and nasalance scores were obtained for specified speech samples using the Nasometer (Kay Elemetrics 6200.3). The relationship between the perceptual ratings and the nasometry results was evaluated using correlation analysis, test sensitivity, specificity, and overall efficiency.Outcomes & Results: Correlation coefficients for perceptual ratings of nasality and nasalance scores ranged from 0.69 to 0.74. The sensitivity of the Nasometer ranged from 0.83 to 0.88; its specificity ranged from 0.78 to 0.95; while its overall efficiency was between 0.82 and 0.92.Conclusions: The strong relationship between perceptual and acoustic assessments of nasality indicated that the Temple Street Scale and the Nasometer are both valid clinical tools for the evaluation of nasality when a carefully constructed speech sample is used. The need to use the Nasometer as a supplement to perceptual assessment is highlighted.
Grammaticality judgements in adolescents with and without language impairment
Authors: Miller Carol A. , Leonard Laurence B. , Finneran Denise 
Published: April 2008

Background: Existing evidence suggests that young children with specific language impairment have unusual difficulty in detecting omissions of obligatory tense‐marking morphemes, but little is known about adolescents' sensitivity to such violations.Aims: The study investigated whether limitations in receptive morphosyntax (as measured by grammaticality judgements) were present at age 16 years, and, if so, whether participants' profiles showed less sensitivity to omissions of tense and agreement morphemes than to (1) inappropriate uses (intrusions) of these same morphemes, and (2) omissions of morphemes that do not encode tense and agreement. The study also compared adolescents with language impairment and non‐verbal IQ more than 1 standard deviation (SD) below the mean (non‐specific language impairment) to adolescents with specific language impairment.Methods & Procedures: Adolescents with specific language impairment (n = 48), adolescents with non‐specific language impairment (n = 25), and adolescents with normal language development (n = 108) performed speeded grammaticality judgements of sentences presented over headphones. Half the sentences were ungrammatical. They included omissions of non‐tense morphemes (‐ing and possessive ‐s), omissions of tense morphemes (‐ed and third‐person singular present ‐s), and intrusions of the same tense morphemes. The A′ statistic was used as the dependent variable for comparisons across groups and item types.Outcomes & Results: Overall, the normal language development group was more sensitive to grammatical violations than the specific language impairment and non‐specific language impairment groups, and there was no significant interaction of group and item type. Post‐hoc analyses showed that the specific language impairment group was less sensitive to violations than the normal language development group on each item type, and the specific language impairment and non‐specific language impairment groups did not differ. Across groups, performance on omission of past tense ‐ed was lowest, and properties of the items that may have contributed to this difference were explored.Conclusions: The adolescents with language impairment in this study showed evidence of reduced sensitivity to morphological errors, including both tense‐marking and non‐tense‐marking morphemes, but no evidence of any extraordinary difficulty in detecting the omission of tense‐marking morphemes, in contrast to results from other research on younger children with specific language impairment. Participants whose non‐verbal IQ score was too low to meet the criteria for specific language impairment performed similarly to their peers with specific language impairment. Grammatical competence is compromised in these adolescents with specific language impairment and non‐specific language impairment. Neither researchers nor clinicians can assume that adolescents with language impairment have fully mastered grammatical morphology.
Economic aspects of a therapy and support service for people with long‐term stroke and aphasia
Authors: van der Gaag Anna , Brooks Richard 
Published: April 2008

Backgound:This paper considers some economic aspects of a therapy and support service for people with stroke and aphasia. This material was part of a broader evaluation of the service, which is reported elsewhere (van derGaaget al.2005, van derGaag and Mowles 2005).Aims:The purpose of this part of the study was to investigate the feasibility of undertaking economic appraisal in a voluntary sector service providing therapy for people with aphasia and their families.Methods & Procedures:The costs of delivering therapy and support services were calculated. These costs were compared with the costs of equivalent services in the National Health Service (NHS). The EQ‐5D health‐related quality of life instrument was used to calculate quality‐adjusted life years (QALYs).Outcomes & Results:The cost of delivering therapy was lower than expected for a customized service of this nature. The study generated cost data for delivering therapy services, allowing some comparisons to be made with equivalent services in NHS settings. QALY data were generated for a sample of 25 clients on one of the programmes.Conclusions:The economics of speech and language therapy service delivery have received scant attention in the published literature. The paper argues that decision‐making about methods of service delivery can be aided by the explicit consideration of the costs and consequences of different programmes.
Variability of Spanish adolescents’ physical activity patterns by seasonality, day of the week and demographic factors
Authors: Peiró‐Velert Carmen , Devís‐Devís Jose , Beltrán‐Carrillo Vicente J. , Fox Kenneth R. 
Published: April 2008

AbstractIn this study, we examined the variability of physical activity (and inactivity) patterns in relation to gender, age, type of school, day of the week, and season of the year among a sample of Spanish adolescents aged 12–16 years. Levels of physical activity engagement, “who” was active/inactive, and “when” they were active/inactive were addressed. A Spanish translation and modification of Cale's Four by One‐Day Physical Activity Questionnaire was administered by interviewer to 323 participants to measure estimated energy expenditure. Activity was assessed for two weekdays and two weekend days on two occasions during the autumn and two occasions during the winter. In an effort to better describe adolescents’ active/inactive lifestyles, energy expenditures were translated into physical activity categories (i.e. active, moderately active, inactive, and very inactive). Results revealed that mean adolescent total daily energy expenditure was 41.46 kcal·kg−1·day−1 (s=7.05), which corresponded to the “active” category. Factorial and mixed analyses of variance showed statistically significant differences in energy expenditure by gender, season, day of the week, and type of school (P<0.001). Female adolescents spent less daily energy than their male counterparts and, consequently, they were less active overall, even though they were more moderately active than boys. Participants were more active in winter than in autumn, which was largely due to the accumulation of time engaged in more lifestyle activities than differences in strenuous exercise. Adolescents were also less active on weekdays than during weekends. An interaction effect emerged for day of the week and type of school with adolescents attending public (or state) schools presenting higher daily energy expenditures than those from private schools during weekends (P<0.01). The results suggest that girls may prefer less vigorous forms of activity. They also indicate that adolescents are investing time in physical activity when they have the freedom to participate or not (i.e. weekends), in particular those from public schools. We suggest that differences in gender, seasonality, and weekends versus weekdays, together with the choice of lifestyle activities, should be considered when designing activity promotion strategies among Spanish adolescents.
MAMOT: hidden Markov modeling tool
Authors: Schütz Frédéric , Delorenzi Mauro 
Published: April 2008

Abstract
Summary: Hidden Markov models (HMMs) are probabilistic models that are well adapted to many tasks in bioinformatics, for example, for predicting the occurrence of specific motifs in biological sequences. MAMOT is a command-line program for Unix-like operating systems, including MacOS X, that we developed to allow scientists to apply HMMs more easily in their research.
One can define the architecture and initial parameters of the model in a text file and then use MAMOT for parameter optimization on example data, decoding (like predicting motif occurrence in sequences) and the production of stochastic sequences generated according to the probabilistic model. Two examples for which models are provided are coiled-coil domains in protein sequences and protein binding sites in DNA. A wealth of useful features include the use of pseudocounts, state tying and fixing of selected parameters in learning, and the inclusion of prior probabilities in decoding.
Availability: MAMOT is implemented in C++, and is distributed under the GNU General Public Licence (GPL). The software, documentation, and example model files can be found at http://bcf.isb-sib.ch/mamot
Contact: Mauro.Delorenzi@isb-sib.ch
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Authors: Strimmer Korbinian 
Published: April 2008

AbstractSummary: False discovery rate (FDR) methodologies are essential in the study of high-dimensional genomic and proteomic data. The R package ‘fdrtool’ facilitates such analyses by offering a comprehensive set of procedures for FDR estimation. Its distinctive features include: (i) many different types of test statistics are allowed as input data, such as P-values, z-scores, correlations and t-scores; (ii) simultaneously, both local FDR and tail area-based FDR values are estimated for all test statistics and (iii) empirical null models are fit where possible, thereby taking account of potential over- or underdispersion of the theoretical null. In addition, ‘fdrtool’ provides readily interpretable graphical output, and can be applied to very large scale (in the order of millions of hypotheses) multiple testing problems. Consequently, ‘fdrtool’ implements a flexible FDR estimation scheme that is unified across different test statistics and variants of FDR.Availability: The program is freely available from the Comprehensive R Archive Network (http://cran.r-project.org/) under the terms of the GNU General Public License (version 3 or later).Contact: strimmer@uni-leipzig.de
Acoustic seabed classification: current practice and future directions
Authors: Anderson John T. , Van Holliday D. , Kloser Rudy , Reid Dave G. , Simard Yvan 
Published: April 2008

Abstract
Anderson, J. T., Holliday, D. V., Kloser, R., Reid, D. G., and Simard, Y. 2008. Acoustic seabed classification: current practice and future directions. – ICES Journal of Marine Science, 65: 1004–1011. Acoustic remote sensing of the seabed using single-beam echosounders, multibeam echosounders, and sidescan sonars combined and individually are providing technological solutions to marine-habitat mapping initiatives. We believe the science of acoustic seabed classification (ASC) is at its nascence. A comprehensive review of ASC science was undertaken by an international group of scientists under the auspices of ICES. The review was prompted by the growing need to classify and map marine ecosystems across a range of spatial scales in support of ecosystem-based science for ocean management. A review of the theory of sound-scattering from seabeds emphasizes the variety of theoretical models currently in use and the ongoing evolution of our understanding. Acoustic-signal conditioning and data quality assurance before classification using objective, repeatable procedures are important technical considerations where standardization of methods is only just beginning. The issue of temporal and spatial scales is reviewed, with emphasis on matching observational scales to those of the natural world. It is emphasized throughout that the seabed is not static but changes over multiple time-scales as a consequence of natural physical and biological processes. A summary of existing commercial ASC systems provides an introduction to existing capabilities. Verification (ground-truthing) methods are reviewed, emphasizing the difficulties of matching observational scales with acoustic-backscatter data. Survey designs for ASC explore methods that extend beyond traditional oceanographic and fisheries survey techniques. Finally, future directions for acoustic seabed classification science were identified in the key areas requiring immediate attention by the international scientific community.
Vasoactive Hormones and the Diabetic Kidney
Authors: Maric Christine 
Published: April 2008

Diabetic nephropathy is the single most common cause of end-stage renal disease (ESRD) and accounts for significant morbidity and mortality. While the incidence of ESRD increased dramatically in the 1980s and 1990s, the U.S. Renal Data System (USRDS) 2005 Annual Data Report shows that 338 out of every million Americans had kidney failure in 2003, down slightly from 340 per million in 2002. This report shows that the numbers of people developing ESRD have stabilized despite the persistent increase in the number of people diagnosed with type 2 diabetes mellitus (T2DM). These data attest to both the efficacy of the currently available therapeutic regimens for the treatment of ESRD as well as better overall patient care. Unfortunately, these encouraging statistics do not apply to all patients. According to the USRDS report, the most marked ESRD decrease was seen in young Caucasian men (<40 years of age), while in other patient groups, particularly African Americans, ESRD has not changed much at all. These observations suggest that more in-depth studies, addressing specific issues, such as race, are needed to understand the disease process fully in order to create novel therapeutic strategies to eradicate the disease completely in all patient populations.The most commonly used therapeutic treatments for diabetic nephropathy are angiotensin-converting enzyme (ACE) inhibitors and angiotensin II (Ang II) receptor blockers (ARBs), implicating the importance of the renin-angiotensin-aldosterone system (RAAS) in the pathophysiology of diabetic nephropathy. The RAAS is not the only vasoactive hormonal system that is involved in the disease process. Over the past decade, studies have suggested that other vasoactive hormones, including endothelin, urotensin II, and the kallikrein-kinin system (KKS), are instrumental in mediating structural and functional alterations in the renal vasculature and parenchyma, leading to the development and progression of diabetic nephropathy. This review will summarize our current understanding of the contribution of vasoactive hormones in the pathophysiology of diabetic nephropathy with specific emphasis on the RAAS, especially the more recently identified components of this hormonal pathway.
Gene Expression and Metabolism in Tomato Fruit Surface Tissues
Authors: Mintz-Oron Shira , Mandel Tali , Rogachev Ilana , Feldberg Liron , Lotan Ofra , Yativ Merav , Wang Zhonghua , Jetter Reinhard , Venger Ilya , Adato Avital , Aharoni Asaph 
Published: April 2008

AbstractThe cuticle, covering the surface of all primary plant organs, plays important roles in plant development and protection against the biotic and abiotic environment. In contrast to vegetative organs, very little molecular information has been obtained regarding the surfaces of reproductive organs such as fleshy fruit. To broaden our knowledge related to fruit surface, comparative transcriptome and metabolome analyses were carried out on peel and flesh tissues during tomato (Solanum lycopersicum) fruit development. Out of 574 peel-associated transcripts, 17% were classified as putatively belonging to metabolic pathways generating cuticular components, such as wax, cutin, and phenylpropanoids. Orthologs of the Arabidopsis (Arabidopsis thaliana) SHINE2 and MIXTA-LIKE regulatory factors, activating cutin and wax biosynthesis and fruit epidermal cell differentiation, respectively, were also predominantly expressed in the peel. Ultra-performance liquid chromatography coupled to a quadrupole time-of-flight mass spectrometer and gas chromatography-mass spectrometry using a flame ionization detector identified 100 metabolites that are enriched in the peel tissue during development. These included flavonoids, glycoalkaloids, and amyrin-type pentacyclic triterpenoids as well as polar metabolites associated with cuticle and cell wall metabolism and protection against photooxidative stress. Combined results at both transcript and metabolite levels revealed that the formation of cuticular lipids precedes phenylpropanoid and flavonoid biosynthesis. Expression patterns of reporter genes driven by the upstream region of the wax-associated SlCER6 gene indicated progressive activity of this wax biosynthetic gene in both fruit exocarp and endocarp. Peel-associated genes identified in our study, together with comparative analysis of genes enriched in surface tissues of various other plant species, establish a springboard for future investigations of plant surface biology.
Tocotrienols, the Unsaturated Forms of Vitamin E, Can Function as Antioxidants and Lipid Protectors in Tobacco Leaves
Authors: Matringe Michel , Ksas Brigitte , Rey Pascal , Havaux Michel 
Published: April 2008

AbstractVitamin E is a generic term for a group of lipid-soluble antioxidant compounds, the tocopherols and tocotrienols. While tocotrienols are considered as important vitamin E components in humans, with functions in health and disease, the protective functions of tocotrienols have never been investigated in plants, contrary to tocopherols. We took advantage of the strong accumulation of tocotrienols in leaves of double transgenic tobacco (Nicotiana tabacum) plants that coexpressed the yeast (Saccharomyces cerevisiae) prephenate dehydrogenase gene (PDH) and the Arabidopsis (Arabidopsis thaliana) hydroxyphenylpyruvate dioxygenase gene (HPPD) to study the antioxidant function of those compounds in vivo. In young leaves of wild-type and transgenic tobacco plants, the majority of vitamin E was stored in thylakoid membranes, while plastoglobules contained mainly δ-tocopherol, a very minor component of vitamin E in tobacco. However, the vitamin E composition of plastoglobules was observed to change substantially during leaf aging, with α-tocopherol becoming the major form. Tocotrienol accumulation in young transgenic HPPD-PDH leaves occurred without any significant perturbation of photosynthetic electron transport. Tocotrienols noticeably reinforced the tolerance of HPPD-PDH leaves to high light stress at chilling temperature, with photosystem II photoinhibition and lipid peroxidation being maintained at low levels relative to wild-type leaves. Very young leaves of wild-type tobacco plants turned yellow during chilling stress, because of the strongly reduced levels of chlorophylls and carotenoids, and this phenomenon was attenuated in transgenic HPPD-PDH plants. While sugars accumulated similarly in young wild-type and HPPD-PDH leaves exposed to chilling stress in high light, a substantial decrease in tocotrienols was observed in the transgenic leaves only, suggesting vitamin E consumption during oxygen radical scavenging. Our results demonstrate that tocotrienols can function in vivo as efficient antioxidants protecting membrane lipids from peroxidation.