bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced protein-energy provision via the enteral route in critically ill patients: a single center feasibility trial of the PEP uP protocol
Authors: Heyland Daren K , Cahill Naomi E , Dhaliwal Rupinder , Wang Miao , Day Andrew G , Alenzi Ahmed , Aris Fiona , Muscedere John , Drover John W , McClave Stephen A 
Published: April 2010

Abstract
Introduction
The purpose of this pilot study is to assess the feasibility, acceptability, and safety of a new feeding protocol designed to enhance the delivery of enteral nutrition (EN).

Methods
In a prospective before and after study, we evaluated a new protocol compared to our standard feeding protocol. Innovative elements of the new protocol included setting daily volume based goals instead of hourly rate targets, initiating motility agents and protein supplements on Day 1, liberalizing the gastric residual volume threshold, and the option to use trophic feeds. Bedside nurses filled out questionnaires to assess the acceptability of the new approach and we assessed patients' nutritional and clinical outcomes.

Results
We enrolled 20 mechanically ventilated patients who stayed in the Intensive Care Unit for more than three days in the before group and 30 such patients in the after group. On a scale where 1 = totally unacceptable and 10 = totally acceptable, 30 nurses rated the new protocol as 7.1 (range 1 to 10) and no incidents compromising patient safety were observed. In the before group, on average, patients received 58.8% of their energy and 61.2% of their protein requirements by EN compared to 67.9% and 73.6% in the after group (P = 0.33 and 0.13). When the subgroup of patients prescribed to receive full volume feeds in the after group were evaluated (n = 18), they received 83.2% and 89.4% of their energy and protein requirements by EN respectively (P = 0.02 for energy and 0.002 for protein compared to the before group). The rates of vomiting, regurgitation, aspiration, and pneumonia were similar between the two groups.

Conclusions
This new feeding protocol seems to be safe and acceptable to critical care nurses. The adoption of this protocol may be associated with enhanced delivery of EN but further trials are warranted to evaluate its effect on nutritional and clinical endpoints.

Trial registration
ClinicalTrials.gov NCT01102348
Optimized design and data analysis of tag-based cytosine methylation assays
Authors: Suzuki Masako , Jing Qiang , Lia Daniel , Pascual Marién , McLellan Andrew , Greally John M 
Published: April 2010

AbstractUsing the type III restriction-modification enzyme EcoP15I, we isolated sequences flanking sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI isoschizomer for massively parallel sequencing. A novel data transformation allows us to normalise HpaII by MspI counts, resulting in more accurate quantification of methylation at >1.8 million loci in the human genome. This HELP-tagging assay is not sensitive to sequence polymorphism or base composition and allows exploration of both CG-rich and depleted genomic contexts.
Progressive Osseous Heteroplasia: A Model for the Imprinting Effects of GNAS Inactivating Mutations in Humans
Authors: Lebrun M. , Richard N. , Abeguilé G. , David A. , Dieux A. Coëslier , Journel H. , Lacombe D. , Pinto G. , Odent S. , Salles J. P. , Taieb A. , Gandon-Laloum S. , Kottler M. L. 
Published: April 2010

Abstract
Context: Heterozygous GNAS inactivating mutations are known to induce pseudohypoparathyroidism type 1a when maternally inherited and pseudopseudohypoparathyroidism when paternally inherited. Progressive osseous heteroplasia (POH) is a rare disease of ectopic bone formation, and studies in different families have shown that POH is also caused by paternally inherited GNAS mutations.
Objective: Our purpose was to characterize parental origin of the mutated allele in de novo cases of POH and to draw phenotype/genotype correlations according to maternal or paternal transmission of a same GNAS mutation.
Design and Setting: We conducted a retrospective study on patients addressed to our referral center for the rare diseases of calcium and phosphorus metabolism.
Patients and Methods: We matched 10 cases of POH with cases of pseudohypoparathyroidism type 1a carrying the same GNAS mutations.
Main Outcome Measures: The parental origin of the mutated allele was studied using informative intragenic polymorphisms and subcloning of PCR products.
Results: Paternal origin of GNAS mutations was clearly demonstrated in eight POH cases including one patient with mutation in exon 1. Genotype/phenotype analyses suggest that there is no direct correlation between the ossifying process and the position of the inactivating GNAS mutation. It is, however, more severe in patients in whom origin of the mutation is paternal. Severe intrauterine growth retardation was clearly evidenced in paternally inherited mutations.
Conclusions: Clinical heterogeneity makes genetic counseling a delicate matter, especially in which paternal inheritance is concerned because it can lead to either a mild expression of pseudopseudohypoparathyroidism or a severe expression of POH.
Perchlorate and Thiocyanate Exposure and Thyroid Function in First-Trimester Pregnant Women
Authors: Pearce Elizabeth N. , Lazarus John H. , Smyth Peter P. A. , He Xuemei , Dall'Amico Daniela , Parkes Arthur B. , Burns Robert , Smith Derek F. , Maina Aldo , Bestwick Jonathan P. , Jooman Mohammed , Leung Angela M. , Braverman Lewis E. 
Published: April 2010

Context: Thyroid hormone, requiring adequate maternal iodine intake, is critical for fetal neurodevelopment. Perchlorate decreases thyroidal iodine uptake by competitively inhibiting the sodium/iodide symporter. It is unclear whether environmental perchlorate exposure adversely affects thyroid function in pregnant women. Thiocyanate, derived from foods and cigarette smoke, is a less potent competitive sodium/iodide symporter inhibitor than perchlorate.
Objective: Our objective was to determine whether environmental perchlorate and/or thiocyanate exposure is associated with alterations in thyroid function in pregnancy.
Design and Setting: We conducted a cross-sectional study at health centers in Cardiff, Wales, and Turin, Italy.
Patients: During 2002–2006, 22,000 women at less than 16 wk gestation were enrolled in the Controlled Antenatal Thyroid Screening Study. Subsets of 261 hypothyroid/hypothyroxinemic and 526 euthyroid women from Turin and 374 hypothyroid/hypothyroxinemic and 480 euthyroid women from Cardiff were selected based on availability of stored urine samples and thyroid function data.
Main Outcome Measures: Urinary iodine, thiocyanate, and perchlorate and serum TSH, free T4 (FT4), and thyroperoxidase antibody were measured.
Results: Urinary iodine was low: median 98 μg/liter in Cardiff and 52 μg/liter in Turin. Urine perchlorate was detectable in all women. The median (range) urinary perchlorate concentration was 5 μg/liter (0.04–168 μg/liter) in Turin and 2 μg/liter (0.02–368 μg/liter) in Cardiff. There were no associations between urine perchlorate concentrations and serum TSH or FT4 in the individual euthyroid or hypothyroid/hypothyroxinemic cohorts. In multivariable linear analyses, log perchlorate was not a predictor of serum FT4 or TSH.
Conclusions: Low-level perchlorate exposure is ubiquitous but did not affect thyroid function in this cohort of iodine-deficient pregnant women.
Large eddy simulation analysis of engine steady intake flows using a mixed-time-scale subgrid-scale model
Authors: Inagaki M , Nagaoka M , Horinouchi N , Suga K 
Published: April 2010

Large eddy simulation (LES) using a mixed-time-scale (MTS) subgrid-scale (SGS) model is applied to the intake flows in simplified internal combustion engine geometry. A modified colocated grid system is employed to obtain results as precise as possible and to perform calculations in a stable way with a central difference scheme for convective terms. The results are compared with corresponding experimental data and the Reynolds averaged Navier—Stokes (RANS) equation model results obtained using the low-Reynolds-number linear k— In addition, it is made clear that when the QUICK scheme is used in LES for the convective terms instead of the central difference scheme, the result obtained deteriorates owing to the numerical viscosity. The importance of the discretization method in practical LES is also confirmed.
On the Importance of Lennard–Jones Parameter Calibration in QM/MM Framework: Reaction Path Tracing via Free Energy Gradient Method for Ammonia Ionization Process in Aqueous Solution
Authors: Koyano Yoshiyuki , Takenaka Norio , Nakagawa Yukinori , Nagaoka Masataka 
Published: April 2010

Abstract
The free energy gradient (FEG) method combined with the QM/MM–MD calculation has realized full-atomic structural optimization of the solute NH3–H2O molecule pair in aqueous solution, exploring successful tracing of the reaction path on the free energy surface from the neutral state (H3N–H2O) to the ionized (H4+N–O−H) through the transition state (H3N···H+···O−H). To reproduce accurately the structural change of the hydrated molecule pair, the LJ parameter calibration in the QM/MM nonelectrostatic interaction was essential for four kinds of QM solute species, i.e., OH−, H2O, NH3, and NH4+, treated in the NDDO-SSRP framework with the ab initio quality. Two linear interpolations of these calibrated LJ parameters optimized at the NSS and ISS were utilized in the path-dependent FEG calculation, as is common in the free energy perturbation treatment. After including the effects of the intramolecular entropic contribution and quantum tunneling, the free energies of activation and reaction were satisfactorily estimated to be 13.8 and 9.8 kcal mol−1 (1 kcal = 4.184 kJ), respectively. It is expected that far more agreement with the experimental values should be reasonably attained if the QM region were extended to three surrounding water molecules to take in the electron delocalization effect adequately.
Synthesis of π-Conjugated Polymers by Organometallic Polycondensation
Authors: Yamamoto Takakazu 
Published: April 2010

Abstract
Organometallic polycondensations give various π-conjugated polymers. For example, nickel complex-promoted dehalogenative polycondensation of dihaloaromatic compounds and dihalogenataed heterocyles, X–Ar–X (Ar = aromatic unit or heterocyclic unit), affords poly(arylene)s and poly(heterocycles), (Ar)n, such as poly(p-phenylene), poly(thiophene-2,5-diyl), poly(3-alkylthiophene-2,5-diyl), and poly(pyridine-2,5-diyl). Pd-catalyzed polycondensation gives poly(aryleneethynylene) type polymers and alternating copolymers of Ar and Ar′. These polymers have well defined bonds between the monomeric units, and they are electrochemically active, electrically conductive, and light-emitting. Their well-characterized linear structure brings about unique packing of the polymer molecules in the solid and alignment of the polymer molecules on the surface of substrates. In this paper, we describe synthesis of π-conjugated polymers by organometallic polycondensations. Basic chemical and physical properties of the synthesized π-conjugated polymers, as well as ordered structures in the solid and applications for electronic and optical devices of the π-conjugated polymers, are also described.
The European Register of Specialists in Clinical Chemistry and Laboratory Medicine: Guide to the Register, Version 3-2010
Authors: McMurray Janet , Zérah Simone , Hallworth Michael , Schuff-Werner Peter , Haushofer Alexander , Szekeres Thomas , Wallemacq Pierre , Tzatchev Kamen , Charilaou Charis , Racek Jaroslav , Johnsen Anders , Tomberg Karel , Harmoinen Aimo , Baum Hannsjörg , Rizos Demetrios , Kappelmayer Janos , O'Mullane John , Nubile Giuseppe , Pupure Silvija , Kucinskiene Zita , Opp Matthias , Jansen Rob , Solnica Bogdan , Reguengo Henrique , Grigore Camelia , Ŝpaňár Július , Ŝtrakl Greta , Queralto Josep , Wallinder Hans , Wieringa Gijsbert 
Published: April 2010

Abstract
In 1997, the European Communities Confederation of Clinical Chemistry and Laboratory Medicine (EC4) set up a Register for European Specialists in Clinical Chemistry and Laboratory Medicine. The operation of the Register is undertaken by a Register Commission (EC4RC). During the last 12 years, more than 2200 specialists in Clinical Chemistry and Laboratory Medicine have joined the Register. In 2007, EC4 merged with the Forum of European Societies of Clinical Chemistry and Laboratory Medicine (FESCC) to form the European Federation of Clinical Chemistry and Laboratory Medicine (EFCC). Two previous Guides to the Register have been published, one in 1997 and another in 2003. The third version of the Guide is presented in this article and is based on the experience gained and development of the profession since the last revision. Registration is valid for 5 years and the procedure and criteria for re-registration are presented as an Appendix at the end of the article.
Clin Chem Lab Med 2010;48:999–1008.
An exercise in a posteriori language sampling
Authors: Dahl Östen 
Published: April 2010

Abstract
A central methodological issue in language typology is sampling  how to choose a representative set of languages for a typological investigation. Most proposed typological sampling methods are a priori in the sense that they are based on assumed, rather than observed, effects of biasing factors  such as genealogical and areal proximity. The advent of the World Atlas of Language Structures (WALS) creates for the first time a chance to attempt a posteriori sampling. The basic idea is to create a sample by removing from the set of available languages one member of each pair of languages whose typological distance  as defined in terms of the features in WALS  does not reach a predefined threshold. In this way, a sample of 101 languages was chosen from an initial set of the 222 languages that are best represented in WALS. The number of languages from different macroareas in this sample can be taken as an indication of the internal diversity of the area in question. Two issues are discussed in some detail: (i) the high diversity of the indigenous languages of the Americas and the tendency for these to be underrepresented by previous sampling methods; (ii) the extreme areal convergence of Mainland South East Asian languages. It is concluded that areal factors cannot be neglected in typological sampling, and that it must be questioned whether the creation of elaborate sampling algorithms makes sense.
Automated classification of the world′s languages: a description of the method and preliminary results
Authors: Brown Cecil H. , Holman Eric W. , Wichmann Søren , Velupillai Viveka 
Published: April 2010

Abstract
An approach to the classification of languages through automated lexical comparison is described. This method produces near-expert classifications. At the core of the approach is the Automated Similarity Judgment Program (ASJP). ASJP is applied to 100-item lists of core vocabulary from 245 globally distributed languages. The output is 29,890 lexical similarity percentages for the same number of paired languages. Percentages are used as a database in a program designed originally for generating phylogenetic trees in biology. This program yields branching structures (ASJP trees) reflecting the lexical similarity of languages. ASJP trees for languages of the sample spoken in Middle America and South America show that the method is capable of grouping together on distinct branches languages of non-controversial genetic groups. In addition, ASJP sub-branching for each of nine respective genetic groups  Mayan, Mixe-Zoque, Otomanguean, Huitotoan-Ocaina, Tacanan, Chocoan, Muskogean, Indo-European, and Austro-Asiatic  agrees substantially with subgrouping for those groups produced by expert historical linguists. ASJP can be applied, among many other uses, to search for possible relationships among languages heretofore not observed or only provisionally recognized. Preliminary ASJP analysis reveals several such possible relationships for languages of Middle America and South America. Expanding the ASJP database to all of the world′s languages for which 100-word lists can be assembled is a realistic goal that could be achieved in a relatively short period of time, maybe one year or even less.
Targeting Angiogenesis with Multitargeted Tyrosine Kinase Inhibitors in the Treatment of Non-Small Cell Lung Cancer
Authors: Scagliotti Giorgio , Govindan Ramaswamy 
Published: April 2010

Abstract
It has been &gt;35 years since the link between angiogenesis and the growth of tumors was first reported. Targeting angiogenesis became feasible with the availability of bevacizumab, an anti–vascular endothelial growth factor monoclonal antibody. Initial studies revealed that the combination of bevacizumab and chemotherapy led to longer overall survival times than with chemotherapy alone in patients with advanced colorectal cancer. Since then, drug development strategies have added small molecule tyrosine kinase inhibitors to the panel of antiangiogenic agents under evaluation; data from numerous trials are now available. The challenge now is to identify the optimal antiangiogenic agent for specific patient groups and to understand not only the mechanistic differences between agents, but also the variability in their antitumor activity across different tumor types and their differing side-effect profiles. As in other solid tumors, angiogenesis contributes to the development of non-small cell lung cancer (NSCLC), and this review summarizes the role of angiogenesis in this disease. We review the current developmental status of antiangiogenic tyrosine kinase inhibitors (including vandetanib, sunitinib, axitinib, sorafenib, vatalanib, and pazopanib) in NSCLC and conclude by briefly discussing the need for optimal patient selection and potential future directions.
Molecular Profiling in Unknown Primary Cancer: Accuracy of Tissue of Origin Prediction
Authors: Greco F. Anthony , Spigel David R. , Yardley Denise A. , Erlander Mark G. , Ma Xiao-Jun , Hainsworth John D. 
Published: April 2010

Abstract

Introduction.
This retrospective, multi-institutional study evaluated the accuracy of tissue-of-origin prediction by molecular profiling in patients with carcinoma of unknown primary site (CUP).

Methods.
Thirty-eight of 501 patients (7.6%) with CUP, seen in 2000–2008, had their latent primary site tumor subsequently identified during life. Twenty-eight of these patients (73.7%) had adequate initial tissue biopsies available for molecular profiling with a reverse transcriptase-polymerase chain reaction (RT-PCR) assay (Cancer Type ID; bioTheranostics, Inc., San Diego, CA). The assay was performed on formalin-fixed paraffin-embedded biopsy specimens in a blinded fashion, and the assay results were compared with clinicopathologic data and the actual latent primary sites.

Results.
Twenty of the 28 (71.4%) RT-PCR assays were successfully completed (eight biopsies had either insufficient tumor or poorly preserved RNA). Fifteen of the 20 assay predictions (75%) were correct (95% confidence interval, 60%–85%), corresponding to the actual latent primary sites identified after the initial diagnosis of CUP. Primary sites correctly identified included breast (four patients), ovary/primary peritoneal (four patients), non-small cell lung (three patients), colorectal (two patients), gastric (one patient), and melanoma (one patient). Three predictions were incorrect (intestinal, testicular, sarcoma) in patients with gastroesophageal, pancreatic, and non-small cell lung cancer, respectively, and two were unclassifiable in patients with non-small cell lung cancer. Clinicopathologic findings were helpful in suggesting the correct primary site in some patients and appear to complement the molecular assay findings.

Conclusions.
These data validate the reliability of this assay in predicting the primary site in CUP patients and may form the basis for more successful site-directed therapy, when used in concert with clinicopathologic data.
Breast Cancer in Latinas: Gene Expression, Differential Response to Treatments, and Differential Toxicities in Latinas Compared with Other Population Groups
Authors: Patel Tejal A. , Colon-Otero Gerardo , Bueno Hume Celyne , Copland John A. , Perez Edith A. 
Published: April 2010

Abstract
Disparities in clinical outcomes of breast cancer have been described among different racial and ethnic groups in the U.S. Convincing data exist showing that Latina women have a lower incidence of breast cancer but a higher breast cancer–related mortality rate compared with white women. Noticeable differences in breast cancer incidence are present even within different Latina subsets with a higher incidence in second- and third-generation women compared with foreign born. An increasing amount of data exists pointing to significant differences in the genetics and biology of breast cancer in Latinas as a significant contributor to the higher mortality, including a higher incidence of triple-negative breast cancers (which do not overexpress HER-2 protein and are negative for estrogen receptors and progesterone receptors). Other social and environmental factors are likely to play a significant role as well, including a lower rate of screening mammography, variable access to medical care, among others. Recent data are inconclusive regarding differences among racial/ethnic groups in the response to chemotherapy. Data on racial/ethnic variations in the pharmacogenomics of chemotherapy, endocrine treatments, and toxicity are more limited, with some data suggesting differences in frequencies of polymorphisms of genes involved in the metabolism of some of these agents. Further studies are needed on this subject.
Identification of the main site factors and management intensity affecting the establishment of Short-Rotation-Coppices (SRC) in Northern Italy through stepwise regression analysis
Authors: Bergante Sara , Facciotto Gianni , Minotta Gianfranco 
Published: April 2010

Abstract
Data collected from 183 poplar and 102 willow SRC experimental plots, located in Central-North Italy, were subjected to stepwise regression analysis to acquire information on the environmental factors affecting plant survival and productivity in the first two-year rotation cycle. Nine Populus ×canadensis Mönch, eight P. deltoids Bartr. clones and four hybrids of Sali× matsudana Koidz were included in analysis. Independent variables were: annual and seasonal water availability (rainfall and irrigation), annual mean air temperature, soil texture, pH, N and organic matter content, planting density and management intensity. Dependent variables were: a) mean annual yield during the first two-year rotation cycle in tons per hectare per year of dry matter (Odt·ha−1·y−1); b) plant survival at the end of the second year from planting (%). Water availability resulted the main variable driving plant survival and biomass production in both poplar and willow clones. Water availability appeared to be the principal factor affecting the establishment of poplar and willow energy plantations in the Po valley. Possible variations in the rainfall regime consequent to climate changes could seriously influence land suitability to SRC. Experimental data also indicate that choice of planting density may increase the biomass yield during the first two-year especially with P. deltoides clones.