bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient piecewise linear model for predicting activity of caspase-3 inhibitors
Authors: Firoozpour Loghman , Sadatnezhad Khadijeh , Dehghani Sholeh , Pourbasheer Eslam , Foroumadi Alireza , Shafiee Abbas , Amanlou Massoud 
Published: September 2012

Abstract

Background and purpose of the study
Multimodal distribution of descriptors makes it more difficult to fit a single global model to model the entire data set in quantitative structure activity relationship (QSAR) studies.

Methods
The linear (Multiple linear regression; MLR), non-linear (Artificial neural network; ANN), and an approach based on “Extended Classifier System in Function approximation” (XCSF) were applied herein to model the biological activity of 658 caspase-3 inhibitors.

Results
Various kinds of molecular descriptors were calculated to represent the molecular structures of the compounds. The original data set was partitioned into the training and test sets by the K-means classification method. Prediction error on the test data set indicated that the XCSF as a local model estimates caspase-3 inhibition activity, better than the global models such as MLR and ANN. The atom-centered fragment type CR2X2, electronegativity, polarizability, and atomic radius and also the lipophilicity of the molecule, were the main independent factors contributing to the caspase-3 inhibition activity.

Conclusions
The results of this study may be exploited for further design of novel caspase-3 inhibitors.
Golgi phosphoprotein 2 in physiology and in diseases
Authors: Kim Ha-Jeong , Lv Dandan , Zhang Yan , Peng Tao , Ma Xiaojing 
Published: September 2012

Abstract
Golgi phosphoprotein 2 (GOLPH2, also termed GP73 and GOLM1) is a type II transmembrane protein residing in the cis and medial-Golgi cisternae. GOLPH2 is predominantly expressed in the epithelial cells of many human tissues. Under poorly defined circumstances, GOLPH2 can be cleaved and released to the extracellular space. Despite of its relatively “young age” since the first description in 2000, the physiological and pathological roles of GOLPH2 have been the subject that has attracted considerable amount of attention in recent years. Here, we review the history of GOLPH2’s discovery and the multitude of studies by many groups around the world aimed at understanding its molecular, cellular, physiological, and pathogenic activities in various settings.
A comparison of the efficacy of transplantation of bone marrow-derived mesenchymal stem cells and unrestricted somatic stem cells on outcome after acute myocardial infarction
Authors: Flynn Aidan , Chen Xizhe , O'Connell Enda , O'Brien Timothy 
Published: September 2012

Abstract
Introduction
A number of questions remain unanswered in the field of cell therapy for acute myocardial infarction, including what is the optimal cell type, and can therapeutic efficacy be enhanced by conditioning regimens. In this study, we sought to address these questions by directly comparing the effect of bone marrow-derived mesenchymal stem cells and unrestricted somatic stem cells delivered 24 hours post-myocardial infarction and by determining if the therapeutic efficacy of unrestricted somatic stem cells could be enhanced by exposing the cells to guiding factors before cell transplantation.

Methods
Unrestricted somatic stem cells were guided by exposure to 50 ng/mL basic fibroblast growth factor, 20 ng/mL hepatocyte growth factor and 20 ng/mL bone morphogenetic protein-2 for 24 hours. Using a Sprague-Dawley rat model of acute myocardial infarction, we transplanted cells by intramyocardial injection 24 hours post-myocardial infarction. Cardiac function was serially measured using echocardiography, and histological analyses of infarct morphology, angiogenesis and apoptosis were obtained. Transcriptomic and proteomic changes were assessed using microarray and real-time quantitative PCR.

Results
When assessed 28 days after the myocardial infarction, the delivery of mesenchymal stem cells 24 hours post-myocardial infarction did not improve ejection fraction (P = 0.19), and did not prevent the decline in ejection fraction observed in the absence of cell therapy (P = 0.17). The administration of unrestricted somatic stem cells also did not improve ejection fraction (P = 0.11), but did prevent a further decline in ejection fraction (P = 0.001). Delivery of guided unrestricted somatic stem cells significantly improved ejection fraction (P = 0.03). Guided unrestricted somatic stem cells restored function to a greater extent than mesenchymal stem cells (P = 0.03). The infarct area (P = 0.2), apoptosis (P = 0.07) and angiogenesis (P = 0.09) did not differ between groups. Microarray analysis revealed that, following pre-implantation guiding, the gene groupings of mitosis, signalling and angiogenesis were highly overrepresented, mediators of apoptosis were overrepresented, and cardiomyocyte-associated genes were not differentially expressed.

Conclusions
These results suggest that guided unrestricted somatic stem cells have a moderate capacity to repair cardiac damage and that they are more effective than mesenchymal stem cells in restoring cardiac function after a myocardial infarction. The mechanism of the benefit was not fully elucidated in this study, but these observations may be mediated by favorable dysregulation of angiogenic and apoptotic gene groupings.
Analytic and clinical validation of a standardized cystatin C particle enhanced turbidimetric assay (PETIA) to estimate glomerular filtration rate
Authors: Voskoboev Nikolay V. , Larson Timothy S. , Rule Andrew D. , Lieske John C. 
Published: September 2012

AbstractCystatin C is an alternative biomarker for assessing glomerular filtration rate (GFR), yet lack of standardization could hinder its widespread use. In this study we analytically and clinically validated a newer cystatin C particle-enhanced turbidimetric assay (PETIA) traceable to a certified reference material and compared it to the more commonly used particle-enhanced nephelometric assay (PENIA).Samples from four patient cohorts at the Mayo Clinic were studied: 1) clinical convenience samples (n=50); 2) samples from patients undergoing iothalamate urinary clearance testing for clinical indications (n=101); 3) volunteers without kidney disease (n=292); 4) samples from 1999–2000 with previous cystatin C measurements.The cystatin C PETIA was analytically robust between 0.15 mg/L and 8.36 mg/L. PETIA cystatin C values were 27.5% higher than PENIA results. Furthermore, PENIA results were 12.9% lower in 2010 than in 2000. PETIA cystatin C values and existing equations performed reasonably well to estimate GFR with an overall –7.4% bias for all patients analyzed. Age and gender specific reference intervals were established for the PETIA cystatin C.Cystatin C can be precisely measured by PETIA traceable to the international reference material, ERM-DA471/IFCC, using a routine chemistry autoanalyzer. There are important biases between this assay and the widely employed Siemens PENIA. This study highlights the importance of assay standardization if cystatin C is to be widely used to estimate GFR.
Eight Decades of Discouragement: The History of Health Care Cost Containment in the USA
Authors: Jost Timothy Stoltzfus 
Published: September 2012

Abstract
This chapter traces the history of attempts at cost control in the United States from the origins of our modern health care financing system in the 1930s and 1940s, through health care cost regulation in the 1970s, and the deregulatory 1980s and 1990s, to the Affordable Care Act.
Biochemical and functional characterization of human phospholipid scramblase 4 (hPLSCR4)
Authors: Francis Vincent Gerard , Gummadi Sathyanarayana N. 
Published: September 2012

Abstract
Human phospholipid scramblase 4 (hPLSCR4), an isoform of the scramblase family, is a type II single-pass transmembrane protein whose function remains unknown. To understand its role, recombinant hPLSCR4 was obtained by cloning the ORF into a pET28 a(+) vector and overexpressed in Escherichia coli. Functional assay showed that Ca2+, Mg2+, and Zn2+ activate hPLSCR4 and mediate scrambling activity independent of the phospholipid head group. Far-UV-CD and fluorescence spectroscopy revealed that Ca2+ and Mg2+ binding induces conformation change in hPLSCR4, exposing hydrophobic patches of the protein, and Ca2+ has more affinity than Mg2+ and Zn2+. Stains-all studies further confirm that hPLSCR4 is a Ca2+-binding protein. Point mutation (Asp290→Ala) in hPLSCR4 decreased the Ca2+-binding affinity as well as Tb3+ luminescence, suggesting residues of the predicted Ca2+-binding motif are involved in Ca2+ binding. Functional reconstitution with (Asp290→Ala) mutant led to ∼50% and ∼40% decrease in scramblase activity in the presence of Ca2+ and Mg2+, respectively.
Social Organization in a Nesting Population of Eastern Willets (Catoptrophorus semipalmatus)
Authors: Howe Marshall A. 
Published: September 2012

Abstract
The breeding ecology of eastern Willets (Catoptrophorus semipalmatus) was studied over a 3-yr period in a salt marsh on the Atlantic coast of Virginia. During the study, 171 adults were color-marked. Willets are strictly monogamous and show strong site and mate fidelity from year to year. Normally a pair bond dissolves only after one member dies or fails to return in the spring. With an estimated annual adult mortality of 15%, the average life of a pair bond is 3 yr. The sexes share in most aspects of breeding, including brood-rearing, but females abandon both mate and brood about 2 weeks after the chicks hatch. Males apparently incubate at night and sometimes relieve the female at the nest during the middle of the day. In this area Willets defend separate nesting and feeding territories, though nest-site defense decreases through the incubation period. When mates are lost, males retain their original nesting and feeding territories, while females pair with available mates near their original nesting territory. Females compete for mates, and males select the most aggressive females.
Nesting was particularly synchronous in lowland marsh sites, where the onset of egg laying was slightly earlier than in upland sites. Nest density was the highest reported for any scolopacid, and the highest densities were in sites closest to the marsh. Nest spacing is achieved through agonistic behavior, but there is evidence of a counter-tendency leading to nest clumping. Several features of the Willet social system resemble characteristics typical of colonial species of birds. These are discussed along with other aspects of social organization and the selective forces operating on it.
The Relationships of the Hawaiian Honeycreepers (Drepaninini) as Indicated by DNA-DNA Hybridization
Authors: Sibley Charles G. , Ahlquist Jon E. 
Published: September 2012

AbstractTwenty-two species of Hawaiian honeycreepers (Fringillidae: Carduelinae: Drepaninini) are known. Their relationships to other groups of passerines were examined by comparing the single-copy DNA sequences of the Apapane (Himatione sanguinea) with those of 5 species of cardueline finches, 1 species of Fringilla, 15 species of New World nine-primaried oscines (Cardinalini, Emberizini, Thraupini, Parulini, Icterini), and members of 6 other families of oscines (Turdidae, Monarchidae, Dicaeidae, Sylviidae, Vireonidae, Corvidae). The DNA-DNA hybridization data support other evidence indicating that the Hawaiian honeycreepers shared a more recent common ancestor with the cardueline finches than with any of the other groups studied and indicate that this divergence occurred in the mid-Miocene, 15-20 million yr ago.The colonization of the Hawaiian Islands by the ancestral species that radiated to produce the Hawaiian honeycreepers could have occurred at any time between 20 and 5 million yr ago. Because the honeycreepers captured so many ecological niches, however, it seems likely that their ancestor was the first passerine to become established in the islands and that it arrived there at the time of, or soon after, its separation from the cardueline lineage. If so, this colonist arrived before the present islands from Hawaii to French Frigate Shoal were formed by the volcanic "hot-spot" now under the island of Hawaii. Therefore, the ancestral drepaninine may have colonized one or more of the older Hawaiian Islands and/or Emperor Seamounts, which also were formed over the "hot-spot" and which reached their present positions as the result of tectonic crustal movement. The cardueline-drepaninine lineage probably diverged from the Fringilla lineage in the late Oligocene, from the New World nine-primaried oscines in the early Oligocene, and from the other oscines in the early Eocene.During this study we also obtained evidence that the vireos (Vireonidae) are not closely related to the New World nine-primaried oscines.
Annual Variation in the Distribution, Abundance, and Habitat Response of the Palila (Loxioides bailleui)
Authors: Scott J. Michael , Mountainspring Stephen , Riper Charles van , Kepler Cameron B. , Jacobi James D. , Burr Timothy A. , Giffin Jon G. 
Published: September 2012

AbstractWe studied the distribution, population size, and habitat response of the Palila (Loxioides bailleui) during the 1980-1984 nonbreeding seasons to infer factors that limit the population and to develop management strategies. Distribution was fairly constant from year to year. Palila were confined to the subalpine woodland on Mauna Kea on the island of Hawaii, occurred between 2,000 and 2,850 m elevation, and reached highest densities on the southwest slopes. The population showed large annual fluctuations, from 6,400 birds in 1981 to 2,000 in 1984. The width of woodland was the most important variable in determining habitat response. Palila were more common in areas with greater crown cover, taller trees, and a higher proportion of native plants in the understory. Annual variation in Palila density within a habitat reflected variation in levels of their staple food, mamane pods. The main limiting factors of the population appeared to be the availability of good habitat and levels of their staple food. Palila had strongly depressed densities in the Pohakuloa flats area. This low density could not be explained by gross habitat features or food levels. Site tenacity, thermal stress, disturbance, and disease were hypothesized explanations. Our study indicated that the most effective management strategies would be the removal of feral ungulates and certain noxious plants from Palila habitat and the extension of the woodland zone to areas now intensively grazed.
Parental Care and Feeding Ecology of Golden Eagle Nestlings
Authors: Collopy Michael W. 
Published: September 2012

AbstractA field study of Golden Eagles (Aquila chrysaetos) nesting in and near the Snake River Birds of Prey Area was conducted during 1977-1979. Patterns of parental care differed between female and male eagles during incubation and chick rearing; males consistently captured more food throughout all phases of brood rearing (1.2 vs. 0.6 prey/day), while females typically fed and tended the offspring. During the 7th through 9th week of chick rearing, when the food requirements of nestlings were greatest, the female contributed 43% of the prey biomass. No differences were observed in mean daily capture rates between 1978 and 1979 or between parents of one-chick broods and parents of two-chick broods. Although there were no differences between the sexes in the mean weight of prey captured, there were significant differences among pairs, suggesting differences in prey availability or hunting ability. The daily food consumption of eaglets increased as chick rearing progressed and peaked between the 7th and 9th week. Comparisons between eaglets in different-sized broods revealed that individuals in multiple-chick broods received more food from adults than those in one-chick broods. Late in chick rearing, however, those chicks competing with siblings for food had lower consumption rates.
Factors Influencing Age-Related Reproductive Success in the Willow Ptarmigan
Authors: Hannon Susan J. , Smith James N. M. 
Published: September 2012

Abstract
In many species, adult birds lay earlier and have higher reproductive success than do yearlings. We found no difference, however, between adult and yearling female Willow Ptarmigan (Lagopus lagopus alexandrae) in date of clutch initiation, clutch size, hatching success, number of fledged young, or territory size. Adult females defended their broods more vigorously, and more were observed with broods, a situation suggesting that more yearlings lost their eggs or young and did not renest. Pairs composed of two adults produced more fledged young than did pairs composed of two yearlings, but clutch size and date of clutch initiation were similar in the two groups. We suggest that the following factors may allow yearlings to reproduce almost as successfully as adults: (1) a reduction in competition with adults for territories because of high population turnover, (2) the presence of extensive male parental care and precocial young, and (3) a dependence on a food source that is readily available and can be obtained without specialized foraging skills.
Exploration of the Visual System: Part 2: In Vivo Analysis Methods: Virtual‐Reality Optomotor System, Fundus Examination, and Fluorescent Angiography
Authors: Marcelli Fabienne , Escher Pascal , Schorderet Daniel F. 
Published: September 2012

AbstractThe mouse has emerged as an animal model for many diseases. At IRO, we have used this animal to understand the development of many eye diseases and treatment of some of them. Precise evaluation of vision is a prerequisite for both these approaches. In this unit we describe three ways to measure vision: testing the optokinetic response, and evaluating the fundus by direct observation and by fluorescent angiography. Curr. Protoc. Mouse Biol. 2:207‐218 © 2012 by John Wiley & Sons, Inc.
Methods for Studying Rodent Intestinal Lipoprotein Production and Metabolism
Authors: Kohan Alison B. , Howles Philip N. , Tso Patrick 
Published: September 2012

AbstractLipid absorption begins with the digestion of dietary triacylglycerol and ultimately results in the secretion of triacylglycerol in chylomicrons into the lymphatics. Additionally, the intestine also secretes numerous proteins and peptides involved in lipid and lipoprotein metabolism in response to food. Ultimately, chylomicrons and these proteins, peptides, and hormones are found in lymph. The lymph fistula rat model has traditionally been used to study this intestinal absorption of nutrients, especially lipids, but recently, this model has also been used for studying the secretion of hormones by the small intestine. The protocols described in this unit include the lymph fistula rat and mouse model, as well as in vivo chylomicron metabolism studies. These experimental models are helpful for the study of metabolic phenotypes, the characterization of intestinal lipid absorption and transport, and determining peripheral metabolism of intestinally derived lipoproteins. Curr. Protoc. Mouse Biol. 2:219‐230 © 2012 by John Wiley & Sons, Inc.
In Vitro and In Vivo Recording of Local Field Potential Oscillations in Mouse Hippocampus
Authors: Forsyth L.H. , Witton J. , Brown J.T. , Randall A.D. , Jones M.W. 
Published: September 2012

AbstractOscillations in hippocampal local field potentials (LFP) reflect the coordinated, rhythmic activity of constituent interneuronal and principal cell populations. Quantifying changes in oscillatory patterns and power therefore provides a powerful metric through which to infer mechanisms and functions of hippocampal network activity at the mesoscopic level, bridging single‐neuron studies to behavioral assays of hippocampal function. Here, complementary protocols that enable mechanistic analyses of oscillation generation in vitro (in slices and a whole hippocampal preparation) and functional analyses of hippocampal circuits in behaving mice are described. Used together, these protocols provide a comprehensive view of hippocampal phenotypes in mouse models, highlighting oscillatory biomarkers of hippocampal function and dysfunction. Curr. Protoc. Mouse Biol. 2:273‐294 © 2012 by John Wiley & Sons, Inc.
General Considerations for Mouse Survival Surgery
Authors: Lyons Bonnie L. , Waterman Linda L. 
Published: September 2012

AbstractPersonnel performing surgery on mice commonly lack formal medical training and most training in mouse surgery focuses on the mechanical skills required for a procedure with less emphasis on perioperative techniques. Consequently, a basic concept that underpins successful surgery, aseptic technique, may not be fully understood or incorporated into the training process. This unit provides a framework in which to plan and carry out surgical procedures in mice using appropriate aseptic technique. Curr. Protoc. Mouse Biol. 2:263‐271 © 2012 by John Wiley & Sons, Inc.
Evaluation of genes involved in limb development, angiogenesis, and coagulation as risk factors for congenital limb deficiencies
Authors: Browne Marilyn L. , Carter Tonia C. , Kay Denise M. , Kuehn Devon , Brody Lawrence C. , Romitti Paul A. , Liu Aiyi , Caggana Michele , Druschel Charlotte M. , Mills James L. 
Published: September 2012

AbstractWe conducted a population‐based case–control study of single nucleotide polymorphisms (SNPs) in selected genes to find common variants that play a role in the etiology of limb deficiencies (LDs). Included in the study were 389 infants with LDs of unknown cause and 980 unaffected controls selected from all births in New York State (NYS) for the years 1998–2005. We used cases identified from the NYS Department of Health (DOH) Congenital Malformations Registry. Genotypes were obtained for 132 SNPs in genes involved in limb development (SHH, WNT7A, FGF4, FGF8, FGF10, TBX3, TBX5, SALL4, GREM1, GDF5, CTNNB1, EN1, CYP26A1, CYP26B1), angiogenesis (VEGFA, HIF1A, NOS3), and coagulation (F2, F5, MTHFR). Genotype call rates were >97% and SNPs were tested for departure from Hardy–Weinberg expectations by race/ethnic subgroups. For each SNP, odds ratios (OR)s and confidence intervals (CI)s were estimated and corrected for multiple comparisons for all LDs combined and for LD subtypes. Among non‐Hispanic white infants, associations between FGF10 SNPs rs10805683 and rs13170645 and all LDs combined were statistically significant following correction for multiple testing (OR = 1.99; 95% CI = 1.43–2.77; uncorrected P = 0.000043 for rs10805683 heterozygous genotype, and OR = 2.37; 95% CI = 1.48–3.78; uncorrected P = 0.00032 for rs13170645 homozygous minor genotype). We also observed suggestive evidence for associations with SNPs in other genes including CYP26B1 and WNT7A. Animal studies have shown that FGF10 induces formation of the apical ectodermal ridge and is necessary for limb development. Our data suggest that common variants in FGF10 increase the risk for a wide range of non‐syndromic limb deficiencies. © 2012 Wiley Periodicals, Inc.
Duplication of OCRL and adjacent genes associated with autism but not Lowe syndrome
Authors: Schroer Richard J. , Beaudet Arthur L. , Shinawi Marwan , Sahoo Trilochan , Patel Ankita , Sun Qin , Skinner Cindy , Stevenson Roger E. 
Published: September 2012

AbstractDisturbances in the form of microduplications and microdeletions have been found throughout the genome and have been associated with autism, intellectual disability, and recognizable malformation syndromes. In our study of 187 probands with autism, we have identified a duplication in Xq25 including full gene duplication of OCRL and six flanking genes. Activity of the enzyme gene product in fibroblasts was elevated to over twice the level in control fibroblasts. The boy had no somatic or neurological findings reminiscent of Lowe syndrome. © 2012 Wiley Periodicals, Inc.