bluuebunny/crossref_metadata_2025_split huggingface dataset:
iLoops: a protein–protein interaction prediction server based on structural features
Authors: Planas-Iglesias Joan , Marin-Lopez Manuel A. , Bonet Jaume , Garcia-Garcia Javier , Oliva Baldo 
Published: July 2013

Abstract
Summary: Protein–protein interactions play a critical role in many biological processes. Despite that, the number of servers that provide an easy and comprehensive method to predict them is still limited. Here, we present iLoops, a web server that predicts whether a pair of proteins can interact using local structural features. The inputs of the server are as follows: (i) the sequences of the query proteins and (ii) the pairs to be tested. Structural features are assigned to the query proteins by sequence similarity. Pairs of structural features (formed by loops or domains) are classified according to their likelihood to favor or disfavor a protein–protein interaction, depending on their observation in known interacting and non-interacting pairs. The server evaluates the putative interaction using a random forest classifier.
Availability: iLoops is available at http://sbi.imim.es/iLoops.php
Contact: baldo.oliva@upf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MIG: Multi-Image Genome viewer
Authors: McGowan Simon J. , Hughes Jim R. , Han Zong-Pei , Taylor Stephen 
Published: July 2013

Abstract
Summary: Multi-Image Genome (MIG) viewer is a web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. This methodology has been used successfully to analyze ChIP-Seq data and RNA-Seq data and to detect somatic mutations in genome resequencing projects.
Availability: MIG is available at https://mig.molbiol.ox.ac.uk/mig/
Contact: simon.mcgowan@imm.ox.ac.uk
The Endocytosis of Cellulose Synthase in Arabidopsis Is Dependent on μ2, a Clathrin-Mediated Endocytosis Adaptin
Authors: Bashline Logan , Li Shundai , Anderson Charles T. , Lei Lei , Gu Ying 
Published: July 2013

Abstract
Clathrin-mediated endocytosis (CME) is the best-characterized type of endocytosis in eukaryotic cells. Plants appear to possess all of the molecular components necessary to carry out CME; however, functional characterization of the components is still in its infancy. A yeast two-hybrid screen identified μ2 as a putative interaction partner of CELLULOSE SYNTHASE6 (CESA6). Arabidopsis (Arabidopsis thaliana) μ2 is homologous to the medium subunit 2 of the mammalian ADAPTOR PROTEIN COMPLEX2 (AP2). In mammals, the AP2 complex acts as the central hub of CME by docking to the plasma membrane while concomitantly recruiting cargo proteins, clathrin triskelia, and accessory proteins to the sites of endocytosis. We confirmed that μ2 interacts with multiple CESA proteins through the μ-homology domain of μ2, which is involved in specific interactions with endocytic cargo proteins in mammals. Consistent with its role in mediating the endocytosis of cargos at the plasma membrane, μ2-YELLOW FLUORESCENT PROTEIN localized to transient foci at the plasma membrane, and loss of μ2 resulted in defects in bulk endocytosis. Furthermore, loss of μ2 led to increased accumulation of YELLOW FLUORESCENT PROTEIN-CESA6 particles at the plasma membrane. Our results suggest that CESA represents a new class of CME cargo proteins and that plant cells might regulate cellulose synthesis by controlling the abundance of active CESA complexes at the plasma membrane through CME.
Identification and Functional Analysis of Tomato BRI1 and BAK1 Receptor Kinase Phosphorylation Sites
Authors: Bajwa Vikramjit S. , Wang Xiaofeng , Blackburn R. Kevin , Goshe Michael B. , Mitra Srijeet K. , Williams Elisabeth L. , Bishop Gerard J. , Krasnyanski Sergei , Allen George , Huber Steven C. , Clouse Steven D. 
Published: July 2013

Abstract
Brassinosteroids (BRs) are plant hormones that are perceived at the cell surface by a membrane-bound receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1). BRI1 interacts with BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) to initiate a signal transduction pathway in which autophosphorylation and transphosphorylation of BRI1 and BAK1, as well as phosphorylation of multiple downstream substrates, play critical roles. Detailed mechanisms of BR signaling have been examined in Arabidopsis (Arabidopsis thaliana), but the role of BRI1 and BAK1 phosphorylation in crop plants is unknown. As a foundation for understanding the mechanism of BR signaling in tomato (Solanum lycopersicum), we used liquid chromatography-tandem mass spectrometry to identify multiple in vitro phosphorylation sites of the tomato BRI1 and BAK1 cytoplasmic domains. Kinase assays showed that both tomato BRI1 and BAK1 are active in autophosphorylation as well as transphosphorylation of each other and specific peptide substrates with a defined sequence motif. Site-directed mutagenesis revealed that the highly conserved kinase domain activation loop residue threonine-1054 was essential for tomato BRI1 autophosphorylation and peptide substrate phosphorylation in vitro. Furthermore, analysis of transgenic lines expressing full-length tomato BRI1-Flag constructs in the weak tomato bri1 allele, curl3-abs1, demonstrated that threonine-1054 is also essential for normal BRI1 signaling and tomato growth in planta. Finally, we cloned the tomato ortholog of TGF-β Receptor Interacting Protein (TRIP1), which was previously shown to be a BRI1-interacting protein and kinase domain substrate in Arabidopsis, and found that tomato TRIP1 is a substrate of both tomato BRI1 and BAK1 kinases in vitro.
Effect of 1‐methyl‐D‐tryptophan and adoptive transfer of dendritic cells on polymicrobial sepsis induced by cecal content injection
Authors: Yim Hong Soon , Choi Kyung Min , Kim Byoungjae , Jung In Duk , Park Yeong‐Min , Kang Yoon Kyu , Lee Min‐Goo 
Published: July 2013

ABSTRACTA mouse model of polymicrobial sepsis induced by cecal content injection (CCI) was developed with the aim of gaining a better understanding of the mechanism of sepsis. This model has a similar survival pattern to the conventional model with the added benefits of ability to vary the severity of sepsis and greater consistency. Administration of 1‐methyl‐D‐tryptophan (1‐MT) to inhibit indoleamine 2,3‐dioxygenase (IDO) in mice with CCI‐induced sepsis increased the survival rate and tended to up‐regulate IL‐10/IL‐12 serum concentrations. The effectiveness of 1‐MT was confirmed by increases in IL‐10 over IL‐12 in bone marrow‐derived dendritic cells (BMDCs) treated with LPS and 1‐MT and a superior survival rate 24 hr after injection of these double treated BMDCs in the CCI‐induced sepsis model. Therefore, CCI is both a useful and reliable technique for investigating polymicrobial sepsis. The present findings using this newly developed model suggest that inhibition of IDO alleviates the severity of polymicrobial sepsis and modulates the immune response even in cases of severe systemic septic inflammation.
Why polar gigantism and Palaeozoic gigantism are not equivalent: effects of oxygen and temperature on the body size of ectotherms
Authors: Verberk Wilco C. E. P. , Atkinson David 
Published: July 2013

Summary

Organisms of gigantic proportions inhabited the world at a time of a hyperoxic prehistoric atmosphere (Palaeozoic gigantism). Extant giants are found in cold polar waters, with large quantities of dissolved oxygen (polar gigantism). Oxygen is usually deemed central to explain such gigantism. Examples of one category of gigantism are often cited in support of the other, but novel insights into the bioavailability of oxygen imply that they cannot be taken as equivalent manifestations of the effect of oxygen on body size.

Recently, the availability of oxygen has been shown to be lower in cold waters, despite greater oxygen solubility. Consequently, gigantism in cold, oxygenated waters and gigantism in an oxygen‐pressurized world are fundamentally different: Palaeozoic gigantism likely arose because of greater oxygen availability, while polar gigantism arises in spite of lower oxygen availability.

The traditional view of respiration focuses on meeting the challenge of extracting sufficient amounts of oxygen, which essentially is a toxic gas. We present a broader perspective, which specifically includes risks of oxygen poisoning. We discuss how challenges pertaining to balancing oxygen uptake capacity and risks of oxygen poisoning are very different for animals breathing either air or water.

We propose a novel explanation for polar gigantism in aquatic ectotherms, arguing that their larger body size represents a respiratory advantage that helps to overcome the larger viscous forces in water. Being large helps organisms to balance the opposing risks of asphyxiation and poisoning, especially in colder, more viscous, water. This results in a selection for larger sizes, with polar gigantism as the extreme manifestation. Hence, a larger size provides respiratory benefits to water‐breathing ectotherms, but not terrestrial ectotherms. This can explain why clines in body size across temperature and latitude are stronger in aquatic ectotherms.
Differential effects of a gelatinase inhibitor on adipocyte differentiation and adipose tissue development
Authors: Van Hul Matthias , Bauters Dries , Lijnen Roger H 
Published: July 2013

Summary

A potential role for the gelatinases in adipocyte differentiation in vitro and adipose tissue development in vivo was investigated using the gelatinase inhibitor tolylsam ((R)‐3‐methyl‐2‐[4‐(3‐p‐tolyl‐[1,2,4]oxadiazol‐5‐yl)‐benzenesulphonylamino]‐butyric acid).

Differentiation of murine 3T3‐F442A preadipocytes (12 days after reaching confluence) into mature adipocytes in vitro was promoted in the presence of tolylsam (10–100 μmol/L).

De novo development of fat tissue in nude mice injected with preadipocytes and kept on a high‐fat diet was significantly impaired following treatment with tolylsam (100 mg/kg per day for 4 weeks).

Adipose tissue development in matrix metalloproteinase (MMP)‐2 deficient mice, kept on a high‐fat diet, was significantly impaired following administration of tolylsam (100 mg/kg per day for 15 weeks). This was associated with markedly enhanced metabolic rate.

Treatment of MMP‐2‐deficient mice with tolylsam (100 mg/kg per day, 15 weeks) was associated with the preservation of collagen and a reduction in blood vessel size in adipose tissues in vivo.

Furthermore, plasma levels of triglycerides and free fatty acids were reduced by tolylsam treatment of MMP‐2‐deficient mice (100 mg/kg per day, 15 weeks), whereas nutrient adsorption in the intestine was not affected.

The results of the present study indicate that tolylsam promotes preadipocyte differentiation in vitro, but impairs adipose tissue development in vivo.
Beyond static assessment of children's receptive vocabulary: the dynamic assessment of word learning (DAWL)
Authors: Camilleri Bernard , Botting Nicola 
Published: July 2013

AbstractBackgroundChildren's low scores on vocabulary tests are often erroneously interpreted as reflecting poor cognitive and/or language skills. It may be necessary to incorporate the measurement of word‐learning ability in estimating children's lexical abilities.AimsTo explore the reliability and validity of the Dynamic Assessment of Word Learning (DAWL), a new dynamic assessment of receptive vocabulary.Methods & ProceduresA dynamic assessment (DA) of word learning ability was developed and adopted within a nursery school setting with 15 children aged between 3;07 and 4;03, ten of whom had been referred to speech and language therapy.Outcomes & ResultsA number of quantitative measures were derived from the DA procedure, including measures of children's ability to identify the targeted items and to generalize to a second exemplar, as well as measures of children's ability to retain the targeted items. Internal, inter‐rater and test–retest reliability of the DAWL was established as well as correlational measures of concurrent and predictive validity.Conclusions & ImplicationsThe DAWL was found to provide both quantitative and qualitative information which could be used to improve the accuracy of differential diagnosis and the understanding of processes underlying the child's performance. The latter can be used for the purpose of designing more individualized interventions.
Anthropometric standardisation and quality control protocols for the construction of new, international, fetal and newborn growth standards: the INTERGROWTH‐21st Project
Authors: Cheikh Ismail L , Knight HE , Ohuma EO , Hoch L , Chumlea WC ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: July 2013

The primary aim of the INTERGROWTH‐21st Project is to construct new, prescriptive standards describing optimal fetal and preterm postnatal growth. The anthropometric measurements include the head circumference, recumbent length and weight of the infants, and the stature and weight of the parents. In such a large, international, multicentre project, it is critical that all study sites follow standardised protocols to ensure maximal validity of the growth and nutrition indicators used. This paper describes in detail the anthropometric training, standardisation and quality control procedures used to collect data for these new standards. The initial standardisation session was in Nairobi, Kenya, using newborns, which was followed by similar sessions in the eight participating study sites in Brazil, China, India, Italy, Kenya, Oman, UK and USA. The intraobserver and inter‐observer technical error of measurement values for head circumference range from 0.3 to 0.4 cm, and for recumbent length from 0.3 to 0.5 cm. These standardisation protocols implemented at each study site worldwide ensure that the anthropometric data collected are of the highest quality to construct international growth standards.
Molecular identification of a pancreatic lipase‐like gene involved in sex pheromone biosynthesis of Bombyx mori
Authors: Zhang Song‐Dou , Li Xun , Bin Zhu , Du Meng‐Fang , Yin Xin‐Ming , An Shi‐Heng 
Published: July 2013

AbstractCytoplasmic lipid droplet (LD) lipolysis is regulated by pheromone biosynthesis activating neuropeptide (PBAN) in Bombyx mori. To elucidate the molecular mechanism of cytoplasm LD lipolysis, the pancreatic lipase‐like gene in B. mori pheromone glands (PGs), designated as B. mori pancreatic lipase‐like gene (BmPLLG), was identified in this study. Spatial expression analysis revealed that BmPLLG is a ubiquitous gene present in all studied tissues, such as PGs, brain, epidermis, egg, midgut, flight muscle and fat body. Temporal expression analysis showed that the BmPLLG transcript begins to express 96 h before eclosion (−96 h), continues to increase, peaks in newly emerged females and steadily decreases after eclosion. Translational expression analysis of BmPLLG using a prepared antiserum demonstrated that BmPLLG was expressed in an age‐dependent pattern at different development stages in B. mori. This finding was similar to the transcript expression pattern. Further RNA interference‐mediated knockdown of BmPLLG significantly inhibited bombykol production. Overall, these results demonstrated that BmPLLG is involved in PBAN‐induced sex pheromone biosynthesis and release.
Macroeconomic Implications of the German Short‐time Work Policy during the Great Recession
Authors: Herzog‐Stein Alexander , Horn Gustav A. , Stein Ulrike 
Published: July 2013

AbstractDespite a sharp fall in GDP, German employment in terms of employees stayed remarkably robust during the Great Recession. At the same time, hours worked per employee declined significantly. This is seen as the core of the German employment ‘miracle’. A general discussion arose about the reasons behind this astonishing labour market performance and the role of short‐time work (STW) as a kind of exportable panacea. In this article we look at the macroeconomic implications of STW and other measures of internal flexibility, in particular focusing on the quantification of safeguarded jobs during the crisis. We find that STW played an important role and helped to safeguard employment in Germany during the Great Recession. However, we show that other measures of internal flexibility (working time accounts, contractual arrangements on working time reductions, reduction of overtime) were equally important. Together with STW these instruments saved around 1 million jobs. To explain and understand the German success story, the features of the German core model – with a strong employer–employee relationship of mutual trust, strong employment protection, traditional standard working contracts and strong works councils at the firm level – are of key importance.
A comparison of the BURP and conventional and modified jaw thrust manoeuvres for orotracheal intubation using the Clarus Video System
Authors: Lee A. R. , Yang S. , Shin Y. H. , Kim J. A. , Chung I. S. , Cho H. S. , Lee J. J. 
Published: July 2013

SummaryWe evaluated the effects of three airway manipulation manoeuvres: (a) conventional (single‐handed chin lift); (b) backward, upward and right‐sided pressure (BURP) manoeuvre; and (c) modified jaw thrust manoeuvre (two‐handed aided by an assistant) on laryngeal view and intubation time using the Clarus Video System in 215 patients undergoing general anaesthesia with orotracheal intubation. In the first part of this study, the laryngeal view was recorded as a modified Cormack–Lehane grade with each manoeuvre. In the second part, intubation was performed using the assigned airway manipulation. The primary outcome was the time to intubation, and the secondary outcomes were the modified Cormack–Lehane grade, the number of attempts and the overall success rate. There were significant differences in modified Cormack–Lehane grade between the three airway manipulations (p < 0.0001). Post‐hoc analysis indicated that the modified jaw thrust improved the laryngeal view compared with the conventional (p < 0.0001) and the BURP manoeuvres (p < 0.0001). The BURP worsened the laryngeal view compared with the conventional manoeuvre (p = 0.0132). The time to intubation in the modified jaw thrust group was shorter than with the conventional manoeuvre (p = 0.0004) and the BURP group (p < 0.0001). We conclude that the modified jaw thrust is the most effective manoeuvre at improving the laryngeal view and shortening intubation time with the Clarus Video System.
Gallbladder bed pocket score as a preoperative measure for assessing the difficulty of laparoscopic cholecystectomy
Authors: Shinozaki Kenta , Ajiki Tetsuo , Okazaki Taro , Ueno Kimihiko , Matsumoto Taku , Ohtsubo Izuru , Murakami Sae , Yoshida Yuko , Matsumoto Ippei , Fukumoto Takumi , Sugimoto Takemi , Ohno Masakazu , Ku Yonson 
Published: July 2013

AbstractIntroductionLaparoscopic cholecystectomy (Lap‐C) is a standard surgery for symptomatic gallbladder stones and acute or chronic cholecystitis. Resident surgeons often perform this operation early in their training, but they sometimes encounter difficulties for various technical reasons. Although encountering a gallbladder buried deep within the gallbladder bed is a common operative difficulty, literature on the subject scarcely exists.MethodsForty‐two patients underwent Lap‐C at our hospitals and were analyzed retrospectively. We defined the gallbladder bed pocket score (GBPS) as the maximum ratio between the height and width of the gallbladder bed measured based on multi‐detector computed tomography (MDCT) images. GBPS and clinical factors were assessed in terms of their correlation with the time required for gallbladder dissection from the gallbladder bed.ResultsOf the 42 patients, 20 had histories of acute or chronic cholecystitis. The mean gallbladder dissection time was 14.9 min, and the mean GBPS was 0.43 in the coronal MDCT section and 0.56 in the sagittal section. The correlation coefficient between the GBPS and gallbladder dissection time was 0.40 (P = 0.01) in the coronal section and 0.38 (P = 0.02) in the sagittal section of the MDCT images. There was no statistically significant correlation between gallbladder dissection time and the surgeon's experience, patient's history of cholecystitis, gallstone size, or blood loss. However, GBPS > 0.4 predicted more difficult and prolonged dissection.ConclusionGBPS is a useful tool for preoperatively predicting the time needed to dissect the gallbladder from the gallbladder bed during Lap‐C. Cases with GBPS < 0.4 seem more suitable for resident surgeons who are performing gallbladder dissection early in their Lap‐C training.
When Intuition is Not Enough. Why the Principle of Procreative Beneficence Must Work Much Harder to Justify Its Eugenic Vision
Authors: Bennett Rebecca 
Published: July 2013

AbstractThe Principle of Procreative Beneficence (PPB) claims that we have a moral obligation, where choice is possible, to choose to create the best child we can. The existence of this moral obligation has been proposed by John Harris and Julian Savulescu and has proved controversial on many levels, not least that it is eugenics, asking us to produce the best children we can, not for the sake of that child's welfare, but in order to make a better society. These are strong claims that require robust justification that can be open to scrutiny and debate.This article argues that robust justifications are currently lacking in the work of Savulescu and Harris. The justifications provided for their conclusions about this obligation to have the best child possible rely heavily on Derek Parfit's Non‐Identity Problem and the intuitive response this provokes in many of us. Unfortunately Harris and Savulescu do not embrace the entirety of the Non‐Identity Problem and the puzzle that it presents. The Non‐Identity Problem actually provides a refutation of PPB. In order to establish PPB as a credible and defendable principle, Harris and Savulescu need to find what has eluded Parfit and many others: a solution to the Non‐Identity Problem and thus an overturning of the refutation it provides for PPB. While Harris and Savulescu do hint at possible but highly problematic solutions to the Non‐Identity Problem, these are not developed or defended. As a result their controversial is left supported by little more than intuition.
Shrinkage Empirical Likelihood Estimator in Longitudinal Analysis with Time‐Dependent Covariates—Application to Modeling the Health of Filipino Children
Authors: Leung Denis Heng‐Yan , Small Dylan S. , Qin Jing , Zhu Min 
Published: July 2013

SummaryThe method of generalized estimating equations (GEE) is a popular tool for analysing longitudinal (panel) data. Often, the covariates collected are time‐dependent in nature, for example, age, relapse status, monthly income. When using GEE to analyse longitudinal data with time‐dependent covariates, crucial assumptions about the covariates are necessary for valid inferences to be drawn. When those assumptions do not hold or cannot be verified, Pepe and Anderson (1994,Communications in Statistics, Simulations and Computation23, 939–951) advocated using an independence working correlation assumption in the GEE model as a robust approach. However, using GEE with the independence correlation assumption may lead to significant efficiency loss (Fitzmaurice, 1995,Biometrics51, 309–317). In this article, we propose a method that extracts additional information from the estimating equations that are excluded by the independence assumption. The method always includes the estimating equations under the independence assumption and the contribution from the remaining estimating equations is weighted according to the likelihood of each equation being a consistent estimating equation and the information it carries. We apply the method to a longitudinal study of the health of a group of Filipino children.