bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity and variation analysis of mutant lines derived from γ-ray and chemical mutagen treatments in blackberry (Rubus fruticosus)
Authors: Ryu Jaihyunk , Ha Bo-Keun , Kim Dong Sub , Kim Jin-Baek , Kim Sang Hoon , Ahn Joon-Woo , Jeong Il Yun , Jo Han-Jik , Kim Ee-Yup , Kang Si-Yong 
Published: July 2014

Blackberry is a fruiting berry species with very high nutrient contents. With the recent increasing consumer demand for blackberries, new sources of germplasm and breeding techniques are required to improve blackberry production. This study was carried out to evaluate the genetic diversity (GD) and relationship among 55 blackberry (Rubus fruticosus) mutants derived from γ-ray treatment (52 lines) and N-methyl-N′-nitrosourea (MNU) treatment (three lines) using an inter-simple sequence repeat marker. A total of 18 bands were amplified with an average of 3.6 bands per primer. Among them, eight bands were identified to be polymorphic with a rate of 44.4%. In addition, the GD information content values were highest in the 60 Gy treatment population and the GD values were higher in the γ-ray treatment populations than in the MNU treatment population. According to a cluster analysis, all the mutant lines can be classified into five categories, and the genetic distance was greatest between the 80 Gy-irradiated population and other populations. These results indicate that mutant lines have high GD and can be effectively utilized for improving blackberry breeding.
Identification of platelet function defects by multi-parameter assessment of thrombus formation
Authors: de Witt Susanne M. , Swieringa Frauke , Cavill Rachel , Lamers Moniek M. E. , van Kruchten Roger , Mastenbroek Tom , Baaten Constance , Coort Susan , Pugh Nicholas , Schulz Ansgar , Scharrer Inge , Jurk Kerstin , Zieger Barbara , Clemetson Kenneth J. , Farndale Richard W. , Heemskerk Johan W. M. , Cosemans Judith M.E.M. 
Published: July 2014

AbstractAssays measuring platelet aggregation (thrombus formation) at arterial shear rate mostly use collagen as only platelet-adhesive surface. Here we report a multi-surface and multi-parameter flow assay to characterize thrombus formation in whole blood from healthy subjects and patients with platelet function deficiencies. A systematic comparison is made of 52 adhesive surfaces with components activating the main platelet-adhesive receptors, and of eight output parameters reflecting distinct stages of thrombus formation. Three types of thrombus formation can be identified with a predicted hierarchy of the following receptors: glycoprotein (GP)VI, C-type lectin-like receptor-2 (CLEC-2)>GPIb>α6β1, αIIbβ3>α2β1>CD36, α5β1, αvβ3. Application with patient blood reveals distinct abnormalities in thrombus formation in patients with severe combined immune deficiency, Glanzmann’s thrombasthenia, Hermansky–Pudlak syndrome, May–Hegglin anomaly or grey platelet syndrome. We suggest this test may be useful for the diagnosis of patients with suspected bleeding disorders or a pro-thrombotic tendency.
Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase
Authors: Leferink Nicole G. H. , Antonyuk Svetlana V. , Houwman Joseline A. , Scrutton Nigel S. , Eady Robert R. , Hasnain S. Samar 
Published: July 2014

AbstractEnzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of catalysis. Evidence for long-range effects on enzyme mechanism resulting from mutations remains sparse, limiting the design/redesign of synthetic catalysts in a predictable way. Here we show that improving the accessibility of the active site pocket of copper nitrite reductase by mutation of a surface-exposed phenylalanine residue (Phe306), located 12 Å away from the catalytic site type-2 Cu (T2Cu), profoundly affects intra-molecular electron transfer, substrate-binding and catalytic activity. Structures and kinetic studies provide an explanation for the lower affinity for the substrate and the alteration of the rate-limiting step in the reaction. Our results demonstrate that distant residues remote from the active site can have marked effects on enzyme catalysis, by driving mechanistic change through relatively minor structural perturbations.
Long-term changes in the ghrelin-CB1R axis associated with the maintenance of lower body weight after sleeve gastrectomy
Authors: Fedonidis C , Alexakis N , Koliou X , Asimaki O , Tsirimonaki E , Mangoura D 
Published: July 2014

Abstract
Objectives:
In the hypothalamus, the molecular actions of receptors for growth hormone secretagogue (ghrelin) receptor-GHSR, leptin receptor-b (LEPRb), Melanocortin-4 receptor (MC4R) and Cannabinoid-1 receptor (CB1R) regulate energy homeostasis and body weight. We hypothesized that the acute loss of stomach tissue upon sleeve gastrectomy (SG), performed to treat obesity, imposes modulations on the expression of these receptors in the brain to sustain weight loss.

Methods:
Rats, induced to obesity with high-fat diet were randomized to SG- or sham-operation groups and killed at 30 or 90 days post surgery, when the expression of Ghrl, Mboat4 and Cnr1 in the stomach, and Ghsr, Leprb, Mc4r and Cnr1 in distinct brain areas was assessed by reverse transcription-PCR and western blotting.

Results:
SG acutely reduced body weight and fat mass and suppressed the remnant stomach mRNA levels of preproghrelin and ghrelin O-acyltransferase, which correlated well with long-term decreases in CB1R mRNA. In the hypothalamus, increases in GHSR and decreases in CB1R and LEPRb by 30 days were followed by further downregulation of CB1R and an increase in MC4R by 90 days.

Conclusions:
Post SG, acyl-ghrelin initiates a temporal hierarchy of molecular events in the gut-brain axis that may both explain the sustained lower body weight and suggest intervention into the cannabinoid pathways for additional therapeutic benefits.
Effects of metformin and other biguanides on oxidative phosphorylation in mitochondria
Authors: Bridges Hannah R. , Jones Andrew J. Y. , Pollak Michael N. , Hirst Judy 
Published: July 2014

The biguanide metformin is widely prescribed for Type II diabetes and has anti-neoplastic activity in laboratory models. Despite evidence that inhibition of mitochondrial respiratory complex I by metformin is the primary cause of its cell-lineage-specific actions and therapeutic effects, the molecular interaction(s) between metformin and complex I remain uncharacterized. In the present paper, we describe the effects of five pharmacologically relevant biguanides on oxidative phosphorylation in mammalian mitochondria. We report that biguanides inhibit complex I by inhibiting ubiquinone reduction (but not competitively) and, independently, stimulate reactive oxygen species production by the complex I flavin. Biguanides also inhibit mitochondrial ATP synthase, and two of them inhibit only ATP hydrolysis, not synthesis. Thus we identify biguanides as a new class of complex I and ATP synthase inhibitor. By comparing biguanide effects on isolated complex I and cultured cells, we distinguish three anti-diabetic and potentially anti-neoplastic biguanides (metformin, buformin and phenformin) from two anti-malarial biguanides (cycloguanil and proguanil): the former are accumulated into mammalian mitochondria and affect oxidative phosphorylation, whereas the latter are excluded so act only on the parasite. Our mechanistic and pharmacokinetic insights are relevant to understanding and developing the role of biguanides in new and existing therapeutic applications, including cancer, diabetes and malaria.
Face-Viewing Patterns in Young Children With Autism Spectrum Disorders: Speaking up for the Role of Language Comprehension
Authors: Åsberg Johnels Jakob , Gillberg Christopher , Falck-Ytter Terje , Miniscalco Carmela 
Published: July 2014

Purpose
The aim was to examine whether viewing patterns toward the mouth, eyes, and nonmouth–noneyes areas differed between young children with autism spectrum disorder (ASD) and typically developing (TD) children when viewing a person speaking. The role of language comprehension in such viewing patterns was also examined.

Method
Eleven children with ASD (approximately 4.5 years old) and 29 TD toddlers (approximately 2.5 years old) participated. The groups were matched on language comprehension raw scores from the Reynell Developmental Language Scales III. All children viewed short films of a woman speaking while their eye movements were recorded with eye-tracking equipment.

Results
Children with ASD spent proportionally less time viewing the mouth and more time viewing the nonmouth–noneyes areas. Time viewing the eyes did not differ between groups. Increased mouth viewing was associated with lower language comprehension in the group with ASD.

Conclusion
Variability in language comprehension is an important factor to monitor when interpreting face-viewing patterns in young children with ASD, particularly with regard to mouth viewing. The results may help explain divergent findings in this field of research.
Assessing Pragmatic Language in Autism Spectrum Disorder: The Yale
in vivo
Pragmatic Protocol
Authors: Simmons Elizabeth Schoen , Paul Rhea , Volkmar Fred 
Published: July 2014

Purpose

This study compared pragmatic language in youths (9–17 years) with autism spectrum disorder (ASD) and those with typical development (TD) on the Yale
in vivo
Pragmatic Protocol (Y
i
PP), a semistructured, dynamic conversational assessment.

Method

Participants (
n
= 118) were divided into groups based on age and diagnosis. Each completed the Y
i
PP, which included 4 pragmatic domains (discourse management, communicative functions, conversational repair, presupposition). The participant's response to each probe was scored correct or incorrect; incorrect scores elicited cues from the examiner, and level of cue required for a correction was also scored.

Results

The Y
i
PP showed high reliability and internal consistency, with moderate concurrent validity, sensitivity, and specificity. The group with ASD performed worse overall on Y
i
PP probes compared to their TD counterparts on both error (
d
= 0.96) and cue (
d
= 0.91) scores. Item analyses revealed greater gaps between older students with ASD and their TD peers than between the 2 younger groups.

Conclusions
These data suggest that a probe measure designed to assess pragmatic abilities in children with ASD within a conversational context has some validity for contributing to diagnostic classification and can identify specific areas of pragmatic vulnerabilities as part of a clinical assessment.

Supplemental Material

https://doi.org/10.23641/asha.6170480
Optimised adaptive power on‐demand routing protocol for mobile ad hoc wireless network
Authors: Bello Lawal , Bakalis Panos , Rapajic Predrag , Anang Kwashie A. 
Published: July 2014

A technique is developed for ad hoc on‐demand routing protocol. The protocol is based on the conventional on‐demand ad hoc routing protocols with the addition of power model. The algorithm design and development is aimed to incorporate the transmitted power consumption function in such a manner that mobile nodes are able to evaluate their power status to decide if they are fit for packet forwarding and reception. This is illustrated through analytical approach supported by computer simulations over mobile ad hoc wireless network containing 80 mobile nodes. The results showed that power savings of 50% were achieved with no delay in the network and increased throughput performance by 60%, as compared to a network with conventional ad hoc on‐demand distance vector and dynamic source routing protocols.
Comparative proteomic study reveals 17β-HSD13 as a pathogenic protein in nonalcoholic fatty liver disease
Authors: Su Wen , Wang Yang , Jia Xiao , Wu Wenhan , Li Linghai , Tian Xiaodong , Li Sha , Wang Chunjiong , Xu Huamin , Cao Jiaqi , Han Qifei , Xu Shimeng , Chen Yong , Zhong Yanfeng , Zhang Xiaoyan , Liu Pingsheng , Gustafsson Jan-Åke , Guan Youfei 
Published: July 2014

Significance
Nonalcoholic fatty liver disease (NAFLD) is a common chronic hepatic disease affecting up to 25% of subjects in the developed world, and represents a progressive illness eventually leading to liver fibrosis and cirrhosis. This study reports an extensive set of human liver lipid droplet (LD)-associated proteins and an array of proteins differentially expressed in human NAFLD. We also uncover 17β-hydroxysteroid dehydrogenase-13, a newly identified LD-associated protein, as a pathogenic molecule in the development of NAFLD. The present study provides a potential link between LD proteins and the pathogenesis of hepatic steatosis.
Insulin-like peptide 5 is an orexigenic gastrointestinal hormone
Authors: Grosse Johannes , Heffron Helen , Burling Keith , Akhter Hossain Mohammed , Habib Abdella M. , Rogers Gareth J. , Richards Paul , Larder Rachel , Rimmington Debra , Adriaenssens Alice A. , Parton Laura , Powell Justin , Binda Matteo , Colledge William H. , Doran Joanne , Toyoda Yukio , Wade John D. , Aparicio Samuel , Carlton Mark B. L. , Coll Anthony P. , Reimann Frank , O’Rahilly Stephen , Gribble Fiona M. 
Published: July 2014

Significance
Hormonal factors from specialized enteroendocrine cells in the gut epithelium link the availability of dietary nutrients to energy utilization and storage. Many gut hormones also affect behaviors such as appetite and foraging, conveying for example the satiating effects of food consumption. Here we identify insulin-like peptide 5 (Insl5) as a product of colonic endocrine L-cells, and show that levels were elevated in calorie-restricted mice and reduced after feeding. Consistent with this profile Insl5 administration stimulated food intake in mice, indicating it should join ghrelin as only the second identified gut hormone that enhances appetite. Modulating the Insl5 axis presents a new strategy for the treatment of metabolic disease and obesity.
Analysis of benzo[c]phenanthridine alkaloids inEschscholtzia californicacell culture using HPLC-DAD and HPLC-ESI-MS/MS
Authors: Son Seok Young , Rhee Hong Soon , Lee Min Woo , Park Jong Moon 
Published: July 2014

AbstractEffective HPLC-DAD and HPLC-ESI-MS/MS methods have been developed for the analysis of eight benzo[c]phenanthridine alkaloids (sanguinarine, chelirubine, macarpine, chelerythrine, dihydrosanguinarine, dihydrochelirubine, dihydromacarpine and dihydrochelerythrine), which are important metabolites in Eschscholtzia californica cell culture. By adopting a ternary gradient pump system, the dihydro-form alkaloids hardly separable from each other could be successfully separated, and all the target alkaloids could be simultaneously quantified with the LOD values of 0.01–0.79 μg/mL and the LOQ values of 0.03–3.59 μg/mL. This HPLC-DAD method was further confirmed by HPLC-ESI-MS/MS system in multiple reaction monitoring mode. Each separated HPLC peak was identified as the target alkaloid, showing its relevant ionized molecule and selected fragment ion. By applying the established method, alkaloid production during the E. californica cell culture could be successfully monitored and some valuable information on its metabolism could be deduced.
Resolving complex tandem repeats with long reads
Authors: Ummat Ajay , Bashir Ali 
Published: July 2014

Abstract
Motivation : Resolving tandemly repeated genomic sequences is a necessary step in improving our understanding of the human genome. Short tandem repeats (TRs), or microsatellites, are often used as molecular markers in genetics, and clinically, variation in microsatellites can lead to genetic disorders like Huntington’s diseases. Accurately resolving repeats, and in particular TRs, remains a challenging task in genome alignment, assembly and variation calling. Though tools have been developed for detecting microsatellites in short-read sequencing data, these are limited in the size and types of events they can resolve. Single-molecule sequencing technologies may potentially resolve a broader spectrum of TRs given their increased length, but require new approaches given their significantly higher raw error profiles. However, due to inherent error profiles of the single-molecule technologies, these reads presents a unique challenge in terms of accurately identifying and estimating the TRs.
Results : Here we present P acmon STR, a reference-based probabilistic approach, to identify the TR region and estimate the number of these TR elements in long DNA reads. We present a multistep approach that requires as input, a reference region and the reference TR element. Initially, the TR region is identified from the long DNA reads via a 3-stage modified Smith–Waterman approach and then, expected number of TR elements is calculated using a pair-Hidden Markov Models –based method. Finally, TR-based genotype selection (or clustering: homozygous/heterozygous) is performed with Gaussian mixture models , using the Akaike information criteria , and coverage expectations.
Availability and implementation: https://github.com/alibashir/pacmonstr
Contact: ajayummat@gmail.com or ali.bashir@mssm.edu
Journaled string tree—a scalable data structure for analyzing thousands of similar genomes on your laptop
Authors: Rahn René , Weese David , Reinert Knut 
Published: July 2014

Abstract
Motivation : Next-generation sequencing (NGS) has revolutionized biomedical research in the past decade and led to a continuous stream of developments in bioinformatics, addressing the need for fast and space-efficient solutions for analyzing NGS data. Often researchers need to analyze a set of genomic sequences that stem from closely related species or are indeed individuals of the same species. Hence, the analyzed sequences are similar. For analyses where local changes in the examined sequence induce only local changes in the results, it is obviously desirable to examine identical or similar regions not repeatedly.
Results : In this work, we provide a datatype that exploits data parallelism inherent in a set of similar sequences by analyzing shared regions only once. In real-world experiments, we show that algorithms that otherwise would scan each reference sequentially can be speeded up by a factor of 115.
Availability : The data structure and associated tools are publicly available at http://www.seqan.de/projects/jst and are part of SeqAn, the C ++ template library for sequence analysis.
Contact : rene.rahn@fu-berlin.de
Edmund Husserl
Authors: Zahavi Dan 
Published: July 2014

Edmund Husserl (b. 1859–d. 1938) is a central figure in 20th-century philosophy. A student of Brentano (b. 1838–d. 1917) and a contemporary of Frege (b. 1848–d. 1925), he is the founding father of phenomenology and thereby a figure with a decisive impact not only on thinkers like Heidegger (b. 1889–d. 1976), Edith Stein (b. 1891–d. 1942), Merleau-Ponty (b. 1908–d. 1961), and Sartre (b. 1905–d. 1980), but also on subsequent theory formations in German and French philosophy. More recently, many of Husserl’s ideas have also been taken up and discussed by analytic philosophers. Husserl is primarily known for his analyses of intentionality, perception, temporality, embodiment, and intersubjectivity, for his rehabilitation of the lifeworld and his commitment to a form of transcendental idealism and for his criticism of reductionism, objectivism, and scientism. Most of Husserl’s writings have been published posthumously and they continue to disclose aspects of his thinking that it would have been difficult to anticipate through the study of the works originally published by Husserl himself. Many of these volumes have not yet been translated into English, and the same holds true for much of the research literature.
Neo-Confucianism
Authors: Angle Stephen 
Published: July 2014

“Neo-Confucianism” refers to the broad revival of Confucian thinking that emerged in the early Song dynasty (960–1279 ce). At the core of this revival was the movement known to its adherents as the “Learning of the Way” (daoxue), but the new directions in which Confucians took their shared tradition are not limited to the texts and terminology of the Learning of the Way movement, and so it makes sense to use the Western neologism “Neo-Confucianism” as a capacious term to cover the whole Confucian revival. When we include both proponents of the Learning of the Way and their critics—the latter of whose views would not have been possible without the Learning of the Way innovations against which to react—it becomes clear that Neo-Confucianism extends temporally from the early Song all the way into the Qing dynasty (1644–1911) and extends spatially into Korea, Japan, and Vietnam. Although there are certainly themes and debates that extend across dynastic or national boundaries, these borders still serve as useful demarcations and are used here as a primary means of organization. The origins of Neo-Confucianism and its ongoing interactions with Daoist and Chinese Buddhist traditions are related because even if the old idea that Neo-Confucianism is a reaction against Buddhism is too simple, there nonetheless are clear resonances between certain Daoist and (especially) Buddhist views and those at the center of the Learning of the Way. Among the many key concepts of Neo-Confucianism, two have occasioned significant independent scholarly attention, so a separate section of the article focuses on li (pattern, coherence, principle) and xing (nature). Finally, this article follows the existing literature in being broadly interdisciplinary. The most common approach to be found here is intellectual history—especially intellectual biography and history of ideas—but particularly in the more recent scholarship, we see philosophy, cultural history, and methods from religious studies. In each of these latter areas, there is substantial room for further development. One promising area has been the degree to which anglophone scholars are engaging with Sinophone scholarship, and vice versa; with this in mind, the article includes some of the best and most influential Chinese-language materials where appropriate.