bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paediatric single mitochondrial DNA deletion disorders: an overlapping spectrum of disease
Authors: Broomfield Alexander , Sweeney Mary G. , Woodward Cathy E. , Fratter Carl , Morris Andrew M. , Leonard James V. , Abulhoul Lara , Grunewald Stephanie , Clayton Peter T. , Hanna Michael G. , Poulton Joanna , Rahman Shamima 
Published: October 2014

AbstractBackgroundSingle large‐scale mitochondrial DNA (mtDNA) deletions (SLSMDs) are amongst the most frequently diagnosed mtDNA disorders in childhood, yet their natural history remains poorly understood. We report the natural history of a large multicentre cohort of such children.MethodsWe reviewed case notes from three different UK centres to determine the clinical course of 34 patients (16 female, 18 male) with childhood‐onset mitochondrial disease caused by SLSMDs. Kaplan–Meier analysis was used to compare survival of patients presenting with haematological features (Pearson syndrome) and those with nonhaematological presentations.ResultsThe most frequent initial presentation was with isolated ptosis (16/34, 47 %). Eleven (32 %) patients presented with transfusion‐dependent anaemia soon after birth and were diagnosed with Pearson syndrome, whilst ten were classified as having Kearns–Sayre syndrome, three as having progressive external ophthalmoplegia (PEO) and seven as having PEO‐plus. Three patients did not conform to any specific mitochondrial syndrome. The most frequently affected organ during the disease course was the kidney, with documented tubular or glomerular dysfunction in 17 of 20 (85 %) cases who had detailed investigations. SLSMDs were present in blood and/or urine cells in all cases tested, indicating that muscle biopsy is not necessary for diagnosis in the paediatric age range. Kaplan–Meier survival analysis revealed significantly worse mortality in patients with Pearson syndrome compared with the rest of the cohort.ConclusionsMitochondrial disease caused by SLSMDs is clinically heterogeneous, and not all cases conform to a classical mitochondrial syndrome. Multisystem disease is the norm, with anaemia, renal impairment and endocrine disturbance being the most frequent extraneurological features. SLSMDs should be considered in the differential diagnosis of all children presenting with ptosis.
Identification of A Novel SBF2 Frameshift Mutation in Charcot–Marie–Tooth Disease Type 4B2 Using Whole-Exome Sequencing
Authors: Chen Meiyan , Wu Jing , Liang Ning , Tang Lihui , Chen Yanhua , Chen Huishuang , Wei Wei , Wei Tianying , Huang Hui , Yi Xin , Qi Ming 
Published: October 2014

Abstract
Charcot–Marie–Tooth disease type 4B2 with early-onset glaucoma (CMT4B2, OMIM 604563) is a genetically-heterogeneous childhood-onset neuromuscular disorder. Here, we report the case of a 15-year-old male adolescent with lower extremity weakness, gait abnormalities, foot deformities and early-onset glaucoma. Since clinical diagnosis alone was insufficient for providing pathogenetic evidence to indicate that the condition belonged to a consanguineous family, we applied whole-exome sequencing to samples from the patient, his parents and his younger brother, assuming that the patient’s condition is transmitted in an autosomal recessive pattern. A frame-shift mutation, c.4571delG (P.Gly1524Glufs∗42), was revealed in the CMT4B2-related gene SBF2 (also known as MTMR13, MIM 607697), and this mutation was found to be homozygous in the proband and heterozygous in his parents and younger brother. Together with the results of clinical diagnosis, this case was diagnosed as CMT4B2. Our finding further demonstrates the use of whole-exome sequencing in the diagnosis and treatment of rare diseases.
Pathway-Based Analysis Tools for Complex Diseases: A Review
Authors: Jin Lv , Zuo Xiao-Yu , Su Wei-Yang , Zhao Xiao-Lei , Yuan Man-Qiong , Han Li-Zhen , Zhao Xiang , Chen Ye-Da , Rao Shao-Qi 
Published: October 2014

Abstract
Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehensive understanding of the molecular mechanisms underlying complex diseases. Extensive studies utilizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods—the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available pathway-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are discussed. This review will provide a useful guide to dissect complex diseases.
TheColletotrichum destructivumspecies complex - hemibiotrophic pathogens of forage and field crops
Authors: Damm U. , O'Connell R.J. , Groenewald J.Z. , Crous P.W. 
Published: October 2014

Colletotrichum destructivumis an important plant pathogen, mainly of forage and grain legumes including clover, alfalfa, cowpea and lentil, but has also been reported as an anthracnose pathogen of many other plants worldwide. SeveralColletotrichumisolates, previously reported as closely related toC. destructivum, are known to establish hemibiotrophic infections in different hosts. The inconsistent application of names to those isolates based on outdated species concepts has caused much taxonomic confusion, particularly in the plant pathology literature. A multilocus DNA sequence analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 83 isolates ofC. destructivumand related species revealed 16 clades that are recognised as separate species in theC. destructivumcomplex, which includesC. destructivum,C. fuscum,C. higginsianum,C. liniandC. tabacum. Each of these species is lecto-, epi- or neotypified in this study. Additionally, eight species, namelyC. americae-borealis,C. antirrhinicola,C. bryoniicola,C. lentis,C. ocimi,C. pisicola,C. utrechtenseandC. vignaeare newly described.
Settling regimes of inertial particles in isotropic turbulence
Authors: Good G. H. , Ireland P. J. , Bewley G. P. , Bodenschatz E. , Collins L. R. , Warhaft Z. 
Published: October 2014

AbstractWe investigate the settling speeds and root mean square (r.m.s.) velocities of inertial particles in isotropic turbulence with gravity using experiments with water droplets in air turbulence from 32 loudspeaker jets and direct numerical simulations (DNS). The dependence on particle inertia, gravity and the scales of both the smallest and largest turbulent eddies is investigated. We isolate the mechanisms of turbulence settling modification and find that the reduced settling speeds of large particles in experiments are due to nonlinear drag effects. We demonstrate using DNS that reduced settling speeds with linear drag (e.g. see Nielsen, J. Sedim. Petrol., vol. 63, 1993, pp. 835–838) only arise in artificial flows that, by design, eliminate preferential sweeping by the eddies. Gravity and inertia both reduce the particle r.m.s. velocities and falling particles are more responsive to vertical than to horizontal fluctuations. The model by Wang & Stock (J. Atmos. Sci., vol. 50, 1993, pp. 1897–1913) captures these trends.
A piglet with surgically induced exocrine pancreatic insufficiency as an animal model of newborns to study fat digestion
Authors: Goncharova Kateryna , Pierzynowski Stefan G. , Grujic Danica , Kirko Siarhei , Szwiec Katarzyna , Wang Jing , Kovalenko Tetiana , Osadchenko Iryna , Ushakova Galyna , Shmigel Halyna , Fedkiv Olexandr , Majda Blanka , Prykhodko Olena 
Published: October 2014

The maldigestion and malabsorption of fat in infants fed milk formula results due to the minimal production of pancreatic lipase. Thus, to investigate lipid digestion and absorption and mimic the situation in newborns, a young porcine exocrine pancreatic insufficient (EPI) model was adapted and validated in the present study. A total of thirteen EPI pigs, aged 8 weeks old, were randomised into three groups and fed either a milk-based formula or a milk-based formula supplemented with either bacterial or fungal lipase. Digestion and absorption of fat was directly correlated with the addition of lipases as demonstrated by a 30 % increase in the coefficient of fat absorption. In comparison to the control group, a 40 and 25 % reduction in total fat content and 26 and 45 % reduction inn-3 andn-6 fatty acid (FA) content in the stool was observed for lipases 1 and 2, respectively. Improved fat absorption was reflected in the blood levels of lipid parameters. During the experiment, only a very slight gain in body weight was observed in EPI piglets, which can be explained by the absence of pancreatic protease and amylase in the gastrointestinal tract. This is similar to newborn babies that have reduced physiological function of exocrine pancreas. In conclusion, we postulate that the EPI pig model fed with infant formula mimics the growth and lipid digestion and absorption in human neonates and can be used to elucidate further importance of fat and FA in the development and growth of newborns, as well as for testing novel formula compositions.
Folk-linguistic landscapes: The visual semiotics of digital enregisterment
Authors: Heyd Theresa 
Published: October 2014

AbstractThis article analyzes folk-linguistic photo blogging as an example of twenty-first-century grassroots prescriptivism. Photo blogs engaged in grassroots prescriptivism usually focus on one specific linguistic phenomenon and collect visual evidence of its usage. Through the overt or covert language policing involved in such displays, folk-linguistic photo blogs contribute to the digital enregisterment of the linguistic practices they focus on as nonstandard or uneducated. This process is closely examined in a case study on emphatic quotation marks, a nonstandard form of punctuation that has been termed ‘greengrocer's quotes’, and its concomitant folk-linguistic photo blog. It is argued here that much of the persuasive power of such blogs can be attributed to their reliance on photographic material depicting signage in public space, and thus on the kind of visual semiotics that also informs many recent approaches in sociolinguistics. The simultaneity of these two phenomena is critically discussed. (Visual semiotics, enregisterment, computer-mediated communication, grassroots prescriptivism, emphatic quotation)*
Categories, stereotypes, and the linguistic perception of sexuality
Authors: Levon Erez 
Published: October 2014

AbstractThis article examines how social stereotypes influence listeners' perceptions of indexical language. Building on recent developments in linguistics and social psychology, I investigate the extent to which stereotypical attitudes and beliefs about categories of speakers serve to enable the association of linguistic features with particular social meanings while simultaneously blocking others. My arguments are based on an analysis of listener perceptions of the intersecting categories of gender, sexuality, and social class among men in the UK. Using a modified matched-guise paradigm to test three category-relevant variables (mean pitch, spectral characteristics of /s/, and TH-fronting), I demonstrate how the perception of social meaning is governed by a combination of both attitudinal and cognitive factors. This finding is important because it illustrates the listener-dependent nature of sociolinguistic perception. Moreover, it also provides further empirical support for an understanding of social meaning as an emergent property of language-in-use. (speech perception, attitudes and stereotypes, sexuality, phonetic variation)*
Reflections on a ‘Happy Ending’: The Case of Cupid and Psyche
Authors: Penwill J.L. 
Published: October 2014

The yo-yo problem: first Psyche is mortal and exposed as though for death (DOWN); then she is rescued and cohabits with Cupid (UP); then she falls from Cupid (DOWN); then she searches and with help almost succeeds in her trials (UP); then she fails and lies in a sleep like death (DOWN); then she is rescued by and married to Cupid (UP).Ken Dowden, ‘Psyche on the Rock’ (1982)Well I've been down so goddam' long, that it looks like up to me.Jim Morrison, ‘Been Down So Long’ (1971)Bella fabella(‘beautiful little story’) exclaims the ass at the conclusion of the unnamed old woman's narration of the tale that we have come to know as ‘Cupid and Psyche’, a tale that occupies 63 chapters of books 4, 5 and 6 of Apuleius'Metamorphoses. The beauty of the tale is enhanced by the contrast with its setting: a bandits' cave whose inhabitants' heroicisation of violence and thuggery is very much in the spirit of Homer's Cyclops or Little Alex in Stanley Kubrick'sA Clockwork Orange, and an audience that comprises two individuals wrenched from their homes and families by these bandits' depredations—Charite, the kidnapped girl, and Lucius, lashed into assisting in the ransacking of his host Milo's house in Hypata. The tale transports us into a world of romance and fairy tale far removed from the difficulties and dangers of what is portrayed as the real world inMetamorphoses1-10.
Repetitions which are not repetitions: the non-redundant nature of tautological compounds
Authors: BENCZES RÉKA 
Published: October 2014

In English morphological literature, the term ‘tautological compound’ has been typically used to refer to two distinct – but closely related – phenomena: (1) compounds composed of a hyponym and a superordinate term (such as oak tree); and/or (2) compounds based upon two synonymous units (such as subject matter). Such combinations are one of the quirkiest – and least researched – phenomena of English compounding. Their oddity can be attributed to two main factors. First, as their name, ‘tautological compound’ implies, at face value such combinations can be considered as prime examples of the redundancy of language. Second, they do not follow normal compound-forming rules in the sense that both constituents can function as the semantic head (as opposed to ‘normal’ English compounds, which follow the Right-Hand Head Rule).Perhaps it is the quirkiness of tautological compounds that accounts for the fact that not much has been said about them in traditional accounts of compounding, which typically relegate them to a marginal area of the English language. However, there is more to tautological compounds than meets the eye. What the present study wishes to demonstrate is that the term ‘tautological compound’ is a misnomer, as such combinations are far from being tautological or redundant in their meaning. Accordingly, the article first clarifies the notion of tautological compound, and then aims to give an account of the various roles that such combinations play in language, thereby demonstrating their non-tautological and non-redundant nature – in order to assign this much-neglected category to its proper, well-deserved place within English word formation.
Reducing the use of seclusion in a secure service for women
Authors: Long Clive G , West Rachel , Afford Matthew , Collins Lesley , Dolley Olga 
Published: October 2014

AbstractReducing the use of seclusion to deal with challenging behaviour is a priority in secure services for women. This study describes the concurrent introduction of a series of initiatives based on recovery principles and the full involvement of patients in their risk management plans.Following change implementation, the first 19 patients who had completed one year of treatment were matched with 19 patients who had completed their first year of treatment before change.A significant decline in both the number of seclusions and risk behaviour post-change was complemented by improved staff ratings of institutional behaviour, increased treatment engagement and a reduction in time spent in medium security. Staff and patients differed in terms of their ratings of the most effective strategies introduced. Patients favoured the Relational Security item of increased individual engagement and timetabled Behaviour Chain Analysis sessions. Staff viewed on ward training and use of de-escalation techniques as most effective.Findings confirm results from mixed gender forensic mental health samples that seclusion can be successfully reduced without an increase in patient violence or alternative coercive strategies. Limitations of the study are discussed along with the need for future evaluations to address issues of fidelity and utilise vigorously designed case studies.
Differentiated Deservedness: Governance through Familialist Social Policies in Singapore
Authors: Teo Youyenn 
Published: October 2014

AbstractThe familialist orientations of the Singapore state on issues of social welfare ought not be taken for granted as static reflections of ‘culture’. Instead, it is a dynamic realm, and a useful site for analysing how and what sorts of state-society relations are forged. We can, moreover, deepen our understanding of governance in Singapore by looking beyond repression and discrimination and paying more attention to the processes of production and differentiation. In this article, I draw on examples from housing, healthcare, and childcare support, to understand how specific social identities and practices are marked as deserving public support. I argue that the logic and practices embedded in policies – what I call ‘differentiated deservedness’ – can be read as a productive and profound form of governance in which specific performances of the familial are generated, and through which norms about state-society relations and citizenship are forged. Scholars and activists who are oriented toward expanding social security and social justice should scrutinise reforms for the extent to which the logic of differentiated deservedness persists or changes.
Iron bioavailability to phytoplankton: an empirical approach
Authors: Lis Hagar , Shaked Yeala , Kranzler Chana , Keren Nir , Morel François M M 
Published: October 2014

Abstract
Phytoplankton are often limited by iron in aquatic environments. Here we examine Fe bioavailability to phytoplankton by analyzing iron uptake from various Fe substrates by several species of phytoplankton grown under conditions of Fe limitation and comparing the measured uptake rate constants (Fe uptake rate/ substrate concentration). When unchelated iron, Fe′, buffered by an excess of the chelating agent EDTA is used as the Fe substrate, the uptake rate constants of all the eukaryotic phytoplankton species are tightly correlated and proportional to their respective surface areas (S.A.). The same is true when FeDFB is the substrate, but the corresponding uptake constants are one thousand times smaller than for Fe′. The uptake rate constants for the other substrates we examined fall mostly between the values for Fe′ and FeDFB for the same S.A. These two model substrates thus empirically define a bioavailability envelope with Fe′ at the upper and FeDFB at the lower limit of iron bioavailability. This envelope provides a convenient framework to compare the relative bioavailabilities of various Fe substrates to eukaryotic phytoplankton and the Fe uptake abilities of different phytoplankton species. Compared with eukaryotic species, cyanobacteria have similar uptake constants for Fe′ but lower ones for FeDFB. The unique relationship between the uptake rate constants and the S.A. of phytoplankton species suggests that the uptake rate constant of Fe-limited phytoplankton has reached a universal upper limit and provides insight into the underlying uptake mechanism.
Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3−/NO2− reduction pathways in Shewanella loihica strain PV-4
Authors: Yoon Sukhwan , Cruz-García Claribel , Sanford Robert , Ritalahti Kirsti M , Löffler Frank E 
Published: October 2014

Abstract
Denitrification and respiratory ammonification are two competing, energy-conserving NO3−/NO2− reduction pathways that have major biogeochemical consequences for N retention, plant growth and climate. Batch and continuous culture experiments using Shewanella loihica strain PV-4, a bacterium possessing both the denitrification and respiratory ammonification pathways, revealed factors that determine NO3−/NO2− fate. Denitrification dominated at low carbon-to-nitrogen (C/N) ratios (that is, electron donor-limiting growth conditions), whereas ammonium was the predominant product at high C/N ratios (that is, electron acceptor-limiting growth conditions). pH and temperature also affected NO3−/NO2− fate, and incubation above pH 7.0 and temperatures of 30 °C favored ammonium formation. Reverse-transcriptase real-time quantitative PCR analyses correlated the phenotypic observations with nirK and nosZ transcript abundances that decreased up to 1600-fold and 27-fold, respectively, under conditions favoring respiratory ammonification. Of the two nrfA genes encoded on the strain PV-4 genome, nrfA0844 transcription decreased only when the chemostat reactor received medium with the lowest C/N ratio of 1.5, whereas nrfA0505 transcription occurred at low levels (≤3.4 × 10−2 transcripts per cell) under all growth conditions. At intermediate C/N ratios, denitrification and respiratory ammonification occurred concomitantly, and both nrfA0844 (5.5 transcripts per cell) and nirK (0.88 transcripts per cell) were transcribed. Recent findings suggest that organisms with both the denitrification and respiratory ammonification pathways are not uncommon in soil and sediment ecosystems, and strain PV-4 offers a tractable experimental system to explore regulation of dissimilatory NO3−/NO2− reduction pathways.
The role of community and population ecology in applying mycorrhizal fungi for improved food security
Authors: Rodriguez Alia , Sanders Ian R 
Published: October 2014

Abstract
The global human population is expected to reach ∼9 billion by 2050. Feeding this many people represents a major challenge requiring global crop yield increases of up to 100%. Microbial symbionts of plants such as arbuscular mycorrhizal fungi (AMF) represent a huge, but unrealized resource for improving yields of globally important crops, especially in the tropics. We argue that the application of AMF in agriculture is too simplistic and ignores basic ecological principals. To achieve this challenge, a community and population ecology approach can contribute greatly. First, ecologists could significantly improve our understanding of the determinants of the survival of introduced AMF, the role of adaptability and intraspecific diversity of AMF and whether inoculation has a direct or indirect effect on plant production. Second, we call for extensive metagenomics as well as population genomics studies that are crucial to assess the environmental impact that introduction of non-local AMF may have on native AMF communities and populations. Finally, we plead for an ecologically sound use of AMF in efforts to increase food security at a global scale in a sustainable manner.