bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of the HLA locus and TNF with type I autoimmune hepatitis susceptibility in New Zealand Caucasians
Authors: Ngu Jing H , Wallace Mary C , Merriman Tony R , Gearry Richard B , Stedman Catherine A M , Roberts Rebecca L 
Published: July 2013

Abstract

Purpose
The precise etiology of autoimmune hepatitis (AIH) remains unknown, although a number of genetic loci have been implicated in the susceptibility of type 1 AIH. The purpose of this study was to test for association of these loci with type 1 AIH in New Zealand Caucasians.

Methods
77 AIH patients and 485 healthy controls were genotyped for the SNPs rs2187668 (HLA-DRB*03:01), rs660895 (HLA-DRB*04:01), rs3749971 (HLA-A1-B8-DR3), rs231775 (CLTLA4), rs1800629 (TNF), and rs1800682 (FAS) using predesigned TaqMan SNP genotyping assays. Chi square analysis was used to test for association of allele and genotype with overall AIH, and with severe fibrosis and ALT levels at 6 months.

Results
Significant risk of AIH was conferred by the minor alleles of rs2187668 (OR = 2.45, 95% CI 1.65-3.61, p < 0.0001), rs3749971 (OR = 1.89, 95% CI 1.21-2.94, p = 0.004) and rs1800629 (OR = 2.06, 95% CI 1.41-3.01, p = 0.0001). Multivariate analysis showed that rs2187668 was independently associated with type 1 AIH susceptibility (OR = 2.40, 95% CI 1.46-3.93, p = 0.001). The C allele of FAS SNP rs1800682 was associated with increased risk of severe fibrosis at diagnosis (OR = 2.03, 95% CI 1.05-3.93, p = 0.035) and with incomplete normalization of ALT levels at 6 months post-diagnosis (OR = 3.94, 95% CI 1.62-9.54, p = 0.0015).

Conclusions
This is the first population-based study to investigate genetic risk loci for type 1 AIH in New Zealand Caucasians. We report significant independent association of HLA-DRB1*03:01 with overall susceptibility to type 1 AIH, as well as FAS with a more aggressive disease phenotype.
Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria
Authors: Al-Awadhi Husain , Dashti Narjis , Khanafer Majida , Al-Mailem Dina , Ali Nidaa , Radwan Samir 
Published: August 2013

Abstract
Culture-dependent methods for bacterial community analysis are currently considered obsolete; therefore, molecular techniques are usually used instead. The results of the current study on hydrocarbonoclastic bacteria in various oily habitats in Kuwait showed however, that the bacterial identities varied dramatically according to the analytical approach used. For six desert and six seawater samples used in this study, the culture-independent and culture-dependent techniques each led to a unique bacterial composition. Problems related to the culture-dependent technique are well known. The results of the current study highlighted bias problems other than those already recorded in the literature for the molecular approaches. Thus, for example, in contrast to the culture-dependent technique, the primers used in the molecular approach preferentially amplified the 16S rDNAs of hydrocarbonoclastic bacteria in total genomic DNAs of all the studied environmental samples, and in addition, failed to reveal in any environmental sample members of the Actinobacteria. The primers used in the molecular approach also amplified certain “pure” 16S rDNAs, but failed to do so when these DNAs were in mixture. In view of these results, it is recommended that the two analytical approaches should be used simultaneously because their combined results would reflect the bacterial community composition more precisely than either of them can do alone.
The effect of different surface treatments of demineralised enamel on microleakage under metal orthodontic brackets
Authors: Moosavi Horieh , Ahrari Farzaneh , Mohamadipour Hamideh 
Published: August 2013

Abstract

Background
The aim of this investigation was to assess the effects of different treatments of demineralised enamel on microleakage under orthodontic brackets.

Methods
Seventy-five intact premolars were randomly assigned to five groups. The teeth in groups 2 through 5 were immersed in a demineralising solution for 16 weeks. In groups 1 (control) and 2 (demineralised/control), conventional acid etching was used. In group 3, sodium hypochlorite (NaOCl) was applied on the enamel surface for 1 min after acid etching, and in group 4, Transbond Plus (3M Unitek, Monrovia, CA, USA) self-etching primer (SEP) was used. The teeth in group 5 were treated with 2% sodium fluoride (NaF) for 4 min before etching. After bracket bonding, the specimens were thermocycled, sealed with nail varnish, immersed in 0.5% basic fuchsine solution for 24 h and sectioned. Microleakage was measured under a stereomicroscope for the enamel-adhesive and adhesive-bracket interfaces of both occlusal and gingival sides.

Results
Demineralised teeth showed more microleakage at the enamel-adhesive interface on both occlusal and gingival sides compared to sound teeth, but the difference was not significant (P > 0.005). Treating the demineralised enamel with 5% NaOCl or Transbond Plus SEP was not effective in reducing microleakage. NaF treatment followed by acid etching of demineralised enamel resulted in significantly lower microleakage in most comparisons (P < 0.005).

Conclusions
The use of 2% NaF on hypomineralised enamel before the bracket bonding procedure is an effective way to decrease microleakage.
All-trans retinoic acid and rapamycin synergize with transforming growth factor-β1 to induce regulatory T cells but confer different migratory capacities
Authors: Jhunjhunwala Siddharth , Chen Leo C , Nichols Erin E , Thomson Angus W , Raimondi Giorgio , Little Steven R 
Published: July 2013

ABSTRACTTregs play important roles in maintaining immune homeostasis, and thus, therapies based on Treg are promising candidates for the treatment for a variety of immune-mediated disorders. These therapies, however, face the significant challenge of obtaining adequate numbers of Tregs from peripheral blood that maintains suppressive function following extensive expansion. Inducing Tregs from non-Tregs offers a viable alternative. Different methods to induce Tregs have been proposed and involve mainly treating cells with TGF-β-iTreg. However, use of TGF-β alone is not sufficient to induce stable Tregs. ATRA or rapa has been shown to synergize with TGF-β to induce stable Tregs. Whereas TGF-β plus RA-iTregs have been well-described in the literature, the phenotype, function, and migratory characteristics of TGF-β plus rapa-iTreg have yet to be elucidated. Herein, we describe the phenotype and function of mouse rapa-iTreg and reveal that these cells differ in their in vivo homing capacity when compared with mouse RA-iTreg and mouse TGF-β-iTreg. This difference in migratory activity significantly affects the therapeutic capacity of each subset in a mouse model of colitis. We also describe the characteristics of iTreg generated in the presence of TGF-β, RA, and rapa.
The LIR motif – crucial for selective autophagy
Authors: Birgisdottir Åsa Birna , Lamark Trond , Johansen Terje 
Published: August 2013

Summary
(Macro)autophagy is a fundamental degradation process for macromolecules and organelles of vital importance for cell and tissue homeostasis. Autophagy research has gained a strong momentum in recent years because of its relevance to cancer, neurodegenerative diseases, muscular dystrophy, lipid storage disorders, development, ageing and innate immunity. Autophagy has traditionally been thought of as a bulk degradation process that is mobilized upon nutritional starvation to replenish the cell with building blocks and keep up with the energy demand. This view has recently changed dramatically following an array of papers describing various forms of selective autophagy. A main driving force has been the discovery of specific autophagy receptors that sequester cargo into forming autophagosomes (phagophores). At the heart of this selectivity lies the LC3-interacting region (LIR) motif, which ensures the targeting of autophagy receptors to LC3 (or other ATG8 family proteins) anchored in the phagophore membrane. LIR-containing proteins include cargo receptors, members of the basal autophagy apparatus, proteins associated with vesicles and of their transport, Rab GTPase-activating proteins (GAPs) and specific signaling proteins that are degraded by selective autophagy. Here, we comment on these new insights and focus on the interactions of LIR-containing proteins with members of the ATG8 protein family.
1,2-Bis(ferrocenyl)dipnictenes: Bimetallic Systems with a Pn=Pn Heavy π-Spacer (Pn: P, Sb, and Bi)
Authors: Sakagami Michiyasu , Sasamori Takahiro , Sakai Heisuke , Furukawa Yukio , Tokitoh Norihiro 
Published: August 2013

Abstract
1,2-Bis(ferrocenyl)dipnictenes bearing a Pn=Pn π-spacer (Pn: P (1), Sb (2), and Bi (3)) between two ferrocenyl units have been synthesized as stable compounds. Not only their molecular structures and fundamental properties but also their redox behavior have been systematically disclosed. Interestingly, in the reduction region, the dipnictenes showed two pseudo-reversible one-electron redox couples at low temperature, suggesting possible generation of the corresponding radical anion and dianion species. On the other hand, they showed three-step one-electron oxidation processes in the oxidation region. The first two oxidation steps would correspond to those of the two ferrocenyl moieties, while the third step would be that of the Pn=Pn π-spacer moiety, respectively. Thus, these 1,2-bis(ferrocenyl)dipnictenes with a Pn=Pn π-spacer should be stable multiredox systems reflecting unique properties of a double bond between heavier 15 group elements. As a result, all Pn=Pn units (Pn: P, Sb, and Bi) were found to work as a more effective π-spacer than those of 2nd row elements such as C=C and N=N.
Protection-free Synthesis of Alkyl Glycosides under Hydrogenolytic Conditions
Authors: Ishihara Masaki , Takagi Yuka , Li Gefei , Noguchi Masato , Shoda Shin-ichiro 
Published: August 2013

Abstract
A convenient protection-free synthetic route for the preparation of alkyl glycosides has been developed. The alcoholysis of one-step preparable glycosyl donors, 4,6-dibenzyloxy-1,3,5-triazin-2-yl (DBT) glycosides, under hydrogenolytic conditions gave the corresponding glycosides in good yields without the addition of any acid promoters. The method could be successfully applied to the glycosylation of an acid-labile oligosaccharide.
The nature and prevalence of chronic pain in homeless persons: an observational study
Authors: Fisher Rebecca , Ewing Judith , Garrett Alice , Harrison E Katherine , Lwin Kimberly KT , Wheeler Daniel W 
Published: July 2013

Background: Homeless people are known to suffer disproportionately with health problems that reduce physical functioning and quality of life, and shorten life expectancy. They suffer from a wide range of diseases that are known to be painful, but little information is available about the nature and prevalence of chronic pain in this vulnerable group. This study aimed to estimate the prevalence of chronic pain among homeless people, and to examine its location, effect on activities of daily living, and relationship with alcohol and drugs.Methods: We conducted face-to-face interviews with users of homeless shelters in four major cities in the United Kingdom, in the winters of 2009-11. Participants completed the Brief Pain Inventory, Short Form McGill Pain questionnaire, Leeds Assessment of Neuropathic Symptoms and Signs, and detailed their intake of prescribed and unprescribed medications and alcohol. We also recorded each participant’s reasons for homelessness, and whether they slept rough or in shelters.Findings: Of 168 shelter users approached, 150 (89.3%) participated: 93 participants (63%) reported experiencing pain lasting longer than three months; the mean duration of pain experienced was 82.2 months. The lower limbs were most frequently affected. Opioids appeared to afford a degree of analgesia for some, but whilst many reported symptoms suggestive of neuropathic pain, very few were taking anti-neuropathic drugs.Interpretation: The prevalence of chronic pain in the homeless appears to be substantially higher than the general population, is poorly controlled, and adversely affects general activity, walking and sleeping. It is hard to discern whether chronic pain is a cause or effect of homelessness, or both. Pain is a symptom, but in this challenging group it might not always be possible to treat the underlying cause. Exploring the diagnosis and treatment of neuropathic pain may offer a means of improving the quality of these vulnerable people’s lives.
De novo genetic variation revealed in somatic sectors of single Arabidopsis plants
Authors: Hopkins Marianne T , Khalid Aaron M , Chang Pei-Chun , Vanderhoek Karen C , Lai Dulcie , Doerr Meghan D , Lolle Susan J 
Published: July 2013

Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives. Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.
Book Reviews
Authors: Rand Graham K. 
Published: August 2013

In Book Reviews, we review an extensive and diverse range of books. They cover theory and applications in operations research, statistics, management science, econometrics, mathematics, computers, and information systems. In addition, we include books in other fields that emphasize technical applications. The editor will be pleased to receive an e-mail from those willing to review a book, with an indication of specific areas of interest. If you are aware of a specific book that you would like to review, or that you think should be reviewed, please contact the editor. The following books are reviewed in this issue of Interfaces, 43(4), July–August, 2013: Value-Added Decision Making for Managers, Kenneth Chelst and Yavuz Burak Canbolat; Risk Analysis in Stochastic Supply Chains: A Mean-Risk Approach, Tsan-Ming Choi and Chun-Hung Chiu; In Pursuit of the Traveling Salesman, William J. Cook; Recent Advances in System Reliability: Signatures, Multi-state Systems and Statistical Inference, Anatoly Lisnianski and Ilia Frenkel, eds.; Dynamic Fleet Management for International Truck Transportation, Steffen Schorpp; and Operative Transportation Planning: Solutions in Consumer Goods Supply Chain, Thorben Seiler.
The assessment of scapular radiographs
Authors: Wijdicks C. A. , Anavian J. , Hill B. W. , Armitage B. M. , Vang S. , Cole P. A. 
Published: August 2013

The glenopolar angle assesses the rotational alignment of the glenoid and may provide prognostic information and aid the management of scapula fractures. We have analysed the effect of the anteroposterior (AP) shoulder radiograph rotational offset on the glenopolar angle in a laboratory setting and used this to assess the accuracy of shoulder imaging employed in routine clinical practice. Fluoroscopic imaging was performed on 25 non-paired scapulae tagged with 2 mm steel spheres to determine the orientation of true AP views. The glenopolar angle was measured on all the bony specimens rotated at 10° increments. The mean glenopolar angle measured on the bone specimens in rotations between 0° and 20° and thereafter was found to be significantly different (p < 0.001). We also obtained the AP radiographs of the uninjured shoulder of 30 patients treated for fractures at our centre and found that none fitted the criteria of a true AP shoulder radiograph. The mean angular offset from the true AP view was 38° (10° to 65°) for this cohort. Radiological AP shoulder views may not fully project the normal anatomy of the scapular body and the measured glenopolar angle. The absence of a true AP view may compromise the clinical management of a scapular fracture.Cite this article: Bone Joint J 2013;95-B:1114–20.
Outcome of limited forefoot amputation with primary closure in patients with diabetes
Authors: Shaikh N. , Vaughan P. , Varty K. , Coll A. P. , Robinson A. H. N. 
Published: August 2013

Limited forefoot amputation in diabetic patients with osteomyelitis is frequently required. We retrospectively reviewed diabetic patients with osteomyelitis, an unhealed ulcer and blood pressure in the toe of > 45 mmHg who underwent limited amputation of the foot with primary wound closure. Between 2006 and 2012, 74 consecutive patients with a mean age of 67 years (29 to 93), and a median follow-up of 31 months, were included. All the wounds healed primarily at a median of 37 days (13 to 210; mean 48). At a median of 6 months (1.5 to 18; mean 353 days), 23 patients (31%) suffered a further ulceration. Of these, 12 patients (16% of the total) required a further amputation. We conclude that primary wound closure following limited amputation of the foot in patients with diabetes is a safe and effective technique when associated with appropriate antibiotic treatment. Cite this article: Bone Joint J 2013;95-B:1083–7.
Is there reduced polyethylene wear and longer survival when using a mobile-bearing design in total knee replacement?
Authors: Zeng Y. , Shen B. , Yang J. , Zhou Z. K. , Kang P. D. , Pei F. X. 
Published: August 2013

The purpose of this study was to undertake a meta-analysis to determine whether there is lower polyethylene wear and longer survival when using mobile-bearing implants in total knee replacement when compared with fixed-bearing implants. Of 975 papers identified, 34 trials were eligible for data extraction and meta-analysis comprising 4754 patients (6861 knees). We found no statistically significant differences between the two designs in terms of the incidence of radiolucent lines, osteolysis, aseptic loosening or survival. There is thus currently no evidence to suggest that the use of mobile-bearing designs reduce polyethylene wear and prolong survival after total knee replacement. Cite this article: Bone Joint J 2013;95-B:1057–63.
A prospective study of a ceramic-on-metal bearing in total hip arthroplasty
Authors: Kazi H. A. , Perera J. R. , Gillott E. , Carroll F. A. , Briggs T. W. R. 
Published: August 2013

We prospectively assessed the efficacy of a ceramic-on-metal (CoM) hip bearing with uncemented acetabular and femoral components in which cobalt­–chrome acetabular liners and alumina ceramic heads were used. The cohort comprised 94 total hip replacements (THRs) in 83 patients (38 women and 45 men) with a mean age of 58 years (42 to 70). Minimum follow-up was two years. All patients had pre- and post-operative assessment using the Western Ontario and McMaster Universities osteoarthritis index (WOMAC), Oxford hip score and Short-Form 12 scores. All showed a statistically significant improvement from three months post-operatively onwards (all p < 0.001). After two years whole blood metal ion levels were measured and chromosomal analysis was performed. The levels of all metal ions were elevated except vanadium. Levels of chromium, cobalt, molybdenum and titanium were significantly higher in patients who underwent bilateral THR compared with those undergoing unilateral THR (p < 0.001). Chromosomal analysis demonstrated both structural and aneuploidy mutations. There were significantly more breaks and losses than in the normal population (p < 0.001). There was no significant difference in chromosomal aberration between those undergoing unilateral and bilateral procedures (all analyses p ≥ 0.62). The use of a CoM THR is effective clinically in the short-term, with no concerns, but the significance of high metal ion levels and chromosomal aberrations in the long-term remains unclear. Cite this article: Bone Joint J 2013;95-B:1040–44.
Endothelin systems in the brain: involvement in pathophysiological responses of damaged nerve tissues
Authors: Koyama Yutaka 
Published: August 2013

AbstractIn addition to their potent vasoconstriction effects, endothelins (ETs) show multiple actions in various tissues including the brain. The brain contains high levels of ETs, and their production is stimulated in many brain disorders. Accumulating evidence indicates that activation of brain ET receptors is involved in several pathophysiological responses in damaged brains. In this article, the roles of brain ET systems in relation to brain disorders are reviewed. In the acute phase of stroke, prolonged vasospasm of cerebral arteries and brain edema occur, both of which aggravate brain damage. Studies using ET antagonists show that activation of ETAreceptors in the brain vascular smooth muscle induces vasospasm after stroke. Brain edema is induced by increased activity of vascular permeability factors, such as vascular endothelial growth factor and matrix metalloproteinases. Activation of ETBreceptors stimulates astrocytic production of these permeability factors. Increases in reactive astrocytes are observed in neurodegenerative diseases and in the chronic phase of stroke, where they facilitate the repair of damaged nerve tissues by releasing neurotrophic factors. ETs promote the induction of reactive astrocytes through ETBreceptors. ETs also stimulate the production of astrocytic neurotrophic factors. Recent studies have shown high expression of ETBreceptors in neural progenitors. Activation of ETBreceptors in neural progenitors promotes their proliferation and migration, suggesting roles for ETBreceptors in neurogenesis. Much effort has been invested in the pursuit of novel drugs to induce protection or repair of damaged nerve tissues. From these studies, the pharmacological significance of brain ET systems as a possible target of neuroprotective drugs is anticipated.