bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlling coherence via tuning of the population imbalance in a bipartite optical lattice
Authors: Di Liberto M. , Comparin T. , Kock T. , Ölschläger M. , Hemmerich A. , Smith C. Morais 
Published: December 2014

AbstractThe control of transport properties is a key tool at the basis of many technologically relevant effects in condensed matter. The clean and precisely controlled environment of ultracold atoms in optical lattices allows one to prepare simplified but instructive models, which can help to better understand the underlying physical mechanisms. Here we show that by tuning a structural deformation of the unit cell in a bipartite optical lattice, one can induce a phase transition from a superfluid into various Mott insulating phases forming a shell structure in the superimposed harmonic trap. The Mott shells are identified via characteristic features in the visibility of Bragg maxima in momentum spectra. The experimental findings are explained by Gutzwiller mean-field and quantum Monte Carlo calculations. Our system bears similarities with the loss of coherence in cuprate superconductors, known to be associated with the doping-induced buckling of the oxygen octahedra surrounding the copper sites.
Spartan deficiency causes genomic instability and progeroid phenotypes
Authors: Maskey Reeja S. , Kim Myoung Shin , Baker Darren J. , Childs Bennett , Malureanu Liviu A. , Jeganathan Karthik B. , Machida Yuka , van Deursen Jan M. , Machida Yuichi J. 
Published: December 2014

AbstractSpartan (also known as DVC1 and C1orf124) is a PCNA-interacting protein implicated in translesion synthesis, a DNA damage tolerance process that allows the DNA replication machinery to replicate past nucleotide lesions. However, the physiological relevance of Spartan has not been established. Here we report that Spartan insufficiency in mice causes chromosomal instability, cellular senescence and early onset of age-related phenotypes. Whereas complete loss of Spartan causes early embryonic lethality, hypomorphic mice with low amounts of Spartan are viable. These mice are growth retarded and develop cataracts, lordokyphosis and cachexia at a young age. Cre-mediated depletion of Spartan from conditional knockout mouse embryonic fibroblasts results in impaired lesion bypass, incomplete DNA replication, formation of micronuclei and chromatin bridges and eventually cell death. These data demonstrate that Spartan plays a key role in maintaining structural and numerical chromosome integrity and suggest a link between Spartan insufficiency and progeria.
MORC1 represses transposable elements in the mouse male germline
Authors: Pastor William A. , Stroud Hume , Nee Kevin , Liu Wanlu , Pezic Dubravka , Manakov Sergei , Lee Serena A. , Moissiard Guillaume , Zamudio Natasha , Bourc’his Déborah , Aravin Alexei A. , Clark Amander T. , Jacobsen Steven E. 
Published: December 2014

AbstractThe Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation.
Benzoate pathway: members, biosynthesis and function.
Authors: Kulma A. , Żuk M. , Kostyn A. , Kostyn K. , Szopa J. 
Published: December 2014

Abstract
Efforts to treat diseases have long involved the use of natural materials placed in contact with human tissues. The main sources of these materials are plant products containing a broad spectrum of compounds capable of restoring, regenerating and even healing tissues. A unique, dual-purpose function is ascribed to benzoate derivatives. Plant protection against environmental stresses on the one hand and strong antimicrobial and antioxidant functions on the other are their potential functions. The benzoate pathway, although very rich in compounds of different and important functions for producers (plant) and consumers, is as yet not fully understood. Signal molecules (salicylate), antimicrobial and antifungal (benzoate, vanillin), local anaesthetic (cocaine) and anticancer (taxol) are all examples of simple benzoate derivatives. Thus, the challenge for biochemists and biotechnologists is to gain more knowledge about the identification and regulation of genes that control this pathway and its application for diversified compound production in plants. The main goal of this review is to summarize knowledge about the route/routes of biosynthesis of benzenoid derivatives (BP) from the phenylpropanoid pathway, as well as about the regulation of the biosynthesis of these compounds, their properties and biotechnological approaches for their production.
Comparison between Hinode/SOT and SDO/HMI, AIA data for the study of the solar flare trigger process
Authors: Bamba Yumi , Kusano Kanya , Imada Shinsuke , Iida Yusuke 
Published: December 2014

Abstract
Understanding the mechanism that produces solar flares is important not only from the scientific point of view but also for improving space weather predictability. There are numerous observational and computational studies that have attempted to reveal the onset mechanism of solar flares. However, the underlying mechanism of flare onset remains elusive. To elucidate the flare trigger mechanism, we analyzed several flare events which were observed by Hinode/Solar Optical Telescope (SOT) in our previous study. Because of the limitation of the SOT field of view, however, only four events in the Hinode data sets have been usable. Therefore, increasing the number of events is required for evaluating the flare trigger models. We investigated the applicability of data obtained by the Solar Dynamics Observatory (SDO) to increase the data sample for a statistical analysis of the flare trigger process. SDO regularly observes the full disk of the sun and all flares, although its spatial resolution is lower than that of Hinode. We investigated the M6.6 flare which occurred on 2011 February 13, and compared the analyzed data of SDO with the results of our previous study using Hinode/SOT data. Filter and vector magnetograms obtained by the Helioseismic and Magnetic Imager and filtergrams from the Atmospheric Imaging Assembly (AIA) 1600 Å were employed. From the comparison of small-scale magnetic configurations and chromospheric emission prior to the flare onset, we confirmed that the trigger region is detectable with the SDO data. We also measured the magnetic shear angles of the active region and the azimuth and strength of the flare trigger field. The results were consistent with our previous study. We concluded that statistical studies of the flare trigger process are feasible with SDO as well as Hinode data. We also investigated the temporal evolution of the magnetic field before the flare onset with SDO.
Sodium Bicarbonate and Renal Function after Cardiac Surgery
Authors: Bailey Michael , McGuinness Shay , Haase Michael , Haase-Fielitz Anja , Parke Rachael , Hodgson Carol L. , Forbes Andrew , Bagshaw Sean M. , Bellomo Rinaldo 
Published: December 2014

AbstractAbstract
The authors have performed a novel, prospectively planned individual patient data meta-analysis of the double-blind randomized trials in this important field. Urinary alkalinization with sodium bicarbonate infusion is not associated with a significant reduction in the overall risk of acute kidney injury in cardiac surgery patients. However, urinary alkalinization was associated with significant renal protection in the subgroup of patients undergoing elective coronary artery bypass graft surgery suggesting that further investigation in these patients is warranted.

Background:
The effect of urinary alkalinization in cardiac surgery patients at risk of acute kidney injury (AKI) is controversial and trial findings conflicting. Accordingly, the authors performed a prospectively planned individual patient data meta-analysis of the double-blind randomized trials in this field.

Methods:
The authors studied 877 patients from three double-blind, randomized controlled trials enrolled to receive either 24 h of intravenous infusion of sodium bicarbonate or sodium chloride. The primary outcome measure was a postoperative increase in serum creatinine concentration of greater than 25% or 0.5 mg/dl (> 44 μm/L) within the first five postoperative days. Secondary outcomes included the raw change in serum creatinine, greater than 50% and greater than 100% rises in serum creatinine, developing AKI (Acute Kidney Injury Network criteria), initiation of renal replacement therapy, morbidity, and mortality.

Results:
Patients were similar in demographics, comorbidities, and cardiac procedures. Sodium bicarbonate increased plasma bicarbonate (P < 0.001) and urine pH (P < 0.001). There were no differences in the development of the primary outcome (Bicarbonate 45% [39–51%] vs. Saline 42% [36–48%], P = 0.29). This result remained unchanged when controlling for study and covariates (odds ratio [OR], 99% confidence interval [CI]: Bicarbonate vs. Control, 1.11 [0.77–1.60], P = 0.45). There was, however, a significant study-adjusted benefit in elective coronary artery bypass surgery patients in terms of renal replacement therapy (Bicarbonate vs. Control, OR: 0.38 [99% CI: 0.25–0.58], P < 0.0001) and the development of an Acute Kidney Injury Network grade = 3 (Bicarbonate vs. Control, OR: 0.45 [99% CI: 0.43–0.48], P < 0.0001).

Conclusions:
Urinary alkalinization using sodium bicarbonate infusion is not associated with an overall lower incidence of AKI; however, it reduces severe AKI and need for renal replacement therapy in elective coronary artery bypass patients.
Two-week Course of Preoperative Radiotherapy for Locally Advanced Rectal Adenocarcinoma
Authors: Zhu Xiang-gao , Li Jin-luan , Li Xiao-fan , Li Yong-heng , Ni Qian-yu , Wang Lin , Zhang Shan-wen , Gu Jin , Cai Yong , Lin Chi 
Published: December 2014

Objectives:
To evaluate local control and survival in locally advanced rectal adenocarcinoma patients who underwent a preoperative 2-week course of radiotherapy (RT) and to identify prognostic factors influencing the survival rate.

Methods:
We analyzed 377 consecutively treated patients with locally advanced (T3/T4 or node positive) rectal adenocarcinoma. All patients underwent a preoperative 2-week course of RT (30 Gy in 10 fractions) followed by curative surgery. Regression model was used to examine prognostic factors for the disease-free survival (DFS) and overall survival (OS) rates. The Statistical Analysis System software package, version 9.3, was used for analysis.

Results:
The median follow-up for all living patients was 63.8 months (range, 5.1 to 131.7). The 5-year DFS and OS rates were 64.5% (95% CI, 59.0-69.4) and 75.6% (95% CI, 70.5-80.0), respectively. The 5-year cumulative incidences of local recurrence and distant metastases were 5.4% (95% CI, 2.9-7.9) and 29.0% (95% CI, 23.9-30.1), respectively. The pathologic complete response rate was achieved in 17 patients (4.5%). The Multivariate Cox Regression model showed that factors affecting DFS were the surgical technique, pre-RT pathologic grade, ypT, ypN, and comorbidity; and factors improving OS were low anterior resection, low pre-RT grade, low ypT, and low ypN.

Conclusions:
Patients treated with preoperative RT with 30 Gy in 10 fractions had similar local control, 5-year DFS and OS to reported long course RT regimen. The surgical technique, pre-RT pathologic grade, ypT, and ypN seemed to affect the OS. Further study on combining a 2-week course of preoperative RT with concurrent chemotherapy would be warranted.
Thyroid V50 Highly Predictive of Hypothyroidism in Head-and-Neck Cancer Patients Treated With Intensity-modulated Radiotherapy (IMRT)
Authors: Sachdev Sean , Refaat Tamer , Bacchus Ian D. , Sathiaseelan Vythialinga , Mittal Bharat B. 
Published: December 2014

Objectives:
Radiation-induced hypothyroidism affects a significant number of patients with head-and-neck squamous cell cancer (HNSCC). We examined detailed dosimetric and clinical parameters to better determine the risk of hypothyroidism in euthyroid HNSCC patients treated with intensity-modulated radiation therapy (IMRT).

Materials and Methods:
From 2006 to 2010, 75 clinically euthyroid patients with HNSCC were treated with sequential IMRT. The cohort included 59 men and 16 females with a median age of 55 years (range, 30 to 89 y) who were treated to a median dose of 70 Gy (range, 60 to 75 Gy) with concurrent chemotherapy in nearly all (95%) cases. Detailed thyroid dosimetric parameters including maximum dose, mean dose, and other parameters (eg, V50—percent volume receiving at least 50 Gy) were obtained. Freedom from hypothyroidism was evaluated using the Kaplan-Meier method. Univariate and multivariate analyses were conducted using Cox regression.

Results:
After a median follow-up period of 50 months, 25 patients (33%) became hypothyroid. On univariate analysis, thyroid V50 was highly correlated with developing hypothyroidism (P=0.035). Other dosimetric paramaters including mean thyroid dose (P=0.11) and maximum thyroid dose (P=0.39) did not reach statistical significance. On multivariate analysis incorporating patient, tumor, and treatment variables, V50 remained highly statistically significant (P=0.037). Regardless of other factors, for V50>60%, the odds ratio of developing hypothyroidism was 6.76 (P=0.002).

Conclusions:
In HNSCC patients treated with IMRT, thyroid V50 highly predicts the risk of developing hypothyroidism. V50>60% puts patients at a significantly higher risk of becoming hypothyroid. This can be a useful dose constraint to consider during treatment planning.
How Globalization Really Happens: Remembering Activism in the Transformation of Istanbul
Authors: Houston Christopher 
Published: December 2014

AbstractOver the past 20 years it has become accepted wisdom that Istanbul has become a ‘global city', transformed in tandem with a raft of neoliberal economic policies. What is the relevant history of this globalization? A muted local knowledge possessed by Istanbul's inhabitants is that the military coup in 1980 was the crucial event in the re‐engineering of the city. Yet exactly here a contradiction emerges: despite this acknowledgement, there is apparently little public memory about what it was like to study, work and agitate in Istanbul in the ‘crisis' years before the coup. Based on extensive interviews with people active in political fractions in the late 1970s, this article privileges a phenomenological approach to identify spatial practices, performances and perceptions of activists that generated and structured Istanbul's expanding urban environment in that period. Further, it shows how this history is relevant for comprehending both the ‘micro‐causes' of the coup as well as important dimensions of Turkish politics in the present, each of which cast illuminating light on Istanbul's experience of globalization.
Clinical oral health of Australia's rural children in a sample attending school dental services
Authors: Ha Diep Hong , Crocombe Leonard A. , C Mejia Gloria 
Published: December 2014

AbstractObjectiveTo examine the association between children's clinical oral health status and their residential location using the latest available data (2009) and to ascertain whether poor oral health among rural children is related to being Indigenous, having less access to fluoridated water or being of lower socioeconomic status (SES), than children from urban areas.DesignCross‐sectional survey.Setting and participantData were collected on 74 467 children aged 5–12 years attending school dental services in Australia (data were not available for Victoria or New South Wales).Main outcome measuresClinical oral health was determined by the mean number of permanent teeth with untreated caries, missing and filled permanent teeth, and the mean decayed, missing and filled permanent teeth index (DMFT) of 8 to 12‐year‐old‐children and the mean number deciduous teeth with untreated caries, missing and filled deciduous teeth, and the mean decayed, missing and filled deciduous teeth index (dmft) of 5–10‐year‐olds.ResultsThe multivariable models that included coefficients on whether the child was Indigenous, from an area with fluoridated water and SES, were controlled for age and sex. The mean DMFT of 8–12‐year‐old children and the mean dmft of 5–10‐year‐old‐children were significantly higher in rural areas compared with urban centres after accounting for Indigenous status, fluoridated water and SES.ConclusionChildren's oral health was poorer in rural areas than in major city areas.
Implementation of a multicomponent intervention to optimise patient safety through improved oxygen prescription in a rural hospital
Authors: Gunathilake Roshan , Lowe Deborah , Wills James , Knight Anne , Braude Peter 
Published: December 2014

AbstractObjectiveTo rationalise oxygen procedures in adult medical and surgical inpatients with a view to improving patient safety.DesignProspective pre‐ and post‐intervention audit.SettingManning Hospital, a rural referral hospital in Taree NSW.ParticipantsPre‐intervention: 82 patients aged 72.7 ± 14.7 years. Post‐intervention: 77 patients aged 73.6 ± 12.4 years.InterventionA multicomponent intervention composed of implementation of a local hospital oxygen policy, introduction of a specific oxygen prescription chart and targeted staff education.Main outcome measuresSatisfactory oxygen prescription, monitoring and titration.ResultsOnly 2/82 (2.4%) patients had satisfactory oxygen prescription specifying target saturation, device and initial flow rate before the intervention compared with 26/77 (34%) patients post‐intervention (χ2 = 56.88, df = 5, P < 0.0001). Percentage of patients with conditions predisposing to hypercapnic respiratory failure who were overtreated with oxygen dropped from 9/19 (47%) to 4/22 (18%) following the study intervention (χ2 = 4.011, df = 1, P = 0.04). Oxygen therapy monitoring was satisfactory during the audit period, but oxygen titration was unsatisfactory and did not significantly improve following the intervention.ConclusionsA multicomponent intervention can achieve a significantly increased rate of satisfactory oxygen prescriptions specifying target saturation, including in those who are at risk of hypercapnic respiratory failure.
A retrospective 15‐year review: survival advantage after switching to sirolimus in hepatitis C virus infected liver graft recipients
Authors: Shah M. , Shankar A. , Gee I. , Nash K. , Hoare M. , Gibbs P. , Davies S. , Alexander G. J. M. 
Published: December 2014

SummaryBackgroundThe use of sirolimus‐based immune suppression in liver transplantation, particularly in hepatitis C virus (HCV)‐infected recipients, remains contentious. There is some evidence that sirolimus retards hepatic fibrosis, is renal sparing and may be of benefit in preventing hepatocellular carcinoma (HCC) recurrence. Sirolimus has not been adopted by many transplant centres because of persistent concerns regarding an increased risk of hepatic artery thrombosis, graft loss and death with de novo sirolimus.AimTo review the impact of switching to sirolimus monotherapy in HCV‐infected liver recipients with respect to survival, graft loss and hepatic fibrosis.MethodsA retrospective review of 190 patients from a single centre undergoing first liver transplantation for HCV over 15 years. 113 patients were switched from calcineurin inhibitor (CNI)‐based therapy to low‐dose sirolimus monotherapy at a median of 15 months after transplantation for HCV‐related fibrosis (72%), renal impairment (14%) or high‐risk HCC (5%).ResultsPatients switched to sirolimus had improved survival (P < 0.001) and slower progression to cirrhosis (P = 0.001). In patients with HCC (n = 91), sirolimus duration rather than strategy was an independent predictor of survival (P = 0.001) and extended time to HCC recurrence (33 vs. 16 months). Patients switched for renal dysfunction showed improvement in serum creatinine (140–108 μmol/L, P = 0.001). Those remaining on CNI‐therapy were more likely to develop post‐transplant diabetes (P = 0.03).ConclusionThese data suggest selective switching to low‐dose sirolimus monotherapy in HCV‐positive liver recipients improves clinical outcome.
Protective effect of aqueous extracts from Rhizopus oryzae on liver injury induced by carbon tetrachloride in rats
Authors: Suzuki Takehito , Fukuoka Hideo , Ushikoshi Setsuo , Sato Reiichiro , Morita Hidetoshi , Takizawa Tatsuya 
Published: December 2014

AbstractHepatoprotective effects of Rhizopus oryzae/ U‐1 aqueous extract (RU) were demonstrated in carbon tetrachloride (CCl4)‐induced liver‐injured rats. In order to investigate the RU effects, the rats were administered RU at a dose of 10 or 100 mg/kg of body weight for 10 days before induction of the liver injury by oral administration of CCl4 (125 mg/kg body weight). (i) Pretreatment with RU caused a significant decrease in serum lactate dehydrogenase (LDH), alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities that were increased by the administration of CCl4. (ii) RU pretreatment (100 mg/kg) increased 5‐bromo‐2′‐deoxyuridine incorporation at 48 h after CCl4 treatment in hepatocytes. (iii) Histological hematoxylin and eosin staining of the liver showed that RU pretreatment reduced the damage induced by CCl4 administration. (iv) Reverse transcriptase PCR analysis showed RU retreatment caused a transient but significant increase in hepatocyte growth factor (HGF) and a sustained and significant increase in insulin‐like growth factor‐I (IGF‐I) gene expression in hepatocytes injured by CCl4 treatment. From these results, we conclude that oral pre‐administration of RU was effective to suppress liver injury induced by the subsequent oral CCl4 administration, and RU‐induced increase in IGF‐I and HGF gene expression may be, even in part, involved in biological actions of RU in rats.