bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody biomarker discovery through in vitro directed evolution of consensus recognition epitopes
Authors: Ballew John T. , Murray Joseph A. , Collin Pekka , Mäki Markku , Kagnoff Martin F. , Kaukinen Katri , Daugherty Patrick S. 
Published: November 2013

Significance
The diagnosis of many diseases is dependent upon accurate detection of particular antibodies present in blood. However, the development of biochemical reagents that can reliably detect these antibodies has proved remarkably challenging. This study describes a process to create biochemical reagents that can accurately and reliably detect disease-associated antibodies, without requiring knowledge of the cause or mechanisms of disease. Simultaneously, this process enabled identification of a critical environmental agent involved in celiac disease. Thus, the process presented here may enable the development of effective diagnostic tests for other medical conditions where such tests are lacking and the identification of environmental factors involved in disease.
tRanslatome: an R/Bioconductor package to portray translational control
Authors: Tebaldi Toma , Dassi Erik , Kostoska Galena , Viero Gabriella , Quattrone Alessandro 
Published: November 2013

Abstract
Summary: High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different ‘-omics’. It has been recently demonstrated that translational control is a widespread phenomenon, with profound and still underestimated regulation capabilities. Although detecting changes in the levels of total messenger RNAs (mRNAs; the transcriptome), of polysomally loaded mRNAs (the translatome) and of proteins (the proteome) is experimentally feasible in a high-throughput way, the integration of these levels is still far from being robustly approached. Here we introduce tRanslatome, a new R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data. The package includes most of the available statistical methods developed for the analysis of high-throughput data, allowing the parallel comparison of differentially expressed genes and the corresponding differentially enriched biological themes. Notably, it also enables the prediction of translational regulatory elements on mRNA sequences. The utility of this tool is demonstrated with two case studies.
Availability and implementation: tRanslatome is available in Bioconductor.
Contact: t.tebaldi@unitn.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Closing the gap by increasing access to clinical dietetic services for urban Aboriginal and Torres Strait Islander people
Authors: Foley Wendy , Houston Annalie 
Published: November 2013

AbstractAimLate in 2010, the dietetic clinic in a Brisbane Indigenous health service increased from one to four days/week. This article presents research to assess the impact of this on access for urban Aboriginal and Torres Strait Islander people to dietetic services.MethodsClinic data on referrals and attendance before and after this change are compared. Focus groups with staff and in‐depth interviews with 13 patients were conducted to ascertain staff and patient experiences of the clinic changes.ResultsThe additional time allowed the dietitian to develop a stronger presence in the community and clinic. This ensured that the dietetic service was culturally safe for clients and strengthened team approaches to patient care in the clinic. Despite space limitations, new referrals more than doubled and occasions of service tripled. New patients were more likely to attend an appointment with the dietitian in 2011 than in 2010 (P < 0.001) and the proportion of patients who did not attend appointments without rescheduling decreased significantly (P = 0.006).ConclusionsVarious factors contributed to improved access for Aboriginal and Torres Strait Islander people to dietetic care. These included fostering the dietitian's cultural awareness and building trust with Indigenous community members, making the dietetic service culturally safe for clients; connecting with patients through appropriate communication styles and inter‐professional teamwork. Providing an expanded and culturally safe dietetic service improved the availability, acceptability and appropriateness for Aboriginal and Torres Strait Islander people.
Fibroblasts from long‐lived species of mammals and birds show delayed, but prolonged, phosphorylation of ERK
Authors: Elbourkadi Najoua , Austad Steven N. , Miller Richard A. 
Published: November 2013

SummaryFibroblasts from long‐lived mutant mice show diminished phosphorylation of the stress‐activated protein kinases ERK1/2 after exposure to peroxide, cadmium, or paraquat. We have now evaluated the kinetics of ERK phosphorylation in fibroblasts from long‐lived and short‐lived species of mammals and birds in response to stress by cadmium or hydrogen peroxide. Fibroblasts from the shorter‐lived species of rodents and birds showed rapid induction of ERK phosphorylation, with a decline to basal level within 60 min. In contrast, cells from longer‐lived species showed slower and more prolonged activation of ERK phosphorylation. These results suggest that fibroblasts from long‐lived species may be less susceptible to the early phases of damage from cadmium or peroxide and suggest that altered kinetics of ERK activity may contribute to their stress resistance properties.
Environmental factors selectively impact co‐occurrence of problem/pathological gambling with specific drug‐use disorders in male twins
Authors: Xian Hong , Giddens Justine L. , Scherrer Jeffrey F. , Eisen Seth A. , Potenza Marc N. 
Published: November 2013

AbstractAimsMultiple forms of drug abuse/dependence frequently co‐occur with problem/pathological gambling (PPG). The current study examines the extent to which genetic and environmental factors contribute to their co‐occurrence.DesignBivariate models investigated the magnitude and correlation of genetic and environmental contributions to problem/pathological gambling and its co‐occurrence with nicotine dependence, cannabis abuse/dependence and stimulant abuse/dependence.SettingComputer‐assisted telephone interviews in the community.ParticipantsParticipants were 7869 male twins in the Vietnam Era Twin Registry, a USA‐based national twin registry.MeasurementsLife‐time DSM‐III‐R diagnoses for problem/pathological gambling, nicotine dependence, cannabis abuse/dependence and stimulant abuse/dependence were determined using the Diagnostic Interview Schedule.FindingsAll drug‐use disorders displayed additive genetic and non‐shared environmental contributions, with cannabis abuse/dependence also displaying shared environmental contributions. Both genetic [genetic correlation rA = 0.22; 95% confidence interval (CI) = 0.10–0.34] and non‐shared environmental components (environmental correlation rE = 0.24; 95% CI = 0.10–0.37) contributed to the co‐occurrence of problem/pathological gambling and nicotine dependence. This pattern was shared by cannabis abuse/dependence (rA = 0.32; 95% CI = 0.05–1.0; rE = 0.36; 95% CI = 0.16–0.55) but not stimulant abuse/dependence (SAD), which showed only genetic contributions to the co‐occurrence with problem/pathological gambling (rA = 0.58; 95% CI = 0.45–0.73).ConclusionsStrong links between gambling and stimulant‐use disorders may relate to the neurochemical properties of stimulants or the illicit nature of using ‘hard’ drugs such as cocaine. The greater contribution of environmental factors to the co‐occurrence between problem/pathological gambling and ‘softer’ forms of drug abuse/dependence (cannabis, tobacco) suggest that environmental interventions (perhaps relating to availability and legality) may help to diminish the relationship between problem/pathological gambling and tobacco‐ and cannabis‐use disorders.
Routine coagulation assays underestimate levels of antithrombin‐dependent drugs but not of direct anticoagulant drugs in plasma from patients with cirrhosis
Authors: Potze Wilma , Arshad Freeha , Adelmeijer Jelle , Blokzijl Hans , van den Berg Arie P. , Porte Robert J. , Lisman Ton 
Published: November 2013

SummaryThere is increasing recognition that thrombotic complications may occur in patients with cirrhosis, and literature on antithrombotic treatment in these patients is rapidly emerging. Due to extensive haemostatic changes in patients with cirrhosis, careful monitoring of anticoagulant therapy may be required. Recent data suggest that plasma levels of low molecular weight heparin (LMWH) are substantially underestimated by the anti‐activated factor X (anti‐Xa) assay in patients with cirrhosis. We studied the in vitro recovery of antithrombin (AT)‐dependent and –independent anticoagulant drugs in plasma from 26 patients with cirrhosis and 30 healthy controls and found substantially reduced anti‐Xa levels when AT‐dependent anticoagulant drugs were added to the plasma of patients with cirrhosis. LMWH (0·2 U/ml) had the poorest recovery in plasma from patients with cirrhosis (0·13 ± 0·06 U/ml, compared to 0·23 ± 0·03 U/ml in controls, P < 0·0001), followed by unfractionated heparin and fondaparinux. In contrast, the recovery of rivaroxaban and dabigatran was identical between patients and controls. These data suggest that the anti‐Xa assay cannot be used to monitor AT‐dependent anticoagulant drugs in patients with cirrhosis, as it substantially underestimates drug levels. The direct factor Xa and IIa inhibitors, however, may be monitored through the respective anti‐Xa and anti‐IIa assays in patients with cirrhosis.
Phase IA/II, multicentre, open‐label study of the CD40 antagonistic monoclonal antibody lucatumumab in adult patients with advanced non‐Hodgkin or Hodgkin lymphoma
Authors: Fanale Michelle , Assouline Sarit , Kuruvilla John , Solal‐Céligny Philippe , Heo Dae S. , Verhoef Gregor , Corradini Paolo , Abramson Jeremy S. , Offner Fritz , Engert Andreas , Dyer Martin J. S. , Carreon Daniel , Ewald Brett , Baeck Johan , Younes Anas , Freedman Arnold S. 
Published: November 2013

SummaryDespite advancements in the treatment of non‐Hodgkin lymphoma (NHL) and Hodgkin lymphoma (HL), patients continue to relapse and thus a need for new targeted therapies remains. The CD40 receptor is highly expressed on neoplastic B cells and activation leads to enhanced proliferation and survival. Lucatumumab (HCD122) is a fully human antagonistic CD40 monoclonal antibody. A phase IA/II study was designed to determine the maximum tolerated dose (MTD) and activity of lucatumumab in patients with relapsed/refractory lymphoma. Determination of the MTD was the primary objective of the phase IA dose escalation portion and clinical response was the primary objective of the phase II dose expansion portion. Patients received escalating doses of lucatumumab administered intravenously once weekly for 4 weeks of an 8‐week cycle. MTD was determined at 4 mg/kg of lucatumumab. A total of 111 patients with NHL (n = 74) and HL (n = 37) were enrolled. Responses were observed across various lymphoma subtypes. The overall response rate by computed tomography among patients with follicular lymphoma (FL) and marginal zone lymphoma of mucosa‐associated lymphatic tissue (MZL/MALT) was 33·3% and 42·9%, respectively. Lucatumumab demonstrates modest activity in relapsed/refractory patients with advanced lymphoma, suggesting that targeting of CD40 warrants further investigation.
Efficacy of robot‐assisted radical cystectomy (RARC) in advanced bladder cancer: results from the International Radical Cystectomy Consortium (IRCC)
Authors: Al‐Daghmin Ali , Kauffman Eric C. , Shi Yi , Badani Ketan , Balbay M. Derya , Canda Erdem , Dasgupta Prokar , Ghavamian Reza , Grubb Robert , Hemal Ashok , Kaouk Jihad , Kibel Adam S. , Maatman Thomas , Menon Mani , Mottrie Alex , Nepple Kenneth , Pattaras John G. , Peabody James O. , Poulakis Vassilis , Pruthi Raj , Palou Redorta Juan , Rha Koon‐Ho , Richstone Lee , Schanne Francis , Scherr Douglas S. , Siemer Stefan , Stöckle Michael , Wallen Eric M. , Weizer Alon , Wiklund Peter , Wilson Timothy , Wilding Gregory , Woods Michael , Guru Khurshid A. 
Published: November 2013

ObjectiveTo characterise the surgical feasibility and outcomes of robot‐assisted radical cystectomy (RARC) for pathological T4 bladder cancer.Patients and MethodsRetrospective evaluation of a prospectively maintained International Radical Cystectomy Consortium database was conducted for 1118 patients who underwent RARC between 2003 and 2012.We dichotomised patients based on pathological stage (≤pT3 vs pT4) and evaluated demographic, operative and pathological variables in relation to morbidity and mortality.ResultsIn all, 1000 ≤pT3 and 118 pT4 patients were evaluated. The pT4 patients were older than the ≤pT3 patients (P = 0.001).The median operating time and blood loss were 386 min and 350 mL vs 396 min and 350 mL for p T4 and ≤pT3, respectively.The complication rate was similar (54% vs 58%; P = 0.64) among ≤pT3 and pT4 patients, respectively. The overall 30‐ and 90‐day mortality rate was 0.4% and 1.8% vs 4.2% and 8.5% for ≤pT3 vs pT4 patients (P < 0.001), respectively.The body mass index (BMI), American Society of Anesthesiology score, length of hospital stay (LOS) >10 days, and 90‐day readmission were significantly associated with complications in pT4 patients.Meanwhile, BMI, LOS >10 days, grade 3–5 complications, 90‐day readmission, smoking, previous abdominal surgery and neoadjuvant chemotherapy were significantly associated with mortality in pT4 patients. On multivariate analysis, BMI was an independent predictor of complications in pT4 patients, but not for mortality.ConclusionsRARC for pT4 bladder cancer is surgically feasible but entails significant morbidity and mortality.BMI was independent predictor of complications in pT4 patients.
Organ allocation in pediatric renal transplants: is there an optimal donor?
Authors: Pitt Susan C. , Vachharajani Neeta , Doyle Maria B. , Lowell Jeffrey A. , Chapman William C. , Anderson Christopher D. , Shenoy Surendra , Wellen Jason R. 
Published: November 2013

AbstractThe 2005 revised allocation scheme for pediatric renal transplantation made the decision of whether to transplant an available living‐donor (LD) kidney or use a deceased‐donor (DD) kidney controversial. The aim of this study was to examine kidney allograft utilization, sensitization, and outcomes of pediatric transplant recipients. Between January 2000 and December 2009, 91 consecutive pediatric kidney recipients (<20 yr) were transplanted. The LD (n = 38) and DD (n = 53) groups were similar in age, gender, dialysis status at transplant, warm ischemia time, and overall patient survival. LD recipients were more likely to be Caucasian (92 vs. 69%), receive older allografts (39 ± 10 vs. 23 ± 9 yr), and have fewer human leukocyte antigen (HLA) mismatches (3.3 ± 1.6 vs. 4.4 ± 1.5, p < 0.01 for all). Graft survival at one, three, and five yr post‐transplant was longer for LD recipients (97%, 91%, 87% vs. DD 89%, 79%, 58%, respectively, p < 0.05). At the time of transplant, 17 (33%) DD recipients had an available LD (mean age 40 yr). A greater proportion of all patients were moderately (PRA 21–79%) sensitized post‐transplant (p < 0.05). A multivariable analysis of graft survival indicated that the advantage in LD organs was likely due to fewer HLA mismatched in this group. Nonetheless, LD organs appear to provide optimal outcomes in pediatric renal transplants when considering the risk of becoming sensitized post‐transplant complicating later use of the LD kidney.
A new approach to develop the Raman carbonaceous material geothermometer for low‐grade metamorphism using peak width
Authors: Kouketsu Yui , Mizukami Tomoyuki , Mori Hiroshi , Endo Shunsuke , Aoya Mutsuki , Hara Hidetoshi , Nakamura Daisuke , Wallis Simon 
Published: November 2013

AbstractThe Raman spectra of carbonaceous material (CM) from 19 metasediment samples collected from six widely separated areas of Southwest Japan and metamorphosed at temperatures from 165 to 655°C show systematic changes with metamorphic temperature that can be classified into four types: low‐grade CM (c. 150–280°C), medium‐grade CM (c. 280–400°C), high‐grade CM (c. 400–650°C), and well‐crystallized graphite (> c. 650°C). The Raman spectra of low‐grade CM exhibit features typical of amorphous carbon, in which several disordered bands (D‐band) appear in the first‐order region. In the Raman spectra of medium‐grade CM, the graphite band (G‐band) can be recognized and several abrupt changes occur in the trends for several band parameters. The observed changes indicate that CM starts to transform from amorphous carbon to crystallized graphite at around 280°C, and this transformation continues until 400°C. The G‐band becomes the most prominent peak at high‐grade CM suggesting that the CM structure is close to that of well‐crystallized graphite. In the highest temperature sample of 655°C, the Raman spectra of CM show a strong G‐band with almost no recognizable D‐band, implying the CM grain is well‐crystallized graphite. In the Raman spectra of low‐ to medium‐grade CM, comparisons of several band parameters with the known metamorphic temperature show inverse correlations between metamorphic temperature and the full width at half maximum (FWHM) of the D1‐ and D2‐bands. These correlations are calibrated as new Raman CM geothermometers, applicable in the range of c. 150–400°C. Details of the methodology for peak decomposition of Raman spectra from the low to medium temperature range are also discussed with the aim of establishing a robust and user‐friendly geothermometer.
An integrative review of nurse‐led community‐based case management effectiveness
Authors: Joo J. Y. , Huber D. L. 
Published: November 2013

BackgroundAccountable, continuous and patient‐centred care in community‐based settings is increasingly needed to reduce fragmented care, especially to reduce patient readmission rates. Case management has been proven effective in reducing healthcare costs and in increasing continuity of care, but its effectiveness in community‐based settings is not clear.AimThe aim of this integrative review is to examine the effectiveness of community‐based case management programmes in improving patient outcomes.MethodsAn integrative review of articles from PubMed, CINAHL and PsycInfo databases was undertaken to synthesize and analyse research about community‐based case management and its outcomes. Studies looking for patient outcomes and empirical studies published since 2000 were included. A total 18 articles were retrieved from 2000 to 2013.ResultsMost of the included studies were conducted in the USA, but international studies with quantitative approaches were reviewed (n = 6). The review revealed that community‐based case management significantly reduced hospital access outcomes, especially readmissions and increased cost effectiveness, patient clinical outcomes and patient satisfaction.LimitationsThis study did not isolate studies of patients with diseases or demographic characteristics in common, resulting in large variations in disease and demographic factors.ConclusionThere is a base of evidence that community‐based case management is effective. Because it provides quality, patient‐centred care, case management should be used for major care coordination.Implications for Nursing and Health PolicyThe benefits of community‐based case management need to be announced to healthcare leaders and policymakers.
Low‐Temperature Sinterable (1−x)Ba3(VO4)2–xLiMg0.9Zn0.1PO4 Microwave Dielectric Ceramics
Authors: Lv Yang , Zuo Ruzhong , Cheng Ying , Zhang Chen 
Published: November 2013

The novel low‐temperature sinterable (1 − x)Ba3(VO4)2–xLiMg0.9Zn0.1PO4 microwave dielectric ceramics were prepared by cofiring the mixtures of pure‐phase Ba3(VO4)2 and LiMg0.9Zn0.1PO4. The phase structure and grain morphology of the ceramics were evaluated using X‐ray diffraction, Raman spectra, and scanning electron microscopy. The results indicated that Ba3(VO4)2 and LiMg0.9Zn0.1PO4 phases can well coexist in the sintered body. Nevertheless, a small amount of LiZnPO4 and some vanadate phases with low melting points were observed, which not only can influence the microwave dielectric properties of the ceramic but also can obviously improve the densification behavior at a relatively low sintering temperature. The near‐zero temperature coefficients of the resonant frequency (τf) could be achieved by adjusting the relative content of the two phases owing to their opposite τf values and simultaneously a desirable quality factor Q × f value can be maintained. No chemical reaction between the matrix ceramic phase and Ag took place after sintering at 800°C for 4 h. The ceramics with 45 vol% LiMg0.9Zn0.1PO4 can be well sintered at only 800°C and exhibit excellent microwave dielectric properties of εr ~ 10, Q × f ~ 64 500 GHz, and τf ~ −2.1 ppm/°C, thus showing a great potential as a low‐permittivity low‐temperature cofired microwave dielectric material.
Inhomogeneous Structure and Magnetic Properties of Aurivillius Ceramics Bi4Bin−3Ti3Fen−3O3n+3
Authors: Li Jing‐Bo , Huang Yong‐Ping , Jin Hai‐Bo , Rao Guang‐Hui , Liang Jing‐Kui 
Published: November 2013

Structures of Aurivillius ceramics Bi4Bin − 3Ti3Fen − 3O3n+3 with n = 3–9 have been investigated by X‐ray powder diffraction and high‐resolution transmission electron microscopy. The Aurivillius ceramics Bi4Bin−3Ti3Fen−3O3n+3 with n = 3–5 exhibit homogeneous layered structure. However, the ceramic samples with n = 6–9 are composed of mixed Aurivillius phases with different layer numbers, in which the stacking faults of the disordered intergrowth of different n‐layered perovskite blocks and the so‐called “side‐stepping” of the (Bi2O2)2+ layers are generally observed. Magnetic measurements indicate that Fe cations couple antiferromagnetically and the inhomogeneity of composition exists in the samples. The magnetic properties are obviously influenced by the inhomogeneous structure and composition.
Schisandrin B attenuates acetaminophen‐induced hepatic injury through heat‐shock protein 27 and 70 in mice
Authors: Li Libo , Zhang Tiran , Zhou Li , Zhou Li , Xing Guihua , Chen Yuhang , Xin Yabing 
Published: November 2013

AbstractBackground and AimSchisandrin B is an active component isolated from Schisandra chinensis (TurcZ.) Baill. that is widely used as an antihepatotoxic agent. Schisandrin B has significant hepatoprotective effect against chemical and immunological liver injury. This study aimed to investigate the effect of Schisandrin B on the expression of 27‐ and 70‐kDa heat‐shock protein (HSP) and its role in protection against acetaminophen‐induced liver injury in mice.MethodsAfter the mice were pretreated, Western blot and real‐time quantitative polymerase chain reaction were used to detect the protein and gene expression of HSP27 and HSP70, respectively; the liver tissues were subjected to histological evaluation, and alanine aminotransferase and aspartate aminotransferase activities in the serum were measured.ResultsOral administration of Schisandrin B increased the expression of HSP27 and HSP70 in a time‐ and dose‐dependent manner. The inducing effect of Schisandrin B on HSP27 and HSP70 was also confirmed by real‐time quantitative polymerase chain reaction. In the acetaminophen‐induced liver injury mouse model, the prior oral administration of Schisandrin B (200 mg/kg) three times in 24 h markedly alleviated liver injury as indicated by the amelioration of histopathological hepatic necrosis and the reduction of alanine aminotransferase and aspartate aminotransferase activities in the serum. However, the earlier actions of Schisandrin B were all suppressed significantly by Quercetin, a known HSP inhibitor.ConclusionThe hepatic cytoprotective action of Schisandrin B against acetaminophen‐induced liver injury is mediated, at least in part, by the induction of HSP27 and HSP70 in mice.