bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐grading bias: subtle problems with assessing power of selected subsets of loci for population assignment
Authors: WAPLES ROBIN S. 
Published: June 2010

AbstractRecognition of the importance of cross‐validation (‘any technique or instance of assessing how the results of a statistical analysis will generalize to an independent dataset’; Wiktionary, en.wiktionary.org) is one reason that the U.S. Securities and Exchange Commission requires all investment products to carry some variation of the disclaimer, ‘Past performance is no guarantee of future results.’ Even a cursory examination of financial behaviour, however, demonstrates that this warning is regularly ignored, even by those who understand what an independent dataset is. In the natural sciences, an analogue to predicting future returns for an investment strategy is predicting power of a particular algorithm to perform with new data. Once again, the key to developing an unbiased assessment of future performance is through testing with independent data—that is, data that were in no way involved in developing the method in the first place. A ‘gold‐standard’ approach to cross‐validation is to divide the data into two parts, one used to develop the algorithm, the other used to test its performance. Because this approach substantially reduces the sample size that can be used in constructing the algorithm, researchers often try other variations of cross‐validation to accomplish the same ends. As illustrated by Anderson in this issue of Molecular Ecology Resources, however, not all attempts at cross‐validation produce the desired result. Anderson used simulated data to evaluate performance of several software programs designed to identify subsets of loci that can be effective for assigning individuals to population of origin based on multilocus genetic data. Such programs are likely to become increasingly popular as researchers seek ways to streamline routine analyses by focusing on small sets of loci that contain most of the desired signal. Anderson found that although some of the programs made an attempt at cross‐validation, all failed to meet the ‘gold standard’ of using truly independent data and therefore produced overly optimistic assessments of power of the selected set of loci—a phenomenon known as ‘high grading bias.’
Cryptic diversity and patterns of host specificity in trematode flatworms
Authors: HAYWARD ALEXANDER 
Published: June 2010

The widespread utilization of molecular markers has revealed that a broad spectrum of taxa contain sets of morphologically cryptic, but genetically distinct lineages (Bickfordet al.2007). The identification of cryptic taxa is important as an accurate appreciation of diversity is crucial for a proper understanding of evolutionary and ecological processes. An example is the study of host specificity in parasitic taxa, where an apparent generalist may be found to contain a complex of several more specific species (Smithet al.2006). Host specificity is a key life history trait that varies greatly among parasites (Poulin & Keeney 2007). While some can exploit a wide range of hosts, others are confined to just a single species. Access to additional hosts increases the resources available to a parasite. However, physiological or ecological constraints can restrict the extension of host range. Furthermore, there may be a trade‐off between relaxed specificity and performance: generalism can decrease a parasites ability to adapt to each individual host species, and increase exposure to competition from other parasites (Poulin 1998). Despite the central role that host specificity plays in parasite life history, relatively little is known about how host range is determined in natural systems, and data from field studies are required to evaluate among competing ideas. In this issue, an exciting paper byLockeet al.(2010)makes a valuable contribution toward the understanding of host specificity in an important group of trematode flatworms. Using molecular methods, Lockeet al.reveal an almost four‐fold increase in the appreciated diversity of their focal group. In combination with a large and elegant sampling design this allows them to accurately assess host specificity for each taxon, and thus draw key insights into the factors that control host range in a dominant parasite group.
Palmoplantar nonpustular psoriasiform dermatitis in a rhesus macaque
Authors: Piedras María José G. M. , García‐Cabezas Miguel Ángel , Sendagorta Elena , Miró‐Murillo Marta , Cavada Carmen 
Published: June 2010

AbstractA case of psoriasiform dermatitis in an adult male rhesus macaque is reported. Appearing spontaneously, the condition presented the clinical and histopathological features of human palmoplantar nonpustular psoriasis. The animal developed multiple scaly plaques on his palms and soles, as well as nail hyperkeratosis and widening of the nail root. Microscopically, the skin lesions showed epidermal hyperkeratosis with multifocal parakeratosis, neutrophil microabscesses in the stratum corneum, a loss of granule cell layer under the microabscesses, acanthosis, and elongation of the rete ridges; the superficial dermis showed a dense inflammatory infiltrate containing lymphocytes, macrophages and neutrophils, as well as dilated and tortuous blood vessels. The lesions improved for 15 days after intramuscular corticosteroid depot therapy and worsened slightly afterwards. Later, a spontaneous, progressive remission coincided with the beginning of spring and lasted until the end of summer; the skin lesions practically disappeared during this period, and the nails looked nearly normal. During the next autumn and winter only nail hyperkeratosis was present. Serum analyses showed hyperproteinaemia and hyperglobulinaemia during the outbreak phase and normal values during remission. The clinical and histopathological features of this case, as well as its evolution, are compared with the three other reported cases of psoriasiform skin lesions in nonhuman primates. To the authors’ knowledge, this is the first report of a definite palmoplantar nonpustular psoriasiform dermatitis in a rhesus macaque.
Serum phosphate and calcium concentrations are associated with reduced patient survival following kidney transplantation
Authors: Moore Jason , Tomson Charles R.V. , Tessa Savage M. , Borrows Richard , Ferro Charles J. 
Published: June 2010

Moore J, Tomson CRV, Tessa Savage M, Borrows R, Ferro CJ. Serum phosphate and calcium concentrations are associated with reduced patient survival following kidney transplantation. Clin Transplant 2011: 25: 406–416. © 2010 John Wiley & Sons A/S.Abstract:  The impact of disordered mineral and bone metabolism following kidney transplantation is not well defined. We studied the association of serum phosphate and calcium concentrations, and surrogate measures of arterial stiffness (augmentation index: AIx and Timing of the reflected wave: Tr), with long‐term kidney transplant recipient and allograft survival. Prevalent adult renal transplant patients (n = 270) were prospectively studied over a median 88‐month follow‐up. Detailed demographic, clinical and laboratory data, in addition to both peripheral and central non‐invasive blood pressure measurements, were recorded. Higher serum phosphate and calcium levels were associated with increased all‐cause mortality (HR: 1.21; 95% CI 1.09,1.35, p < 0.001 and HR: 1.22; 95% CI 1.01,1.48; p < 0.04, respectively; adjusted Cox model) and death‐uncensored graft loss (p < 0.001 and p = 0.03, respectively). In addition, serum calcium and phosphate were associated with death‐censored graft loss on univariable analysis (p < 0.001 and p = 0.02, respectively), but did not retain significance on multivariable analysis. AIx and Tr were not associated with mortality or graft loss on multivariable analysis. This is the first report to demonstrate that both higher serum phosphate and calcium levels are associated with increased mortality in kidney transplant recipients. It highlights the need for randomized trials assessing current interventions available for improving disordered mineral–bone metabolism post transplantation.
Pharmacodynamic monitoring of cyclosporine A by NFAT‐regulated gene expression and the relationship with infectious complications in pediatric renal transplant recipients
Authors: Billing Heiko , Giese Thomas , Sommerer Claudia , Zeier Martin , Feneberg Reinhard , Meuer Stefan , Tönshoff Burkhard 
Published: June 2010

Billing H, Giese T, Sommerer C, Zeier M, Feneberg R, Meuer S, Tönshoff B. Pharmacodynamic monitoring of cyclosporine A by NFAT‐regulated gene expression and the relationship with infectious complications in pediatric renal transplant recipients. Pediatr Transplantation 2010: 14:844–851. © 2010 John Wiley & Sons A/S.Abstract:  Pharmacokinetic monitoring of CsA is unsatisfactory, because at comparable CsA blood concentrations, the frequency and severity of adverse effects vary considerably among patients. We have therefore recently developed a precise, reliable, and robust whole‐blood pharmacodynamic assay that measures the suppression of CsA‐target genes in T lymphocytes. Because of the different characteristics of CsA pharmacokinetics in children and the higher propensity for infectious complications, this assay requires validation in the pediatric patient population. We therefore quantified in a prospective study of 45 pediatric renal transplant recipients the residual expression of NFAT‐regulated genes in lymphocytes by RT‐PCR and correlated these findings with the frequency of recurrent infections in the maintenance period post‐transplant. Patients with recurrent infections showed a significantly stronger inhibition of NFAT‐regulated gene expression (18.2%) than patients without recurrent infections (31.7%; p = 0.012). This difference was specific, because various PK parameters of CsA and the concomitant immunosuppressive therapy were comparable between patients. Multivariate regression analysis showed that patient age and residual NFAT‐regulated gene expression were the only independent determinants of recurrent infections. By ROC curve analysis, a cutoff value of 23% residual NFAT‐regulated gene expression had the highest sensitivity (71.1%) and specificity (65.4%) for the discrimination of patients with and without recurrent infections. Pharmacodynamic monitoring of CsA by measurement of residual NFAT‐regulated gene expression in T lymphocytes has the potential to identify over‐immunosuppressed pediatric renal transplant recipients and is therefore a useful tool for the optimization of CsA therapy.
Methanogenesis, sulfate reduction and crude oil biodegradation in hot Alaskan oilfields
Authors: Gieg Lisa M. , Davidova Irene A. , Duncan Kathleen E. , Suflita Joseph M. 
Published: June 2010

SummaryPetrochemical and geological evidence suggest that petroleum in most reservoirs is anaerobically biodegraded to some extent. However, the conditions for this metabolism and the cultivation of the requisite microorganisms are rarely established. Here, we report on microbial hydrocarbon metabolism in two distinct oilfields on the North Slope of Alaska (designated Fields A and B). Signature anaerobic hydrocarbon metabolites were detected in produced water from the two oilfields offering evidence of in situ biodegradation activity. Rate measurements revealed that sulfate reduction was an important electron accepting process in Field A (6–807 µmol S l−1 day−1), but of lesser consequence in Field B (0.1–10 µmol S l−1 day−1). Correspondingly, enrichments established at 55°C with a variety of hydrocarbon mixtures showed relatively high sulfate consumption but low methane production in Field A incubations, whereas the opposite was true of the Field B enrichments. Repeated transfer of a Field B enrichment showed ongoing methane production in the presence of crude oil that correlated with ≥ 50% depletion of several component hydrocarbons. Molecular‐based microbial community analysis of the methanogenic oil‐utilizing consortium revealed five bacterial taxa affiliating with the orders Thermotogales, Synergistales, Deferribacterales (two taxa) and Thermoanaerobacterales that have known fermentative or syntrophic capability and one methanogen that is most closely affiliated with uncultured clones in the H2‐using family Methanobacteriaceae. The findings demonstrate that oilfield‐associated microbial assemblages can metabolize crude oil under the thermophilic and anaerobic conditions prevalent in many petroleum reservoirs.
Bladder outlet obstruction: progression from inflammation to fibrosis
Authors: Metcalfe Peter D. , Wang JianFei , Jiao Haiyan , Huang Yue , Hori Keijiro , Moore Ronald B. , Tredget Edward E. 
Published: June 2010

Study Type – Aetiology (case control) Level of Evidence 3bOBJECTIVETo investigate the progression of urodynamic changes, as well as histological and biochemical outcomes over a prolonged period of partial bladder outlet obstruction (pBOO) in an animal model with physiologically relevant pBOO.MATERIALS AND METHODSHealthy, adult, female Fischer rats underwent surgical creation of a pBOO for either 2, 4, 8, or 13 weeks and were compared with sham‐operated rats. Urodynamic measurements were used to compare bladder volumes and pressure. Tissue was grossly analysed with light microscopy and bladder weights and thicknesses were compared. Reverse transcription‐polymerase chain reaction for collagen, transforming growth factor β (TGF‐β), connective tissue growth factor (CTGF), hypoxia inducible factor 1α (HIF‐1α), and platelet‐derived growth factor (PDGF‐A) was performed on all samples, as well as immunohistochemistry (IHC) for α‐smooth muscle actin (α‐SMA). Finally, mass spectrometry was used to quantify the collagen content of the bladders as a measure of fibrosis.RESULTSAfter induction of pBOO, all rats remained healthy. Initial urodynamics showed an increase in capacity while maintaining normal pressures, but then deteriorated into small capacity, high‐pressure bladders. Haematoxylin and eosin (H&E) staining showed an initial inflammatory response, and this was confirmed with significantly increased mRNA levels of TGF‐β, CTGF, HIF‐1α, and PDGF. The progression to smooth muscle hypertrophy was evident on H&E and confirmed with increased bladder mass and thickness. IHC for α‐SMA showed a progressive increase associated with the elevated bladder pressures. Masson’s trichrome and mass spectrometry showed a progressive increase in collagen to 13 weeks.CONCLUSIONWith this model, we have effectively replicated the clinical scenario, with significant pathophysiological changes occurring insidiously in otherwise healthy rats. We believe that our observed changes represent distinct phases of bladder decompensation; with an initial inflammatory response to the stress of the pBOO, smooth muscle hypertrophy to overcome the increased urethral resistance, and eventual decompensation to fibrosis. The time course of the inflammatory markers implies the need for early intervention to prevent this cascade. Novel strategies targeting these observed physiological responses could lead to improved preventative strategies, with respect to biochemical pathways and the time course of their initiation.
The prevalence of chronic constipation and faecal incontinence among men and women with symptoms of overactive bladder
Authors: Coyne Karin S. , Cash Brooks , Kopp Zoe , Gelhorn Heather , Milsom Ian , Berriman Sandra , Vats Vasudha , Khullar Vik 
Published: June 2010

Study Type – Symptom prevalence (non‐consecutive cohort) Level of Evidence 4 What’s known on the subject? and What does the study add? There have been no previous studies examining the overlap of chronic constipation and overactive bladder in the US population. Limited research to date based on samples of elderly, Asian and pediatric populations suggests that there is substantial overlap. The results of this study suggest that the prevalence of chronic constipation is increased in people with overactive bladder who are ≥40 years and should be considered by healthcare providers treating these patients.OBJECTIVETo estimate the prevalence and overlap of overactive bladder (OAB), chronic constipation (CC) and faecal incontinence (FI) among a general population sample of adults in the USA.PATIENTS AND METHODSA cross‐sectional internet‐based survey of randomly selected panel members who were ≥40 years of age was conducted. Participants reported how often they experienced symptoms of OAB, CC and FI using Likert scales and modified Rome III criteria. Analyses were conducted to examine the overall prevalence of OAB, CC and FI in men and women separately and to characterize the extent of overlap between these conditions in participants with OAB vs those without OAB, and those participants with continent vs incontinent OAB.RESULTSThe response rate for the survey was 62.2% and the final sample (N= 2000) included 927 men and 1073 women. The overall prevalence of OAB [defined as a response of ≥‘sometimes’ to urinary urgency (i.e. ‘sometimes’ or more often) or ‘yes’ to urinary urgency incontinence (UUI)] was 26.1% in men and 41.2% in women. The overall prevalence of CC was significantly lower in men than in women (15.3 vs 26.3%), but both men and women with OAB were significantly more likely to report CC (22.3 and 35.9% vs 5.7 and 6.7%, respectively, P < 0.0001). The overall prevalence of FI reported ‘rarely’ or more was 16.7% of men and 21.9% of women. Men and women with OAB were significantly more likely to report FI than those without OAB. FI was also more common in participants with incontinent OAB than in those with continent OAB. Logistic regressions controlling for demographic factors and comorbid conditions suggest that OAB status is a very strong predictor of CC, FI and overlapping CC and FI (odds ratios, range 3.55–7.96).CONCLUSIONSChronic constipation, FI and overlapping CC and faecal incontinence occur more frequently in patients with OAB and should be considered when evaluating and treating patients with OAB. These findings suggest a shared pathophysiology among these conditions. Additional study is needed to determine if successful treatment of one or more of these conditions is accompanied by commensurate improvement in symptoms referable to the other organ system.
The impact of preoperative erectile dysfunction on survival after radical prostatectomy
Authors: Han Misop , Trock Bruce J. , Partin Alan W. , Humphreys Elizabeth B. , Bivalacqua Trinity J. , Guzzo Thomas J. , Walsh Patrick C. 
Published: June 2010

Study Type – Prognosis (case series) Level of Evidence 4PURPOSEErectile dysfunction (ED) and cardiovascular disease (CVD) share etiology and pathophysiology. The underlying pathology for preoperative ED may adversely affect survival following radical prostatectomy (RP). We examined the association between preoperative ED and survival following RP.MATERIALS AND METHODSBetween 1983 and 2000, a single surgeon performed RP on 2511 men, with preoperative ED (ED group, n= 231, 9.2%) or without ED (No ED group, n= 2280, 90.8%). We retrospectively analysed their CVD‐specific survival (CVDSS), prostate cancer‐specific survival (PCSS), non‐PCSS (NPCSS) and overall survival (OS) from time of surgery.RESULTSWith median follow‐up of 13 years after RP, 449 men (18%) died (140 from prostate cancer, 309 from other causes). Kaplan–Meier analyses demonstrated significant differences in CVDSS (P < 0.001), NPCSS (P < 0.001) and OS (P < 0.001), but not in PCSS (P= 0.12), between the ED group vs No ED group. In univariate proportional hazards analyses, preoperative ED was associated with a significant decrease in OS, hazard ratio (HR), 1.71 (95% CI, 1.34–2.23), P < 0.001. However, in multivariable analyses, the association of ED with survival became non‐significant (HR, 1.25 (95% CI, 0.97–1.66), P= 0.111) after adjusting for other prognostic factors, such as age, preoperative prostate‐specific antigen (PSA) level, Gleason score, pathologic stage, body mass index and Charlson Comorbidity Index.CONCLUSIONSPreoperative ED is associated with decreased overall survival and survival from causes other than prostate cancer following RP. However, preoperative ED was not an independent predictor of overall survival after adjusting for other predictors of survival. Urologists should carefully assess pretreatment ED status to enhance appropriate treatment recommendation for men with prostate cancer.
Phase II study of docetaxel re‐treatment in docetaxel‐pretreated castration‐resistant prostate cancer
Authors: Di Lorenzo Giuseppe , Buonerba Carlo , Faiella Adriana , Rescigno Pasquale , Rizzo Mimma , Autorino Riccardo , Perdonà Sisto , Riccardi Nando , Scagliorini Sarah , Scognamiglio Florinda , Masala Daniele , Ferro Matteo , Palmieri Giovannella , Aieta Michele , Marinelli Alfredo , Altieri Vincenzo , De Placido Sabino , Cartenì Giacomo 
Published: June 2010

Study Type – Therapy (cohort) Level of Evidence 2b What’s known on the subject? and What does the study add? We show that (i) docetaxel re‐treatment, after a treatment‐free interval, preserves activity; (ii) the treatment is especially well tolerated in patients who were effectively pretreated with docetaxel; and (iii) it could be speculated that combining docetaxel with other agents in this setting might be safe and result in greater activity.OBJECTIVETo determine the activity and tolerability of docetaxel re‐treatment after first‐line therapy with docetaxel in castration‐resistant prostate cancer (CRPC).PATIENTS AND METHODSBetween November 2005 and January 2009, 45 patients initially responding to docetaxel and then experiencing disease progression after a period of biochemical remission of at least 5 months were enrolled in a prospective multicenter study and re‐treated with docetaxel. The primary endpoint was the biochemical response (biochemical partial response defined as >50% prostate‐specific antigen [PSA] decline); secondary endpoints were objective response, toxicity, progression‐free survival (PFS) and overall survival (OS).RESULTSPartial PSA responses were observed in 11 patients (24.5%), 4 (25%) of whom also had an objective response. The treatment was well tolerated, with grade 1–2 neutropenia, thrombocytopenia, vomiting and peripheral neuropathy noted in 18 (40%), 11 (24.5%), 8 (17.8%), and 6 (13.3%) patients, respectively. The most common grade 3 toxicity was neutropenia, which was observed in 8 patients (17.8%). Median PFS was 5 months and median OS was 13 months.CONCLUSIONSDocetaxel re‐treatment preserves anti‐tumour activity and is well tolerated in a selected population of pretreated patients with CRPC. Further randomized trials are needed to confirm our preliminary results.
An application of belief‐importance theory with reference to trait emotional intelligence, mood, and somatic complaints
Authors: PETRIDES K. V. 
Published: June 2010

Petrides, K.V. (2011). An application of belief‐importance theory with reference to trait emotional intelligence, mood, and somatic complaints. Scandinavian Journal of Psychology 52, 161–167.This article describes the basic principles of belief‐importance (belimp) theory and tests them in two empirical studies. Belimp theory hypothesizes that personality traits confer a propensity to perceive convergences and divergences between our belief that we can attain goals and the importance that we place on these goals. Belief and importance are conceptualized as two coordinates, together defining the belimp plane. Four distinct quadrants can be identified within the belimp plane (Hubris, Motivation, Depression and Apathy), broadly corresponding to the personality dimensions of trait emotional intelligence, conscientiousness, neuroticism and introversion. Study 1 (N = 365) defines the four quadrants in relation to goals about financial security and shows that they score differently on trait emotional intelligence, mood and somatic complaints. Study 2 (N = 230) defines the quadrants in relation to goals about appearance and, separately, in relation to goals about popularity, and replicates the findings of the first study. Strategies and requirements for testing belimp theory are presented, as are a number of theoretical and practical advantages that it can potentially offer.