bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological niche models in phylogeographic studies: applications, advances and precautions
Authors: Alvarado‐Serrano Diego F. , Knowles L. Lacey 
Published: October 2013

AbstractThe increased availability of spatial data and methodological developments in species distribution modelling has lead to concurrent advances in phylogeography, broadening the scope of questions studied, as well as providing unprecedented insights. Given the species‐specific nature of the information provided by ecological niche models (ENMs), whether it is on the environmental tolerances of species or their estimated distribution, today or in the past, it is perhaps not surprising that ENMs have rapidly become a common tool in phylogeographic analysis. Such information is essential to phylogeographic tests that provide important biological insights. Here, we provide an overview of the different applications of ENMs in phylogeographic studies, detailing specific studies and highlighting general limitations and challenges with each application. Given that the full potential of integrating ENMs into phylogeographic cannot be realized unless the ENMs themselves are carefully applied, we provide a summary of best practices with using ENMs. Lastly, we describe some recent advances in how quantitative information from ENMs can be integrated into genetic analyses, illustrating their potential use (and key concerns with such implementations), as well as promising areas for future development.
Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set
Authors: Dong Wenpan , Cheng Tao , Li Changhao , Xu Chao , Long Ping , Chen Chumming , Zhou Shiliang 
Published: October 2013

AbstractThe ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region of rbcL performs as a barcode in species discrimination. We found that the rbcLb region was more variable than the frequently used rbcLa region. Both universal and plant group‐specific primers were designed to amplify rbcLb, and the performance of rbcLa and rbcLb was tested in several ways. Using blast, both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for rbcLa and from 22.09% to 98.43% for rbcLb in species‐rich families, and from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in species‐rich genera. Both regions performed better for lower plants than for higher plants, although rbcLb performed significantly better than rbcLa overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbcLb as a universal plant barcode.
Geometry of the Randomized Evidence for Treatments of Pulmonary Hypertension
Authors: Tonelli Adriano R. , Zein Joe , Ioannidis John P.A. 
Published: October 2013

SummaryObjectiveWe studied the entire agenda of randomized clinical trials in pulmonary hypertension (PH) using sociological methods. We explored the geometry of the PH network to interpret the evidence on multiple competing treatments for the same indication.DesignWe searched MEDLINE, Embase and Cochrane Library Databases for published studies. We queried clinicaltrials.gov and WHO International Clinical Trials Registry platform for non‐published studies.ResultsWe found 75 randomized trials (41 published [n = 4136 participants] and 34 registered unpublished [planned n = 3470 participants]). Of the published randomized studies, all used placebo as the comparator arm except for two nonindustry‐sponsored comparisons between phosphodiestearase‐5 (PDE‐5) inhibitors and endothelin receptor antagonists (ERA), and one study comparing two different regimens of treprostinil. Similarly, only five unpublished/ongoing trials used an active PH treatment as comparator (PDE‐5 inhibitors versus ERA (n = 3), different doses of sildenafil (n = 1) and two formulations of epoprostenol (n = 1). Of the 75 trials, 47 were sponsored by the manufacturer of the tested active product(s), and only two trials were sponsored by two companies comparing their products.ConclusionsThe relative merits of different treatment options are not directly known, as there are very few head‐to‐head comparisons. A limited number of ongoing studies are using active FDA‐approved PH‐treatments for comparison. This lack of information can be overcome by carefully designing comparative effectiveness trials.
Potential of a 70 kDa IL‐10‐like factor in synovial fluid from rheumatoid arthritis patients to augment superoxide generation by human neutrophils
Authors: Nakamura Tadashi , Yamamoto Tetsuro 
Published: October 2013

AbstractAimTo elucidate the role of polymorphonuclear leukocytes (PMNs) in joint destruction during the inflammatory process in rheumatoid arthritis (RA) as related to superoxide generation.MethodsSuperoxide generation by human peripheral PMNs was measured by using a water‐soluble formazan dye, 2‐(4‐iodophenyl)‐3‐(4‐nitrophenyl)‐5‐(2, 4‐disulfophenyl)‐2H‐tetrazolium, monosodium salt, under PMN stimulation with N‐formylmethionyl‐leucyl‐phenylalanine (fMLP) and cytochalasin B. Factors in synovial fluids (SF) from RA patients that may augment PMN superoxide generation were characterized via high‐performance liquid chromatography and isoelectric focusing.ResultsThe formazan dye allowed measurement of superoxide generated in the xanthine‐xanthine oxidase system and by PMNs stimulated by cytochalasin B and fMLP in the presence of the intermediate electron transporter phenazine methosulfate. By using chromatography and electrophoresis, an RA‐SF protein with an apparent molecular size of 70 kDa and an isoelectric point of 8.3 was isolated and was demonstrated to increase superoxide generation by PMNs. The factor was heat‐labile and susceptible to protease treatment. This enhancing activity of the factor was absorbed by human PMNs and was somewhat immunoadsorbed with a specific monoclonal antibody against interleukin (IL)‐10.ConclusionThe 70‐kDa protein factor in RA‐SF increased superoxide generation by human PMNs, which suggests the possibility of its being related to IL‐10. This factor may have a pathological role in RA joint destruction caused by PMNs and coinciding with rheumatoid inflammation, which suggests that PMNs, via superoxide generation, play an important role in RA joint destruction. IL‐10 therefore likely has biological activity toward PMNs during synovial inflammatory chain reactions in RA.
sigmaS, a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition
Authors: Landini Paolo , Egli Thomas , Wolf Johannes , Lacour Stephan 
Published: October 2013

SummaryBacterial cells often face hostile environmental conditions, to which they adapt by activation of stress responses. In Escherichia coli, environmental stresses resulting in significant reduction in growth rate stimulate the expression of the rpoS gene, encoding the alternative σ factor σS. The σS protein associates with RNA polymerase, and through transcription of genes belonging to the rpoS regulon allows the activation of a ‘general stress response’, which protects the bacterial cell from harmful environmental conditions. Each step of this process is finely tuned in order to cater to the needs of the bacterial cell: in particular, selective promoter recognition by σS is achieved through small deviations from a common consensus DNA sequence for both σS and the housekeeping σ70. Recognition of specific DNA elements by σS is integrated with the effects of environmental signals and the interaction with regulatory proteins, in what represents a fascinating example of multifactorial regulation of gene expression. In this report, we discuss the function of the rpoS gene in the general stress response, and review the current knowledge on regulation of rpoS expression and on promoter recognition by σS.
The Fair Value of Cash Flow Hedges, Future Profitability, and Stock Returns
Authors: Campbell John L. 
Published: October 2013

AbstractThe SEC and FASB recently expressed concerns that investors do not fully assimilate all of the information provided by complex and incomplete derivatives and other comprehensive income (OCI) disclosures. My evidence supports these concerns. Specifically, I examine the information content of unrealized cash flow hedge gains/losses for future profitability and stock returns. An unrealized gain on a cash flow hedge suggests that the price of the underlying hedged item (i.e., commodity price, foreign currency exchange rate, or interest rate) moved in a direction that will impair the firm's profits after the hedge expires. Consequently, I find that unrealized cash flow hedge gains/losses are negatively associated with future gross profit after the firm's existing hedges have expired. This association only holds after the firm has reclassified its hedges into earnings, and is weaker for firms that can pass input price changes on to their customers. Finally, investors do not immediately price the cash flow hedge information. Instead, investors appear surprised by future realizations of gross margin, consistent with the view that complex and incomplete disclosures delay pricing. These results are relevant to policymakers involved in the current FASB and IASB project designed to simplify the accounting and disclosure for derivatives and, in particular, cash flow hedges.
Paliperidone palmitate long‐acting injection – prospective year‐long follow‐up of use in clinical practice
Authors: Attard A. , Olofinjana O. , Cornelius V. , Curtis V. , Taylor D. 
Published: October 2013

ObjectiveTo follow‐up patients prescribed paliperidone palmitate long‐acting injection (PP) over 1 year to determine factors predicting continuation with PP treatment.MethodNaturalistic observation of patients registered as starting PP in a single healthcare unit in London, UK. Monovariate and multivariate (Cox regression) analysis of factors predicting continuation at 1 year.ResultsData were available for 210 patients consecutively prescribed PP of whom 10 were lost to follow‐up. At 1 year, 65% of 200 patients (176 with a diagnosis of schizophrenia or schizoaffective disorder) started on PP were still receiving it. The main reason for discontinuation was perceived ineffectiveness (52% of discontinuers); only 10 subjects (5% of total) discontinued because of adverse effects. Initiation as an out‐patient [hazard ratio (HR) 0.39, 95%CI, 0.20, 0.67, P = 0.001]; being switched from risperidone (HR 0.56, 95%CI 0.32, 0.94, P = 0.026) and correct initiation (HR 0.56, 95%CI 0.34, 0.93, P = 0.024) were significantly associated with a lower likelihood of discontinuation.ConclusionPaliperidone palmitate was effective and well tolerated in this naturalistic cohort. Optimising treatment by targeting PP for patients identified as having lower risk of discontinuation can give rise to continuation rates approaching 80% at 1 year.
Medication adherence in a comparative effectiveness trial for bipolar disorder
Authors: Sylvia L. G. , Reilly‐Harrington N. A. , Leon A. C. , Kansky C. I. , Calabrese J. R. , Bowden C. L. , Ketter T. A. , Friedman E. S. , Iosifescu D. V. , Thase M. E. , Ostacher M. J. , Keyes M. , Rabideau D. , Nierenberg A. A. 
Published: October 2013

ObjectivePsychopharmacology remains the foundation of treatment for bipolar disorder, but medication adherence in this population is low (range 20–64%). We examined medication adherence in a multisite, comparative effectiveness study of lithium.MethodThe Lithium Moderate Dose Use Study (LiTMUS) was a 6‐month, six‐site, randomized effectiveness trial of adjunctive moderate dose lithium therapy compared with optimized treatment in adult out‐patients with bipolar I or II disorder (N = 283). Medication adherence was measured at each study visit with the Tablet Routine Questionnaire.ResultsWe found that 4.50% of participants reported missing at least 30% of their medications in the past week at baseline and non‐adherence remained low throughout the trial (<7%). Poor medication adherence was associated with more manic symptoms and side‐effects as well as lower lithium serum levels at mid‐ and post‐treatment, but not with poor quality of life, overall severity of illness, or depressive symptoms.ConclusionParticipants in LiTMUS were highly adherent with taking their medications. The lack of association with possible predictors of adherence, such as depression and quality of life, could be explained by the limited variance or other factors as well as by not using an objective measure of adherence.
Psychiatric comorbidity in treatment‐seeking substance use disorder patients with and without attention deficit hyperactivity disorder: results of the IASP study
Authors: van Emmerik‐van Oortmerssen Katelijne , van de Glind Geurt , Koeter Maarten W. J. , Allsop Steve , Auriacombe Marc , Barta Csaba , Bu Eli Torild H. , Burren Yuliya , Carpentier Pieter‐Jan , Carruthers Susan , Casas Miguel , Demetrovics Zsolt , Dom Geert , Faraone Stephen V. , Fatseas Melina , Franck Johan , Johnson Brian , Kapitány‐Fövény Máté , Kaye Sharlene , Konstenius Maija , Levin Frances R. , Moggi Franz , Møller Merete , Ramos‐Quiroga J. Antoni , Schillinger Arild , Skutle Arvid , Verspreet Sofie ,   IASP research group, van den Brink Wim , Schoevers Robert A. 
Published: October 2013

AbstractAimsTo determine comorbidity patterns in treatment‐seeking substance use disorder (SUD) patients with and without adult attention deficit hyperactivity disorder (ADHD), with an emphasis on subgroups defined by ADHD subtype, taking into account differences related to gender and primary substance of abuse.DesignData were obtained from the cross‐sectional International ADHD in Substance use disorder Prevalence (IASP) study.SettingForty‐seven centres of SUD treatment in 10 countries.ParticipantsA total of 1205 treatment‐seeking SUD patients.MeasurementsStructured diagnostic assessments were used for all disorders: presence of ADHD was assessed with the Conners' Adult ADHD Diagnostic Interview for DSM‐IV (CAADID), the presence of antisocial personality disorder (ASPD), major depression (MD) and (hypo)manic episode (HME) was assessed with the Mini International Neuropsychiatric Interview‐Plus (MINI Plus), and the presence of borderline personality disorder (BPD) was assessed with the Structured Clinical Interview for DSM‐IV Axis II (SCID II).FindingsThe prevalence of DSM‐IV adult ADHD in this SUD sample was 13.9%. ASPD [odds ratio (OR) = 2.8, 95% confidence interval (CI) = 1.8–4.2], BPD (OR = 7.0, 95% CI = 3.1–15.6 for alcohol; OR = 3.4, 95% CI = 1.8–6.4 for drugs), MD in patients with alcohol as primary substance of abuse (OR = 4.1, 95% CI = 2.1–7.8) and HME (OR = 4.3, 95% CI = 2.1–8.7) were all more prevalent in ADHD+ compared with ADHD− patients (P < 0.001). These results also indicate increased levels of BPD and MD for alcohol compared with drugs as primary substance of abuse. Comorbidity patterns differed between ADHD subtypes with increased MD in the inattentive and combined subtype (P < 0.01), increased HME and ASPD in the hyperactive/impulsive (P < 0.01) and combined subtypes (P < 0.001) and increased BPD in all subtypes (P < 0.001) compared with SUD patients without ADHD. Seventy‐five per cent of ADHD patients had at least one additional comorbid disorder compared with 37% of SUD patients without ADHD.ConclusionsTreatment‐seeking substance use disorder patients with attention deficit hyperactivity disorder are at a very high risk for additional externalizing disorders.
Efficacy of different solvents in removing gutta‐percha from curved root canals: A micro‐computed tomography study
Authors: Sağlam Baran Can , Koçak Mustafa Murat , Türker Sevinç Aktemur , Koçak Sibel 
Published: October 2013

AbstractThe aim of this study was to compare the root filling material that remained after retreatment of curved root canals with chloroform and Endosolv R as solvents. The evaluation employed micro‐computed tomography (CT) imaging. Thirty‐six extracted molar teeth with curved roots were selected. After preparation with ProTaper rotary instruments, the canals were filled with gutta‐percha and AH26 sealer. The teeth were randomly divided into three groups according to solvent used (n = 12) as follows: group 1: chloroform; group 2: Endosolv R; group 3: no solvent (negative control). ProTaper Universal Retreatment files were used to remove each root canal filling and then the self‐adjusting file was applied for two minutes. Preoperative and postoperative micro‐CT images were used to assess the percentage of residual filling material. The mean percentage of residual filling material was quantified. There were no statistically significant differences between the groups in terms of percentage volume of residual root canal filling.
Effect of ferrule height and glass fibre post length on fracture resistance and failure mode of endodontically treated teeth
Authors: Abdulrazzak Shurooq S. , Sulaiman Eshamsul , Atiya Basim K. , Jamaludin Marhazlinda 
Published: October 2013

AbstractThe purpose of this study was to evaluate the combined effect of ferrule height and post length on fracture resistance and failure mode of endodontically treated teeth restored with glass fibre posts, composite resin cores and crowns. Ninety human maxillary central incisors were endodontically treated and divided into three groups (n = 30) according to the ferrule heights: 4, 2 and 0 mm, respectively. Post spaces in each group were prepared at 2/3, 1/2 and 1/3 of the root length (n = 10). The specimens were received fibre posts, composite resin core build up and cast metal crowns. After thermocycling, compressive static load was applied at an angle of 135° to the crowns. Two‐way analysis of variance showed significant differences in the failure load in the ferrule height groups, no significant differences in post length groups and no significant interaction between ferrule heights and post lengths. More restorable failure modes were observed.
Effect of Oxytocin, IBMX and dbcAMP on Rabbit Ovarian Follicles
Authors: Balazi A. , Sirotkin A. V. , Pivko J. , Chrenek P. 
Published: October 2013

SummaryOxytocin (OT) and protein kinase A (PKA), a possible intracellular mediator of hormone action in the ovary, can be potent activators of ovarian functions and fertility. Nevertheless, action of OT on ovarian follicle atresia has not been studied yet. Only single administration of PKA activators [3‐isobutyl‐1‐methyl‐xanthine (IBMX) and dibutyryl cyclic adenosine monophosphate (dbcAMP)] on ovarian follicle atresia was studied previously. The aim of this study was to examine the effect of OT (single treatment per one reproductive cycle, multiple treatments for three cycles), IBMX and dbcAMP (multiple treatments) on folliculogenesis and follicular atresia in rabbit. The ovarian cycle in control females was induced only by gonadotropins. Experimental females received co‐administration of gonadotropins with OT, IBMX or dbcAMP (at 50 μg/female). All females were artificially inseminated. Single‐treated females were euthanized after 18–19 h. Multiple‐treated females were euthanized after the third reproductive cycle. Histological sections of the ovaries were prepared and evaluated by a light microscopy. The follicles were divided into four classes according to the structure of granulosa and theca cells as follows: none or small atresia, cystic atresia, obliterative atresia and atresia associated with luteinization. The ovaries from the control and experimental females, treated during one reproductive cycle or three cycles, were compared. Single OT co‐administration increased proportion of follicles with atresia associated with luteinization, but not other types of atresia. No influence of multiple OT co‐administration on follicular atresia was recorded. Multiple IBMX and dbcAMP co‐administration decreased the proportion of atretic follicles and increased the proportion of healthy follicles without atresia.
Morphological and Cytochemical Studies of Peripheral Blood Cells of Schizothorax prenanti
Authors: Fang J. , Chen K. , Cui H. M. , Peng X. , Li T. , Zuo Z. C. 
Published: October 2013

SummaryThe morphological and cytochemical studies of peripheral blood cells of Schizothorax prenanti were studied by light and electron microscopy. Erythrocytes, thrombocytes and three types of leucocytes, lymphocytes, neutrophils and monocytes, were distinguished and characterized. In addition to mature erythrocytes, immature and dividing erythrocytes were observed. A few organelles such as mitochondria were distributed in the cytoplasm of erythrocytes. Lymphocytes with heavily clumped heterochromatic nucleus and minimal cytoplasm were classified into small and large lymphocytes. Three different populations of granules, with distinctive ultrastructural aspect, were observed in neutrophils. Monocytes were the fewest leucocytes possessing rich organelles, phagocytized materials and vacuoles. Thrombocytes with various types were the most abundant blood cells among leucocytes and contained a prominent nucleus with dense bands of heterochromatin and many cytoplasmic vacuoles. Periodic acid‐Schiff staining was positive in neutrophils, monocytes, lymphocytes and thrombocytes, but not in erythrocytes. Peroxidase‐positive staining was observed in neutrophils and monocytes, but not in erythrocytes, lymphocytes and thrombocytes. Only neutrophils were positive for oil red O. Except for erythrocytes, the other blood cells stained positively for acid phosphatase. Only neutrophils and monocytes were positive for α‐naphthyl acetate esterase. None of the cells studied were positive for alkaline phosphatase. The morphologic and cytochemical features of blood cells of S. prenanti are similar to those of other fish. This investigation may be helpful as a tool to monitor the health status of cultured S. prenanti and will grant early detection of clinical pathology.
Increased Nuclear Expression of Nuclear Factor Kappa‐B p65 Subunit in the Eutopic Endometrium and Ovarian Endometrioma of Women with Advanced Stage Endometriosis
Authors: Kim Sung Hoon , Ihm Hyo Jin , Oh Young Sang , Chae Hee Dong , Kim Chung‐Hoon , Kang Byung Moon 
Published: October 2013

ProblemWe evaluated whether the expression of NF‐кB p65 subunit is increased in the eutopic endometrium and/or in the ovarian endometrioma of women with advanced stage endometriosis, and ascertained in vitro effects of proinflammatory cytokines on the expression and DNA binding of NF‐кB p65 subunit in endometrial cells.Method of StudyImmunohistochemistry was performed to compare the nuclear NF‐кB p65 subunit immunoreactivity between women with and without advanced stage endometriosis. The nuclear NF‐кB p65 subunit expression and DNA binding were also analyzed in endometrial cells treated with tumor necrosis factor‐alpha (TNF‐α) or interleukin‐1beta (IL‐1β) utilizing Western blot analysis, enzyme‐linked immunosorbent assay, and electrophoretic mobility shift assay.ResultsThe immunoreactivity of the nuclear NF‐кB p65 subunit was significantly increased in the eutopic endometrium as well as in the ovarian endometrioma of women with endometriosis compared with the controls. In vitro treatment of endometrial cells with TNF‐α and IL‐1β led to a significant increase in nuclear NF‐кB p65 subunit expression and DNA binding.ConclusionsThe nuclear expression of NF‐κB p65 is increased in the eutopic endometrium and ovarian endometrioma of women with advanced stage endometriosis, which strongly suggests that NF‐кB signaling plays a crucial role in the pathogenesis and/or pathophysiology of endometriosis.