bluuebunny/crossref_metadata_2025_split huggingface dataset:
YCF1: A Green TIC: Response to the de Vries et al. Commentary
Authors: Nakai Masato 
Published: June 2015

Abstract
This response to a recent Commentary article by de Vries et al. highlights critical errors in the annotation and identification of Ycf1 homologs in the sequenced chloroplast genomes. Contrary to what is reported by de Vries et al., the majority of chloroplast genomes sequenced to date appear to have retained a typical Ycf1 sequence (i.e., including the N-terminal 6TM domain and a variable hydrophilic C-terminal domain) as my group previously reported. Our evidence continues to support the model that Ycf1 forms an essential component of a “green TIC” that is largely conserved among the Chlorophyta and land plants. Since the establishment of this green TIC with Tic20 as the core component, some cases of loss of Ycf1 during the evolution of the green lineages might be regarded as modifications or alterations of the complex. Here, I discuss our working model that the presence of an alternative “nonphotosynthetic-type” or “ancestral-type” TIC might explain other (or specific) cases of the lack of Ycf1, not only in early lineages, including Glaucophyta and Rhodophyta, but also in the grasses.
Sarcomatoid carcinoma arising in the congenital pigmented nevus after treatment with carbon dioxide snow freezing method
Authors: Nakajima Rina , Komine Mayumi , Miyamoto Yukiko , Fusumae Takayuki , Fujita Yurika , Maekawa Takeo , Murata Satoru , Fukushima Noriyoshi , Ohtsuki Mamitaro 
Published: June 2015

AbstractWe report a case of sarcomatoid carcinoma of the skin in a 63‐year‐old man who was treated with the carbon dioxide snow freezing method for a huge congenital pigmented nevus that extended from the right upper extremity to the right trunk during childhood. He had an exophytic red tumor on the nevus in the right upper extremity that grew slowly for 4 years and rapidly recently. Histological and immunohistochemical studies revealed both epithelial and mesenchymal malignancy in the same tumor. The epithelial component was composed of basaloid cells forming multiple nests with peripheral palisading, positive for keratins and BerEP4, implying basal cell carcinoma. The mesenchymal component was composed of spindle‐shaped cells negative for keratins and positive for vimentin, suggesting sarcoma. This is, to our knowledge, the first report of sarcomatoid carcinoma arising in the primary pigmented nevus that had been treated by the carbon dioxide snow freezing method.
Successful treatment of hypertrophic herpes simplex genitalis in HIV‐infected patient with topical imiquimod
Authors: Deza Gustavo , Martin‐Ezquerra Gemma , Curto‐Barredo Laia , Villar García Judit , Pujol Ramon M. 
Published: June 2015

AbstractHypertrophic herpes simplex genitalis is an atypical presentation of genital herpes described in the context of immunosuppression, particularly HIV‐positive patients. This situation can become a diagnostic and therapeutic challenge. For this reason, alternative therapies are currently being discussed in the literature. We report a case of hypertrophic genital herpes in a HIV‐positive patient who was successfully treated with topical 5% imiquimod after treatment failures with oral and i.v. antivirals.
Case of H syndrome with massive skin involvement, retroperitoneal fibrosis and Raynaud's phenomenon with a novel mutation in the SLC29A3 gene
Authors: Fujita Etsuko , Komine Mayumi , Tsuda Hidetoshi , Adachi Akimasa , Murata Satoru , Kamata Yasuyuki , Minota Seiji , Ohtsuki Mamitaro 
Published: June 2015

AbstractWe describe a case of H syndrome with massive skin involvement, retroperitoneal fibrosis and Raynaud's phenomenon. A 48‐year‐old man with parents of a consanguineous marriage, first appeared with decreased urine output, skin sclerosis on his inner thighs and short stature (142 cm, 47 kg). The patient had suffered from hearing loss since the age of 1 year, and his secondary sexual characteristics had not developed. Computed tomography showed periaortic fibrosis, bilateral ureteral stenosis, hydronephrosis and sclerosis of the germinal cords. A biopsy from the retroperitoneal mass revealed remarkable fibrosis with chronic inflammatory cells. Biopsies from the skin lesion showed thick collagen bundles through the dermis and lymphohistiocytic infiltration with numerous plasma cells. Serum inflammatory markers, such as C‐reactive protein, vascular endothelial factor, transforming growth factor‐β and soluble interleukin‐2 receptor, were elevated. Prednisolone was effective in treating skin lesions and in lowering serum inflammatory markers. After a long period of follow up, genomic DNA of the patient was obtained, and we identified a homozygous mutation in exon 5, c.625G>A, which caused transition of glycine to arginine, p.Gly208Arg, in the patient, but not in DNA samples from another 50 healthy individuals. This is the first case of H syndrome with Raynaud's phenomenon and retroperitoneal fibrosis, and the first Japanese case of H syndrome reported in the English published work with a novel mutation in the SLC29A3 gene.
Reliability and validity assessment of the revised Symptom Checklist 90 for alopecia areata patients in China
Authors: Tan Huan , Lan Xue‐mei , Yu Nan‐lan , Yang Xi‐chuan 
Published: June 2015

AbstractNo study has tested the reliability and validity of the revised Symptom Checklist 90 (SCL‐90‐R) for patients with alopecia areata (AA), and few have used it to evaluate the mental health of AA patients. To assess the psychological status in Chinese AA patients using the SCL‐90‐R, and to evaluate its reliability and validity, the psychological status of 168 patients and 100 controls was evaluated with the Chinese‐version SCL‐90‐R. From this study, we found that The Global Severity Index and nine subscale scores on the SCL‐90‐R were significantly higher in AA patients than that in the controls. Moreover, The Global Severity Index and nine subscale scores on the SCL‐90‐R were associated with disease duration, age of onset, sex and type of AA. In addition, the SCL‐90‐R presented good internal consistency (whole scale α = 0.98 and split‐half coefficient = 0.95). The intercorrelations between the nine subscales and their correlations with the total scale were 0.58–0.93. Factor analysis produced 22 factors with eigenvalues more than 1.0; the first factor explained 33.88% of the variance. Only hostility and paranoid ideation merged into one factor. Taken together, our data indicated that Chinese AA patients demonstrate greater psychopathology than healthy controls. The SCL‐90‐R can be used to assess global psychological distress in AA patients with good reliability and validity.
On the variety of methods for calculating confidence intervals by bootstrapping
Authors: Puth Marie‐Therese , Neuhäuser Markus , Ruxton Graeme D. 
Published: June 2015

Summary

Researchers often want to place a confidence interval around estimated parameter values calculated from a sample. This is commonly implemented by bootstrapping. There are several different frequently used bootstrapping methods for this purpose.

Here we demonstrate that authors of recent papers frequently do not specify the method they have used and that different methods can produce markedly different confidence intervals for the same sample and parameter estimate.

We encourage authors to be more explicit about the method they use (and number of bootstrap resamples used).

We recommend the bias corrected and accelerated method as giving generally good performance; although researchers should be warned that coverage of bootstrap confidence intervals is characteristically less than the specified nominal level, and confidence interval evaluation by any method can be unreliable for small samples in some situations.
Tax Avoidance and the Implications of Weak Internal Controls
Authors: Bauer Andrew M. 
Published: June 2015

AbstractI examine whether corporate tax avoidance is associated with internal control weaknesses (ICWs) disclosed under the Sarbanes‐Oxley Act (SOX). ICWs disclosed under SOX are frequently related to a firm's tax function. When pervasive ICWs exist, the likelihood increases that these frequent tax‐related ICWs spill over from financial reporting issues to tax avoidance objectives. Thus, my research helps corporate stakeholders understand the implications of internal controls beyond simply financial reporting objectives. Results indicate that, on average, firms with a tax‐related ICW have a 4 percent higher three‐year cash effective tax rate relative to firms without any such weaknesses. Further estimates reveal that this negative relation stems from pervasive, company‐level tax ICWs. Analysis of remediation suggests a causal link. I find that after remediating tax‐related ICWs, firms report higher levels of tax avoidance in the future. Broadly, these findings support that internal control quality represents a proxy for internal governance, and thus the strength of alignment between managers and shareholders. Furthermore, tax‐related internal controls represent an important underlying determinant of tax avoidance with significant cash flow effects, and implications beyond financial reporting.
The Effect of Investor Status on Investors' Susceptibility to Earnings Fixation
Authors: Harris Ling L. , Hobson Jessen L. , Jackson Kevin E. 
Published: June 2015

AbstractThis study investigates whether an individual's status as a current or a prospective investor affects the investor's susceptibility to earnings fixation and proposes a mechanism to reduce earnings fixation. Our experimental results suggest that current investors are more susceptible to earnings fixation than prospective investors, and that current investors can reduce earnings fixation by explicitly forecasting future earnings as part of their evaluation process. We provide theory‐consistent evidence that current investors' prevention focus makes them elevate the importance of summary earnings in their evaluation of a company. However, after forecasting future earnings, current investors view summary earnings as only one of several similarly important evaluation inputs rather than as one substantially more important input (relative to its components). Our study contributes to research on earnings fixation and investor status. We also contribute to practice by documenting the moderating effect of investor status on earnings fixation and by identifying a simple mechanism that current investors can use to reduce their susceptibility to earnings fixation.
When Do Ineffective Audit Committee Members Experience Turnover?
Authors: Kachelmeier Steven J. , Rasmussen Stephanie J. , Schmidt Jaime J. 
Published: June 2015

AbstractWe use information extracted from a major proxy advisory service to test predictions from institutional theory regarding when and why audit committee (AC) members experience turnover because of evidence of ineffective governance. First, we broadly categorize AC ineffectiveness concerns as either (i) financial reporting failures or (ii) characteristics of individual AC members. Institutional theory suggests that the visible nature of the first category is more likely to threaten perceptions of AC legitimacy and hence prompt turnover, which is what we find. We then enrich the analysis by interacting the AC‐member ineffectiveness indicators with the extent of shareholder protest votes, finding that shareholder dissent elevates the turnover effects of both categories of ineffectiveness, as institutional theory would predict. Finally, we find that otherwise effective AC members face an increased likelihood of turnover if they serve on the AC when financial reporting failures are discovered, even if they were not on the AC when the events precipitating the failures occurred. Overall, our findings support the institutional theoretic premise that boards take remedial actions when necessary to restore perceived legitimacy.
Simple ways to calculate stable isotope discrimination factors and convert between tissue types
Authors: Greer Amanda L. , Horton Travis W. , Nelson Ximena J. 
Published: June 2015

Summary

Traditional methods to determine stable isotope discrimination factors (Δ) between an animal's diet and tissue(s) are costly and time‐consuming. Consequently, data are only available for relatively few species and are completely absent from some orders, including parrots (Order: Psittaciformes).

We present simple and cost‐effective methodologies for establishing discrimination factors and converting between tissue types. We investigated Δ13Cdiet‐feather and Δ15Ndiet‐feather values for the kea parrot Nestor notabilis by comparing the isotope values from feathers of a population held under their regular conditions at a local zoo, with the δ13C and δ15N values from their weekly diet of >30 food items. We mathematically controlled for dietary elemental concentration, and the potential impacts of metabolic routing, the exclusive consumption of preferred foods and the large‐scale consumption of self‐sourced plants and invertebrates, resulting in Δ13Cdiet‐feather = 4·00‰ ± 0·03 and Δ15Ndiet‐feather = 3·10‰ ± 0·20.

We also determined regression equations for predicting feather δ13C and δ15N values from whole blood values by sampling simultaneously grown feathers and blood from wild kea nestlings. These are the first feather–blood discrimination equations determined for terrestrial birds in the wild. Our δ13C feather–blood discrimination equation was similar to an equation developed for use across marine birds; however, the δ15N feather–blood discrimination equation for marine birds consistently underestimated kea feather δ15N values.

These methodologies, while developed for use in birds, can easily be applied to other animal classes given the appropriate selection of tissues.
Sleep disturbances are associated with reduced health‐related quality of life in patients with substance use disorders
Authors: Magnée Ellis H. B. , de Weert‐van Oene Gerdien H. , Wijdeveld Toon A. G. M. , Coenen Anton M. L. , de Jong Cor A. J. 
Published: June 2015

Background and ObjectivesSleep problems and substance use are strongly linked. Sleep problems play a role in the etiology of substance use, but also may be a result of it. After detoxification, sleep problems may worsen leading to relapse. Nowadays, most substance dependence treatment programs aim at recovery rather than total abstinence, and in that view health‐related quality of life (HRQL) is a relevant construct. This article describes the association between self‐perceived sleep problems and HRQL in a naturalistic population of polydrug‐using inpatients.MethodsAt the start of treatment, 388 polydrug‐using inpatients completed questionnaires concerning their sleep quality and HRQL. Three categories were established based on reported sleep problems: patients without sleep problems (21.6%), those with clinically relevant sleep problems (34.5%), and patients with sleep disorders (43.8%).ResultsMean grades for quality of sleep were M = 7.3 (sd 1.7), M = 6.6 (sd 1.7) and M = 5.3 (sd 1.9) for the three categories, respectively. In addition, patients in the disorder category perceived a lower HRQL than those in the other categories. In the explanation of HRQL, both sleep problems and sleep disorders added significantly to the model when controlling for baseline characteristics.Discussion and ConclusionsOur findings stress the need for clinicians to pay attention to the quality of sleep of recovering polydrug users, since this may play an important role in the recovery process. Monitoring sleep during treatment is advocated. This study adds to the knowledge about the way HRQL and sleep are related in a naturalistic sample of substance‐dependent patients. (Am J Addict 2015;24:515–522)
Viral Infection‐Induced Differential Expression of LncRNAs Associated with Collagen in Mouse Placentas and Amniotic Sacs
Authors: Pan Jing , Mor Gil , Ju Weina , Zhong Julia , Luo Xiucui , Aldo Paulomi Bole , Zhong Mei , Yu Yanhong , Jenkins Edmund C. , Brown William T. , Zhong Nanbert 
Published: June 2015

ProblemWe have previously determined that long non‐coding RNAs (lncRNAs) are differentially expressed in preterm premature rupture of membranes (PPROM) and hypothesized that the collagenolysis ubiquitin–proteasome system may be activated by infection and inflammation. However, direct evidence of the involvement of lncRNAs in transcriptional and posttranscriptional regulation of the infection‐triggered alteration of collagen is lacking.Method of studyA previously developed mouse model with MHV68 viral infection was assessed to determine whether viral infection may induce differential expression of lncRNAs in mouse placentas and amniotic sacs.ResultsDifferential expression of lncRNAs that are associated with collagen was found in HMV68 viral‐infected, compared to non‐infected, mouse placentas and amniotic sacs. Differential expression of messenger RNAs (mRNAs) of collagen was also documented.ConclusionsOur data demonstrate, for the first time, that viral infection may induce the differential expression of lncRNAs that are associated with collagen. Based on this finding, we propose that lncRNA may have involved in regulating of infection‐induced collagen transcription.
A review of the use of direct seeding and seedling plantings in restoration: what do we know and where should we go?
Authors: Palma Ana Cristina , Laurance Susan G.W. 
Published: June 2015

AbstractQuestionsTo select the best method to restore an ecosystem requires an understanding of the various outcomes commonly achieved through different restoration techniques. What method results in the most timely and cost‐effective means of reinstating biodiversity and restoring ecosystem functions and services?MethodsWe explored the efficacy and costs of two re‐vegetation techniques commonly used in ecosystem restoration: direct seeding and planting of seedlings. Our analysis focused on 120 scientific peer‐reviewed publications reporting on experiments using seeds or seedlings, and encompassed a range of ecosystems such as wetlands, savannas and forests. We examined current restoration issues, including species diversity, survival, species selection, costs and how future climate change may influence restoration efforts.ResultsDirect seeding experiments used more species than seedling studies, yet showed lower survivorship. Species availability is the major constraint in the selection of which species were used, regardless of the approach employed. Although costs are extremely important when planning a restoration project, few published findings report on the economic aspects of ecosystem restoration. Further, we did not find any study addressing the impacts of global climate change on restoration programmes or how studies should consider future shifts in the environment.ConclusionsOur results highlight the need for restoration experiments to explore more species. Restoration efforts are in need of detailed reporting that includes time frames and costs. We need to consider future climate scenarios that will affect ecosystem restoration efforts.
A comparative framework for broad‐scale plot‐based vegetation classification
Authors: De Cáceres Miquel , Chytrý Milan , Agrillo Emiliano , Attorre Fabio , Botta‐Dukát Zoltán , Capelo Jorge , Czúcz Bálint , Dengler Jürgen , Ewald Jörg , Faber‐Langendoen Don , Feoli Enrico , Franklin Scott B. , Gavilán Rosario , Gillet François , Jansen Florian , Jiménez‐Alfaro Borja , Krestov Pavel , Landucci Flavia , Lengyel Attila , Loidi Javier , Mucina Ladislav , Peet Robert K. , Roberts David W. , Roleček Jan , Schaminée Joop H.J. , Schmidtlein Sebastian , Theurillat Jean‐Paul , Tichý Lubomír , Walker Donald A. , Wildi Otto , Willner Wolfgang , Wiser Susan K. 
Published: June 2015

AbstractAimsClassification of vegetation is an essential tool to describe, understand, predict and manage biodiversity. Given the multiplicity of approaches to classify vegetation, it is important to develop international consensus around a set of general guidelines and purpose‐specific standard protocols. Before these goals can be achieved, however, it is necessary to identify and understand the different choices that are made during the process of classifying vegetation. This paper presents a framework to facilitate comparisons between broad‐scale plot‐based classification approaches.ResultsOur framework is based on the distinction of four structural elements (plot record, vegetation type, consistent classification section and classification system) and two procedural elements (classification protocol and classification approach). For each element we describe essential properties that can be used for comparisons. We also review alternative choices regarding critical decisions of classification approaches; with a special focus on the procedures used to define vegetation types from plot records. We illustrate our comparative framework by applying it to different broad‐scale classification approaches.ConclusionsOur framework will be useful for understanding and comparing plot‐based vegetation classification approaches, as well as for integrating classification systems and their sections.
Drug Metabolism – From In Vitro to In Vivo, From Simple to Complex
Authors: Pelkonen Olavi 
Published: June 2015

AbstractDrug metabolism is the crucial part of pharmaco‐ and toxicokinetics and consequently is associated with both desirable and adverse effects of most xenobiotics, compounds foreign to the body. This minireview follows some advances of the field over the last 50 years or so through the experiences and work of one scientist. Thus, this minireview represents a rather personal view of research in one research field. Drug metabolism is affected and controlled by a huge number of factors and conditions such as individual development, species differences, drug–drug interactions and various environmental, host and genetic factors working via a variable set of regulatory mechanisms. All these different factors create wide individual, population and species variability with obvious repercussions to clinical drug therapy and chemical risk assessment. This minireview also provides glimpses to methodological developments over recent decades and ends up presenting a few promising approaches and techniques such as various omics and high‐content and high‐throughput techniques feeding huge amounts of data to computational integration and modelling, which constitute the basis for systems or network pharmacology and toxicology.