bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dispersal increases ecological selection by increasing effective community size
Authors: Ron Ronen , Fragman-Sapir Ori , Kadmon Ronen 
Published: October 2018

Significance
A basic challenge of ecology is to understand the mechanisms that generate changes in the composition of ecological communities. At the most fundamental level, any change in species composition results from the interplay between two contrasting forces: selection (representing deterministic forces) and drift (representing stochastic forces). Here we provide experimental evidence that the relative importance of these two forces depends on the magnitude of dispersal. Specifically, increasing dispersal increases the effective size of the communities, thereby diminishing the relative importance of demographic stochasticity and increasing the relative importance of selective forces as drivers of community assembly. Our findings, supported by computer simulations, have important implications for understanding the ecological consequences of dispersal.
From Co-Actionality to Extended Intersubjectivity: Drawing on Language Change and Ontogenetic Development
Authors: TANTUCCI Vittorio 
Published: October 2018

Abstract
This article combines research results centred on theory of mind (ToM) from cognitive and developmental psychology (Goldman 2006; Apperly 2010; Wilkinson and Ball 2012) with the notion of intersubjectivity in usage-based linguistics (i.a. Verhagen 2005; Nuyts 2012; Traugott 2012). It identifies some of the controversies in the literature from both domains and suggests the desiderata for a hybrid approach to intersubjectivity, which is distinctively designed to tackle applied research in social and cognitive sciences. This model is based on a mismatch between interaction as mere ‘co-action’ vs. interaction as spontaneously communicated awareness of an(other) mind(s). It provides a case study centred on the first language acquisition of pre-nominal usage of this/that and such. From, respectively, a distinctive collexeme (Gries and Stefanowitsch 2004) and behavioural profile analysis (Gries 2010) will emerge that beyond expressions of joint attention, children’s ToM ability progressively underpins ‘ad-hoc’ generalized instantiations based on extended intersubjectivity, viz. the socio-cognitive skill to problematize what a general persona would act, feel, or think in a specific context.
ICD-10-CM Diagnosis Coding for Neuropsychological Assessment
Authors: Uysal Suzan 
Published: October 2018

Abstract

Objective
This paper summarizes the basic principles of diagnosis coding for neuropsychological evaluation of patients with known or suspected brain injury or disease.

Method
The resources forming the basis of this article are the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) and the ICD-10-CM Official Guidelines for Coding and Reporting.

Conclusion
Diagnosis codes are used to communicate the specific reason for health care encounters and the conditions treated. All health care providers in all health care settings are mandated to implement ICD-10-CM for coding all health care encounters and transactions. It is the providers of health care services who ultimately are responsible for medical record documentation and diagnosis coding. The neuropsychologist’s knowledge base, therefore, should include a basic understanding of the structure of the ICD-10-CM, the conventions and rules for diagnosis coding, and the rules for what constitutes accurate coding.
BMDExpress 2: enhanced transcriptomic dose-response analysis workflow
Authors: Phillips Jason R , Svoboda Daniel L , Tandon Arpit , Patel Shyam , Sedykh Alex , Mav Deepak , Kuo Byron , Yauk Carole L , Yang Longlong , Thomas Russell S , Gift Jeff S , Davis J Allen , Olszyk Louis , Merrick B Alex , Paules Richard S , Parham Fred , Saddler Trey , Shah Ruchir R , Auerbach Scott S 
Published: October 2018

Abstract

Summary
A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams’ trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community.

Availability and implementation
BMDExpress 2 is available at https://github.com/auerbachs/BMDExpress-2/releases.

Supplementary information
Supplementary data are available at Bioinformatics online.
A non-invasive biomarker of type III collagen degradation reflects ischaemia reperfusion injury in rats
Authors: Rasmussen Daniel Guldager Kring , Nielsen Per Mose , Kasab-Oglo Özlem Yashar , Nielsen Signe Holm , Kierulf-Lassen Casper , Karsdal Morten Asser , Genovese Federica , Nørregaard Rikke 
Published: October 2018

Abstract

Background
Maintenance of kidney function in kidney allografts remains a challenge, as the allograft often progressively develops fibrosis after kidney transplantation. Fibrosis is caused by the accumulation of extracellular matrix proteins like type I and III collagen (COL I and III) that replace the functional tissue. We assessed the concentrations of a neo-epitope fragment of COL III generated by matrix metalloproteinase-9 cleavage (C3M) in two rat models resembling the ischaemic injury taking place following kidney transplantation.

Methods
We measured C3M in urine (U-C3M) and plasma (P-C3M) samples of rats subjected to unilateral nephrectomy followed by sham operation (NTx) or ischaemia reperfusion injury (NTxIRI) as well as in rats subjected to bilateral ischaemia reperfusion injury (BiIRI). Levels of U-C3M were normalized to urinary creatinine and were correlated to plasma creatinine, blood urea nitrogen, messenger ribonucleic acid (mRNA) of markers of kidney injury, and mRNA and protein levels of markers of tissue repair and fibrosis.

Results
Levels of U-C3M were significantly elevated 7 days after ischaemia reperfusion in the NTxIRI. BiIRI animals showed higher levels of U-C3M after 7 and 14 days of reperfusion but not at 21 days. P-C3M did not change in any of the models. There was a significant correlation between U-C3M and mRNA levels of fibronectin, COL I alpha 1 chain (COL Ia1) and neutrophil gelatinase-associated lipocalin (NGAL), and protein levels of alpha smooth muscle actin (αSMA), fibronectin and COL III in NTxIRI but not in NTx animals. Levels of U-C3M increased significantly in the BiIRI animals subsequent to reperfusion, and mirrored the histological alterations. Furthermore, U-C3M was associated with the extent of fibrosis, and remained elevated even after plasma creatinine levels decreased.

Conclusions
These results demonstrate that degradation of COL III increases after ischaemia reperfusion injury, and that U-C3M may be a non-invasive marker of tissue repair and fibrosis in the ischaemic kidney.
Vapes, E-cigs, and Mods: What Do Young Adults Call E-cigarettes?
Authors: Pearson Jennifer L , Reed Domonique M , Villanti Andrea C 
Published: October 2018

Abstract

Introduction
A diverse class of products, “e-cigarettes” present surveillance and regulatory challenges because of nonstandard terminology used to describe subtypes, especially among young adults, where occasional e-cig use is most prevalent.

Methods
Young adults (n = 3364) in wave 9 (Spring 2016) of the Truth Initiative Young Adult Cohort were randomized to see two of five photos of common e-cig products (three varieties of first-generation e-cigs and one variety each of second- and third-generation e-cigs). Qualitative responses were coded into nine classifications: “e-cigarette, e-hookah, vape-related, mod, other or more than one kind of e-cig, marijuana-related, non-e-cig tobacco product, misidentified, and don’t know.” We characterized the sample and survey responses and conducted multivariable logistic regression to identify participant characteristics associated with correctly identifying the devices as e-cigs. Data were weighted to represent the young adult population in the United States in 2016.

Results
The majority of participants identified the pictured devices as some type of e-cig (57.7%–83.6%). The white first-generation e-cig, as well as the second- and third-generation e-cigs caused the greatest confusion, with a large proportion of individuals responding “don’t know” (12.2%–25.1%, depending on device) or misidentifying the e-cig as a non-nicotine product (3.4%–16.1%, depending on device) or non-e-cig tobacco product (1.4%–14.6%, depending on device).

Conclusions
Accurate surveillance and analyses of the effect of e-cigs on health behavior and outcomes depend on accurate data collection on users’ subtype of e-cig. Carefully chosen images in surveys may improve reporting of e-cig use in population studies.

Implications
Survey researchers using images to cue respondents, especially young adult respondents, should consider avoiding use of white or colorful first-generation e-cigs, which were commonly misidentified in this research, in preference for black or dark colored first-generation e-cigs, such as the blu brand e-cig. Given the sizable proportion of respondents who classified second- and third-generation e-cigs with terminology related to vaping, surveys specifically aimed at assessing use of these types of e-cigs should include the term “vape” when describing this subclass of devices.
The Effects of Wheel Running on Skeletal Muscle Function During and Following Doxorubicin Treatment
Authors: Hochberg Leanne M. , Busekrus Raquel B. , Hydock David S. 
Published: October 2018

Doxorubicin (DOX) is a powerful chemotherapeutic agent, but its use is associated with adverse side effects including skeletal muscle dysfunction. Exercise prior to DOX treatment has been shown to attenuate muscle dysfunction, but the effects of exercise on DOX myotoxicity during and following treatment remain unknown.

Purpose:
The purpose of this study was therefore to explore the effects of endurance exercise during and following DOX treatment on skeletal muscle function.

Methods:
Male rats received DOX or saline weekly for 6 weeks and were housed in either voluntary running wheel cages or sedentary condition. Grip force was measured at baseline, week 5, and week 10, and ex vivo skeletal muscle function was assessed at week 10.

Results:
Wheel running during and following DOX treatment attenuated late-onset grip force reduction and promoted improved function in type I, or slow muscle.

Conclusion:
Skeletal muscle function can be preserved during and following DOX treatment with low-volume endurance exercise, but this protection may be limited to type I muscle.
Extensive CD34-to-CD90 Fibroblast Transition Defines Regions of Cutaneous Reparative, Hypertrophic, and Keloidal Scarring
Authors: Ho Jonathan Dale , Chung Hye Jin , MS Barron Alexander , Ho Djavila Amari , Sahni Debjani , Browning Jeffrey L. , Bhawan Jag 
Published: October 2018

Background:
CD90+ fibroblasts have been described arising from and replacing the homeostatic CD34+ network in scleroderma, but have not been specifically examined in other forms of cutaneous fibrosis.

Objectives:
To address expression, timelines, and spatial relationships of CD90, CD34, and smooth muscle actin (SMA) expressing fibroblasts in scars and to examine for the presence of a CD34-to-CD90 transition.

Methods:
One hundred and seventeen scars (reparative/hypertrophic/keloidal) were evaluated for CD90, CD34, and SMA expression. Double-staining immunohistochemistry for CD90/CD34 was performed to identify CD90+/CD34+ transitioning cells, confirmed by double-color immunofluorescence. In addition, some scars were double-stained with CD90/SMA, CD90/procollagen-1, or SMA/procollagen-1 to evaluate spatial relationships and active collagen synthesis. Expression was graded as diffuse, minority, and negative.

Results:
Most scars demonstrate a CD90diffuse/CD34negative/minority pattern, and dual CD90+/CD34+ fibroblasts were observed in 91% of scars. In reparative scars, CD90 expression reverses to a CD34+/CD90− state with maturation. Pathologic scars exhibit prolonged CD90 expression. Both CD90+ and SMA+ fibroblasts collagenize scars, although CD90+ fibroblasts are more prevalent.

Conclusions:
CD90+ fibroblasts likely arise from the resting CD34+ fibroblastic network. Actively collagenizing scar fibroblasts exhibit a CD90diffuse/CD34negative/minority phenotype, which is prolonged in pathologic scars. CD90+ fibroblasts are likely important players in cutaneous scarring.
Simultaneous Quantification of Nine Antimicrobials by LC-MS/MS for Therapeutic Drug Monitoring in Critically Ill Patients
Authors: Neugebauer Sophie , Wichmann Christina , Bremer-Streck Sibylle , Hagel Stefan , Kiehntopf Michael 
Published: October 2018

Background:
Adequate antibiotic treatment is a prerequisite for the successful treatment of systemic infections. Based on accumulating scientific evidence, a fixed dosage regimen can lead to insufficient and ineffective antibiotic therapy. Thus, the aim of this study was to develop and validate a simplified, but sensitive method for the simultaneous quantification of antimicrobials by using liquid chromatography with tandem mass spectrometry (LC-MS/MS) for the development of personalized therapy regimens using therapeutic drug monitoring.

Methods:
A method was developed for the simultaneous quantification of 9 antimicrobials (aciclovir, ampicillin, cefuroxime, ciprofloxacin, meropenem, metronidazole, piperacillin, rifampicin, and tazobactam) in lithium–heparin plasma. A simple sample preparation method and a chromatographic run time of 10 minutes enabled the quick processing of the samples. The method was validated according to the guidelines for bioanalytical method validation of the European Medicines Agency and addressed sensitivity, specificity, linearity, accuracy, precision, dilution integrity, carry-over, recovery, matrix effects, and stability.

Results:
The chromatographic run time was 10 minutes and antimicrobials eluted at retention times ranging from 1.1 to 2.2 minutes. Calibration curve for all antimicrobials was linear over a range of 1–100 mg/L, and a 2-fold or 5-fold dilution of the samples was possible. The method accuracy ranged from 85.1% to 114.9% for all measured antimicrobials, and the within- and between-run precision values were <11.9% and <16.5% for the lower limit of quantification. No interferences and carry-over were observed. The samples were stable for at least 5 hours at room temperature or in the autosampler (10°C).

Conclusions:
The LC-MS/MS method developed in this study is appropriate and practical for the therapeutic drug monitoring of antimicrobials in the daily clinical laboratory practice because of its short analysis time, the need for a small amount of plasma, high specificity, and accuracy.
Embracing the future for emergency nurse practitioners and specialty practice: Implications for research, clinical practice, education, and health policy
Authors: Evans Dian Dowling , Hoyt Karen Sue , Wilbeck Jennifer , Schumann Lorna , Ramirez Elda , Tyler Diane , Agan Donna 
Published: October 2018

ABSTRACT
The emergency nurse practitioner (ENP) specialty has grown rapidly, responding and adapting to changes within emergency care. Designation and advancement of nurse practitioner (NP) specialties follows a systematic process as defined by the profession. This includes establishment of scope and standards of practice, educational standards, and policy initiatives to ensure quality and safety within the profession. This article describes how the ENP specialty has used evidence to meet health system needs and chart a transformational future. Current recommendations for advancing health care transformation, as described by the American Association of Colleges of Nursing-Manatt Report, inform and frame the processes by which the ENP specialty has collaborated with diverse stakeholders to create a research and policy agenda to ensure that ENPs are appropriately prepared to lead and provide access to safe, affordable, quality health care. These processes provide a future-oriented model that promotes advancement of the NP profession through provision of new NP specialty designations as they emerge to meet changing health care system needs.
Direct-to-consumer genetic testing for breast cancer risk
Authors: Reed E. Kate , Edelman Emily A. 
Published: October 2018

ABSTRACT
Increasingly, individuals are interested in genetic testing to find out if they are at increased risk for breast cancer and other diseases. Through direct-to-consumer genetic testing, people can receive information about many different traits, including some risk information about hereditary breast and ovarian cancer syndrome. With more people getting this information outside of the medical setting, clinicians should be aware of the benefits and limitations of such testing.
Pulmonary embolism critical care update: prognosis, treatment, and research gaps
Authors: Chodakowski Jason D. , Courtney D. Mark 
Published: October 2018

Purpose of review
We provide a timely update on treatment care issues facing clinicians and patients with acute pulmonary embolism accompanied by either right ventricular strain (sub-massive pulmonary embolism) or shock (massive pulmonary embolism).

Recent findings
Care and research changes over the last several years have resulted in four important trends: more consensus and accuracy in the way acute pulmonary embolism severity is described and communicated among acute care clinicians and researchers, increased availability and use of risk prediction scoring systems, increased use of advanced invasive therapy in the setting of severe right ventricular dysfunction, and emergence of multidisciplinary pulmonary embolism response teams to guide standard care decision-making.

Summary
Pulmonary embolism with shock should be treated with either systemic or catheter-based thrombolytic therapy in the absence of contraindications. Patients with sub-massive pulmonary embolism accompanied by right heart dysfunction who are treated with thrombolytic therapy likely will experience more rapid improvement in RV function and are less likely to progress to hemodynamic decompensation. This comes, however, with an increased risk of major bleeding. Our recommendation is to consider catheter-based or systemic fibrinolytic therapy in sub-massive pulmonary embolism cases where patients demonstrate high-risk features such as: severe RV strain on echo or CT, and importantly worsening over time trends in pulse, SBP, and oxygenation despite anticoagulation. Understanding the impact of advanced therapy beyond standard anticoagulation on patient-centered outcomes, such as functional status and quality of life represent a research knowledge gap.
Place of Sterotactic Radiotherapy in Treatment of Extramedullary Plasmocytoma
Authors: Cihan Yasemin Benderli 
Published: October 2018

Abstract
In conclusion, extramedullary plasmacytoma (EMPs) initially develop as localized disease. These tumors are quite sensitive to radiotherapy (RT) and the response is often complete recovery after RT. In addition, highly sensitive, conformal radiosurgery can be preferred to conventional RT; however, further studies are needed to define indications and therapeutic fractions in stereotactic RT of plasmacytoma since guidelines and clinical trials are lacking. Although general principles are valid, radiosurgery may be planned based on anatomical localization of EMP.
An Unusual Case of Schwannoma in the Infraorbital Region
Authors: Pirimoglu Berhan , Kantarci Mecit 
Published: October 2018

Abstract
Schwannoma is usually an uncommon benign encapsulated slow-growing neural tumor that originates from Schwann cells of peripheral, cranial, and autonomic nerves. It constitutes 1% to 8% of all head and neck neoplasms. Extracranial schwannoma are very rarely seen originating from the infraorbital nerve. Most of the schwannomas are usually solitary and not associated with NF1. The typical presentation is a slow-growing soft-tissue mass. Treatment of schwannoma is surgical resection.
Does Glossopharyngeal Neuralgia Need Rhizotomy in Neurovascular Decompression Surgery?
Authors: Wang Ji , Yu Rui , Qu Chuncheng , Jiang Jun , Wang Chengwei , Meng Qinghu , Wei Shengcheng 
Published: October 2018

Objective:
To evaluate and compare the long-term efficacy and safety of microvascular decompression (MVD) and glossopharyngeal nerve roots rhizotomy (GNR) in the treatment of glossopharyngeal neuralgia (GN).

Patients and Methods:
The data of 37 patients with glossopharyngeal neuralgia undergoing MVD alone and MVD + GNR from July 2004 to March 2017 were analyzed retrospectively. Among them, 22 were MVD alone and 15 were MVD + GNR. All patients underwent preoperative cocaine experiments to verify diagnoses, preoperative magnetic resonance imaging examinations to detect compressing vessels near the root entry zone of the glossopharyngeal nerve. Operation via retrosigmoid approach, keyhole craniotomy, and postoperative efficacy was followed up.

Results:
Efficacy: In the 22 patients with MVD alone, 19 patients were cured and 3 patients improved. In the 15 patients with MVD + GNR, 14 patients were cured and 1 patient improved. There was no significant difference between the 2 groups (χ2 test, P > 0.05). Complications: Postoperative complications in MVD group: 2 patients had short-term hoarseness and drinking cough, 1 patient with cerebrospinal fluid leakage, 1 patient with intracranial infection, 1 patient with ipsilateral hearing loss, and no deaths; postoperative complications in MVD + GNR group: permanent hoarseness in 2 patients, short-term drinking cough and hoarseness in 4 patients, ipsilateral facial paralysis in 1 patient, 1 patient with cerebrospinal fluid leakage, no intracranial infection and death. The incidence of postoperative hoarseness and drinking cough in MVD + GNR group was higher than that in MVD group (χ2 test, P < 0.05).

Conclusion:
The MVD alone was a safe and effective method for the treatment of primary glossopharyngeal neuralgia, the efficacy was equivalent to MVD + GNR, and had low incidence of hoarseness and drinking cough.