bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical Coherence Tomography Angiography Findings in X-Linked Retinoschisis
Authors: Mastropasqua Rodolfo , Toto Lisa , Di Antonio Luca , Parodi Maurizio Battaglia , Sorino Luca , Antonucci Ivana , Stuppia Liborio , Di Nicola Marta , Mariotti Cesare
Published: September 2018

BACKGROUND AND OBJECTIVE:

The aim of the study was to determine optical coherence tomography angiography (OCTA) findings and to identify mutations in the
RS1
gene in a three-generation family with X-linked juvenile retinoschisis (XLRS).

PATIENTS AND METHODS:

Clinical and genetic assessments were performed in 12 family members. OCTA was performed at baseline (12 members including cases and carriers) and after acetazolamide administration (three cases). Twenty healthy subjects (20 eyes, controls) were chosen for comparison. Molecular genetic analysis of the
RS1
gene was performed in all family members.

RESULTS:

Deep capillary plexus density was reduced in cases compared with controls (
P
< .01) and was negatively related with retinal thickness (
P
< .05). After treatment, retinal thickness decreased (
P
< .05) and deep capillary plexus density increased (
P
< .05) in cases. In three cases and in four carriers, p.Arg197 His mutation was found.

CONCLUSION:

OCTA shows reduced macular deep vessel density in patients with XLRS probably related to vessel displacement and disruption due to schitic cysts.

[
Ophthalmic Surg Lasers Imaging Retina
. 2018;49:e20–e31.]
The Correlation of Pars Plana Incision and Transient Hypotony After Silicone Oil Removal
Authors: Zhang Xian , Chen Bo , Yang Huajing , Song Yinwei , Zhang Di , Soetikno Brian T. , Sun Xufang
Published: September 2018

BACKGROUND AND OBJECTIVE:

To evaluate the correlation between pars plana incision and transient hypotony after silicone oil removal in aphakic eyes

PATIENTS AND METHODS:

Twenty-two patients with aphakia and a high degree of myopia with silicone oil tamponade were recruited for this prospective study and randomly scheduled to two groups for silicone oil removal: 3.5-mm corneal incision with suture corneal or 20-gauge pars plana incision with suture. Intraocular pressure (IOP) was measured and fundus and anterior structure were examined preoperatively on the first, third, and seventh postoperative day and at 1 month after surgery.

RESULTS:

IOPs in the pars plana group were significantly lower than the corneal group on the first and third day after surgery (P < .001). Nine of the 11 patients in the pars plana group suffered ciliary detachment accompanied by hypotony (IOP < 8 mm Hg), among whom three patients exhibited excessive hypotony (IOP < 5 mm Hg), whereas the ciliary bodies remained tightly attached and IOP was normal in the corneal group. Among these nine patients, six eyes were observed to have multiple silicone oil granules in the supraciliary cavity, three exhibited gaps of pars plana below the scleral incision site, and two had vitreous hemorrhage. Hypotony spontaneously relieved at the seventh postoperative day for all patients.

CONCLUSION:

Pars plana incision is the crucial cause of ciliary detachment and consequent transient hypotony after silicone oil removal. Using corneal limbus incision in patients with aphakic eyes to avoid the par plana incision is expected to reduce the incidence of hypotony with minimal complications.

[
Ophthalmic Surg Lasers Imaging Retina
. 2018;49:e44–e51.]
Peripheral Persistent Fetal Vasculature: A Report of Three Cases
Authors: Dedania Vaidehi S. , Ozgonul Cem , Besirli Cagri G.
Published: September 2018

The authors report three cases of persistent fetal vasculature (PFV) presenting with an atypical peripheral fibrovascular stalk. A 5-month-old with congenital exotropia with a vitreous hemorrhage in the right eye underwent vitrectomy, and a mid-peripheral vitreal vascular stalk was visualized within the area of hemorrhage. The second case is of an 8-year-old with two fetal vascular remnants in the right eye: (1) a stalk superotemporally extending from the pars plana to the mid-peripheral retina that was associated with a retinal break and (2) a focal lens opacity. The third case is a 12-year-old with a history of familial exudative vitreoretinopathy and peripapillary choroidal neovascular membrane found to have a peripheral vitreal stalk in the right eye. These cases demonstrate a rare form of PFV with primarily peripheral remnants.

[
Ophthalmic Surg Lasers Imaging Retina
. 2018;49:e83–e88.]
First Locally Acquired Congenital Zika Syndrome Case in the United States: Neonatal Clinical Manifestations
Authors: Ventura Camila V. , Bandstra Emmalee S. , Fernandez Maria P. , Cooper Joshua M. , Saigal Gaurav M. , Bauer Charles R. , Hofheimer Julie A. , Berkovits Michelle D. , Fifer Robert C. , Pensirikul Alyssa D. , Gonzalez Ivan A. , Curry Christine L. , Andreansky Samita , Younis Ramzi T. , Liu Xue Z. , Banker Tanuj P. , Dubovy Sander R. , Langer Samantha M. , Berrocal Audina M. ,   Consortium Investigators
Published: September 2018

In the spring of 2017, a full-term infant with microcephaly was delivered in South Florida. During first trimester, the mother presented with fever, nausea, and vomiting. She reported no foreign travel for herself or her partner. The infant's neurologic, ophthalmologic, neuroradiologic, and audiologic findings were highly suggestive of congenital Zika syndrome (CZS), confirmed by IgM antibodies and plaque reduction neutralization test. New observations, including peripheral temporal retinal avascularity and peripapillary retinal nerve fiber layer thinning, are presented from this first known case of non-travel-associated CZS in the United States.

[
Ophthalmic Surg Lasers Imaging Retina
. 2018;49:e93–e98.]
Therapeutic Potential of Mesenchymal Cell–Derived miRNA-150-5p–Expressing Exosomes in Rheumatoid Arthritis Mediated by the Modulation of MMP14 and VEGF
Authors: Chen Zhe , Wang Hanqi , Xia Yang , Yan Fuhua , Lu Yong
Published: September 2018

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial tissue inflammation and joint destruction associated with the activation of angiogenesis. Exosomes, which play a role in cell-to-cell communication as carriers of genetic information, transfer microRNAs (miRNAs or miRs) between cells and have been studied as delivery vehicles for therapeutic molecules. The aim of the current study was to investigate the therapeutic effect of mesenchymal stem cell (MSC)–derived miR-150-5p exosomes on joint destruction in RA. The expression and secretion of miR-150-5p, matrix metalloproteinase (MMP) 14, and vascular endothelial growth factor (VEGF) in RA patients and fibroblast-like synoviocytes (FLS) were examined by quantitative RT-PCR, ELISA, and Western blotting. Immunohistochemistry was used to assess angiogenesis. MSCs were transfected with an miR-150-5p expression plasmid, and MSC-derived exosomes were harvested. The effect of MSC-derived miR-150-5p exosomes (Exo-150) on MMP14 and VEGF expression was examined. The effects of Exo-150 on cell migration and invasion in cytokine-stimulated FLS from RA patients were examined by HUVEC tube formation and transwell assays. The effect of Exo-150 in vivo was examined in a collagen-induced arthritis mouse model. Exo-150 decreased migration and invasion in RA FLS and downregulated tube formation in HUVECs by targeting MMP14 and VEGF. Injection of Exo-150 reduced hind paw thickness and the clinical arthritic scores in collagen-induced arthritis mice. Exo-150 reduced joint destruction by inhibiting synoviocyte hyperplasia and angiogenesis. Exosomes facilitate the direct intracellular transfer of miRNAs between cells and represent a potential therapeutic strategy for RA.
KlimaSeniorinnen: lessons from the Swiss senior women's case for future climate litigation
Authors: Bähr Cordelia Christiane , Brunner Ursula , Casper Kristin , Lustig Sandra H
Published: September 2018

As older women are particularly vulnerable to climate change impacts, a group of senior women in Switzerland founded the association KlimaSeniorinnen Schweiz (Senior Women for Climate Protection Switzerland) in order to fight for ambitious climate action by legally challenging the Swiss government's inadequate climate policies and mitigation measures. The KlimaSeniorinnen filed a legal request with the authorities, claiming that the Swiss authorities are failing to fulfil their duty to protect them as required by the Swiss Constitution and by the European Convention on Human Rights. This article provides a detailed analysis of the KlimaSeniorinnen case within the context of climate litigation worldwide. It argues that the case's human rights arguments, which are grounded in climate science, the United Nations Framework Convention on Climate Change (UNFCCC), the Paris Agreement, environmental principles and international law, are generally transferable to almost any country. Therefore, vulnerable individuals and groups can learn from the KlimaSeniorinnen litigation that there are strong legal grounds to bring human-rights-based climate lawsuits against governments and thus governments should expect more litigation if their climate actions or omissions contravene international law and violate constitutional principles.
Inverse modelling of CF4 and NF3 emissions in East Asia
Authors: Arnold Tim , Manning Alistair J. , Kim Jooil , Li Shanlan , Webster Helen , Thomson David , Mühle Jens , Weiss Ray F. , Park Sunyoung , O'Doherty Simon
Published: September 2018

Abstract. Decadal trends in the atmospheric abundances of carbon tetrafluoride
(CF4) and nitrogen trifluoride (NF3) have been well characterised
and have provided a time series of global total emissions. Information on
locations of emissions contributing to the global total, however, is
currently poor. We use a unique set of measurements between 2008 and 2015
from the Gosan station, Jeju Island, South Korea (part of the Advanced Global
Atmospheric Gases Experiment network), together with an atmospheric transport
model, to make spatially disaggregated emission estimates of these gases in
East Asia. Due to the poor availability of good prior information for this
study, our emission estimates are largely influenced by the atmospheric
measurements. Notably, we are able to highlight emission hotspots of
NF3 and CF4 in South Korea due to the measurement location. We
calculate emissions of CF4 to be quite constant between the years 2008 and
2015 for both China and South Korea, with 2015 emissions calculated at 4.3±2.7 and 0.36±0.11 Gg yr−1, respectively.
Emission estimates of NF3 from South Korea could be made with relatively
small uncertainty at 0.6±0.07 Gg yr−1 in 2015, which equates to
∼1.6 % of the country's CO2 emissions. We also apply
our method to calculate emissions of CHF3 (HFC-23) between 2008 and
2012, for which our results find good agreement with other studies and which
helps support our choice in methodology for CF4 and NF3.
Exploring hydrological similarity during soil moisture recession periods using time dependent variograms
Authors: Mälicke Mirko , Hassler Sibylle K. , Weiler Markus , Blume Theresa , Zehe Erwin
Published: September 2018

Abstract. This study proposes a new method for identifying temporally stable spatial patterns in soil moisture. Soil moisture patterns during rainfall-driven wetting conditions and during radiation-driven drying essentially reflect different processes with specific underlying controls. Consequently we expect that these patterns exhibit different covariance structures, and their spatial analysis should be separated accordingly. More specifically we hypothesize that: (H1): An ensemble of distributed soil moisture observations will converge to a rank-stable configuration during long-term drying periods and re-organize to stable ranks after disturbances; (H2): Variograms of these soil moisture ranks converge towards a stable configuration during drying periods, reflecting the covariance of the underlying time-invariant controls. These hypotheses were tested using soil moisture measurements which were recorded within the CAOS research unit in Luxembourg. We found evidence of stable rank configurations for time spans of several weeks. During rainfall events, these stable ranks were disturbed but later reorganized into the same pre-event configuration. Coupling time-shifting variograms with a density-based clustering algorithm enabled us to identify a convergence towards stable spatial variogram configurations. Moreover, the spatial organization of soil moisture showed preferred states with distinct patterns, depending on their respective drivers. This corroborates that the proposed method can be used to disentangle spatial structure originating from rainfall patterns from those controlled by the internal terrestrial system properties. Furthermore, we conclude that during stable states variogram aggregates originating from the density-based clustering could in principle be used for interpolation purposes, as they represent a temporally stable covariance. In contrast, an interpolation can be problematic while covariance is not stable in time. While the method has been developed and tested based on spatially distributed soil moisture data, it is also suitable for analyzing other state variables.
Evaluation of impacts of future climate change and water use scenarios on regional hydrology
Authors: Chang Seungwoo , Graham Wendy , Geurink Jeffrey , Wanakule Nisai , Asefa Tirusew
Published: September 2018

Abstract. General circulation models (GCMs) have been widely used to simulate current
and future climate at the global scale. However, the development of
frameworks to apply GCMs to assess potential climate change impacts on
regional hydrologic systems, ability to meet future water demand, and
compliance with water resource regulations is more recent. In this study
eight GCMs were bias-corrected and downscaled using the bias correction and
stochastic analog (BCSA) downscaling method and then used, together with
three ET0 methods and eight different water use scenarios, to drive an
integrated hydrologic model previously developed for the Tampa Bay region in
western central Florida. Variance-based sensitivity analysis showed that
changes in projected streamflow were very sensitive to GCM selection, but
relatively insensitive to ET0 method or water use scenario. Changes in
projections of groundwater level were sensitive to both GCM and water use
scenario, but relatively insensitive to ET0 method. Five of eight GCMs
projected a decrease in streamflow and groundwater availability in the future
regardless of water use scenario or ET method. For the business as usual
water use scenario all eight GCMs indicated that, even with active water
conservation programs, increases in public water demand projected for 2045
could not be met from ground and surface water supplies while achieving
current groundwater level and surface water flow regulations. With adoption
of 40 % wastewater reuse for public supply and active conservation four
of the eight GCMs indicate that 2045 public water demand could be met while
achieving current environmental regulations; however, drier climates would
require a switch from groundwater to surface water use. These results
indicate a high probability of a reduction in future freshwater supply in the
Tampa Bay region if environmental regulations intended to protect current
aquatic ecosystems do not adapt to the changing climate. Broad interpretation
of the results of this study may be limited by the fact that all future water
use scenarios assumed that increases in water demand would be the result of
intensification of water use on existing agricultural, industrial, and urban
lands. Future work should evaluate the impacts of a range of potential land
use change scenarios, with associated water use change projections, over a
larger number of GCMs.
Review article: Climate change impacts on dam safety
Authors: Fluixá-Sanmartín Javier , Altarejos-García Luis , Morales-Torres Adrián , Escuder-Bueno Ignacio
Published: September 2018

Abstract. Dams as well as protective dikes and levees are critical
infrastructures whose associated risk must be properly managed in a
continuous and updated process. Usually, dam safety management has been
carried out assuming stationary climatic and non-climatic conditions.
However, the projected alterations due to climate change are likely to affect
different factors driving dam risk. Although some reference institutions
develop guidance for including climate change in their decision support
strategies, related information is still vast and scattered and its
application to specific analyses such as dam safety assessments remains a
challenge. This article presents a comprehensive and multidisciplinary review of the
impacts of climate change that could affect dam safety. The global effect
can be assessed through the integration of the various projected effects
acting on each aspect of the risk, from the input hydrology to the
calculation of the consequences of the flood wave on population and assets at
risk. This will provide useful information for dam owners and dam safety
practitioners in their decision-making process.
Macroprudential Policy: Resolution and Continued Challenges
Authors: Tomic Igor M , Angelidis John
Published: September 2018

In this paper we address three issues; 1) The importance of knowing the exact damage caused by a failing firm, as that knowledge assists in creating more efficient policy responses. The failure of a large and complex financial firm, Lehman Brothers, experienced a very difficult and lengthy process in its resolution; the damage was much greater than expected, leading to a change in policies and specifically to a requirement for stress tests; 2) Macroprudential policies are very helpful as the can address issues in a specific sector, something that monetary policy is not designed for. This means that monetary policy designed to bring output and price stability, when combined with macroprudential tools, provides more financial stability; 3) Although macroprudential policies have stabilized the financial industry, some threats remain and therefore several threats are explored.
Perception of registered nurses and midwives on maternal health education in Nigeria
Authors: Nwankwo Clementina U. , Ezenwaka Chidum E.
Published: September 2018

Objective: To assess the views of Nigerian Nurses and Midwives on Maternal Health Education (MHE) and the barriers to its implementation.Methods: A total of 238 qualified nurses and midwives who participated in Mandatory Continuing Professional Development Programme (MCPDP) in South-eastern state of Nigeria voluntarily completed the self-administered research questionnaire. To avoid receiving duplicate copies of the questionnaires, all were serially numbered and all personal identifiers were removed. Of 348 participants that completed the questionnaires, only 238 met the inclusion criteria which included experience in antenatal clinics and qualifications in midwifery.Results: The majority of the study participants (86%) had both nursing and midwifery qualifications and the majority (98%) believed that MHE is beneficial to pregnant mothers particularly in reducing maternal morbidity and mortality (95.3%). A high percentage of the respondents (92%) agreed that MHE should be intensified for pregnant mothers in their work places. The identified major barriers to MHE include attitude of some health professionals (79%), some cultural practices (77%), inadequate economic resources (75%) and insufficient health personnel (71%). 18% of the respondents agreed that the hospital policy of their work places does not promote MHE.Conclusions: This study has demonstrated that nurses and midwives are aware of the importance of MHE in reducing maternal mortality and morbidity. There are still negative perceptions on the preparedness of the healthcare institutions towards MHE coupled with economic and cultural barriers. We recommend integrated MHE in the antenatal care plans of the pregnant woman.
Inheriting Possibility
Authors: Dixon-Román Ezekiel J.
Published: September 2018

Inheriting Possibility is concerned with the ways we have come to understand and produce knowledge about the reproduction of power relations and how those understandings have rested on a premise that nature is made of fixed universals that create the stage for the play of culture. It is said that “truth” exists in nature and that culture contaminates our access to these “truths.” It is argued that this same dualism underpins theories and research on inheritance, social reproduction, and human learning and development.
Given work in the physical and biological sciences and new materialist philosophy, it is not only argued that nature is culture but also that the assumed nature/culture binary has ultimately limited our understanding of how power relations are reproduced. Thus, Inheriting Possibility develops new arguments about the forces of inheritance (i.e., the double injunction and intra-action of material-discursive forces, timespace, and assemblages) and rethinks approaches to quantitative inquiry on social reproduction in education.
Inheriting Possibility delineates how the limitations of knowledge production have been due to the false assumptions about the possibilities of unlocking nature’s “truths” with quantification. It puts forward an alternative ontology, epistemology, and methodology that attempt to carve out a space within critical inquiry for quantitative methods. Inheriting Possibility empirically demonstrates how parenting practices and grandchild SAT performance are both results of myriad forces that are multigenerational, events, and material phenomena that cannot be reduced to pathology or deficiency but rather convey the inheritance of reconfiguring and enfolding historialities of differential patterns of possibility.
Feasibility of Implementing an Exercise Program in a Geriatric Assessment Unit: the SPRINT Program
Authors: Juneau Andréanne , Bolduc Aline , Nguyen Philippe , Leclerc Bernard-Simon , Rousseau Jacqueline , Dubé François , Ringuet Marie-Ève , Kergoat Marie-Jeanne
Published: September 2018

BackgoundAn exercise program involving patients, caregivers, and professionals, entitled SPecific Retraining in INTerdisciplinarity (SPRINT), has been developed to prevent functional decline during hospitalization of older patients.GoalAssess the feasibility of implementing SPRINT in the context of a Geriatric Assessment Unit (GAU).MethodsGAU’s health-care professionals were instructed with the SPRINT. All new patients were evaluated by a physiotherapist shortly after admission to validate the eligibility criteria and allocation category of exercises. Questionnaires on physical activities were filled out by professionals, patients, and caregivers at baseline and after intervention. Quantitative and qualitative information was collected on adherence to the program.ResultsSPRINT was applied to 19 of the 50 patients admitted during the three-month pilot study. A daily average of one exercise session per patient was performed, most frequently with a nurse (37%), physician (20%), care attendant (13%) or by the patient alone (22%). The caregivers participated only 4% of the time. Barriers and facilitators in applying SPRINT have been identified.ConclusionsSPRINT appears relevant and applicable within GAUs. Future studies should be conducted to assess its safety and effectiveness in preventing hospital-related functional decline.
Incorporation of Cervista Human Papillomavirus 16/18 Assay Into Algorithms for Classifying Human Papillomavirus Status in Formalin-Fixed, Paraffin-Embedded Head and Neck Squamous Carcinoma Specimens
Authors: Guo Ming , Khanna Abha , Wang Jianping , Williams Michelle D. , Kalhor Neda , Gong Yun , Xu Li , Sturgis Erich M. , Staerkel Gregg
Published: September 2018

Context.—

Human papillomavirus (HPV) DNA in situ hybridization (ISH) assay and p16 immunohistochemistry (IHC) are used to determine high-risk HPV status in formalin-fixed, paraffin-embedded (FFPE) tissues in oropharyngeal squamous cell carcinoma (SCC). Although high sensitivity and specificity for HPV can be obtained by combined p16 IHC and HPV DNA ISH, the occasional discrepancy between these assays has prompted evaluation of Cervista HPV assays in FFPE tissue from patients with oropharyngeal SCC.

Objective.—

To compare the efficacy of Cervista HPV 16/18 and Cervista HPV HR assay to that of HPV DNA ISH assay and p16 IHC in FFPE tissue in head and neck squamous cell carcinoma of oropharyngeal origin.

Design.—

Archived FFPE tissue from 84 patients with SCC of oropharyngeal origin and available HPV DNA ISH and p16 IHC test results were tested with the Cervista HPV 16/18 assay and further verified by polymerase chain reaction (PCR)–based HPV16/18 genotyping tests in cases with discrepancy.

Results.—

Of the 84 specimens, 75% (63 of 84) were positive and 16% (13 of 84) had discrepant or equivocal findings by p16 IHC and HPV DNA ISH testing. Use of Cervista HPV assays, either to clarify discrepant/equivocal findings or as confirmation after initial p16 IHC/HPV DNA ISH tests, identified 81% (68 of 84) of HPV-positive cases without equivocal HPV results. Five of 13 cases with discrepancy or equivocal HPV DNA ISH results tested positive for HPV16 or HPV18 by Cervista HPV 16/18 assay, which was further confirmed by PCR-based HPV 16/18 genotyping.

Conclusions.—

The Cervista HPV assays are a reasonable alternative to HPV DNA ISH in determining HPV status in FFPE tissue specimens from patients with oropharyngeal SCC.
Análisis de la evaluación y las prescripciones morales sobre el comportamiento de las mujeres líderes en la literatura managerial
Authors: Medina-Vicent María
Published: September 2018

El papel de las mujeres en el mundo de la gerencia parece haberse convertido en uno de los temas centrales de la agenda política y mediática actual. Una de las herramientas de difusión de los modelos de liderazgo asociados a dicho grupo es la literatura gerencial o managerial, que difunde modas de gestión empresarial entre la clase directiva y el público general. Con el objetivo de identificar si el modelo de liderazgo asociado a las mujeres se aleja del rol de género femenino tradicional, trataremos de identificar los valores que se les asignan a través de un análisis de la literatura managerial. Así pues, en el presente artículo se realizará una propuesta de aplicación metodológica de la Appraisal Theory para el estudio de la evaluación y las prescripciones morales contenidas en la literatura managerial.The role of women in management world seems to have become one of the central themes of the current political and media agenda. One of the dissemination tools of the leadership models associated with this group is the managerial literature, which spreads management fashions to the directive class and the general public. In order to identify if the roles assigned to women leaders move away from the traditional femenine gender stereotype, we will try to identify the values that are associated to them through an analysis of managerial literature. Thus, in the present article a proposal of methodological application of the Appraisal Theory will be made for the study of the moral prescriptions contained in the managerial literature.
”Urfolk” og ”mangfold” i skolens læreplaner
Authors: Olsen Torjer Andreas , Andreassen Bengt-Ove
Published: September 2018

Since 1974, the curriculum for the Norwegian school has had a overarching part that puts the school and its content into a bigger social and political context. As such, this part of the curriculum is a highly political and ideological text that expresses the state's purpose and interest related to the school. This article looks into how indigenous people, minorities and diversity is represented in the general part of the curriculum from 1974 to 2017. The changing curricula show changes in the official politics and views on diversity. Through an analysis of the curricula we explore which terms and concepts that are used in the description of people and groups in Norwegian society. We focus primarily on the representation of the Sami, who move from being people in "mixed language districts" with limited rights, via being an "ethnic minority", to being an indigenous people with a set of rights. Further, we look into how the diverse society is represented, from the use of "alien workers", via "immigrants", to just "diversity". We argue that the concepts or strategies of politics of recognition and politics of integration respectively can be used to describe the curricula. Norway's educational policy towards minorities and indigenous people seems to exist between these two. In the end, this leave diversity competence as an important concept in the future Norwegian school.
Towards computational reproducibility: researcher perspectives on the use and sharing of software
Authors: AlNoamany Yasmin , Borghi John A.
Published: September 2018

Research software, which includes both source code and executables used as part of the research process, presents a significant challenge for efforts aimed at ensuring reproducibility. In order to inform such efforts, we conducted a survey to better understand the characteristics of research software as well as how it is created, used, and shared by researchers. Based on the responses of 215 participants, representing a range of research disciplines, we found that researchers create, use, and share software in a wide variety of forms for a wide variety of purposes, including data collection, data analysis, data visualization, data cleaning and organization, and automation. More participants indicated that they use open source software than commercial software. While a relatively small number of programming languages (e.g., Python, R, JavaScript, C++, MATLAB) are used by a large number, there is a long tail of languages used by relatively few. Between-group comparisons revealed that significantly more participants from computer science write source code and create executables than participants from other disciplines. Differences between researchers from computer science and other disciplines related to the knowledge of best practices of software creation and sharing were not statistically significant. While many participants indicated that they draw a distinction between the sharing and preservation of software, related practices and perceptions were often not aligned with those of the broader scholarly communications community.
20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration
Authors: Thessen Anne E. , Poelen Jorrit H. , Collins Matthew , Hammock Jen
Published: September 2018

Biodiversity information is made available through numerous databases that each have their own data models, web services, and data types. Combining data across databases leads to new insights, but is not easy because each database uses its own system of identifiers. In the absence of stable and interoperable identifiers, databases are often linked using taxonomic names. This labor intensive, error prone, and lengthy process relies on accessible versions of nomenclatural authorities and fuzzy-matching algorithms. To approach the challenge of linking diverse data, more than technology is needed. New social collaborations like the Global Unified Open Data Architecture (GUODA) that combines skills from diverse groups of computer engineers from iDigBio, server resources from the Advanced Computing and Information Systems (ACIS) Lab, global-scale data presentation from EOL, and independent developers and researchers are what is needed to make concrete progress on finding relationships between biodiversity datasets. This paper will discuss a technical solution developed by the GUODA collaboration for faster linking across databases with a use case linking Wikidata and the Global Biotic Interactions database (GloBI). The GUODA infrastructure is a 12-node, high performance computing cluster made up of about 192 threads with 12 TB of storage and 288 GB memory. Using GUODA, 20 GB of compressed JSON from Wikidata was processed and linked to GloBI in about 10–11 min. Instead of comparing name strings or relying on a single identifier, Wikidata and GloBI were linked by comparing graphs of biodiversity identifiers external to each system. This method resulted in adding 119,957 Wikidata links in GloBI, an increase of 13.7% of all outgoing name links in GloBI. Wikidata and GloBI were compared to Open Tree of Life Reference Taxonomy to examine consistency and coverage. The process of parsing Wikidata, Open Tree of Life Reference Taxonomy and GloBI archives and calculating consistency metrics was done in minutes on the GUODA platform. As a model collaboration, GUODA has the potential to revolutionize biodiversity science by bringing diverse technically minded people together with high performance computing resources that are accessible from a laptop or desktop. However, participating in such a collaboration still requires basic programming skills.
Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013
Authors: Quinn Brady K.
Published: September 2018

This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs,Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 257 monthly environmental variables and performing stepwise multiple regression analyses. Crab densities in a given year were best explained by potential settlement during the summer and the maximum sea-surface temperature during March of the same year. However, potential roles of other factors (e.g., autumn winds, summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the area, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region.
Zooming into plant-flower visitor networks: an individual trait-based approach
Authors: Rumeu Beatriz , Sheath Danny J. , Hawes Joseph E. , Ings Thomas C.
Published: September 2018

Understanding how ecological communities are structured is a major goal in ecology. Ecological networks representing interaction patterns among species have become a powerful tool to capture the mechanisms underlying plant-animal assemblages. However, these networks largely do not account for inter-individual variability and thus may be limiting our development of a clear mechanistic understanding of community structure. In this study, we develop a new individual-trait based approach to examine the importance of individual plant and pollinator functional size traits (pollinator thorax width and plant nectar holder depth) in mutualistic networks. We performed hierarchical cluster analyses to group interacting individuals into classes, according to their similarity in functional size. We then compared the structure of bee-flower networks where nodes represented either species identity or trait sets. The individual trait-based network was almost twice as nested as its species-based equivalent and it had a more symmetric linkage pattern resulting from of a high degree of size-matching. In conclusion, we show that by constructing individual trait-based networks we can reveal important patterns otherwise difficult to observe in species-based networks and thus improve our understanding of community structure. We therefore recommend using both trait-based and species-based approaches together to develop a clearer understanding of the properties of ecological networks.
EIciRNA‐mediated gene expression: tunability and bimodality
Authors: Hu Qi , Zhou Tianshou
Published: September 2018

Biological experiments have verified that EIciRNAs (a class of circRNA) produced from pre‐mRNA can regulate gene expression, but the effect of regulation remains unexplored. Here, we refine a mechanistic gene model from experimental facts, in which we assume pre‐mRNA synthesizes EIciRNAs and mRNAs in a probabilistic manner, with the probability called the pathway strength, and the resulting EIciRNAs positively regulate the pre‐mRNA synthesis. We show that there is a critical pathway strength such that the mRNA mean and the mRNA noise reach the highest and lowest levels, respectively. The EIciRNA can induce the unimodal and bimodal mRNA expressions, as well as the transition between them. Our investigation hints that EIciRNA is a non‐negligible factor affecting cell‐to‐cell variability in gene expression.
Extending Near‐Term Emissions Scenarios to Assess Warming Implications of Paris Agreement NDCs
Authors: Gütschow Johannes , Jeffery Mairi Louise , Schaeffer Michiel , Hare Bill
Published: September 2018

In the Paris Agreement countries have agreed to act together to hold global warming well below 2°C over preindustrial levels and to pursue efforts to limit warming to 1.5°C. To assess if the world is on track to meet this long‐term temperature goal, countries' pledged emissions reductions (Nationally Determined Contributions, NDCs) need to be analyzed for their implied warming. Several research groups and nongovernmental organizations have estimated this warming and arrived at very different results but have invariably concluded that the current pledges are inadequate to hold warming below 2°C, let alone 1.5°C. In this paper we analyze different methods to estimate 2100 global mean temperature rise implied by countries' NDCs, which often only specify commitments until 2030. We present different methods to extend near‐term emissions pathways that have been developed by the authors or used by different research groups and nongovernmental organizations to estimate 21st century warming consequences of Paris Agreement commitments. The abilities of these methods to project both low and high warming scenarios in line with the scenario literature is assessed. We find that the simpler methods are not suitable for temperature projections while more complex methods can produce results consistent with the energy and economic scenario literature. We further find that some methods can have a strong high or low temperature bias depending on parameter choices. The choice of methods to evaluate the consistency of aggregated NDC commitments is very important for reviewing progress toward the Paris Agreement's long‐term temperature goal.
Mirror, Mirror: Learning to “Become” Together
Authors: Smith L. Shakiyla , Nicolaides Aliki
Published: September 2018

Intentional communities of inquiry can serve as important informal learning contexts for adults to grow their meaning‐making complexity and capacity to manage ambiguity through and in relationship.
Heterogeneity in association of remote herpesvirus infections and pediatric MS
Authors: Nourbakhsh Bardia , Rutatangwa Alice , Waltz Michael , Rensel Mary , Moodley Manikum , Graves Jennifer , Casper Theron Charles , Waldman Amy , Belman Anita , Greenberg Benjamin , Goyal Manu , Harris Yolanda , Kahn Ilana , Lotze Timothy , Mar Soe , Schreiner Teri , Aaen Gregory , Hart Janace , Ness Jayne , Rubin Jennifer , Tillema Jan‐Mendelt , Krupp Lauren , Gorman Mark , Benson Leslie , Rodriguez Moses , Chitnis Tanuja , Rose John , Candee Meghan , Weinstock‐Guttman Bianca , Shao Xiaorong , Barcellos Lisa , James Judith , Waubant Emmanuelle ,   On behalf of the US Network of Pediatric MS Centers
Published: September 2018

Objective

While prior Epstein–Barr virus (EBV) infection has been consistently associated with subsequent risk of developing multiple sclerosis (MS), the association with other common herpesviruses has been more controversial. Our objectives were to determine whether remote infection with EBV and other common herpesviruses affect the susceptibility to pediatric MS and if there are interactions between genetic and demographic factors and viral infections.

Methods

Cases with pediatric‐onset MS or clinically isolated syndrome within 4 years of disease onset, and controls were recruited from 16 American pediatric MS centers. Logistic regression models adjusted for potential confounders assessed the association between case status and serological evidence for past infection with EBV, cytomegalovirus (CMV), Herpes Simplex viruses‐1 (HSV‐1) and ‐2. We determined the heterogeneity of the effect of viral infection on the risk of having MS according to race, ethnicity and HLA‐DRB1:1501 status.

Results

A total of 356 pediatric cases and 493 controls were recruited. In multivariable models, EBV‐viral capsid antigen (VCA) seropositivity was associated with increased odds of having MS by 7.4 times (95% CI: 4.5–12.0, P < 0.001). Seropositivity for HSV‐1 was also associated with increased odds of having MS (OR 1.54, 95% CI: 1.06–2.25, P = 0.025) but this increase was seen only in Whites (OR = 2.18, 95% CI 1.35–3.52, P < 0.001) and those negative for HLA‐DRB1*1501 (OR = 1.89, 95% CI 1.17–3.03, P = 0.009). The effect of remote EBV infection on the risk of pediatric MS depended on race and HLA‐DRB1*15:01 status.

Interpretation

EBV seropositivity is strongly associated with pediatric MS, as is HSV‐1 seropositivity in subjects negative for HLA‐DRB1*15:01. Our report of interactions between select viral exposures, and age, race and DRB1 status suggests a complex effect of environmental and genetic risk factors on MS development.
Biopsy‐Proven Small‐Fiber Neuropathy in Primary Sjögren's Syndrome: Neuropathic Pain Characteristics, Autoantibody Findings, and Histopathologic Features
Authors: Birnbaum Julius , Lalji Aliya , Saed Aveen , Baer Alan N.
Published: September 2018

Objective

Painful small‐fiber neuropathies (SFNs) in primary Sjögren's syndrome (SS) may present as pure or mixed with concurrent large‐fiber involvement. SFN can be diagnosed by punch skin biopsy results that identify decreased intra‐epidermal nerve‐fiber density (IENFD) of unmyelinated nerves.

Methods

We compared 23 consecutively evaluated patients with SS with pure and mixed SFN versus 98 patients without SFN. We distinguished between markers of dorsal root ganglia (DRG) degeneration (decreased IENFD in the proximal thigh versus the distal leg) versus axonal degeneration (decreased IENFD in the distal leg versus the proximal thigh).

Results

There were no differences in pain intensity, pain quality, and treatment characteristics in the comparison of 13 patients with pure SFN versus 10 patients with mixed SFN. Ten patients with SFN (approximately 45%) had neuropathic pain preceding sicca symptoms. Opioid analgesics were prescribed to approximately 45% of patients with SFN. When compared to 98 patients without SFN, the 23 patients with SFN had an increased frequency of male sex (30% versus 9%; P < 0.01), a decreased frequency of anti–Ro 52 (P = 0.01) and anti–Ro 60 antibodies (P = 0.01), rheumatoid factor positivity (P < 0.01), and polyclonal gammopathy (P < 0.01). Eleven patients had stocking‐and‐glove pain, and 12 patients had nonstocking‐and‐glove pain. Skin biopsy results disclosed patterns of axonal (16 patients) and DRG injury (7 patients).

Conclusion

SS SFN had an increased frequency among male patients, a decreased frequency of multiple antibodies, frequent treatment with opioid analgesics, and the presence of nonstocking‐and‐glove pain. Distinguishing between DRG versus axonal injury is significant, especially given that mechanisms targeting the DRG may result in irreversible neuronal cell death. Altogether, these findings highlight clinical, autoantibody, and pathologic features that can help to define mechanisms and treatment strategies.
Engineering Neural Tissue from Human Pluripotent Stem Cells Using Novel Small Molecule Releasing Microspheres
Authors: De la Vega Laura , Karmirian Karina , Willerth Stephanie Michelle
Published: September 2018

Here a novel technique for engineering neural tissue consisting of motor neurons by combining human‐induced pluripotent stem cells (hiPSCs) with small molecules releasing microspheres is demonstrated. First, the small molecule purmorphamine (puro) is successfully encapsulated into poly ε‐caprolactone (PCL) microspheres using a single emulsion oil‐in‐water (o/w) method for the first time with an efficiency of (84% ± 2.12%). These microspheres release 91% ± 1.7% of the encapsulated puro in a controlled fashion over 46 days. Puro microspheres, along with previously characterized retinoic acid (RA) releasing microspheres, are then incorporated into hiPSC aggregates to engineer neural tissue. The combination of puro and RA microspheres promotes hiPSC differentiation as indicated by the expression of multiple neural markers, including the neuronal marker β‐tubulin III (βT‐III), and the transcription factor Olig2 (7.69 ± 8.38%) on day 28. These tissues express the motor neuron marker HB9 (24.85 ± 4.51%) on day 35, and the mature motor neuron marker ChaT (12.35 ± 4.17%) on day 60. These engineered tissues can be used for regenerative medicine applications such as treating spinal cord injury (SCI), disease modeling, and drug screening.
Subtractive Manufacturing of Microfluidic 3D Braid Mixers
Authors: Salieb‐Beugelaar Georgette Bernice , Liu Kegang , Hunziker Patrick
Published: September 2018

Subtractive manufacturing using the thread template approach is an emerging technique for rapid prototyping of complex, true 3D microfluidic systems, offering advantages to photolithography in terms of process complexity, and achieving excellent structure fidelity compared to 3D printing and micro‐milling. This paper explores subtractive manufacturing for novel high‐performance microfluidic 3D braid mixers. The broad freedom of design with subtractive manufacturing, that is achievable with minimal process complexity is exploited to study the impact of design parameters of such braid mixers on mixing performance. The braid mixer is compared by computational fluid dynamics and experimentally with a number of existing mixer designs using colorimetric chemical reactions. The use of a braid mixer in a streamlined production of nanomaterials in a multistep procedure, shows highly competitive performance compared to other microfluidic designs and nanoparticle assembly methods.