bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geological surveys as research-focused organizations: New Zealand's experience and opportunities
Authors: Rattenbury Mark , Jolly Gill , Benfell Peter , Smillie Robert 
Published: November 2019

Abstract
GNS Science is New Zealand's geological survey with an applied earth science research focus yet without traditional government department accountabilities. As one of New Zealand's Crown Research Institutes established in 1992, GNS Science is owned by the New Zealand Government but has higher levels of self-determination, fiscal independence and impartiality than a government department. Securing competitive research funding and commissioned research is a business imperative and because of this the institute is able to respond and adapt to changing societal expectations. GNS Science can also influence outcomes based on its discretionary research investment. New Zealand's geological setting astride an active plate boundary attracts many international partners endeavouring to better understand geological processes in an accessible and logistically well-resourced natural laboratory. Partnerships like these substantially increase technological and financial resources and these enable diverse and often ambitious projects.
Real‐World Associations of Renin–Angiotensin–Aldosterone System Inhibitor Dose, Hyperkalemia, and Adverse Clinical Outcomes in a Cohort of Patients With New‐Onset Chronic Kidney Disease or Heart Failure in the United Kingdom
Authors: Linde Cecilia , Bakhai Ameet , Furuland Hans , Evans Marc , McEwan Phil , Ayoubkhani Daniel , Qin Lei 
Published: November 2019

Background

Dosing of renin–angiotensin–aldosterone system inhibitors (
RAAS
i) may be modified to manage associated hyperkalemia risk; however, this approach could adversely affect cardiorenal outcomes. This study investigated real‐world associations of
RAAS
i dose, hyperkalemia, and adverse clinical outcomes in a large cohort of
UK
cardiorenal patients.

Methods and Results

This observational study included
RAAS
i‐prescribed patients with new‐onset chronic kidney disease (n=100 572) or heart failure (n=13 113) first recorded between January 2006 and December 2015 in Clinical Practice Research Datalink and linked Hospital Episode Statistics databases. Odds ratios associating hyperkalemia and
RAAS
i dose modification were estimated using logistic generalized estimating equations with normal (<5.0 mmol/L) serum potassium level as the reference category. Patients with serum potassium ≥5.0 mmol/L had higher risk of
RAAS
i down‐titration (adjusted odds ratios, chronic kidney disease: 1.79 [95%
CI
, 1.64–1.96]; heart failure: 1.33 [95% CI, 1.08–1.62]). Poisson models were used to estimate adjusted incident rate ratios of adverse outcomes based on total
RAAS
i exposure (<50% and ≥50% of the guideline‐recommended
RAAS
i dose). Incidence of major adverse cardiac events and mortality was consistently higher in the lower dose group (adjusted incident rate ratios: chronic kidney disease: 5.60 [95% CI, 5.29–5.93] for mortality and 1.60 [95% CI, 1.55–1.66] for nonfatal major adverse cardiac events; heart failure: 7.34 [95% CI, 6.35–8.48] for mortality and 1.85 [95% CI, 1.71–1.99] for major adverse cardiac events).

Conclusions

The results of this real‐world analysis highlight the potential negative impact of suboptimal
RAAS
i dosing and the need for strategies that allow patients to be maintained on appropriate therapy, avoiding
RAAS
i dose modification or discontinuation.
Risk of New‐Onset Atrial Fibrillation Among Asian Chronic Hepatitis C Virus Carriers: A Nationwide Population‐Based Cohort Study
Authors: Yang Yao‐Hsu , Chiang Hsin‐Ju , Yip Hon‐Kan , Chen Ko‐Jung , Chiang John Y. , Lee Mel S. , Sung Pei‐Hsun 
Published: November 2019

Background

Hepatitis C virus (
HCV
) infection not only links closely to systemic inflammation but also has numerous extrahepatic manifestations. Chronic inflammation also increases the risk of new‐onset atrial fibrillation (AF). However, little is known regarding the clinical association between
HCV
infection and new‐onset AF.

Methods and Results

We conducted a population‐based cohort study using Taiwan's National Health Insurance Research Database during 1997 to 2013. A total of 11 771
HCV
‐infected patients were included in this study, and each of them was matched in a ratio of 1:4. Because of higher mortality among
HCV
cohorts, we used both Cox proportional hazard regression and competing risk regression models to compute the hazard ratios accompanying 95%
CI
s after adjustment for relevant confounder. The results demonstrated that the patients with chronic
HCV
infection had significantly higher incidence rate (332.0 versus 265.8 in 100 000 person‐years,
P
<0.0001) of new‐onset AF compared with the non‐
HCV
population. The adjusted hazard ratio of
HCV
for new‐onset AF was 1.32 (95%
CI
, 1.20–1.44;
P
<0.0001) and 1.20 (95%
CI,
1.10–1.31;
P
=0.0001) while calculated with Cox proportional hazard regression model and competing risk model, respectively. Intriguingly, we observed that the patients with HCV treated with antiviral agents had significantly lower incidental
AF
than those without anti‐
HCV
treatment (1.2% versus 6.0%;
P
<0.0001).

Conclusions

Chronic
HCV
infection was associated with an increased risk of incidental
AF
probably through sharing common pathology of chronic inflammation. Furthermore, a well‐designed study is needed to clarify whether anti‐
HCV
therapy can provide protection against the occurrence of
AF
.
Spirit Ecologies and Customary Governance in Post-conflict Timor-Leste
Authors: Palmer Lisa , McWilliam Andrew 
Published: November 2019

Abstract
In post-conflict Timor-Leste, the concepts of spirit ecologies and intergenerational wellbeing direct our attention to the ways in which Timorese people derive strength from house-based family networks as well as protective and productive spiritual relations with living nature. These practices of exchange resonate with a comparative body of research that has described similar ‘spiritscapes’ elsewhere in Southeast Asia and their relevance for social and environmental governance. Exploring the diverse ontologies of particular Timorese ‘spirit ecologies’ and their embedding in a concept of more-than-human ‘intergenerational wellbeing’, in this article we investigate the renewed significance of these ‘house-based’ practices for social and environmental governance in Timor-Leste. We argue that despite the challenges, multiple engagements of mutually appropriated, transgenerational debt obligations and ritually regulated forms of resource governance are emerging as cultural, and increasingly state-sanctioned, strategies aimed at rebuilding the social and environmental commons.
More on the Taṇḍa in Old Javanese Literature
Authors: Acri Andrea 
Published: November 2019

Abstract
This article adds to the discussion on the figure of the taṇḍa in Old Javanese literature, recently revived by Jiří Jákl in ‘The figure of the taṇḍa in Old Javanese literary and epigraphical records’, published in Bijdragen 175 (2019). In this contribution, the author clarifies his position on some points criticized by Jákl, and adds a few more thoughts on the elusive taṇḍa.
Asylum Seekers’ and Refugees’ Decision-Making in Transit in Indonesia
Authors: Missbach Antje 
Published: November 2019

Abstract
Asylum seekers and refugees currently living in Indonesia tend to see Indonesia as a transit rather than a destination country, despite the fact that their stays are increasing in length. Based on contact with Muhamad (not his real name), a young refugee from Iran currently residing in Indonesia whose adjustment and development I observed over four years, I illustrate the changing priorities in his decision-making, the constant flux of circumstances and context, and the extreme complexity of primary and secondary factors that come into play in planning for the future. Combining a macro perspective with a case study, in which I present excerpts from several life-story interviews, helps to exemplify these generic migratory challenges and distil a range of relevant parameters that influence the decision-making of asylum seekers and refugees in transit. A (self-)critical reflection on ethical and methodological challenges underpins my analysis and argument, not least because politicians and policymakers are increasingly interested in influencing migratory decision-making processes to gain political advantage. Of particular interest in my analysis is the role of Australia’s deterrence policies in asylum seekers’ decision-making. Despite the ethical challenges associated with studying migratory decision-making—as public knowledge of migration strategies can also suppress aspirations of mobility—I argue for more in-depth and longitudinal research. At the very least, this is because more intensive, yet considerate studies of decision-making will help us to take seriously the migratory aspirations of people with limited choices.
<p class="HeadingRunIn"><strong>The ontogeny of parapodia and setae in <em>Laeonereis culveri</em> (Webster) (Polychaeta: Nereididae)</strong></p>
Authors: MAZURKIEWICZ MICHAEL 
Published: November 2019

The ontogeny of parapodia on the first four larval trunk segments was followed toward maturity in the nereidid Laeonereis culveri. The morphologies ultimately attained by the parapodia include cephalic, uniramous, and biramous forms. Setal types and arrangements were also determined for all setigers present on discrete life history stages from larva to adult. The results showed pronounced differences in parapodial morphology and setation between larvae, postlarval juveniles, and adults. These differences stem from the sequential development of parapodial processes and setae. Taxonomists rely heavily on adult setation and parapodial morphology to characterize nereidid species, but since these features vary ontogenetically, their adult states cannot be used to distinguish species during earlier life history phases.
<strong>Polychaete fauna in the vicinity of bluefin tuna sea-cages in Ensenada, Baja California, Mexico</strong>
Authors: DÍAZ-CASTAÑEDA VICTORIA , VALENZUELA-SOLANO SANTIAGO 
Published: November 2019

This paper describes the polychaete fauna in Salsipuedes Bay, Baja California. Sea-cage farming results in a rain of organic matter onto the underlying benthos. There is growing concern over the effects of tuna sea-cages on the local sediment chemistry and benthic communities. Eighteen stations were sampled with a Van Veen grab (0.1 m2) from the oceanographic vessel Francisco de Ulloa in March 2003 and October 2004. Redox potential in 2003 ranged between ‑113 and ‑200 mV, while in 2004 it ranged between ‑110 and ‑302 mV. Organic carbon concentrations varied between 0.20% and 2.53 %, lowest values were located in the southern part of the bay; highest concentrations were found at stations 18–22 situated in the northern section, west of the tuna pens. Organic N varied between 0.02% and0.12%, highest concentrations (0.07–0.12%) were located at stations 16–21 in the northern section of the bay; stations situated at the south and near the coast presented the lowest N concentrations (0.02–0.04%). A total of 9,291 organisms belonging to seven phyla were collected: Polychaeta, Mollusca, Crustacea, Echinodermata, Cnidaria, Sipuncula, and Bryozoa. Polychaetes accounted for 62% of all invertebrate macrofauna, with 5,765 specimens representing 34 families and 146 species. The best represented families in 2003 and 2004 were Paraonidae, Cirratulidae, Spionidae, Capitellidae, Syllidae, Nephtyidae, Lumbrineridae, and Glyceridae. Polychaetes were dominant at almost all sampling stations. Families with the highest species richness were Paraonidae (14 spp.), Spionidae (11 spp.), Onuphidae (11 spp.), Maldanidae (10 spp.), Syllidae (9 spp.), Cirratulidae and Ampharetidae with 7 species each. Among the most abundant species were Aphelochaeta multifilis, Mediomastus ambiseta, Prionospio steenstrupi Spiophanes bombyx, Apoprionospio pygmaea, Paraonella sp., Monticellina sp., Aricidea (Allia) ramosa, Spiophanes bombyx, Spiophanes duplex, and Levinsenia gracilis. The dominant trophic group was deposit-feeders, followed by carnivores. In 2003 Shannon index varied between 2.26 and 3.40 bits/ind.; the highest diversity values were found in the southern section of Salsipuedes Bay. In 2004 diversity fluctuated between 2.31and 3.35; the highest values were found at three stations in the northern section south of the tuna pens. Stress-predictability modeling characterized 85% of stations in 2003 and 78% in 2004 as presenting favorable and stable conditions, the rest were considered moderately disturbed. Non-metric multidimensional scaling (MDS) separated stations depending on the distance to the tuna pens. Our results indicate that Salsipuedes Bay is still a favorable environment for polychaetes. Apparently local circulation has at least partially dispersed the excess organic matter.
<strong>Tetranychidae of China: a review of progress, with a checklist</strong>
Authors: HONG XIAO-YUE , ZHANG ZHI-QIANG , LI GUO-QING 
Published: November 2019

This paper reviews the research on the family Tetranychidae in China, with an updated checklist of 212 species belonging to 28 genera. Major contributions to the Chinese fauna of the Tetranychidae were made by Wang Hui-Fu and her colleagues who discovered and described about 40 species, Ma En-Pei and Yuan Yi-Lan who discovered over 30 species, and Tseng Yi-Hsiung and his co-authors who added over 20 new species. There have been a lot of studies on the biology and control of the spider mites in China and recent studies are briefly reviewed.
<p class="HeadingRunIn"><strong>The <em>Trichoptera Literature Database</em>: a collaborative bibliographic resource for world caddisfly research</strong></p>
Authors: K. Mendez Patina , Holzenthal Ralph W. , Steiner Joshua W. H. 
Published: November 2019

In addition to a list of valid names and synonyms, as provided by the Trichoptera World Checklist, access to the primary literature itself is essential for research in Trichoptera taxonomy and systematics. To improve access to bibliographic information, we established the Trichoptera Literature Database, http://www.trichopteralit.umn.edu, a bibliographic database of over 8,500 citations of literature on Trichoptera. In addition to compiling bibliographical information, we provided access to over 450 high quality Portable Document Format files (PDFs) of historically important, rare, or out-of-print older works as well as more current literature. To provide universal web access to this bibliographical resource, we constructed a dynamic, custom-designed, web application (PHP, Symfony framework) created to import Extensible Markup Language (XML) from the EndNote data file. The database allows the user to search by author and year of publication, displays citations in a standard bibliographic format, and provides download links to available PDF literature. Existing bibliographies of Trichoptera literature and online access to Zoological Record databases were used to accumulate citations. Protocols for scanning literature, issues regarding copyright, and procedures for uploading citations and PDFs to the database are established. We hope to create a collaborative framework of contributors by seeking regional, subject, or language organizers from the community of Trichoptera workers to assist in completing and maintaining this resource with the goal of lowering barriers to efficient access to taxonomic information.
C-fibers may modulate adjacent Aδ-fibers through axon-axon CGRP signaling at nodes of Ranvier in the trigeminal system
Authors: Edvinsson Jacob C. A. , Warfvinge Karin , Krause Diana N. , Blixt Frank W. , Sheykhzade Majid , Edvinsson Lars , Haanes Kristian A. 
Published: November 2019

Abstract

Background
Monoclonal antibodies (mAbs) towards CGRP or the CGRP receptor show good prophylactic antimigraine efficacy. However, their site of action is still elusive. Due to lack of passage of mAbs across the blood-brain barrier the trigeminal system has been suggested a possible site of action because it lacks blood-brain barrier and hence is available to circulating molecules. The trigeminal ganglion (TG) harbors two types of neurons; half of which store CGRP and the rest that express CGRP receptor elements (CLR/RAMP1).

Methods
With specific immunohistochemistry methods, we demonstrated the localization of CGRP, CLR, RAMP1, and their locations related to expression of the paranodal marker contactin-associated protein 1 (CASPR). Furthermore, we studied functional CGRP release separately from the neuron soma and the part with only nerve fibers of the trigeminal ganglion, using an enzyme-linked immunosorbent assay.

Results
Antibodies towards CGRP and CLR/RAMP1 bind to two different populations of neurons in the TG and are found in the C- and the myelinated Aδ-fibers, respectively, within the dura mater and in trigeminal ganglion (TG). CASPR staining revealed paranodal areas of the different myelinated fibers inhabiting the TG and dura mater. Double immunostaining with CASPR and RAMP1 or the functional CGRP receptor antibody (AA58) revealed co-localization of the two peptides in the paranodal region which suggests the presence of the CGRP-receptor. Double immunostaining with CGRP and CASPR revealed that thin C-fibers have CGRP-positive boutons which often localize in close proximity to the nodal areas of the CGRP-receptor positive Aδ-fibers. These boutons are pearl-like synaptic structures, and we show CGRP release from fibers dissociated from their neuronal bodies. In addition, we found that adjacent to the CGRP receptor localization in the node of Ranvier there was PKA immunoreactivity (kinase stimulated by cAMP), providing structural possibility to modify conduction activity within the Aδ-fibers.

Conclusion
We observed a close relationship between the CGRP containing C-fibers and the Aδ-fibers containing the CGRP-receptor elements, suggesting a point of axon-axon interaction for the released CGRP and a site of action for gepants and the novel mAbs to alleviate migraine.
PyBDA: a command line tool for automated analysis of big biological data sets
Authors: Dirmeier Simon , Emmenlauer Mario , Dehio Christoph , Beerenwinkel Niko 
Published: November 2019

AbstractBackgroundAnalysing large and high-dimensional biological data sets poses significant computational difficulties for bioinformaticians due to lack of accessible tools that scale to hundreds of millions of data points.ResultsWe developed a novel machine learning command line tool called PyBDA for automated, distributed analysis of big biological data sets. By using Apache Spark in the backend, PyBDA scales to data sets beyond the size of current applications. It uses Snakemake in order to automatically schedule jobs to a high-performance computing cluster. We demonstrate the utility of the software by analyzing image-based RNA interference data of 150 million single cells.ConclusionPyBDA allows automated, easy-to-use data analysis using common statistical methods and machine learning algorithms. It can be used with simple command line calls entirely making it accessible to a broad user base. PyBDA is available athttps://pybda.rtfd.io.
A simple, fast and reliable scan-based technique as a novel approach to quantify intracellular bacteria
Authors: Sarshar Meysam , Scribano Daniela , Tranquilli Giulia , Di Pietro Marisa , Filardo Simone , Zagaglia Carlo , Sessa Rosa , Palamara Anna Teresa , Ambrosi Cecilia 
Published: November 2019

Abstract

Background
Quantification of intracellular bacteria is fundamental in many areas of cellular and clinical microbiology to study acute and chronic infections. Therefore, rapid, accurate and low-cost methods represent valuable tools in determining bacterial ability to persist and proliferate within eukaryotic cells.

Results
Herein, we present the first application of the immunofluorescence In-Cell Western (ICW) assay aimed at quantifying intracellular bacteria in in vitro infection models. The performance of this new approach was evaluated in cell culture infection models using three microorganisms with different lifestyles. Two facultative intracellular bacteria, the fast-growing Shigella flexneri and a persistent strain of Escherichia coli, as well as the obligate intracellular bacterium Chlamydia trachomatis were chosen as bacterial models. The ICW assay was performed in parallel with conventional quantification methods, i.e. colony forming units (CFUs) and inclusion forming units (IFUs). The fluorescence signal intensity values from the ICW assay were highly correlated to CFU/IFUs counting and showed coefficients of determination (R2), ranging from 0,92 to 0,99.

Conclusions
The ICW assay offers several advantages including sensitivity, reproducibility, high speed, operator-independent data acquisition and overtime stability of fluorescence signals. All these features, together with the simplicity in performance, make this assay particularly suitable for high-throughput screening and diagnostic approaches.
Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis
Authors: Zhang Peng , Zhong Kaizhen , Zhong Zhengzheng , Tong Hanhua 
Published: November 2019

AbstractBackgroundThe genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice.ResultsGenome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting’s core collection constructed from 2262 Ting’s collections with more than 3.8 million SNPs. Within Ting’s core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes likeNRAT1, ART1andSTAR1were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance.ConclusionsThe present study provided important information for further using these elite genes existing in Ting’s core collection for improvement of rice Al tolerance.