bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interoperable genetic lab test reports: mapping key data elements to HL7 FHIR specifications and professional reporting guidelines
Authors: Khalifa Aly , Mason Clinton C , Garvin Jennifer Hornung , Williams Marc S , Del Fiol Guilherme , Jackson Brian R , Bleyl Steven B , Alterovitz Gil , Huff Stanley M 
Published: September 2021

Abstract

Objective
In many cases, genetic testing labs provide their test reports as portable document format files or scanned images, which limits the availability of the contained information to advanced informatics solutions, such as automated clinical decision support systems. One of the promising standards that aims to address this limitation is Health Level Seven International (HL7) Fast Healthcare Interoperability Resources Clinical Genomics Implementation Guide-Release 1 (FHIR CG IG STU1). This study aims to identify various data content of some genetic lab test reports and map them to FHIR CG IG specification to assess its coverage and to provide some suggestions for standard development and implementation.

Materials and Methods
We analyzed sample reports of 4 genetic tests and relevant professional reporting guidelines to identify their key data elements (KDEs) that were then mapped to FHIR CG IG.

Results
We identified 36 common KDEs among the analyzed genetic test reports, in addition to other unique KDEs for each genetic test. Relevant suggestions were made to guide the standard implementation and development.

Discussion and Conclusion
The FHIR CG IG covers the majority of the identified KDEs. However, we suggested some FHIR extensions that might better represent some KDEs. These extensions may be relevant to FHIR implementations or future FHIR updates.
The FHIR CG IG is an excellent step toward the interoperability of genetic lab test reports. However, it is a work-in-progress that needs informative and continuous input from the clinical genetics’ community, specifically professional organizations, systems implementers, and genetic knowledgebase providers.
Deep significance clustering: a novel approach for identifying risk-stratified and predictive patient subgroups
Authors: Huang Yufang , Liu Yifan , Steel Peter A D , Axsom Kelly M , Lee John R , Tummalapalli Sri Lekha , Wang Fei , Pathak Jyotishman , Subramanian Lakshminarayanan , Zhang Yiye 
Published: September 2021

Abstract

Objective
Deep significance clustering (DICE) is a self-supervised learning framework. DICE identifies clinically similar and risk-stratified subgroups that neither unsupervised clustering algorithms nor supervised risk prediction algorithms alone are guaranteed to generate.

Materials and Methods
Enabled by an optimization process that enforces statistical significance between the outcome and subgroup membership, DICE jointly trains 3 components, representation learning, clustering, and outcome prediction while providing interpretability to the deep representations. DICE also allows unseen patients to be predicted into trained subgroups for population-level risk stratification. We evaluated DICE using electronic health record datasets derived from 2 urban hospitals. Outcomes and patient cohorts used include discharge disposition to home among heart failure (HF) patients and acute kidney injury among COVID-19 (Cov-AKI) patients, respectively.

Results
Compared to baseline approaches including principal component analysis, DICE demonstrated superior performance in the cluster purity metrics: Silhouette score (0.48 for HF, 0.51 for Cov-AKI), Calinski-Harabasz index (212 for HF, 254 for Cov-AKI), and Davies-Bouldin index (0.86 for HF, 0.66 for Cov-AKI), and prediction metric: area under the Receiver operating characteristic (ROC) curve (0.83 for HF, 0.78 for Cov-AKI). Clinical evaluation of DICE-generated subgroups revealed more meaningful distributions of member characteristics across subgroups, and higher risk ratios between subgroups. Furthermore, DICE-generated subgroup membership alone was moderately predictive of outcomes.

Discussion
DICE addresses a gap in current machine learning approaches where predicted risk may not lead directly to actionable clinical steps.

Conclusion
DICE demonstrated the potential to apply in heterogeneous populations, where having the same quantitative risk does not equate with having a similar clinical profile.
Use of machine learning to transform complex standardized nursing care plan data into meaningful research variables: a palliative care exemplar
Authors: Macieira Tamara G R , Yao Yingwei , Keenan Gail M 
Published: September 2021

Abstract
The aim of this article was to describe a novel methodology for transforming complex nursing care plan data into meaningful variables to assess the impact of nursing care. We extracted standardized care plan data for older adults from the electronic health records of 4 hospitals. We created a palliative care framework with 8 categories. A subset of the data was manually classified under the framework, which was then used to train random forest machine learning algorithms that performed automated classification. Two expert raters achieved a 78% agreement rate. Random forest classifiers trained using the expert consensus achieved accuracy (agreement with consensus) between 77% and 89%. The best classifier was utilized for the automated classification of the remaining data. Utilizing machine learning reduces the cost of transforming raw data into representative constructs that can be used in research and practice to understand the essence of nursing specialty care, such as palliative care.
Electrical polarity-dependent gating and a unique subconductance of RyR2 induced by S-adenosyl methionine via the ATP binding site
Authors: Kampfer Angela J , Balog Edward M 
Published: September 2021

Abstract
S-Adenosyl-L-methionine (SAM) was used to probe the functional effects exerted via the cardiac RyR isoform (RyR2) adenine nucleotide binding site. Single channel experiments revealed that SAM applied to the cytoplasmic face of RyR2 had complex voltage dependent effects on channel gating and conductance. At positive transmembrane holding potentials, SAM caused a striking reduction in channel openings and a reduced channel conductance. In contrast, at negative potentials, SAM promoted a clearly resolved subconductance state. At membrane potentials between −75 and −25 mV, the open probability of the subconductance state was independent of voltage. ATP, but not the non-adenosine-based ryanodine receptor (RyR) activator 4-chloro-m-cresol, interfered with the effects of SAM at both negative and positive potentials. This suggests that ATP and SAM interact with a common binding site. Molecular docking showed SAM bound to the adenine nucleotide binding site and formed a hydrogen bond to Glu4886 in the C-terminal end of the S6 alpha helix. In this configuration, SAM may alter the conformation of the RyR2 ion conduction pathway. This work provides novel insight into potential functional outcomes of ligand binding to the RyR adenine nucleotide binding site.
Lemur tail kinase 1 (LMTK1) regulates the endosomal localization of β-secretase BACE1
Authors: Komaki Keisuke , Takano Tetsuya , Sato Yutaka , Asada Akiko , Ikeda Shikito , Yamada Kaoru , Wei Ran , Huo Anni , Fukuchi Aoi , Saito Taro , Ando Kanae , Murayama Shigeo , Araki Wataru , Kametani Fuyuki , Hasegawa Masato , Iwatsubo Takeshi , Tomomura Mineko , Fukuda Mitsunori , Hisanaga Shin-ichi 
Published: September 2021

AbstractLemur tail kinase 1 (LMTK1), previously called apoptosis-associated tyrosine kinase (AATYK), is an endosomal Ser/Thr kinase. We recently reported that LMTK1 regulates axon outgrowth, dendrite arborization and spine formation via Rab11-mediated vesicle transport. Rab11, a small GTPase regulating recycling endosome trafficking, is shown to be associated with late-onset Alzheimer’s disease (LOAD). In fact, genome-wide association studies identified many proteins regulating vesicle transport as risk factors for LOAD. Furthermore, LMTK1 has been reported to be a risk factor for frontotemporal dementia. Then, we hypothesized that LMTK1 contributes to AD development through vesicle transport and examined the effect of LMTK1 on the cellular localization of AD-related proteins, amyloid precursor protein (APP) and β-site APP cleaving enzyme 1 (BACE1). The β-cleavage of APP by BACE1 is the initial and rate-limiting step in Aβ generation. We found that LMTK1 accumulated BACE1, but not APP, to the perinuclear endosomal compartment, whereas the kinase-negative(kn) mutant of LMTK1A did not. The β-C-terminal fragment was prone to increase under overexpression of LMTK1A kn. Moreover, the expression level of LMTK1A was reduced in AD brains. These results suggest the possibility that LMTK1 is involved in AD development through the regulation of the proper endosomal localization of BACE1.
Relative growth ofEurynolambrus australisH. Milne Edwards & Lucas, 1841 (Decapoda: Brachyura: Majidae): use of epibionts to interpret moulting patterns and maturation
Authors: McLay Colin L , Woods Chris M C 
Published: September 2021

AbstractMales of the brachyuran crab Eurynolambrus australisH. Milne Edwards & Lucas, 1841 have three phases of growth recognizable by breaks in relative growth in the chelipeds in relation to carapace width. Females have two growth phases marked by increased abdomen width and pleopod length at sexual maturity. The difference between the maximum size of E. australis and the maximum size of the preceding phase in both sexes is large and may not be achieved in a single moult, suggesting that post-pubertal moulting could occur. Relative growth could involve both growth- and size-allometry. This is supported to some extent by the distribution of spirorbid tube worms. The lack of correlation between number and size of tube worms and crab carapace width suggests that epibionts do not accumulate over time. Crabs without attached tube worms (suggesting recent moulting) occur in all growth phases, but some of these may have recently moulted. Some large specimens, however, do carry a load of epibionts large enough to suggest terminal moulting. The possibility of post-pubertal moulting remains an open question.
Technical Features of Asynchronous and Synchronous Community Platforms and their Effects on Community Cohesion: A Comparative Study of Forum-based and Chat-based Online Mental Health Communities
Authors: Li Han , Kraut Robert E , Zhu Haiyi 
Published: September 2021

AbstractAcross online support communities, community cohesion varies by platform and can impact the self-disclosure of members and their exchanges of social support. Through a comparative study of forum and chat-based mental health communities, this research examines how technical features of both platforms influence community cohesion by affecting communication patterns among members, including evenness of communication, speed of communication, and number of participants. This study collected four weeks of data from 20 forum-based and 20 chat-based mental health communities in mainland China. Multilevel mediation analyses show that chat-based communities were more cohesive with higher member retention, network connectedness, and language conformity. Chat-based platforms facilitated faster communication and greater evenness of receiving messages among participants which in turn fostered community cohesion.
De novo RNA-Seq and Annotation of Sesquiterpenoid and Ecdysteroid Biosynthesis Genes and MicroRNAs in a Spider MiteEotetranychus kankitus
Authors: Li Gang , Zhang Jun , Liu Xun-Yan , Niu Jinzhi , Wang Jin-Jun 
Published: September 2021

AbstractEotetranychus kankitus is an important mite pest in citrus, but molecular data on the developmental processes of E. kankitus are lacking. The different development stages mix of E. kankitus was used to sequence for transcriptome and small RNAs to identify genes and predict miRNAs associated with sesquiterpenoid and ecdysteroid biosynthesis and signaling pathways. More than 36 million clean reads were assembled and 67,927 unigenes were generated. Of the unigenes, 19,300 were successfully annotated through annotation databases NR, SwissProt, COG, GO, KEGG, PFAM, and KOG. The transcripts were involved in sesquiterpenoid biosynthesis (11 genes) and ecdysteroid biosynthesis and signaling pathway (13 genes). Another, small RNA library was obtained and 31 conserved miRNAs were identified. Five most abundant miRNAs were Ek-miR-5735, Ek-miR-1, Ek-miR-263a, Ek-miR-184, and Ek-miR-8. The target genes related to sesquiterpenoid and ecdysteroid showed that 10 of the conserved miRNAs could potentially target the sesquiterpenoid and ecdysteroid pathway according to four-prediction software, sRNAT, miRanda, RNAhybrid, and Risearch2. Thus, the results of this study will provide bioinformatics information for further molecular studies of E. kankitus which may facilitate improved pest control strategies.
Comparative Capture ofTrogoderma granarium(Coleoptera: Dermestidae) andT. variabilein Floor Traps in Single Species Releases With Previously Captured Conspecific or Heterospecific Individuals
Authors: Gourgouta Marina , Baliota Georgia V , Morrison William R , Domingue Michael J , Athanassiou Christos G 
Published: September 2021

AbstractIn the present work, a series of tests were performed to examine the effect of previously captured adults in floor traps, on the captures of Τrogoderma granarium Everts and T. variabile Ballion, in single species releases. In a first series of tests, a single trap with kairomone oil and dead adults of single or both species was placed in a plastic container, which was used as the release arena. Subsequently, adults of both species were separately released in the arena, and the adult capture was recorded 24 h later. In a second series of trials, two traps were placed in the same arena, containing different numbers of prior seeded adults, and adult capture was similarly recorded. For T. granarium, in all cases, more adults were found inside the trap than under the trap or on the trap walls. In contrast, for T. variabile, most adults were recorded on the trap walls. In general, T. variabile had a stronger response to the traps than T. granarium. This work illustrates that previous captures of either species do not negatively affect captures of new live adults and may tend to enhance captures in some cases. This has important implications for the use of traps for the biosureveillance of these two important dermestid species.
Impacts of COVID-19 on Canadian Beekeeping: Survey Results and a Profitability Analysis
Authors: Bixby Miriam E F , Polinsky Matthew , Scarlett Rod , Higo Heather , Common Julia , Hoover Shelley E , Foster Leonard J , Zayed Amro , Cunningham Morgan , Guarna M Marta 
Published: September 2021

Abstract
To gauge the impact of COVID-19 on the Canadian beekeeping sector, we conducted a survey of over 200 beekeepers in the fall of 2020. Our survey results show Canadian beekeepers faced two major challenges: 1) disrupted importation of honey bees (Hymenoptera: Apidae) (queen and bulk bees) that maintain populations; and 2) disrupted arrival of temporary foreign workers (TFWs). Disruptions in the arrival of bees and labor resulted in fewer colonies and less colony management, culminating in higher costs and lower productivity. Using the survey data, we develop a profitability analysis to estimate the impact of these disruptions on colony profit. Our results suggest that a disruption in either foreign worker or bee arrival allows beekeepers to compensate and while colony profits are lower, they remain positive. When both honey bee and foreign workers arrivals are disrupted for a beekeeper, even when the beekeeper experiences less significant colony health and cost impacts, a colony with a single pollination contract is no longer profitable, and a colony with two pollination contracts has significantly reduced profitability. As COVID-19 disruptions from 2020 and into 2021 become more significant to long-term colony health and more costly to a beekeeping operation, economic losses could threaten the industry’s viability as well as the sustainability of pollination-dependent crop sectors across the country. The economic and agricultural impacts from the COVID-19 pandemic have exposed a vulnerability within Canada’s beekeeping industry stemming from its dependency on imported labor and bees. Travel disruptions and border closures pose an ongoing threat to Canadian agriculture and apiculture in 2021 and highlight the need for Canada’s beekeeping industry to strengthen domestic supply chains to minimize future risks.
Recent Youth-Led and Rights-Based Climate Change Litigation in Canada: Reconciling Justiciability, Charter Claims and Procedural Choices
Authors: Cameron Camille , Weyman Riley 
Published: September 2021

Abstract
This analysis examines three recent and ongoing Canadian climate change litigation cases: ENvironnement JEUnesse c Procureur général du Canada, La Rose v Canada and Mathur v Ontario. Consistent with international climate change litigation trends, these cases are youth-led and rights-based and they advance claims for present and future generations. They present apparently conflicting judicial views on the justiciability of climate change claims and on the use of the Canadian Charter of Rights and Freedoms to advance such claims. We examine these issues. We also analyse the insights the cases offer into the connections between litigants’ procedural choices and early success, either in withstanding a motion to strike, or in obtaining court authorisation to proceed by way of class action.
A Path Toward Sustainable Development Along the Belt and Road
Authors: Lorenzo Johanna Aleria P 
Published: September 2021

ABSTRACT
The article scrutinizes the purported synergies between the Belt and Road Initiative (BRI) and the United Nations (UN) 2030 Agenda for Sustainable Development by evaluating the transnational legal order regulating environmental and social impacts of BRI economic activities. From the perspective of international law and sustainable development, three problematic features are identified. First, the bilateral character of agreements between China and BRI-participating States produces fragmented and variable sustainability standards. Second, the informality of State-to-State arrangements often hinder parliamentary and public deliberation in host States. Lastly, BRI decision-making processes restrict non-State actor participation and thereby disregard the very communities harmed by infrastructure projects.
To clear its path to sustainability and bring it closer to the UN agenda, BRI’s legal and regulatory framework must become multilateral, transparent, and inclusive. The proposal entails bringing to fore the relevant background international legal norms, especially on environmental, labor, and human rights protection, and consolidating them in a framework agreement that sets minimum sustainability safeguards for transboundary economic activities like foreign-funded infrastructure projects. Reforms are imperative because the subject matter of the Initiative requires international cooperation and involves not only the economic, environmental, and social concerns of two States but also implicates the goals and interests of the international community.
Special and Differential Treatment Under the World Trade Organization: A Legal Typology
Authors: Hegde Vineet , Wouters Jan 
Published: September 2021

ABSTRACT
The World Trade Organization (WTO) Secretariat has developed a typology to categorize various Special and Differential Treatment (SDT) provisions in WTO agreements. This typology is based on the aims and intended effects of such provisions. However, it fails to highlight their legal effects. A legal typology is particularly important because the developed Members note that the developing Members have taken advantage of the system through this treatment and intend to abolish SDT for certain advanced developing Members, whereas developing Members have called SDT a non-negotiable and treaty-embedded ‘right’. Moreover, developing Members have called for an effective operation of SDT provisions. These claims give rise to two questions: (i) do SDT provisions provide legal rights to developing Members? (ii) if so, what provisions confer differential treatment rights? In this article we devise a legal typology for SDT by distinguishing the provisions that confer rights and duties from provisions that constitute merely political commitments. We also consider the types, and the scope, of rights and duties that result in a special or differential treatment. Our results, inter alia, highlight that only 21% of SDT provisions oblige developed Members to provide differential treatment to developing Members. The rest are mere best-effort endeavors and political commitments. We provide our observations for this design feature and explain the underlying rationale of developing Members’ position on SDT. Lastly, we provide a blueprint to resolve the North–South deadlock.
Influence of European Beech (Fagales: Fagaceae) Rot Hole Habitat Characteristics on Invertebrate Community Structure and Diversity
Authors: Cuff Jordan P , Windsor Fredric M , Gilmartin Emma C , Boddy Lynne , Jones T Hefin 
Published: September 2021

AbstractHollows of veteran trees (i.e., rot holes) provide habitat for many rare and threatened saproxylic invertebrates. Rot holes are highly heterogeneous, particularly in terms of substrate and microclimate conditions. There is, however, a dearth of information regarding the differences in biological communities inhabiting rot holes with different environmental conditions. Invertebrates were sampled from European beech (Fagus sylvatica) rot holes in Windsor, Savernake, and Epping Forests (United Kingdom). For each rot hole, physical and environmental conditions were measured, including tree diameter, rot hole dimensions, rot hole height, substrate density, water content, and water potential. These parameters were used to assess the influence of environmental conditions and habitat characteristics on invertebrate communities. Rot hole invertebrate communities were extremely diverse, containing both woodland generalist and saproxylic specialist taxa. Large variation in community structure was observed between rot holes and across woodlands; all sites supported threatened and endangered taxa. Environmental conditions in rot holes were highly variable within and between woodland sites, and communities were predominantly structured by these environmental conditions. In particular, turnover between invertebrate communities was linked to high β-diversity. The linked heterogeneity of environmental conditions and invertebrate communities in rot holes suggests that management of deadwood habitats in woodlands should strive to generate environmental heterogeneity to promote invertebrate diversity. Additional research is required to define how management and conservation activities can further promote enhanced biodiversity across rot holes.