bluuebunny/crossref_metadata_2025_split huggingface dataset:
An evaluation of information sharing schemes to identify what motivates fishers to share catch information
Authors: Calderwood Julia , Marshall C Tara , Haflinger Karl , Alfaro-Shigueto Joanna , Mangel Jeffrey C , Reid David G 
Published: December 2021

AbstractAvoiding unwanted catches and reducing discards is an important objective of fisheries management. Fishers can avoid unwanted catches to some extent by improving selectivity of their fishing operations. This can be achieved through technical measures and gear modifications but also by adjusting when and where fishing takes place. Having access to real-time information, as provided through information sharing within a fleet, can help fishers avoid unwanted catches. Yet, there often remains a reluctance to share catch information with others. This paper compiles information from 15 case study examples of existing information sharing schemes in fisheries throughout the world. We compare the structure and operation of each of these schemes and determine what motivated participants to join and share potentially sensitive catch information. While there is no one-size-fits-all approach to designing and implementing information sharing schemes in fisheries, this paper highlights how industry and stakeholder support is often important, and understanding the needs, concerns, and motivations of any group of fishers is fundamental in developing and expanding such approaches.
Psilocybin Therapy of Psychiatric Disorders Is Not Hampered by hERG Potassium Channel–Mediated Cardiotoxicity
Authors: Hackl Benjamin , Todt Hannes , Kubista Helmut , Hilber Karlheinz , Koenig Xaver 
Published: December 2021

Abstract
Psilocybin, a hallucinogen contained in “magic” mushrooms, holds great promise for the treatment of various psychiatric disorders, and early clinical trials are encouraging. Adverse cardiac events after intake of high doses of psilocybin and a trial reporting QT interval prolongation in the electrocardiogram attributed to the drug’s main metabolite, psilocin, gave rise to safety concerns. Here we show that clinical concentrations of psilocin do not cause significant human ether-a-go-go-related gene (hERG) potassium channel inhibition, a major risk factor for adverse cardiac events. We conclude that hERG channel blockage by psilocin is not liable for psilocybin- associated cardiotoxic effects.
Finite-time stabilization of nonlinear polytopic systems: a control Lyapunov function approach
Authors: Kumar Soni Sandeep , Kamal Shyam , Ghosh Sandip , Olaru Sorin 
Published: December 2021

Abstract
This paper addresses the finite-time stabilization of nonlinear polytopic systems. Sufficient conditions are proposed for the existence of a continuous time-invariant finite-time stabilizing state feedback controller through a robust control Lyapunov function. It is shown that the obtained sufficient condition is also necessary if there exists a state feedback controller such that the closed-loop system has a robust Lyapunov function for all possible uncertainties. Finally, to verify the efficacy of the proposed control design, a numerical example is presented.
Impact of Dapivirine and Placebo Vaginal Rings on the Microbiota of Adolescent, Lactating, and Postmenopausal Females
Authors: Austin Michele N , Meyn Leslie A , Avolia Hilary A , Petrina Melinda A , Cosentino Lisa A , Alphonse Calins , Chen Beatrice A , Bunge Katherine , Noguchi Lisa , Beigi Richard , Squires Kathleen , Hillier Sharon L 
Published: December 2021

Abstract

Background
A 25-mg dapivirine vaginal ring has been demonstrated to reduce risk of human immunodeficiency virus (HIV) acquisition in nonpregnant adult women. In this secondary analysis of studies conducted in US adolescent, lactating, and postmenopausal females, vaginal microbiota was assessed prior to and after ring use, and between dapivirine and placebo ring users.

Methods
Vaginal fluid swabs were collected before and after product use for the evaluation of microbiota using Nugent criteria, quantitative culture, and quantitative polymerase chain reaction.

Results
Vaginal ring use did not impact bacterial vaginosis prevalence among the 3 populations and was associated with minimal shifts in microbiota. Adolescents in both arms demonstrated an increased prevalence of Lactobacillus crispatus and a decrease in quantity of Megasphaera lornae. Postmenopausal active and placebo ring users demonstrated an increased prevalence of lactobacilli and non-albicans yeast, while dapivirine ring users demonstrated an increased prevalence of Candida albicans and increased quantity of group B Streptococcus and non-albicans yeasts. Prevotella species were increased in lactating women, whereas Prevotella timonensis increased in prevalence and concentration among adolescent and postmenopausal females and Prevotella bivia increased in prevalence among adolescent dapivirine ring users.

Conclusions
Dapivirine vaginal ring use was associated with minimal changes in the vaginal microbiota that are likely not clinically significant.
Migrating a research data warehouse to a public cloud: challenges and opportunities
Authors: Kahn Michael G , Mui Joyce Y , Ames Michael J , Yamsani Anoop K , Pozdeyev Nikita , Rafaels Nicholas , Brooks Ian M 
Published: December 2021

Abstract

Objective
Clinical research data warehouses (RDWs) linked to genomic pipelines and open data archives are being created to support innovative, complex data-driven discoveries. The computing and storage needs of these research environments may quickly exceed the capacity of on-premises systems. New RDWs are migrating to cloud platforms for the scalability and flexibility needed to meet these challenges. We describe our experience in migrating a multi-institutional RDW to a public cloud.

Materials and Methods
This study is descriptive. Primary materials included internal and public presentations before and after the transition, analysis documents, and actual billing records. Findings were aggregated into topical categories.

Results
Eight categories of migration issues were identified. Unanticipated challenges included legacy system limitations; network, computing, and storage architectures that realize performance and cost benefits in the face of hyper-innovation, complex security reviews and approvals, and limited cloud consulting expertise.

Discussion
Cloud architectures enable previously unavailable capabilities, but numerous pitfalls can impede realizing the full benefits of a cloud environment. Rapid changes in cloud capabilities can quickly obsolete existing architectures and associated institutional policies. Touchpoints with on-premise networks and systems can add unforeseen complexity. Governance, resource management, and cost oversight are critical to allow rapid innovation while minimizing wasted resources and unnecessary costs.

Conclusions
Migrating our RDW to the cloud has enabled capabilities and innovations that would not have been possible with an on-premises environment. Notwithstanding the challenges of managing cloud resources, the resulting RDW capabilities have been highly positive to our institution, research community, and partners.
Early specialized palliative care for patients with metastatic lung cancer receiving chemotherapy: a feasibility study of a nurse-led screening-triggered programme
Authors: Matsumoto Yoshihisa , Umemura Shigeki , Okizaki Ayumi , Fujisawa Daisuke , Kobayashi Naoko , Tanaka Yuko , Sasaki Chiyuki , Shimizu Ken , Ogawa Asao , Kinoshita Hiroya , Uchitomi Yosuke , Yoshiuchi Kazuhiro , Matsuyama Yutaka , Morita Tatsuya , Goto Koichi , Ohe Yuichiro 
Published: December 2021

Abstract

Background
Strategies to implement early specialized palliative care have not yet been established. The present study investigated the feasibility of a nurse-led, screening-triggered early specialized palliative care intervention programme and obtained data to design a randomized controlled trial.

Methods
Patients with metastatic lung cancer undergoing first-line platinum-based chemotherapy were eligible. The intervention consisted of (1) a questionnaire-based screening programme and (2) advanced-level nurse counselling and care coordination with interdisciplinary team approach. The primary endpoint was the completion rate of the assessment questionnaire after the second course of first-line chemotherapy (T2). Secondary endpoints included changes in Functional Assessment of Cancer Therapy-Lung scores, depression and anxiety rates based on the Patient Health Questionnaire 9 and the Hospital Anxiety and Depression Scale, and the contents of specialized palliative care.

Results
A total of 50 patients were enrolled between August 2012 and March 2014. Median age was 66 years (range, 40–78 year) and 84% were male. A total of 38 patients had stage IV non-small cell lung carcinoma and 12 had extensive disease small-cell lung carcinoma. The completion rate was 70% (95% confidence interval 56.0–81.0). The median duration between baseline and T2 was 53 days. Improvement from baseline were observed at T2 in Functional Assessment of Cancer Therapy-Lung scores (86.0 ± 18.1 vs 94.9 ± 18.2, P = 0.057), depression (16.0 vs 5.7%; P = 0.26) and anxiety (32.0 vs 22.9%; P = 0.65); however, these results were not statistically significant.

Conclusions
This early specialized palliative care intervention is feasible and could be useful in improving patients’ quality of life. The present results justify the initiation of a randomized control trial.
Fungal oxysterol-binding protein-related proteins promote pathogen virulence and activate plant immunity
Authors: Chen Meng-Meng , Yang Si-Ru , Wang Jian , Fang Ya-Li , Peng You-Liang , Fan Jun 
Published: December 2021

AbstractOxysterol-binding protein-related proteins (ORPs) are a conserved class of lipid transfer proteins that are closely involved in multiple cellular processes in eukaryotes, but their roles in plant–pathogen interactions are mostly unknown. We show that transient expression of ORPs of Magnaporthe oryzae (MoORPs) in Nicotiana benthamina plants triggered oxidative bursts and cell death; treatment of tobacco Bright Yellow-2 suspension cells with recombinant MoORPs elicited the production of reactive oxygen species. Despite ORPs being normally described as intracellular proteins, we detected MoORPs in fungal culture filtrates and intercellular fluids from barley plants infected with the fungus. More importantly, infiltration of Arabidopsis plants with recombinant Arabidopsis or fungal ORPs activated oxidative bursts, callose deposition, and PR1 gene expression, and enhanced plant disease resistance, implying that ORPs may function as endogenous and exogenous danger signals triggering plant innate immunity. Extracellular application of fungal ORPs exerted an opposite impact on salicylic acid and jasmonic acid/ethylene signaling pathways. Brassinosteroid Insensitive 1-associated Kinase 1 was dispensable for the ORP-activated defense. Besides, simultaneous knockout of MoORP1 and MoORP3 abolished fungal colony radial growth and conidiation, whereas double knockout of MoORP1 and MoORP2 compromised fungal virulence on barley and rice plants. These observations collectively highlight the multifaceted role of MoORPs in the modulation of plant innate immunity and promotion of fungal development and virulence in M. oryzae.
Plant iron nutrition: the long road from soil to seeds
Authors: Murgia Irene , Marzorati Francesca , Vigani Gianpiero , Morandini Piero 
Published: December 2021

Abstract
Iron (Fe) is an essential plant micronutrient since many cellular processes including photosynthesis, respiration, and the scavenging of reactive oxygen species depend on adequate Fe levels; however, non-complexed Fe ions can be dangerous for cells, as they can act as pro-oxidants. Hence, plants possess a complex homeostatic control system for safely taking up Fe from the soil and transporting it to its various cellular destinations, and for its subcellular compartmentalization. At the end of the plant’s life cycle, maturing seeds are loaded with the required amount of Fe needed for germination and early seedling establishment. In this review, we discuss recent findings on how the microbiota in the rhizosphere influence and interact with the strategies adopted by plants to take up iron from the soil. We also focus on the process of seed-loading with Fe, and for crop species we also consider its associated metabolism in wild relatives. These two aspects of plant Fe nutrition may provide promising avenues for a better comprehension of the long pathway of Fe from soil to seeds.
Fatty alcohol oxidase 3 (FAO3) and FAO4b connect the alcohol- and alkane-forming pathways in Arabidopsis stem wax biosynthesis
Authors: Yang Xianpeng , Cui Lili , Li Shipeng , Ma Changle , Kosma Dylan K , Zhao Huayan , Lü Shiyou 
Published: December 2021

Abstract
The alcohol- and alkane-forming pathways in cuticular wax biosynthesis are well characterized in Arabidopsis. However, potential interactions between the two pathways remain unclear. Here, we reveal that mutation of CER4, the key gene in the alcohol-forming pathway, also led to a deficiency in the alkane-forming pathway in distal stems. To trace the connection between the two pathways, we characterized two homologs of fatty alcohol oxidase (FAO), FAO3 and FAO4b, which were highly expressed in distal stems and localized to the endoplasmic reticulum. The amounts of waxes from the alkane-forming pathway were significantly decreased in stems of fao4b and much lower in fao3 fao4b plants, indicative of an overlapping function for the two proteins in wax synthesis. Additionally, overexpression of FAO3 and FAO4b in Arabidopsis resulted in a dramatic reduction of primary alcohols and significant increases of aldehydes and related waxes. Moreover, expressing FAO3 or FAO4b led to significantly decreased amounts of C18–C26 alcohols in yeast co-expressing CER4 and FAR1. Collectively, these findings demonstrate that FAO3 and FAO4b are functionally redundant in suppressing accumulation of primary alcohols and contributing to aldehyde production, which provides a missing and long-sought-after link between these two pathways in wax biosynthesis.
Molybdenum: More than an essential element
Authors: Huang Xin-Yuan , Hu Da-Wei , Zhao Fang-Jie 
Published: December 2021

Abstract
Molybdenum (Mo) is an essential element for almost all living organisms. After being taken up into the cells as molybdate, it is incorporated into the molybdenum cofactor, which functions as the active site of several molybdenum-requiring enzymes and thus plays crucial roles in multiple biological processes. The uptake and transport of molybdate is mainly mediated by two types of molybdate transporters. The homeostasis of Mo in plant cells is tightly controlled, and such homeostasis likely plays vital roles in plant adaptation to local environments. Recent evidence suggests that Mo is more than an essential element required for plant growth and development; it is also involved in local adaptation to coastal salinity. In this review, we summarize recent research progress on molybdate uptake and transport, molybdenum homeostasis network in plants, and discuss the potential roles of the molybdate transporter in plant adaptation to their local environment.
The effect of dwarf galaxies on the tidal tails of globular clusters
Authors: El-Falou Nada , Webb Jeremy J 
Published: December 2021

ABSTRACT
The tidal tails of globular clusters have been shown to be sensitive to the external tidal field. We investigate how Galactic globular clusters with observed tails are affected by satellite dwarf galaxies by simulating tails in galaxy models with and without dwarf galaxies. The simulations indicate that tidal tails can be subdivided into three categories based on how they are affected by dwarf galaxies: (1) dwarf galaxies perturb the progenitor cluster’s orbit (NGC 4590, Pal 1, Pal 5), (2) dwarf galaxies perturb the progenitor cluster’s orbit and individual tail stars (NGC 362, NGC 1851, NGC 4147, NGC 5466, NGC 7492, Pal 14, Pal 15), and (3) dwarf galaxies negligibly affect tidal tails (NGC 288, NGC 5139, NGC 5904, Eridanus). Perturbations to a cluster’s orbit occur when dwarf galaxies pass within its orbit, altering the size and shape of the orbital and tail path. Direct interactions between one or more dwarf galaxies and tail stars lead to kinks and spurs, however we find that features are more difficult to observe in projection. We further find that the tails of Pal 5 are shorter in the galaxy model with dwarf galaxies as it is closer to apocentre, which results in the tails being compressed. Additional simulations reveal that differences between tidal tails in the two galaxy models are primarily due to the Large Magellanic Cloud. Understanding how dwarf galaxies affect tidal tails allows for tails to be used to map the distribution of matter in dwarf galaxies and the Milky Way.
Reconstructing orbits of galaxies in extreme regions (ROGER) – II: reliability of projected phase-space in our understanding of galaxy populations
Authors: Coenda Valeria , Rios Martín de los , Muriel Hernán , Cora Sofía A , Martínez Héctor J , Ruiz Andrés N , Vega-Martínez Cristian A 
Published: December 2021

ABSTRACT
We connect galaxy properties with their orbital classification by analysing a sample of galaxies with stellar mass M⋆ ≥ 108.5h−1M⊙ residing in and around massive and isolated galaxy clusters with mass M200 &gt; 1015h−1M⊙ at redshift z = 0. The galaxy population is generated by applying the semi-analytic model of galaxy formation sag on the cosmological simulation MultiDark Planck 2. We classify galaxies considering their real orbits (3D) and their projected phase-space position using the roger code (2D). We define five categories: cluster galaxies, galaxies that have recently fallen into a cluster, backsplash galaxies, infalling galaxies, and interloper galaxies. For each class, we analyse the 0.1(g − r) colour, the specific star formation rate (sSFR), and the stellar age, as a function of the stellar mass. For the 3D classes, we find that cluster galaxies have the lowest sSFR, and are the reddest and the oldest, as expected from environmental effects. Backsplash galaxies have properties intermediate between the cluster and recent infaller galaxies. For each 2D class, we find an important contamination by other classes. We find it necessary to separate the galaxy populations in red and blue to perform a more realistic analysis of the 2D data. For the red population, the 2D results are in good agreement with the 3D predictions. Nevertheless, when the blue population is considered, the 2D analysis only provides reliable results for recent infallers, infalling galaxies and interloper galaxies.
Rapid turn-on of a luminous X-ray source in the candidate Lyman continuum emitting galaxy Tol 0440-381
Authors: Kaaret P , Bluem J , Prestwich A H 
Published: December 2021

ABSTRACT
Chandra observations of the nearby candidate Lyman continuum (LyC) emitting galaxy Tol 0440-381 show brightening of an X-ray source by at least a factor of 4 to a luminosity of $1.6 \times 10^{40} \rm \, erg \, s^{-1}$ over 3.8 d. The X-ray emission likely arises from either a low-luminosity active galactic nucleus or an ultraluminous X-ray source. The properties of the X-ray source are similar to those found in Haro 11 and Tololo 1247-232, the only other LyC emitting galaxies that have been resolved in X-rays. All three galaxies host luminous, variable, and hard-spectrum X-ray sources that are likely accretion-powered. Accretion on to compact objects produces powerful outflows and ionizing radiation that could help enable LyC escape.
Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis
Authors: Carroll Brittany L , Zahn Karl E , Hanley John P , Wallace Susan S , Dragon Julie A , Doublié Sylvie 
Published: December 2021

Abstract
Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.
Foster thy young: enhanced prediction of orphan genes in assembled genomes
Authors: Li Jing , Singh Urminder , Bhandary Priyanka , Campbell Jacqueline , Arendsee Zebulun , Seetharam Arun S , Wurtele Eve Syrkin 
Published: December 2021

AbstractProteins encoded by newly-emerged genes (‘orphan genes’) share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.
Development of a genome-targeting mutator for the adaptive evolution of microbial cells
Authors: Eom Ga-eul , Lee Hyunbin , Kim Seokhee 
Published: December 2021

Abstract
Methods that can randomly introduce mutations in the microbial genome have been used for classical genetic screening and, more recently, the evolutionary engineering of microbial cells. However, most methods rely on either cell-damaging agents or disruptive mutations of genes that are involved in accurate DNA replication, of which the latter requires prior knowledge of gene functions, and thus, is not easily transferable to other species. In this study, we developed a new mutator for in vivo mutagenesis that can directly modify the genomic DNA. Mutator protein, MutaEco, in which a DNA-modifying enzyme is fused to the α-subunit of Escherichia coli RNA polymerase, increases the mutation rate without compromising the cell viability and accelerates the adaptive evolution of E. coli for stress tolerance and utilization of unconventional carbon sources. This fusion strategy is expected to accommodate diverse DNA-modifying enzymes and may be easily adapted to various bacterial species.