bluuebunny/crossref_metadata_2025_split huggingface dataset:
An assessment of the impact of 1.5 versus 2 and 2.5°C global temperature increase on flooding in Jamaica: a case study from the Hope watershed
Authors: Mandal Arpita , Stephenson Tannecia , Campbell Jayaka , Taylor Michael , Watson Shavel , Clarke Leonardo , Smith David , Darsan Junior , Wilson Matthew 
Published: February 2022

Climate change models project that, within the Caribbean basin, rainfall intensity is likely to increase toward the end of this century, although the region is projected to be drier overall. This may affect the frequency and severity of floods in Jamaica and the Caribbean Small Island Developing States. We investigate how flood hazards may be affected by increases in global mean surface temperature of 1.5, 2.0 and 2.5°C above pre-industrial levels using a case study of a Jamaican watershed. Rainfall projections from the PRECIS regional climate model for the Caribbean are analysed. Six members from the Quantifying Uncertainty in Model Predictions (AENWH, AEXSA, AEXSC, AEXSK, AEXSL and AEXSM) were used to create 100-year flood inundation maps for the Hope river for different global warming levels using hydrological and hydraulic models. Model runs projected peak discharges at 2.0, 2.5 and 1.5°C warming that were higher than discharges in the historical record of events that damaged sections of the watershed. Projections from the hydraulic model show increased flow area, depth and extent for 1.5 followed by 2.0 and 2.5°C rises in temperature. These results imply continued flood risk for the vulnerable areas of the watershed.
This article is part of the theme issue 'Developing resilient energy systems'.
Sea-level rise, coastal salinity and vegetation changes in Sri Lanka
Authors: Mathiventhan Thavanayagam , Gorman Daniel , Jayasingam Thangamuthu 
Published: February 2022

Sea-level rise is a key component of many climate change scenarios. Such increases are expected to cause greater coastal inundation by seawater, reduce the depth of the freshwater-saline water lens and have a range of consequences for coastal ecosystems. Soil salinity determines the distribution patterns of coastal vegetation across a sea-to-land gradient, and sea-level rise would be expected to alter these distributions. Our study done along the east coast of Sri Lanka shows that soil salinity decreases predictably from sea to land, varying between 21‰ and 30‰ over a distance of 50 m from the mean high water springs level. Soil salinity also showed declines with increasing soil depth (0, 10, 50 cm) although this was marginally non-significant. The emergence of terrestrial vegetation coincided with a cross-shore ecotone where the soil salinity approached 0‰. Our predictions suggest that if the mean sea-level were to increase by 1 m in the Batticaloa region (Sri Lanka), this would cause landward communities to be inundated with brackish water at various depths. The present permanent coastal vegetation front would likely shift landward by 30–45 m under scenarios involving a 1 m increase in sea level. Sea-level rise and its consequences could result in a variety of changes to coastal vegetation such as altered physiognomy and diversity, colonization of new territory, expansion of salt-tolerant species such as mangroves and saltmarsh and will therefore greatly influence adaptive management and future planning.
This article is part of the theme issue ‘Developing resilient energy systems’.
Low-cost and open-source super-resolution fluorescence microscope with autofocus for teaching and research
Authors: Hanselman Justin D. , Kopek Benjamin G. 
Published: February 2022

AbstractSuper-resolution fluorescence microscopy revolutionized optical microscopy by breaking the theoretical resolution limit and thus providing an unprecedented view of biological structure in exquisite detail. Additionally, the relative ease of use and implementation for some super-resolution microscopes provided hope that this technology would be widely available and accessible. Despite initial excitement, super-resolution microscopy is still largely limited to facilities that can afford expensive commercial instruments or with personnel experienced in optical engineering that can construct an instrument. Recently, the open scientific hardware movement has attempted to make scientific instrumentation more widely available and accessible in a similar way to the open software movement. The widespread availability and affordability of prototyping devices, such as three-dimensional printers and interfaces (e.g., Arduino) have all contributed to unlocking the potential of the open hardware movement, turning expensive “black box” hardware into open-source, affordable, and robust instrumentation. Many others have recognized the potential of describing low-cost implementations of super-resolution microscope designs. However, we have found these microscope designs lacking in the documentation and details required to meet the requirements of open-source hardware. In this paper, we attempt to provide the documentation, details, and instructions necessary for the construction of an open-source and low-cost super-resolution microscope at a targeted cost of <$15,000.
A community-based ANP-led integrated oncology care model for adults receiving oral anticancer medication-protocol for a pilot study
Authors: Richmond J.P. , Johnston A. , Murphy P.J. , Gillespie P. , Murphy A.W. 
Published: February 2022

AbstractOncology has been undergoing a profound transition in the last ten years or more with the increased usage in oral anti-cancer medication (OAM). Approximately 25% of all anti-cancer medication is now designed for oral use and this is likely to increase prospectively. Oral anti-cancer medications have the potential to alleviate capacity issues in cancer treating units as patients receive their treatment at home. There remains however a requirement for safe and efficient assessment and monitoring but this does not necessarily require them to repeatedly attend a hospital day unit. Therefore the opportunity exists to transition this cohort to a community-based setting to be assessed by a specialist such as an Advanced Nurse Practitioner (ANP) in nurse-led clinics. Having an OAM assessment closer to their home would be more convenient to the patient. Furthermore, this could help alleviate hospital capacity issues which were brought into sharp focus with the onset of the COVID-19 pandemic and the use of nurse-led clinics are promoted in the aims of the current healthcare system reform process in Ireland.Within the context of the Irish healthcare system reform and the COVID-19 pandemic this protocol will outline a collaboration between an Oncology Department in Letterkenny University Hospital in Ireland and the National University of Ireland, Galway aimed to develop and pilot a community-based Advanced Nurse Practitioner-led integrated oncology care model for adults receiving OAM. Phase 1 of this two-phase study commenced in September 2020 and comprised a scoping review, a benchmarking exercise and a qualitative analysis of relevant stakeholders. This protocol paper presents a pilot to be undertaken in phase 2 as OAM care is transitioned to an ANP-led community-based model, which is a radical shift for oncology care in Ireland. The pilot outlined will provide data that will identify potential refinements to the model and address specific uncertainties about a definitive trial.
A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2
Authors: Popp Bernt , Brugger Melanie , Poschmann Sibylle , Bartolomaeus Tobias , Radtke Maximilian , Hentschel Julia , Di Donato Nataliya , Rump Andreas , Gburek-Augustat Janina , Graf Elisabeth , Wagner Matias , Lemke Johannes , Meitinger Thomas , Jamra Rami Abou , Strehlow Vincent , Brunet Theresa 
Published: February 2022

ABSTRACTPurposeNSD2 dimethylates histone H3 at lysine 36 (H3K36me2) and is located in the Wolf-Hirschhorn syndrome (WHS) region. Recent descriptions delineated loss-of-function (LoF) variants in NSD2 with a distinct disorder. The oncogenic missense variant p.Glu1099Lys occures somatically in leukemia and has a gain-of-function (GoF) effect.MethodsWe describe two unrelated individuals carrying c.3295G>A, p.Glu1099Lys as heterozygous de novo germline variants identified by exome sequencing of blood DNA and subsequently confirmed in two ectodermal tissues. We use omics data from the Cancer Cell Line Encyclopedia to analyze the GoF effect.ResultsClinically these individuals are characterized by intellectual disability, coarse/ square facial gestalt, abnormalities of the hands and organomegaly. We confirmed increased K36me2 methylation in lines with either NSD2 GoF variants or duplications. Cells with GoF variants showed increased DNA promoter methylation and dysregulated RNA expression, influencing cellular modules involved in white blood cell activation, cell growth and organ development.ConclusionNSD2 GoF caused by the missense variant p.Glu1099Lys leads to a novel syndromic phenotype distinct from both the previously described LoF phenotypes. Other variants causing NSD2 hyperactivation or overexpression may cause a similar phenotype. This syndrome should be distinguished from the recently named Rauch-Steindl syndrome caused by NSD2 haploinsufficiency.
Genome-wide study on 72,298 Korean individuals in Korean biobank data for 76 traits identifies hundreds of novel loci
Authors: Nam Kisung , Kim Jangho , Lee Seunggeun 
Published: February 2022

AbstractGenome-wide association studies (GWAS) on diverse ancestry groups are lacking, resulting in deficits of genetic discoveries and polygenic scores. We conducted GWAS for 76 phenotypes in Korean biobank data, namely Korean Genome and Epidemiology Study (KoGES, n=72,298). Our analysis discovered 2,237 associated loci, including 117 novel associations, many of which replicated in Biobank Japan (BBJ) GWAS. We also applied several up-to-date methods for genetic association tests to increase the power, discovering additional associations that are not identified in simple case-control GWAS. We evaluated genetic pleiotropy to investigate genes associated with multiple traits. Following meta-analysis of 32 phenotypes between KoGES and Biobank Japan (BBJ), we further identified 379 novel associations and demonstrated the improved predictive performance of polygenic risk scores by using the meta-analysis results. The summary statistics of 76 KoGES GWAS phenotypes are publicly available, contributing to a better comprehension of the genetic architecture of the East Asian population.
Quantifying antibody dynamics of severe and non-severe patients with COVID-19
Authors: Ordoñez-Jiménez Fernanda , Blanco-Rodríguez Rodolfo , Almocera Alexis Erich S. , Chinney-Herrera Gustavo , Hernández-Vargas Esteban 
Published: February 2022

ABSTRACTCOVID-19 pandemic is a major public health threat with unanswered questions regarding the role of the immune system in the severity level of the disease. In this paper, based on antibody kinetic data of patients with different disease severity, topological data analysis highlights clear differences in the shape of antibody dynamics between three groups of patients, which were non-severe, severe, and one intermediate case of severity. Subsequently, different mathematical models were developed to quantify the dynamics between the different severity groups. The best model was the one with the lowest media value of Akaike Information Criterion for all groups of patients. Although it has been reported high IgG level in severe patients, our findings suggest that IgG antibodies in severe patients may be less effective than non-severe patients due to early B cell production and early activation of the seroconversion process from IgM to IgG antibody.
Monitoring peripheral hemodynamic response to changes in blood pressure via photoacoustic imaging
Authors: Mantri Yash , Dorobek Tyler R. , Tsujimoto Jason , Penny William F. , Garimella Pranav S. , Jokerst Jesse V. 
Published: February 2022

AbstractChronic wounds and amputations are common in chronic kidney disease patients needing hemodialysis (HD). HD is often complicated by drops in blood pressure (BP) called intra-dialytic hypotension. Whether intra-dialytic hypotension is associated with detectable changes in foot perfusion, a risk factor for wound formation and impaired healing remains unknown. Photoacoustic (PA) imaging is ideally suited to study perfusion changes. We scanned the feet of 20 HD and 11 healthy subjects. HD patients were scanned before and after a dialysis session whereas healthy subjects were scanned twice at rest and once after a 10 min exercise period while BP was elevated. Healthy (r=0.70, p<0.0001) and HD subjects (r=0.43, p<0.01) showed a significant correlation between PA intensity and systolic BP. Furthermore, HD cohort showed a significantly reduced PA response to changes in BP compared to the healthy controls (p<0.0001). Hence showing that PA can monitor hemodynamic changes due to changes in BP.
Effectiveness of the third dose of BNT162b2 vaccine on neutralizing Omicron variant in the Japanese population
Authors: Kawasuji Hitoshi , Morinaga Yoshitomo , Tani Hideki , Saga Yumiko , Kaneda Makito , Murai Yushi , Ueno Akitoshi , Miyajima Yuki , Fukui Yasutaka , Nagaoka Kentaro , Ono Chikako , Matsuura Yoshiharu , Niimi Hideki , Yamamoto Yoshihiro 
Published: February 2022

ABSTRACTIntroductionThe vaccine against SARS-CoV-2 provides humoral immunity to fight COVID-19; however, the acquired immunity gradually declines. Booster vaccination restores reduced humoral immunity; however, its effect on newly emerging variants, such as the Omicron variant, is a concern. As the waves of COVID-19 cases and vaccine programs differ between countries, it is necessary to know the domestic effect of the booster.MethodsSerum samples were obtained from healthcare workers (20-69 years old) in the Pfizer BNT162b2 vaccine program at the Toyama University Hospital 6 months after the second dose (6mA2D, n = 648) and 2 weeks after the third dose (2wA3D, n = 565). The anti-SARS-CoV-2 antibody level was measured, and neutralization against the wild-type and variants (Delta and Omicron) was evaluated using pseudotyped viruses. Data on booster-related events were collected using questionnaires.ResultsThe median anti-SARS-CoV-2 antibody was >30.9-fold elevated after the booster (6mA2D, 710.0 U/mL [interquartile range (IQR): 443.0–1068.0 U/mL]; 2wA3D, 21927 U/mL [IQR: 15321.0–>25000.0 U/mL]). Median neutralizing activity using 100-fold sera against wild-type-, Delta-, and Omicron-derived variants was elevated from 84.6%, 36.2%, and 31.2% at 6mA2D to >99.9%, 99.1%, and 94.6% at 2wA3D, respectively. The anti-SARS-CoV-2 antibody levels were significantly elevated in individuals with fever ≥37.5 °C, general fatigue, and myalgia, local swelling, and local hardness.ConclusionThe booster effect, especially against the Omicron variant, was observed in the Japanese population. These findings contribute to the precise understanding of the efficacy and side effects of the booster and the promotion of vaccine campaigns.
Oxidation-reduction and photophysical properties of isomeric forms of Safranin
Authors: Andersen Eskil M.E. , Wang Hsin , Khoo Joshua S.H. , Cerda Jose , Koder Ronald L. 
Published: February 2022

AbstractSafranine O is widely used in the bioenergetics community as an indicator dye to determine membrane potentials and as an electron transfer mediator in potentiometric titrations. Here we show that two different commercial preparations of Safranine O contain less than sixty percent by weight of the title compound, with the rest primarily consisting of two closely related safranine isomers. All three major isomer components were isolated using reverse phase HPLC and their structures determined using mass spectrometry and two-dimensional NMR. These Safranines have two-electron midpoint potentials ranging from −272 to −315 mV vs. SHE. We have also investigated the absorption and fluorescence spectra of the compounds and found that they display distinct spectral and photophysical properties. While this mixture may aid in Safranine O’s utility as a mediator compound, membrane potential measurements must take this range of dye potentials into account.
Temporal matches and mismatches between monarch butterfly and milkweed population changes over the past 12,000 years
Authors: Boyle John H. , Strickler Susan , Twyford Alex , Ricono Angela , Powell Adrian , Zhang Jing , Xu Hongxing , Dalgleish Harmony J. , Jander Georg , Agrawal Anurag A. , Puzey Joshua R. 
Published: February 2022

AbstractIn intimate ecological interactions, the interdependency of species may result in correlated demographic histories. For species of conservation concern, understanding the long-term dynamics of such interactions may shed light on the drivers of population decline. Here we address the demographic history of the monarch butterfly, Danaus plexippus, and its dominant host plant, the common milkweed Asclepias syriaca, using broad-scale sampling and genomic inference. Because genetic resources for milkweed have lagged behind those for monarchs, we first release a chromosome-level genome assembly and annotation for common milkweed. Next, we show that despite its enormous geographic range across eastern North America, A. syriaca is best characterized as a single, roughly panmictic population. Using Approximate Bayesian Computation via Random Forests (ABC-RF), a machine learning method for reconstructing demographic histories, we show that both monarchs and milkweed experienced concurrent range expansion during the most recent recession of North American glaciers ∼12,000 years ago. Our data identify an expansion of milkweed during the large-scale clearing of eastern forests (∼200 years ago) but was inconclusive as to expansion or contraction of the monarch butterfly population during this time. Finally, our results indicate that neither species experienced a population contraction over the past 75 years. Thus, the well-documented decline of monarch abundance over the past 40 years is not visible in our genomic dataset, reflecting a possible mismatch of the overwintering census population to effective population size in this species.
A molecular mechanism for high salt taste in Drosophila
Authors: McDowell Sasha A. T. , Stanley Molly , Gordon Michael D. 
Published: February 2022

SUMMARYDietary salt detection and consumption are crucial to maintaining fluid and ionic homeostasis. To optimize salt intake, animals employ salt-dependent activation of multiple taste pathways. Generally, sodium activates attractive taste cells, but attraction is overridden at high salt concentrations by cation non-selective activation of aversive taste cells. In flies, high salt avoidance is driven by both ‘bitter’ taste neurons and a class of glutamatergic ‘high salt’ neurons expressing pickpocket23 (ppk23). Although the cellular basis of salt taste has been described, many of the molecular mechanisms remain elusive. Here, we show that ionotropic receptor 7c (IR7c) is expressed in glutamatergic high salt neurons, where it functions with co-receptors IR76b and IR25a to detect high salt. Misexpression of IR7c in sweet neurons, which endogenously express IR76b and IR25a, confers responsiveness to non-sodium salts, indicating that IR7c is sufficient to convert a sodium-selective receptor to a cation non-selective receptor. Furthermore, the resultant transformation of taste neuron tuning switches potassium chloride from an aversive to an attractive tastant. This research provides insight into the molecular basis of monovalent and divalent salt taste coding and the full repertoire of IRs needed to form a functional salt receptor.
Meta-Analysis of the Functional Neuroimaging Literature with Probabilistic Logic Programming
Authors: Abdallah Majd , Iovene Valentin , Zanitti Gaston , Wassermann Demian 
Published: February 2022

AbstractInferring reliable brain-behavior associations requires synthesizing evidence from thousands of functional neuroimaging studies through meta-analysis. However, existing meta-analysis tools are limited to investigating simple neuroscience concepts and expressing a restricted range of questions. Here, we expand the scope of neuroimaging meta-analysis by designing NeuroLang: a domain-specific language to express and test hypotheses using probabilistic first-order logic programming. By leveraging formalisms found at the crossroads of artificial intelligence and knowledge representation, NeuroLang provides the expressivity to address a larger repertoire of hypotheses in a meta-analysis, while seamlessly modelling the uncertainty inherent to neuroimaging data. We demonstrate the language’s capabilities in conducting comprehensive neuroimaging meta-analysis through use-case examples that address questions of structure-function associations. Specifically, we infer the specific functional roles of three canonical brain networks, support the role of the visual word-form area in visuospatial attention, and investigate the heterogeneous organization of the fronto-parietal control network.
Morphometric characters in the taxonomic recognition of the species of Dolichopus pennatus group (Diptera: Dolichopodidae)
Authors: Chursina M.A. , Selivanova O.V. 
Published: February 2022

AbstractSexually dimorphic structures (ornaments) on the legs are important diagnostic features for Dolichopus males, whereas females of those males are often morphologically similar and their species diagnostics is difficult. To assessing the relevance and feasibility of setting diagnostic characters for five sister species of the genus Dolichopus Latreille, 1796 (D. argyrotarsis, D. lineaticornis, D. pennatus, D. popularis, D. subpennatus) analysis of morphometric trait was used: comparison of wing shape by methods of geometric morphometry, as well as comparison of the ratios of the leg segments lengths. Comparative analysis of morphometric characters with molecular data made it possible to study the phylogenetic signal of male leg ornaments. It was shown for Dolichopus species, that modifications of the males’ middle legs occurred independently several times in the genus. In addition, the evolutionary pattern in the formation of similar ornaments was also associated with changes in the morphometric features of the legs and wings. Based on wing and legs morphometry, new diagnostic characters were proposed for females of the studied species group.