bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes
Authors: Frühe Larissa , Cordier Tristan , Dully Verena , Breiner Hans‐Werner , Lentendu Guillaume , Pawlowski Jan , Martins Catarina , Wilding Thomas A. , Stoeck Thorsten 
Published: April 2020

AbstractIncreasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate‐monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.
Illuminating the mysteries of wolf history
Authors: Schweizer Rena M. , Wayne Robert K. 
Published: April 2020

One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter & Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.
Community structure – Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function
Authors: Meyer Kyle M. , Hopple Anya M. , Klein Ann M. , Morris Andrew H. , Bridgham Scott D. , Bohannan Brendan J. M. 
Published: April 2020

AbstractBelowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4)‐cycling processes in soil samples collected along a wetland‐to‐upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high‐affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine‐scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
Laudato Si's View on Integral Ecology in Light of the Planetary Boundaries Concept
Authors: De Tavernier Johan , Ndubueze Kingsley 
Published: April 2020

AbstractPromoting ecological awareness and sustainability of God's creation is now considered as a primary task of the CST. However, from its beginning with Rerum Novarum, CST emphasizes the promotion of social justice and equity, and highlights the dangers of economic inequalities between richer and poorer nations and the need for distributive justice. To that effect, human development was its central theme, which is favored by the dominion mandate and is known nowadays as the Anthropocene. Important documents like Gaudium et Spes and Populorum Progressio are illustrative for this anthropocentric stance, while less attention is given to the wellbeing of nonhuman creatures and natural ecosystems. Nevertheless, from Octogesima Adveniens onwards, the CST starts to look into environmental issues. Pope Francis' Laudato Si' in 2015 introduces a significant shift by referring to nonhuman creatures as ‘our fellow creatures’, thereby extending ‘intrinsic value’ to all nonhuman creatures. In his integral ecology, he promotes a sustainable and integral development that favors the wellbeing of both human and natural environments. In this article, we assess Laudato Si's view on sustainability and integral development in confrontation with the wider framework of the Planetary Boundaries's concept of sustainable development.
Vasogenic edema in the medial temporal lobe during treatment of diabetic ketoacidosis in an elderly patient
Authors: Wakabayashi Hikaru , Kobayashi Zen , Kakei Takeshi , Ishihara Shoichiro , Tomimitsu Hiroyuki , Shintani Shuzo 
Published: April 2020

AbstractA 68‐year‐old woman presented with a 1‐month history of appetite loss and weight loss, followed by vertigo and a decreased level of consciousness. A diagnosis of diabetic ketoacidosis (DKA) was made, and treatment of DKA was initiated. Her level of consciousness gradually improved, but time‐related disorientation as well as recent memory disturbance persisted even after a decrease in the level of blood glucose. Brain MRI demonstrated vasogenic edema in the left medial temporal lobe. Vasogenic cerebral edema during the treatment of DKA should be considered not only in children and young adults, but also in elderly patients.
The canalization hypothesis – challenges and alternatives
Authors: Ravichandran Sree Janani , Linh Nguyen Manh , Scarpella Enrico 
Published: April 2020

SummaryThe ‘canalization hypothesis’ was suggested 50 years ago by Tsvi Sachs to account for the formation of vascular strands in response to wounding or auxin application. The hypothesis proposes that positive feedback between auxin movement through a cell and the cell's auxin conductivity leads to the gradual selection of narrow ‘canals’ of polar auxin transport that will differentiate into vascular strands. Though the hypothesis has provided an invaluable conceptual framework to understand the patterned formation of vascular strands, evidence has been accumulating that seems to be incompatible with the hypothesis. We suggest that the challenging evidence is incompatible with current interpretations of the hypothesis but not with the concept at the core of the hypothesis' original formulation.
RLP/K enrichment sequencing; a novel method to identify receptor‐like protein (RLP) and receptor‐like kinase (RLK) genes
Authors: Lin Xiao , Armstrong Miles , Baker Katie , Wouters Doret , Visser Richard G. F. , Wolters Pieter J. , Hein Ingo , Vleeshouwers Vivianne G. A. A. 
Published: April 2020

Summary

The identification of immune receptors in crop plants is time‐consuming but important for disease control. Previously, resistance gene enrichment sequencing (RenSeq) was developed to accelerate mapping of nucleotide‐binding domain and leucine‐rich repeat containing (NLR) genes. However, resistances mediated by pattern recognition receptors (PRRs) remain less utilized.

Here, our pipeline shows accelerated mapping of PRRs. Effectoromics leads to precise identification of plants with target PRRs, and subsequent RLP/K enrichment sequencing (RLP/KSeq) leads to detection of informative single nucleotide polymorphisms that are linked to the trait.

Using Phytophthora infestans as a model, we identified Solanum microdontum plants that recognize the apoplastic effectors INF1 or SCR74. RLP/KSeq in a segregating Solanum population confirmed the localization of the INF1 receptor on chromosome 12, and led to the rapid mapping of the response to SCR74 to chromosome 9. By using markers obtained from RLP/KSeq in conjunction with additional markers, we fine‐mapped the SCR74 receptor to a 43‐kbp G‐LecRK locus.

Our findings show that RLP/KSeq enables rapid mapping of PRRs and is especially beneficial for crop plants with large and complex genomes. This work will enable the elucidation and characterization of the nonNLR plant immune receptors and ultimately facilitate informed resistance breeding.
The influence of lateral flows in an aquifer on the agricultural value of groundwater
Authors: Kovacs Kent F. , Durand‐Morat Alvaro 
Published: April 2020

AbstractValuation of water in an aquifer depends on reliable information about the hydrologic conditions of an aquifer. Regions of depression emerge in an aquifer because groundwater cannot seamlessly flow between shallow and deep aquifer locations, and our analysis shows that the degree of lateral flow influences the value of the water in the aquifer. The assumption that groundwater declines uniformly over a landscape, a bathtub aquifer, leads to an underestimate of the value of a unit of water in an aquifer but an overestimate of the wealth that the aquifer represents. For the alluvial aquifer in Arkansas, USA, the average accounting price of water in an aquifer is almost 40% higher if there is no lateral flow, but the groundwater wealth is 10% lower. The value of an aquifer with the limited lateral flow is less sensitive to changes in agricultural markets, the discount rate, or the natural recharge of the aquifer.Recommendations for Resource Managers
Average value of water in an aquifer with limited lateral flows is nearly 40% higher than the value of an aquifer with high lateral flows.
Groundwater wealth weights the accounting prices of water in the aquifer by the amount water underneath each site. As lateral flows decline, the wealth of the aquifer rises and then falls because the distribution of accounting prices change so most water is beneath sites with lower accounting prices.
The average value of water in an aquifer is less sensitive to changes in hydro‐economic model parameters such as the natural recharge or discount rate when the lateral flows are less.
Methylene blue and monosodium glutamate improve neurologic signs after fluoroacetate poisoning
Authors: DeLey Cox Vanessa E. , Hartog Matthew A. , Pueblo Erin , Racine Michelle , Jennings Laura , Tressler Justin , Tuet Wing Y. , Stone Samuel , Pierce Samuel A. , Thompson Lily , Dukes Aliyah , Hoard‐Fruchey Heidi , Wong Benjamin , McCranor Bryan J. 
Published: April 2020

AbstractFluoroacetate (FA) is a tasteless, odorless, water‐soluble metabolic poison with severe toxicological effects. Characterized in the mid‐1900s, it has been used as a rodenticide but is comparably lethal to all mammals. Many countries have restricted its use, and modern‐day accidental human exposures are rare, but recently, concerns have been raised about its application as a chemical weapon with no known antidote. A combined treatment of methylene blue (MB), an antioxidant, and monosodium glutamate (MSG), a precursor of the citric acid cycle substrate alpha‐ketoglutarate, has been recommended as an effective countermeasure; however, no peer‐reviewed articles documenting the efficacy of this therapy have been published. Using a rodent model, we assessed the effects of MB and MSG on the neurologic, cardiac, and pulmonary systems. Transcriptomic analysis was used to elucidate inflammatory pathway activation and guide bioassays, which revealed the advantages and disadvantages of these candidate countermeasures. Results show that MB and MSG can reduce neurologic signs observed in rats exposed to sodium FA and improve some effects of intoxication. However, while this strategy resolved some signs of intoxication, ultimately it was unable to significantly reduce lethality.
Characterization of ovarian development in girls from birth to 9 months
Authors: Chin Helen B. , Baird Donna D. , Kaplan Summer L. , Darge Kassa , Adgent Margaret A. , Ford Eileen G. , Rogan Walter J. , Stallings Virginia A. , Umbach David M. 
Published: April 2020

AbstractBackgroundThe minipuberty of infancy is a period of increased reproductive axis activity. Changes in reproductive hormone concentrations and organ size occur during this period, but longitudinal changes have not been well described.ObjectivesThe objective of this study was to characterize ovarian growth trajectories and ovarian follicle development during the first 9 months of life in a large longitudinal cohort of healthy girls.MethodsData from the Infant Feeding and Early Development Study, a longitudinal cohort study of oestrogen‐responsive outcomes in healthy infants, were used to estimate ovarian growth trajectories and describe the presence of ovarian antral follicles in girls 0‐9 months old. Ovarian ultrasound evaluations were performed on the infants within 72 hours of birth (newborn visit) and at 4, 8, 16, 24, and 32 weeks of age. Mixed‐effects regression splines were used to characterize changes in ovarian volume during infancy and assess the association between the presence of ovarian follicles at the newborn visit and ovarian growth.ResultsThis analysis included 163 girls with two or more ovarian ultrasounds in the study. Results from the estimated overall ovarian growth trajectory show that ovarian volume increases more than sixfold during the first 16 weeks after birth and then remains relatively stable in the later weeks of infancy. Among girls with observable ovaries at the newborn visit (n = 133), girls with at least one visible ovarian follicle showed more rapid initial ovarian growth compared with girls without visible follicles.ConclusionsInfant ovarian volume increased to a peak at 16 weeks, which was influenced by the number and size of developing follicles. This research contributes to future development of reference ranges for postnatal ovarian growth in healthy, term infants.
MicroRNA regulation of Toll‐like receptor, RIG‐I‐like receptor and Nod‐like receptor pathways in teleost fish
Authors: Chu Qing , Xu Tianjun 
Published: April 2020

AbstractThe innate immune system is the first‐line defence against invading pathogens, and the main molecules involved in recognizing invading pathogens are the pattern recognition receptors. Accumulating evidences have demonstrated that activation and termination of the immune responses are regulated by various layers of regulators and mechanisms. MicroRNAs (miRNAs) are a group of small non‐coding RNAs that emerged as critical component of the complex regulatory networks in fish immune responses. In this review, we have summarized miRNA regulation in teleost fish, which can provide new insights into the regulation of innate immune receptor pathways in fish. Meanwhile, we comprehensively discuss the recent researches on how teleost miRNAs respond to the signalling pathways of innate immune receptors, including Toll‐like receptors, retinoic acid‐inducible gene‐I‐like receptors and Nod‐like receptors.
Facilitators and barriers associated with the implementation of a Swedish psychosocial dementia care programme in Japan: a secondary analysis of qualitative and quantitative data
Authors: Nakanishi Miharu , Ziylan Canan , Bakker Ton , Granvik Eva , Nägga Katarina , Nishida Atsushi 
Published: April 2020

BackgroundA psychosocial dementia care programme for challenging behaviour (DEMBASE®) was developed in collaboration with a Swedish BPSD‐registry team for in‐home care services use in Japan. The programme consisted of a web‐based tool for the continued assessment of challenging behaviours and interdisciplinary discussion meetings. Effectiveness of the adapted programme was verified through a cluster‐randomised controlled trial. The Tokyo Metropolitan Government provided municipal funding to introduce the programme into daily practice beginning in April 2018.ObjectivesTo investigate both facilitators and barriers associated with programme implementation.DesignA secondary analysis of qualitative and quantitative data.SettingsData were collected in naturalistic long‐term care settings from April 2018 to March 2019.ParticipantsA total of 138 professionals and 157 people with dementia participated in the programme.MethodsChallenging behaviour in persons with dementia was assessed by professionals using a total Neuropsychiatric Inventory score. Data on expected facilitators and barriers were extracted for qualitative analysis from a debriefing meeting between professionals.ResultsOf the 157 persons with dementia, 81 (51.6%) received follow‐up behavioural evaluations by March 2019. The average level of challenging behaviour was significantly reduced for 81 persons from baseline to their most recent follow‐up evaluations. Facilitators included ‘programme available for care managers’, ‘visualised feedback on professionals’ work’, ‘affordable for providers and professionals’ and ‘media coverage’. Barriers included ‘professionals from different organisations’, ‘unpaid work’, ‘operation requirement for municipalities’ and ‘conflict with daily benefit‐oriented framework’.ConclusionsA follow‐up evaluation was not fully achieved. Further strategies to address barriers may include the development of a benefit‐rewarding scheme for interdisciplinary discussion meetings, an e‐learning system capable of substituting training course portions and a cross‐municipality training course.
Psychometric evaluation of the Swedish Quality of Dyadic Relationships scale – homogeneity and construct validity
Authors: Gudjonsdottir Johanna , Eklund Mona , Ingberg Edvin , Ström Jakob O. 
Published: April 2020

AbstractRationale and aimsThe Quality of Dyadic Relationships is a self‐assessment scale used to evaluate various aspects of relationship quality. Psychometric evaluation by the developers of the instrument has led to a nontested amended version. Further psychometric testing is thus warranted, and the aim of this study was to evaluate homogeneity, construct validity (in terms of concurrent, discriminant and known‐groups validity) and any floor and ceiling effects of the Quality of Dyadic Relationships.MethodsForty‐seven cohabitant couples (47 women with a mean age of 30.0 years and 47 men with a mean age of 31.5 years) answered the Quality of Dyadic Relationships, the Relationship Assessment Scale (to test concurrent validity) and the Perceived Stress Scale (to test discriminant validity). Homogeneity (internal consistency) was calculated by Cronbach’s alpha. Concurrent and discriminant validity were estimated as correlations between Quality of Dyadic Relationships and the other instruments. Assessment of known‐groups validity was based on the variables of parental status and gender. Floor and ceiling effects were evaluated according to frequency distribution.ResultsThe overall homogeneity was good with acceptable Cronbach’s alpha values (α > 0.70) for all subscales but dyadic sexuality. Concurrent validity and discriminant validity were found. Known‐groups validity was indicated by significant differences between individuals with different parental status on the total QDR index, where the ones without children scored higher. No difference between the genders was found. No significant floor effects were found, but a significant ceiling effect was found in the subscale dyadic sensuality, with 27.7% of respondents scoring maximum.ConclusionIn all, the QDR showed promising psychometric properties and may be used for screening and follow‐up purposes. However, it can benefit from further development, as suggested by the ceiling effect in the subscale dyadic sensuality and the low internal consistency in the subscale dyadic sexuality.
Uncertainties in BP management in dialysis patients
Authors: Doulton Timothy W. R. , Swift Pauline A. , Murtaza Asam , Dasgupta Indranil 
Published: April 2020

AbstractHypertension in dialysis patients is extremely common. In this article, we review the current evidence for blood pressure (BP) goals in hemodialysis patients, and consider the effectiveness of interventions by which BP may be lowered, including manipulation of dietary and dialysate sodium; optimization of extracellular water; prolongation of dialysis time; and antihypertensive medication. Although two meta‐analyses suggest lowering BP using antihypertensive drugs might be beneficial in reducing cardiovascular events and mortality, there are insufficient rigorously designed trials in hypertensive hemodialysis populations to determine preferred antihypertensive drug classes. We suggest aiming for predialysis systolic BP between 130 and 159 mm Hg, while at the same time acknowledge the significant limitations of the data upon which it is based. We conclude by summarizing current knowledge as regards management of hypertension in the peritoneal dialysis population and make recommendations for future research in this field.