bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference
Authors: Bocharov Sergey , Harris Simon , Kominek Emma , Mooers Arne Ø. , Steel Mike
Published: September 2021

Abstract

In the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate λ for timet. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges toastgrows, and thus is essentially independent oft. However, the behaviour of the lengthLof thelongestpendant edge reveals remarkably different behaviour:Lconverges tot/2 as the expected number of leaves grows. Extending this model to allow an extinction rateμ(whereμ< λ), we also establish a similar result for birth-death trees, except thatt/2 is replaced byt/2 · (1 –μ/λ). This ‘complete’ tree may contain subtrees that have died out before timet; for the ‘reduced tree’ that just involves the leaves present at timetand their direct ancestors, the longest pendant edge lengthLagain converges tot/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.
The Drosophila TMEM184B ortholog Tmep ensures proper locomotion by restraining ectopic firing at the neuromuscular junction
Authors: Cho Tiffany S. , Beigaitė Eglė , Klein Nathaniel E. , Sweeney Sean T. , Bhattacharya Martha R.C.
Published: September 2021

TMEM184B is a putative seven-pass membrane protein that promotes axon degeneration after injury. TMEM184B mutation causes aberrant neuromuscular architecture and sensory and motor behavioral defects in mice. The mechanism through which TMEM184B causes neuromuscular defects is unknown. We employed Drosophila melanogaster to investigate the function of the TMEM184B ortholog, Tmep (CG12004) at the neuromuscular junction. We show that Tmep is required for full adult viability and efficient larval locomotion. Tmep mutant larvae have a reduced body contraction rate compared to controls, with stronger deficits in females. Surviving adult Tmep mutant females show “bang sensitivity,” a phenotype associated with epileptic seizures. In recordings from body wall muscles, Tmep mutants show substantial hyperexcitability, with many post-synaptic potentials fired in response to a single stimulation, consistent with a role for Tmep in restraining synaptic excitability. Neuromuscular junctions in Tmep mutants show modest structural defects and satellite boutons, which could also contribute to poor locomotor performance. Tmep is expressed in endosomes and synaptic vesicles within motor neurons, suggesting a possible role in synaptic membrane trafficking. Using RNAi knockdown, we show that Tmep is required in motor neurons for proper larval locomotion and excitability. Locomotor defects can be rescued by presynaptic knock-down of endoplasmic reticulum calcium channels or by reducing evoked release probability, suggesting that excess synaptic activity drives behavioral deficiencies. Our work establishes a critical function for the TMEM184B ortholog Tmep in the regulation of synaptic transmission and locomotor behavior.
High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome
Authors: Eble Holger , Joswig Michael , Lamberti Lisa , Ludington William B.
Published: September 2021

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Yet biological interactions between genes (1, 2), species (3–6), and different environmental contexts (7–9) change the individual effects due to non-additive interactions, known as epistasis. In the fitness landscape concept, each gene/organism/environment is modeled as a separate biological dimension (10), yielding a high dimensional landscape, with epistasis adding local peaks and valleys to the landscape. Massive efforts have defined dense epistasis networks on a genome-wide scale (2), but these have mostly been limited to pairwise, or two-dimensional, interactions (11). Here we develop a new mathematical formalism that allows us to quantify interactions at high dimensionality in genetics and the microbiome. We then generate and also reanalyze combinatorically complete datasets (two genetic, two microbiome). In higher dimensions, we find that key genes (e.g. pykF) and species (e.g. Lactobacillus plantarum) distort the fitness landscape, changing the interactions for many other genes/species. These distortions can fracture a “smooth” landscape with one optimal fitness peak into a landscape with many local optima, regulating evolutionary or ecological diversification (12), which may explain how a probiotic bacterium can stabilize the gut microbiome.
Post-encoding modulation of spatial memory by a GABAA-agonist
Authors: Iggena Deetje , Maier Patrizia M. , Häußler Sophia M. , Menk Mario , Olze Heidi , Larkum Matthew E. , Finke Carsten , Ploner Christoph J.
Published: September 2021

We investigated the role of the post-encoding period for consolidation of self-centered (egocentric) and world-centered (allocentric) spatial memory in neurologically normal human subjects. We used the GABAA-ergic anesthetic propofol to transiently modulate neural activity during the early stage of spatial memory consolidation. A total of 52 patients undergoing minor surgery learned to navigate to a target in a five-armed maze derived from animal experiments immediately prior to injection of propofol (early group) or more than 60 minutes before injection (late group). Two hundred and forty minutes after anesthesia, subjects were tested for memory-guided navigation. Our results show a selective impairment of memory-guided navigation in the early group and near-normal performance in the late group. Both egocentric and allocentric navigation were affected, albeit with distinct error patterns. In the egocentric condition, early group patients navigated significantly more often to a wrong alley of the maze but showed normal navigation times, thus suggesting a deficit mainly for memory of sequences of path segments. By contrast, in the allocentric condition, early group patients mostly navigated to the correct alley of the maze but showed a significant increase in detours and prolonged navigation times, thus suggesting a weakened representation of the relationship between landmarks. We conclude that presumably hippocampus-dependent networks contribute to early consolidation of representations underlying both egocentric and allocentric memory-guided navigation. Distinct aspects of these representations are susceptible to GABAA-ergic modulation within a post-encoding time-window of less than 60 minutes, indicating a redistribution and reconfiguration of spatial memory networks early during consolidation.

Significance statement

Propofol modulates consolidation of spatial representations underlying human spatial navigation.

Following administration of propofol, memory-guided navigation using self-centered (egocentric) and world-centered (allocentric) spatial information is impaired.

Error patterns after administration of propofol suggest modulation of a post-encoding integration process relevant for ego- and allocentric memory representations.

The transient susceptibility of this process to GABAA-ergic modulation is consistent with rapid reconfiguration of networks for spatial memory shortly after learning.

Propofol provides a pharmacological tool to investigate spatial memory consolidation in humans.
SAMD1 Distribution Patterns in Mouse Atherosclerosis Models Suggest Roles in LDL Retention, Antigen Presentation, and Cell Phenotype Modulation
Authors: Campbell Bruce , Bourassa Patricia , Aiello Robert
Published: September 2021

The theory that lesions formed by retention of circulating LDL can then progress to complicated atherosclerotic lesions has been a subject of debate, as has the mechanism of retention. In earlier work, we identified SAMD1, a protein expressed by intimal smooth muscle cells in human lesions that appears to irreversibly bind apoB-Lps in extracellular matrix near the lumen. We hypothesized this binding could contribute to the formation of lesions in mice, and that inhibiting binding could reduce lesion growth. In mouse models of atherosclerosis, we found that SAMD1 binds LDL; that SAMD1/apoB complex is ingested by intimal cells; and that recognizable epitopes of the SAMD1/apoB complex survive some degree of catabolism in foam cell. These data appear to support the SAMD1/LDL retention hypothesis of lesion growth. Despite apparently irreversible binding of human LDL to full-length human SAMD1, efficient anti-SAMD1-antibody inhibitors were created. In vivo lesion targeting of inhibitors was demonstrated by MRI, ultrasound, and ex vivo microscopy. However, only non-statistically significant reductions in spontaneous lesion size in apoE-/- mice were seen after 12 weeks of treatment with PEG-fab inhibitors of SAMD1/LDL binding. In contrast, these inhibitors substantially reduced LDL retention in carotid injury lesions in apoE-/- and LDLR-/- mice 7 days after injury. The most obvious difference between injury lesions and early spontaneous lesions is the presence of numerous smooth muscle cells and associated extracellular matrix in the injury lesions. Thus, SAMD1 may be involved in retention of apoB-Lps in mouse lesions, but not until smooth muscle cells have entered the intima. In addition, SAMD1 is seen throughout arteries in changing patterns that suggest broader and more complicated roles in atherosclerosis.
Computation of the mitochondrial age distribution along the axon length
Authors: Kuznetsov Ivan A. , Kuznetsov Andrey V.
Published: September 2021

We describe a compartmental model of mitochondrial transport in axons, which we apply to compute mitochondrial age at different distances from the soma. The model predicts that at the tip of an axon that has a length of 1 cm, the average mitochondrial age is approximately 22 hours. The mitochondria are youngest closest to the soma and their age scales approximately linearly with distance from the soma. To the best of the authors’ knowledge, this is the first attempt to predict the spatial distribution of mitochondrial age within an axon. A sensitivity study of the mean age of mitochondria to various model parameters is also presented.
Full-length NLRP3 forms oligomeric cages to mediate NLRP3 sensing and activation
Authors: Andreeva Liudmila , David Liron , Rawson Shaun , Shen Chen , Pasricha Teerithveen , Pelegrin Pablo , Wu Hao
Published: September 2021

The nucleotide-binding domain and leucine-rich-repeat (LRR) containing protein 3 with a pyrin domain (NLRP3) is emerging to be a critical intracellular inflammasome sensor of membrane integrity and a highly important clinical target against chronic inflammation. Here we report that the endogenous, stimulus-responsive form of full-length NLRP3 is a 12-16 mer double ring cage held together by LRR-LRR interactions with the pyrin domains shielded within the assembly to avoid premature activation. Surprisingly, this NLRP3 form is predominantly membrane localized, which is consistent with previously noted localization of NLRP3 at various membrane organelles. Structure-guided mutagenesis reveals that trans-Golgi network dispersion into vesicles, an early event observed for all NLRP3 activating stimuli, requires the double ring cages of NLRP3. Double ring-defective NLRP3 mutants further abolish inflammasome punctum formation, caspase-1 processing and cell death. Thus, unlike other inflammasome sensors that are monomeric when inactive, our data uncover a unique NLRP3 oligomer on membrane that is poised to sense diverse signals to induce inflammasome activation.
Therapeutic efficacy of an oral nucleoside analog of remdesivir against SARS-CoV-2 pathogenesis in mice
Authors: Schäfer Alexandra , Martinez David R. , Won John J. , Moreira Fernando R. , Brown Ariane J. , Gully Kendra L. , Kalla Rao , Chun Kwon , Du Pont Venice , Babusis Darius , Tang Jennifer , Murakami Eisuke , Subramanian Raju , Barrett Kimberly T , Bleier Blake J. , Bannister Roy , Feng Joy Y. , Bilello John P. , Cihlar Tomas , Mackman Richard L. , Montgomery Stephanie A. , Baric Ralph S. , Sheahan Timothy P.
Published: September 2021

The COVID-19 pandemic remains uncontrolled despite the rapid rollout of safe and effective SARS-CoV-2 vaccines, underscoring the need to develop highly effective antivirals. In the setting of waning immunity from infection and vaccination, breakthrough infections are becoming increasingly common and treatment options remain limited. Additionally, the emergence of SARS-CoV-2 variants of concern with their potential to escape therapeutic monoclonal antibodies emphasizes the need to develop second-generation oral antivirals targeting highly conserved viral proteins that can be rapidly deployed to outpatients. Here, we demonstrate the in vitro antiviral activity and in vivo therapeutic efficacy of GS-621763, an orally bioavailable prodrug of GS-441524, the parental nucleoside of remdesivir, which targets the highly conserved RNA-dependent RNA polymerase. GS-621763 exhibited significant antiviral activity in lung cell lines and two different human primary lung cell culture systems. The dose-proportional pharmacokinetic profile observed after oral administration of GS-621763 translated to dose-dependent antiviral activity in mice infected with SARS-CoV-2. Therapeutic GS-621763 significantly reduced viral load, lung pathology, and improved pulmonary function in COVID-19 mouse model. A direct comparison of GS-621763 with molnupiravir, an oral nucleoside analog antiviral currently in human clinical trial, proved both drugs to be similarly efficacious. These data demonstrate that therapy with oral prodrugs of remdesivir can significantly improve outcomes in SARS-CoV-2 infected mice. Thus, GS-621763 supports the exploration of GS-441524 oral prodrugs for the treatment of COVID-19 in humans.
Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR
Authors: Zehnder Johannes , Cadalbert Riccardo , Yulikov Maxim , Künze Georg , Wiegand Thomas
Published: September 2021

Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the “blind sphere” around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (~14 Å) than for nitroxide (~11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.
Experimental confirmation that an uncommon, yet clinically relevant mutation (G878A) in the rrs gene of Mycobacterium tuberculosis confers resistance to streptomycin
Authors: Domenech Pilar , Mouhoub Esma , Reed Michael B.
Published: September 2021

The effective treatment of patients diagnosed with drug resistant tuberculosis (TB) is highly dependent upon the ability to rapidly and accurately determine the antibiotic resistance/ susceptibility profile of the Mycobacterium tuberculosis isolate(s) involved. Thus, as more and more clinical microbiology laboratories advance towards the routine use of DNA sequence-based diagnostics, it is imperative that their predictive functions extend beyond the well-known resistance-conferring mutations, in order to also encompass as many of the lower-frequency mutations as possible. However, in most cases, the fundamental experimental proof that links these uncommon mutations with phenotypic resistance is still lacking. One such example is the G878A polymorphism within the rrs gene encoding the 16s rRNA. We, and others, have identified this mutation within a small number of drug-resistant M. tuberculosis isolates, although prior to this study a consensus regarding exactly which aminoglycoside antibiotic(s) it conferred resistance toward seems not to have been reached. Here we have employed oligo-mediated recombineering to specifically introduce the G878A polymorphism into the rrs gene of M. bovis BCG - a species very closely related to M. tuberculosis - and demonstrate that it confers low-level resistance to streptomycin alone. In our hands, it does not confer cross-resistance towards amikacin, capreomycin, nor kanamycin. We also demonstrate that the rrsG878A mutation exerts a substantial fitness defect in vitro, that may at least in part explain why clinical M. tuberculosis isolates bearing this mutation appear to be quite rare. Overall, this study provides clarity to the resistance phenotype attributable to the rrsG878A mutation and is relevant to the future implementation of genomics-based diagnostics, as well as the clinical management of patients in situations where this particular polymorphism is encountered.
Unsteady squeezing second order of nanofluid flow through an infinite channel
Authors: Salahuddin Taimoor , Haider Ali , Alghamdi Metib
Published: September 2021

Purpose

The current investigation is communicated to analyze the characteristics of squeezed second grade nanofluid flow enclosed by infinite channel in the existence of both heat generation and variable viscosity. The leading non-linear energy and momentum PDEs are converted into non-linear ODEs by using suitable analogous approach.

Design/methodology/approach

Then the acquired non-linear problem is numerically calculated by using Bvp4c (built in) technique in MATLAB.

Findings

The influence of certain appropriate physical parameters, namely, squeezed number, fluid parameter, Brownian motion, heat generation, thermophoresis parameter, Prandtl number, Schmidt number and variable viscosity parameter on temperature, velocity and concentration distributions are studied and deliberated in detail. Numerical calculations of Sherwood number, Nusselt number and skin friction for distinct estimations of appearing parameters are analyzed through graphs and tables. It is examined that for large values of squeezing parameter, the velocity profile increases, whereas opposite behavior is noticed for large values of variable viscosity and fluid parameter. Moreover, temperature profile increases for large values of Brownian motion, thermophoresis parameter and squeezed parameter and decreases by increases Prandtl number and heat generation. Moreover, concentration profile increases for large values of Brownian motion parameter and decreases by increases thermophoresis parameter, squeezed parameter and Schmidt number.

Originality/value

No one has ever taken infinite squeezed channel having second grade fluid model with variable viscosity and heat generation.
Analysis of risk spillover effect of copper option in China
Authors: Ye Wuyi , Wang Yiqi , Zhao Jinhai
Published: September 2021

Purpose

The purpose of this paper is to compare the changes in the risk spillover effects between the copper spot and futures markets before and after the issuance of copper options, analyze the risk spillover effects between the three markets after the issuance of the options and can provide effective suggestions for regulators and investors who hedge risks.

Design/methodology/approach

The MV-CAViaR model is an extended form of the vector autoregressive model (VAR) to the quantile model, and it is also a special form of the MVMQ-CAViaR model. Based on the VAR quantile model, this model has undergone continuous promotion of the Conditional Autoregressive Value-at-Risk Model (CAViaR) and the Multi-quantile Conditional Autoregressive Value-at-Risk Model (MQ-CAViaR), and finally got the current form of the model.

Findings

The issuance of options has led to certain changes in the risk spillover effect between the copper spot and its derivative markets, and the risk aggregation effect in the futures market has always been significant. Therefore, when supervising the copper product market and investors using copper derivatives to avoid market risks, they need to pay attention to the impact of futures on the spot market, the impact of options on the futures market and the risk spillover effects of spot and futures on the options market.

Practical implications

The empirical results of this paper can be used to hedge market risk investment strategies, and the changes in market relationships also provide an effective basis for the supervision of the copper product market by the supervisory authority.

Originality/value

It is the first literature research to discuss the risk and the impact of spillover effects of copper options on China copper market and its derivative markets. The MV-CAViaR model can capture the mutual risk influence between markets by modeling multiple markets simultaneously.
Case study: why Paysend is moving to remote-first working
Authors: Nicolaus Alex
Published: September 2021

Purpose

With the COVID-19 pandemic causing businesses to shake up social and work practices, the purpose of this paper is to explore why global fintech Paysend has decided to shift toward a new norm of remote-first working.

Design/methodology/approach

A real-world case study.

Findings

Although some organizations, especially larger ones, are urging employees to return to a daily office commute, a remote first set up is definitely here to stay.

Originality/value

Paysend was one of the very first fintechs that moved to a fully remote model at the start of the pandemic in early March 2020.
The Remaking of Conservatism: Boris Johnson and the Politics of Brexit
Authors: Gamble ANDREW
Published: September 2021

Why has the Conservative Party been such a successful political party? One of the reasons lies in the ability of its leaders to understand and navigate the pressure of the politics of power and the politics of support, adjusting to changing circumstances and being focussed on what is needed in order to gain and hold power in the particular circumstances of the British political system. Since the publication of The Conservative Nation in 1974 the party has reinvented itself twice, first under Thatcher and now under Johnson. The character of the remaking under Johnson is analysed together with some of the problems for pursuing a successful post‐Brexit statecraft, particularly delivering the ‘levelling‐up’ agenda and the ‘global Britain’ agenda in ways which will consolidate rather than fragment the new Conservative coalition, and preserve the Union.
Echolocation among the blind: an argument for an ontogenetic turn
Authors: Downey Greg
Published: September 2021

Proponents of the ontological turn typically advance a highly conceptual understanding of variation in ontology. In contrast, this article argues theoretically that cultural canalizations of embodied ontogenetic processes — especially the development of local neurologies — underwrite distinct lived worlds. This theoretical argument for a corporeal basis of world‐making draws on the case of vision‐impaired individuals who actively echolocate, or perceive space using sound. Neurological evidence shows that echolocators’ sensory practices over developmental time produce specialized brain adaptations to behaviour. Human echolocation thus demonstrates how enculturation effaces the distinction between biology and culture in a behavioural‐developmental spiral with implications for our understanding of human being.
Idiopathic granulomatous mastitis associated with erythema nodosum may indicate a worse prognosis
Authors: Velidedeoğlu Mehmet , Papila Kundaktepe Berrin , Mete Bilgul , Uğurlu Serdal
Published: September 2021

Introduction

Idiopathic granulomatous mastitis (IGM) is a chronic inflammatory breast disease of unknown etiology, and erythema nodosum (EN) is a rare extramammary manifestation of this entity characterized by reddish, tender nodules of the lower legs. We aimed to investigate whether the association of IGM with EN has a role as a prognostic indicator. There are few case reports, and only 1 original article including 12 IGM patients with EN has been reported.

Methods

We present 43 women with IGM coexisting with EN and 43 with a diagnosis of IGM only, who were randomly selected from 610 patients for a control group. To the best of our knowledge, this paper comprises the first comparative study of the coexistence of IGM and EN to be reported in the literature.

Results

Our findings show that the association of IGM with EN indicates a more aggressive disease course. White blood cells, erythrocyte sedimentation rate, and C‐reactive protein were significantly higher in the EN‐positive group (P < .05). Arthralgia, breast feeding, fistula distribution and recurrence distributions were significantly higher in the EN‐positive group (P < .05).

Conclusion

Since fistula distribution and recurrence rates were higher in EN‐positive group, association of IGM with EN may be an indictor of a worse prognosis. The present study highlights the importance of dermatological care. All physicians should not neglect questioning breast complaints in patients with EN since EN may be caused by IGM.
Trophic ecology of two amphibian species in patches and core forest of Atlantic Forest: A dietary and isotopic approach
Authors: de Oliveira Mateus , Moser Camila Fernanda , Rebelato Marluci Muller , de Camargo Plínio Barbosa , Tozetti Alexandro Marques
Published: September 2021

Species richness and abundance, as well as trophic relationships, are affected by habitat configuration. Smaller habitat patches suffer greater external interference, being more susceptible to diversity loss and could also receive more trophic subsidies from outside or matrix, which can favour the maintenance of populations even in small patches. Natural mosaics of forest patches in a grassland matrix in southern Brazil are good places to analyse such a process. Our objective was to analyse the effect of habitat patching on trophic relationships based on the evaluation of two forest amphibian species (Physalaemus lisei and P. carrizorum) and compare those from habitat patches versus core/contiguous habitat. We compared isotopic carbon (δ13C) and nitrogen ratios (δ15N) in two anuran species as well the variation in their diet at different forest patch sizes. We chose carbon isotopes since they act as a proxy for inferences on the original habitat from which the matter flows towards the anurans, while nitrogen reveals their tropic level. Our results revealed that trophic sources for these amphibians derives predominantly from primary forest productivity. However, Physalaemus lisei δ13C values indicated that the contribution of grassland trophic sources in the diet was higher in frogs from forests patches (<100 ha) than in those from core forest habitat. In smaller patches, P. lisei consumed predominantly ants, which was the most abundant prey on habitat. On the other hand, in the core forest, where isopods were the most abundant prey, most of its consumption was beetles, spiders and ants. In contrast, P. carrizorum showed no significant changes in isotopic ratios or diet across habitats. Isotopic data suggested that both species occupied lower trophic levels in smaller forests than in core forests. Our data showed a tendency towards the increase of grassland contribution and decrease of amphibian trophic position in patched habitats in comparison to continuous habitat.
Study on the concordance between different SNP‐genotyping platforms in sheep
Authors: Marina H. , Chitneedi P. , Pelayo R. , Suárez‐Vega A. , Esteban‐Blanco C. , Gutiérrez‐Gil B. , Arranz J. J.
Published: September 2021

Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false‐positive results in genome‐wide association studies. Currently, whole‐genome resequencing (WGR) also offers the potential for variant calling analysis and high‐throughput genotyping. WGR might overshadow array‐based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP‐chip technologies, namely, Affymetrix and Illumina, for high‐throughput genotyping in sheep considering high‐coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP‐chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low‐reliability markers before exploiting genomic information for gene mapping analyses or genomic prediction.
Satisfaction with general practitioner obstetrician‐led maternity care in rural Western Australia
Authors: Roxburgh Carly , Moore Sarah , McCulloch Claudia , Valli Kelsey , Zuidersma Danika , Pikora Terri , Ngo Hanh
Published: September 2021

Objective

To measure satisfaction with general practitioner obstetrician‐led maternity care in Western Australia and to explore perspectives of maternity service users

Design

Women were recruited at antenatal visits with their general practitioner obstetrician. Participants completed a validated three‐part survey about their satisfaction with antenatal, intrapartum and postpartum care. They were all offered a semi‐structured interview.

Setting

Nine general practitioner obstetrician practices located in regional Western Australia.

Participants

155 women receiving general practitioner obstetrician‐led maternity care within the South West or Great Southern regions of Western Australia. 13 of these women also participated in an interview.

Main Outcome Measures

We quantified satisfaction with aspects of antenatal, intrapartum and postpartum care using a Likert scale. Descriptive variables included demographic information and birth outcomes. Qualitative data described valued aspects of maternity care.

Results

116 women completed all 3 surveys. General practitioner obstetrician‐led care resulted in high rates of satisfaction across all 3 stages of care, with 78%‐100% agreement with positively worded satisfaction statements. Thematic analysis identified four key aspects of care women valued when receiving maternity care: the woman‐centred care experience, the skills of the general practitioner obstetrician, support from the health care team and the health care environment.

Conclusion

General practitioner obstetrician‐led maternity care is a highly regarded model of maternity care, valued by rural women with high rates of satisfaction.
Successful outcomes with transplanting kidneys from deceased donors with acute kidney injuryon temporary renal replacement therapy
Authors: Budhiraja Pooja , Heilman Raymond L. , Jadlowiec Caroline C. , Smith Maxwell L. , Ryan Margaret S. , Khamash Hasan A. , Kodali Lavanya , Moss Adyr A. , Mathur Amit K. , Reddy Kunam S.
Published: September 2021

Background and objectives

We aimed to determine outcomes with transplanting kidneys from deceased donors with severe acute kidney injury requiring acute renal replacement therapy (RRT).

Materials and methods

A total of 172 recipients received a kidney from donors with acute kidney injury stage 3 (AKIN3) requiring RRT. We compared the study group to 528 recipients who received a kidney from donors with AKIN stage 3 not on RRT and 463 recipients who received < 85% Kidney Donor Profile Index (KDPI) AKIN stage 0 kidney.

Results

The study group donors were younger compared to the 2 control groups. Despite higher DGF in the study group, the length of hospital stay and acute rejection were similar. Death censored graft survival (96% AKIN3‐RRT vs. 97%AKIN3 no RRT vs. 96% KDPI < 85% AKIN0,P = 0.26) and patient survival with functioning graft at 1 year (95% across all groups,P = 0.402) were similar. The estimated glomerular filtration rate were similar across the 3 groups after first month. Interstitial fibrosis and tubular atrophy score ≥ 2 on protocol biopsy at time 0, 4 and 12 months were similar. Primary nonfunction was rare and associated with high KDPI.

Conclusions

Transplanting selected kidneys from deceased donors with AKIN3 requiring RRT is safe and has good outcomes.
Association of donor hypertension and outcomes in orthotopic heart transplantation
Authors: Kim Samuel T. , Hadaya Joseph , Tran Zachary , Iyengar Amit , Williamson Catherine G. , Rabkin David , Benharash Peyman
Published: September 2021

The present study examined the impact of donor hypertension on recipient survival and offer acceptance practices in the United States. This was a retrospective study of all patients undergoing OHT from 1995 to 2019 using the United Network for Organ Sharing and Potential Transplant Recipient file databases. Hypertensive donors were stratified by Short (0–5 years) and Prolonged (> 5 years) hypertension. Multivariable logistic regression was used to analyze offer acceptance practices while Cox proportional‐hazards models were used to compare mortality across groups. Of 38,338 heart transplants meeting study criteria, 5662 were procured from hypertensive donors (69% Short and 31% Prolonged). After adjustment, Prolonged donor hypertension was associated with increased mortality (hazard ratio, HR, 1.31, 95% confidence interval, CI, 1.04–1.64), while recipients of Short donors experienced no decrement in post‐transplant survival. Both Short and Prolonged hypertension were independently associated with decreased odds of offer acceptance (odds ratio, OR .92 95%CI: .88–.96 and OR .93 95%CI: .88–.99, respectively). While prolonged untreated hypertension in OHT donors is associated with a slight decrement in recipient survival, donors with ≤5 years of hypertension yielded similar outcomes. Donor hypertension was associated with reduced organ offer acceptance, highlighting a potential source of organ underutilization.
Quantifying adaptive divergence of the snowfinches in a common landscape
Authors: She Huishang , Jiang Zhiyong , Song Gang , Ericson Per G. P. , Luo Xu , Shao Shimiao , Lei Fumin , Qu Yanhua
Published: September 2021

Aim

Species living in a shared environment face similar selective pressures and often evolve adaptive divergence to avoid competition. Quantifying phenotypic divergence and its genetic parallelism among sympatric species is important for understanding of ecologically moderated biodiversity. Here, we integrate ecologic, phenotypic and genomic datasets to study to what extent three sympatrically snowfinches (Montifringilla adamsi, Pyrgilauda ruficollis and Onychostruthus taczanowskii) differ in their adaptations in order to co‐exist in a shared environment.

Location

Qinghai–Tibetan Plateau.

Methods

We used principal component analysis to summarize and compare environmental and phenotypic divergence. We compared phenotypes relevant to body and beak sizes (n = 68) because they are indicators of niche and food segregation, thus critical for establishing co‐existence of sympatric birds. We used comparative genomics (n = 33) to identify genetic loci that are highly divergent between species as well as loci unique for each of species. Using vector analyses, we integrated correlation and permutation to quantify parallelism between phenotypic and genetic divergences.

Results

We found that body and beak sizes are significantly different among three snowfinches. The phenotypic differentiations are greater in species that share similar ecological conditions than in those that do not. We showed that genes related to developmental process are over‐represented within highly divergent genomic regions and unique genetic loci of each species. We found that the extent of phenotypic divergence between snowfinch pairs is more strongly correlated with the magnitude of divergence in developmental genes than in the whole genome.

Main conclusions

Adaptive divergence of sympatric snowfinches is highly constrained on developmental genes. As this genetic divergence is strongly correlated with divergence of the traits related to segregation in niche and food resources, this correlation reflects either causal effects or indirect consequences of ecological mediated changes. Our study provides novel insights into the mechanisms underlying evolutionary versatility and ecological success among sympatric species.
Free‐PhaseGas Detection in Groundwater Wells via Water Pressure and Continuous Field Parameters
Authors: Morais Tiago A. , Ladd Bethany , Fleming Neil A. , Ryan M. Cathryn
Published: September 2021

Detection of free‐phase gas (FPG) in groundwater wells is critical for accurate assessment of dissolved gas concentrations and the occurrence of FPG in the subsurface, with consequent implications for understanding groundwater contamination and greenhouse gas emissions. However, identifying FPG is challenging during routine groundwater monitoring and there is poor agreement on the best approach to detect the occurrence of FPG in groundwater. In this study, laboratory experiments in a water column were designed to mimic nonflowing and flowing conditions in a groundwater well to evaluate how the presence of FPG affects water pressure and commonly used continuous field parameters. The laboratory results were extrapolated to interpret field data at an abandoned exploration well with episodic release of free‐gas CO2. The FPG effect on water pressure varied between flowing and nonflowing wells, and depending on whether the FPG was above or below the sensor. Electrical conductivity values were decreased and/or behaved erratically when FPG was present in the water column. Findings from this study have shown that the combined measurement of water pressure, electrical conductivity, and total dissolved gas pressure can provide information about the occurrence of FPG in groundwater wells. Measurement of these parameters at different depths can also provide information about relative depths and amounts of FPG within the well water column. This approach can be used for long‐term monitoring of groundwater gases, managing gas‐locking in production wells with gassy groundwater, and measuring fugitive greenhouse gas emissions from groundwater wells.
Leachability and basicity of Na‐ and K‐based geopolymer powders and lattices used as biodiesel catalysts
Authors: Botti Renata , Innocentini Murilo D. M. , Faleiros Thais A. , Paschoalato Cristina F. P. R. , Mello Murilo F. , Franchin Giorgia , Colombo Paolo
Published: September 2021

Geopolymer powders and 3D‐printed lattices have shown promising preliminary results as heterogeneous catalysts for the transesterification of vegetable oils to produce biodiesel. However, questions about the basicity of catalytic sites and the leaching characteristics of metals (K, Na) and hydroxyl groups in the reactional mixtures remained. The leaching of alkaline ions in methanol and biodiesel for powder and printed geopolymer formulations based on K, Na, or Na+K activators and treated at 110 to 700°C was investigated, as well as the physiochemical modifications of the materials. The Hammett indicators were used to determine base strength, and both leachable and total basicities were quantified. The amount of Na and K leached into the biodiesel phase was negligible (<1% wt.%). Methanol leaching reached a maximum of 29.3%. The base strength ranged between 11.0 and 18.4. Potassium‐based geopolymer lattices presented the highest basicity, followed by sodium and sodium‐potassium geopolymer catalysts. The basicity of all formulations decreased gradually as the calcination temperature increased. When compared to the homogeneous catalysts NaOH and KOH, the level of biodiesel contamination with Na and K is 81–93% lower. The findings support the heterogeneous nature of geopolymers as biodiesel catalysts and further validates their use for this application.
Pocket closure and residual pockets after non‐surgical periodontal therapy: A systematic review and meta‐analysis
Authors: Citterio Filippo , Gualini Giacomo , Chang Moontaek , Piccoli Gian Marco , Giraudi Marta , Manavella Valeria , Baima Giacomo , Mariani Giulia Maria , Romano Federica , Aimetti Mario
Published: September 2021

Aim

To analyse the efficacy of non‐surgical therapy (NST) in terms of pocket closure (PC) and changes in percentage and number of pockets.

Materials and Methods

Three databases (PubMed, EMBASE, and Scopus) were searched up to January 2020. Prospective studies with a minimum follow‐up of 12 months and presenting data in terms of PC or number or percentage of pocket depths (PDs) before and after NST on systemically healthy patients were included. Random‐effect meta‐analyses were performed.

Results

After screening 4610 titles and abstracts, 27 studies were included. Of these, 63.9% of PC was reported by one study. The percentage of PDs ≤3 mm changed from 39.06% to 64.11% with a weighted mean difference (WMD) of 26.14% (p < .001). This accounted for a relative increase of healthy sites of 64.13%. The mean percentage of PD ≥5 mm was 28.23% and 11.71% before and after treatment, respectively, with a WMD of 15.50% (p < .001). The WMD in the number of PDs ≥5 mm before and after treatment was 24.42 (p = .036). The mean number of residual PPD ≥5 after NST was 14.13.

Conclusions

NST is able to eradicate the majority of the pockets. However, residual pockets after NST may remain and should be considered cautiously for further treatment planning.
An ultrasound‐assisted extraction system to accelerate production of Mhiskey, a rice spirit‐based product, inside oak barrel: Total phenolics, color, and energy consumption
Authors: Gavahian Mohsen , Chu Rachael , Ratchaneesiripap Paphawarin
Published: September 2021

Rice spirit‐based (RSB) products, such as rice wine, are commonly used in several Asian cuisines. While RSB can be enriched with phenolic compounds (e.g., through extraction from oak barrel) to develop a healthier product with a new flavor, such a process is expected to be time‐consuming. At the same time, the culinary and adult beverage industry demands approaches for developing innovative products based on affordable alternatives to barley. Therefore, an ultrasound‐based system was set up in a 10‐L oak barrel to develop a new RSB product that referred to as “Mhiskey” in this study. The system was run at 0, 275, and 550 W, and changes in total phenolics, color values (L*, a*, b*, color intensity, and overall color changes), pH, and degrees Brix were studied during the extraction process. According to the results, this system reduced the extraction time, enhanced the total phenolic compounds, and produced a Mhiskey with similar physical properties to those of the conventional method. Increasing sonication power reduced the extraction time significantly but did not affect the specific energy consumption. In terms of total phenolics, the final products had up to 162 mg GAE per L sample. This new system is scalable and can be implemented in the industry after further economic and technical evaluations. Furthermore, the product developed in the present study might be evaluated for commercialization (e.g., for culinary purposes) after sensory and market research.

Practical applications

This study proposed a new extraction system based on ultrasound technology that can be used to process rice spirit‐based (RSB). The system is scalable and can be adopted in the industry to reduce the processing time which can provide benefits for wineries. Also, the energy consumption can be reduced by optimizing the processing parameters. The technical information reported in this work can also be used as a base for process optimization at an industrial scale. At the same time, the final product of this process, that is, Mhiskey, has the potential to be sold in the market at a competitive price.
Early detection of hearing loss for infants in Western Australia: Comparison to international benchmarks
Authors: Reid Allison , Firns Sarah , Tao Karina , Maywood Erin , Herbert Hayley , Mulders Wilhemina A M , Kuthubutheen Jafri , Brennan‐Jones Christopher
Published: September 2021

Aim

To assess the degree to which timely audiological assessment of congenital hearing loss is achieved at our institution ‐ Perth Children's Hospital, Western Australia, and to review cases which breached this timeframe in order to address barriers to timely assessment. The benchmark used to determine timely assessment is that set out by The Joint Committee on Infant Hearing (JCIH) in which diagnostic audiological testing occurs by three months of age for those who do not pass newborn hearing screening.

Methods

A retrospective chart review of infants who underwent diagnostic auditory assessment at Perth Children's Hospital between 2016‐2019. A total of 151 children were identified as meeting the inclusion criteria and their medical files were reviewed. Time to first dABR was the time point for whether testing was achieved within the 3 month timeframe.

Results

Of the 151 children who underwent dABR assessments, 1 was identified as having breached the 90 day time limit (tested on day 91) for which no valid reason for delay could be identified. The timely delivery of dABR assessments in 99.3% of cases within this cohort compares favourably with the literature.

Conclusions

Conclusion Timely diagnostic audiological assessment is achievable for children with congenital hearing loss. The reasons for patients breaching this timeframe are explored in the paper along with factors which may help avoid delays.