bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptome profiles of eggplant (Solanum melongena) and its wild relativeS. dasyphyllumunder different levels of osmotic stress provide insights into response mechanisms to drought
Authors: Villanueva Gloria , Vilanova Santiago , Plazas Mariola , Prohens Jaime , Gramazio Pietro
Published: November 2022

Defence mechanisms to abiotic stresses, like drought, are very broad and RNA sequencing (RNA-Seq) can help in understanding the complex responses triggered. In this study, we performed RNA-Seq of the transcriptomes of eggplant (Solanum melongena) and its related wild species (S. dasyphyllum) under two PEG concentrations (20% and 30%), two different times (after 0.5 h and 2 h of osmotic stress) and at two plant phenological stages (three and five true fully developed leaves).Solanum dasyphyllumwas more tolerant to osmotic stress, and a differential expression pattern of drought-related genes was identified between the two species. Plants subjected to a higher osmotic potential, at a more adult stage and at a higher stress exposure time displayed a higher number of DEGs (differential expressed genes). Gene ontology (GO) enrichment analysis revealed that, compared toS. melongena, S. dasyphyllumtriggered the regulation of a wide range of transcription factors (AP2/ERF, DREB, bZIP, WRKY and bHLH). In both species, the abscisic acid (ABA) signaling response pathway played a crucial role leading to stomatal closure. Other important pathways involved in abiotic stresses tolerance including flavonoid, carotenoid and phenylpropanoid biosynthesis, chlorophyll metabolism and photosynthesis pathway among others were found to have a relevant role under both moderate and severe osmotic stresses. Our results reveal thatS. dasyphyllumis a potential source of genes for breeding resilient eggplant varieties.
Metals and metal isotopes in insect wings: Implications for diet, geolocation and pollution exposure
Authors: Reich Megan S. , Kindra Mira , Dargent Felipe , Hu Lihai , Tyler Flockhart D.T. , Norris D. Ryan , Kharouba Heather , Talavera Gerard , Bataille Clément P.
Published: November 2022

Anthropogenic activities are exposing insects to abnormal levels of toxic metals, with unknown implications for migratory insects. Simultaneously, metals and metal isotopes have become promising tools for the geolocation of migratory insects. Furthering our understanding of metal cycling in insect tissues is essential, both for the development of metals and metal isotopes as geolocation tools, and for assessing the toxicity risks of metals to insects. We conducted a diet-switching experiment on monarch butterflies (Danaus plexippus) with controlled larval and adult diets to evaluate the dietary and environmental sources of 23 metals and metalloids, strontium isotopes, and lead isotopes to insect wing tissues over a period of 8 weeks. Concentrations of Ca, Co, and Sb differed between the sexes. Ni and Zn bioaccumulated in the insect wing tissues over time, likely from the adult diet, while increases in Al, Cr, Cd, Cu, Fe, and Pb were likely from external sources (i.e., dust aerosols). Bioaccumulation of Pb in the monarch wings was confirmed by Pb isotopes to be from external anthropogenic sources, revealing the potential of Pb isotopes to become an indicator and tracer of metal pollution exposure along migratory paths. Concentrations of Ba, Cs, Mg, Na, Rb, Sr, Ti, Tl, and U appeared to be unaffected by dietary or environmental contamination and should be further developed for geolocation purposes. Strontium isotope ratios remained indicative of the larval diet, at least in males, supporting its potential as a geolocation tool. However, the difference in strontium isotope ratios between sexes, as well as the possibility of external contamination by wetting, requires further investigation. Our results demonstrate the complexity of metal cycling in insects and the need for further investigations, as well as the value of studying metals to develop new tools to quantify pollution exposure, metal toxicity and insect mobility.
Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance
Authors: Connor Ryan , Yarmosh David A. , Maier Wolfgang , Shakya Migun , Martin Ross , Bradford Rebecca , Brister J. Rodney , Chain Patrick SG , Copeland Courtney A. , di Iulio Julia , Hu Bin , Ebert Philip , Gunti Jonathan , Jin Yumi , Katz Kenneth S. , Kochergin Andrey , LaRosa Tré , Li Jiani , Li Po-E , Lo Chien-Chi , Rashid Sujatha , Maiorova Evguenia S. , Xiao Chunlin , Zalunin Vadim , Pruitt Kim D.
Published: November 2022

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.
Environmental micro‐niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield
Authors: Rolli Eleonora , Marasco Ramona , Fusi Marco , Scaglia Barbara , Schubotz Florence , Mapelli Francesca , Ciccazzo Sonia , Brusetti Lorenzo , Trombino Luca , Tambone Fulvia , Adani Fabrizio , Borin Sara , Daffonchio Daniele
Published: November 2022

The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m2 area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co‐occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high‐throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche‐specific role of the micro‐environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico‐chemical and micro‐climatic variations at the site‐spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.
Primary teachers' knowledge and attitudes about autism, and experience of good practice approaches: implications for policy and practice in Croatia
Authors: Stošić Jasmina , Lisak Šegota Natalija , Preece David
Published: November 2022

Education in Croatia is based upon principles of inclusion and individualisation. However, the effective inclusion of learners with special educational needs, including those with autism, has been identified as limited. To better understand the situation within primary education in the country, a survey of specialist teachers from mainstream and special primary schools was undertaken (n = 99), to investigate such teachers' knowledge and attitudes regarding autism, and their experience of ‘good autism practice’ methods and approaches. Knowledge was inconsistent, and inaccurate understandings were common. Attitudes regarding the inclusion of learners with autism were ambivalent. Training in ‘good practice’ approaches was extremely limited; however, despite low confidence, the use of these approaches was common. Teachers' education needs in autism were identified, and implications for future teacher education in autism, practice and policy initiatives are discussed.
Teaching, learning and philosophising as metaphysical animals: Introduction
Authors: Jamieson Lesley
Published: November 2022

In recent years, a new scholarly gaze has been cast on four women-Elizabeth Anscombe, Philippa Foot, Mary Midgley, and Iris Murdoch-who have come to be known as the ‘Wartime Quartet’. During the postwar period, when women were still scarce in the discipline, these four flourished as philosophers. New details about their wartime education give us materials to reflect on what enabled them to develop their unique philosophical voices. Their work dispels widespread philosophical dogmas, especially scientistic interpretations of naturalism that exclude value from the fabric of reality. Through their attention to the details of ordinary life, they avoid flattening the complexities of moral learning, especially where this involves navigating intergenerational differences. The articles in this Suite look to the Wartime Quartet's writings and learning conditions to show that, far from being of purely historical interest, they shed fresh light on the aims and challenges of moral education and offer a critical perspective on current pedagogical practices-particularly in the teaching of philosophy.
Patients with low body mass index are more likely to develop shoulder pain after laparoscopy
Authors: Jiang Yuxia , Wu Yijun , Lu Shentao , Que Yuni , Chi Yugang , Liu Qianfen
Published: November 2022

Introduction

Shoulder pain is one of the most common complications after laparoscopy. Previous studies have found a number of methods to reduce shoulder pain after laparoscopic surgery, but these methods have not been targeted to specific populations. The purpose of this study was to identify people who are more likely to develop shoulder pain.

Material and methods

A total of 203 patients underwent laparoscopy for benign gynecological diseases between July 2020 and February 2021. Patients were divided into two groups according to the Chinese overweight standard, body mass index less than 24 kg/m2 group and 24 kg/m2 or more group. The baseline characteristics and intraoperative data between the two groups were compared. The intensity of the shoulder pain was quantified using a visual analog scale (VAS).

Results

The incidence and the VAS scores of shoulder pain were significantly higher in the less than 24 kg/m2 group (63.64% vs 38.03%, p < 0.001 in incidence; median 5 (interquartile range [IQR] 3–7) vs 3 (IQR 2–5), p < 0.001 in VAS scores), and the chance of shoulder pain within 24 hours after laparoscopy was higher in the less than 24 kg/m2 group (89.29% vs 66.67%, p = 0.013). In univariate and multivariate logistic regression analysis, BMI less than 24 kg/m2 was an independent risk factor of shoulder pain after laparoscopic surgery (p = 0.001, p = 0.031, respectively). Shoulder pain scores were inversely correlated with BMI (r = −0.300, p = 0.001).

Conclusions

Patients with low body mass index are more likely to develop shoulder pain after laparoscopy, with earlier onset and higher pain scores.
Adaptability and emotional, behavioural and cognitive aspects of self‐regulated learning: Direct and indirect relations with academic achievement and life satisfaction
Authors: Feraco Tommaso , Casali Nicole , Ganzit Elena , Meneghetti Chiara
Published: November 2022

Background

Adaptability regulates individuals' cognitive, behavioural and emotional responses to new, unexpected and uncertain situations, but to date no study has analysed whether adaptability contemporarily favours cognitive, behavioural and emotional aspects of learning.

Aims

This study aims to address this gap by examining (i) the direct relations between adaptability and achievement emotions, self‐regulated learning strategies and academic self‐efficacy and (ii) the direct and indirect relations between adaptability and academic achievement and life satisfaction through and over the other study‐related factors.

Sample

A total of 1083 students (415 males, Mage = 13.37, SDage = 1.97, age range = 10–18) in grades 6–12 participated to the study.

Method

Questionnaires were used to measure students' adaptability, positive and negative achievement emotions, self‐regulated learning strategies, academic self‐efficacy and life satisfaction. Schools provided grades obtained by each student at the end of the academic year.

Results

A path analysis based on 1083 students (10–18 years old) confirmed that adaptability directly relates to the three study‐related factors considered and to life satisfaction and indirectly relates to academic achievement and life satisfaction—through the mediation of the other variables.

Conclusions

The results, discussed in accordance with the self‐regulated learning theory, enlarge the nomological framework of adaptability and highlight its importance for emotional, behavioural and cognitive aspects of self‐regulated learning.
Phase II trial of a novel chemotherapy regimen CVEP (cyclophosphamide, vinblastine, etoposide and prednisolone) for acquired immunodeficiency syndrome (AIDS)‐associated lymphomas
Authors: Sengar Manju , Jain Hasmukh , Shet Tanuja , Sridhar Epari , Gota Vikram , Rangarajan Venkatesh , Laskar Siddhartha S. , Alahari Aruna , Thorat Jayashree , Agarwal Archi , Sharma Neha , Gupta Himanshi , Kannan Sadhana , Kumar Shikhar , Nayak Lingaraj , Menon Hari , Gujral Sumeet , Bagal Bhausaheb
Published: November 2022

Management of acquired immunodeficiency syndrome (AIDS)‐related diffuse large B‐cell (DLBCL) and plasmablastic lymphomas (PBL) poses significant challenges. The evidence supports use of dose‐adjusted EPOCH (etoposide, prednisone, vincristine, cyclophosphamide and doxorubicin) with or without rituximab as first‐line therapy. The need for central venous access, growth factors and significant toxicities limits its use in resource‐constrained settings. To address these challenges, we have developed a novel regimen, CVEP (cyclophosphamide, vinblastine, etoposide, and prednisolone) based on the pharmacodynamic principles of dose‐adjusted EPOCH. This single‐centre phase II study evaluated the efficacy and safety of CVEP regimen in patients with de novo systemic AIDS‐related DLBCL and PBL. The primary objective was complete response (CR) rates as assessed by positron emission tomography‐computed tomography. The secondary objectives were incidence of Grade 3/4 toxicities, toxicities requiring hospitalisation, and disease‐free survival. From May 2011 to February 2017, 42 patients were enrolled. At the end of therapy the CR rates were 69% (29/42) in the intention‐to‐treat population and 80.5% (29/36) in evaluable patients. At a median follow‐up of 69 months, the 5‐year disease‐free survival was 65.3%. Out of 217 cycles administered, febrile neutropenia occurred in 19.3% and hospitalisation was required in 18.3% of cycles. There were two treatment‐related deaths. The CVEP regimen is an active and safe regimen for AIDS‐related DLBCL and PBL.
The perceived helpfulness of structural family therapy in caring for Hong Kong Chinese families of an adolescent with intellectual disabilities: A qualitative inquiry
Authors: Lo Julia W. K. , Ma Joyce L. C.
Published: November 2022

Background

Previous literature pinpointed the limitations of behavioural treatment in helping families of people with intellectual disabilities to transit lifecycle adjustment and suggested the contributions of systemic intervention made to this population.

Methods

This study aimed to explore the applicability of structural family therapy to helping Hong Kong Chinese families of adolescents with intellectual disabilities from the perspective of family members. Nine members from four families of adolescents with intellectual disabilities were recruited. Family or individual interviews were conducted. A thematic analysis was adopted for data analysis.

Findings

The families experienced two major changes after the therapy, that is, sharing the care responsibilities among family members and using more open communication styles in the family. Structural family therapy was found to be helpful in mediating family problems and promoting the active involvement of adolescents with intellectual disabilities in family interactions. However, the family participants expected clear guidance for the future development of adolescents with intellectual disabilities in a family treatment process.

Conclusions

Structural family therapy can be a promising approach to working with Chinese families of adolescents with intellectual disabilities.
Does a tax deduction scheme matter for jobs and investment by multinational and domestic enterprises?
Authors: Konings Jozef , Lecocq Catherine , Merlevede Bruno
Published: November 2022

Many countries have reduced corporate income tax rates or introduced tax deductions, exclusions and credits to attract foreign direct investment. This paper analyzes the introduction of the notional interest deduction (NID) in Belgium, which allows companies to deduct from their taxable income an interest that is calculated based on the company's equity. We use an event type study approach to analyze the evolution of employment and investment of foreign affiliates in Belgium. We find that the tax deduction has increased employment and investment in the Belgian affiliates on average by 7.4 and 6.1%, respectively, in the period after the introduction of the NID. The NID, however, also provides a higher after‐tax return on investment to domestic Belgian firms. Using a matching analysis, we find that domestic Belgian firms with low external financial dependence also respond to the NID but somewhat less strongly, domestic firms with high external financial dependence do not show NID‐driven investment nor employment creation.
Mechanism and application of ozone fading: Oxidative decolorisation of disperse dyes and waste‐dyed polyester fabrics
Authors: Lou Jiangfei , Ren Lamei , Yuan Jiugang , Xu Jin , Gu Zhengbiao , Fan Xuerong
Published: November 2022

As the most common synthetic fibre, polyester has consistently been in high demand and usage, but its recycling has always been a problem for the textile industry. The decolorisation of dyed polyester is the key to expanding its recycling use, and there is no rapid, effective and simple decolorisation method. In this study, ozone was used to decolorise dispersed dyes developed for polyester. Ozone was effective in decolorising CI Disperse Orange 30 and CI Disperse Blue 60, and the process was extended to the decolorisation of dyed polyester fabric. Based on single factor analysis, the optimum decolorisation technological conditions were: an ozone feed rate of 130 mg L−1 min−1, treatment time of 2 hours, wet pick‐up of 100% and pH value of 3, with which the decolorisation rate and colour difference values could exceed 45% and 6%, respectively. The changes in dye structure during the process of ozone decolorisation were analysed using scanning electron microscopy, X‐ray diffraction and Fourier Transform–infrared spectroscopy, and the mechanism of ozone decolorisation was also investigated. The results showed that the crystallinity decreased from 41.18% to 36.30% with a strength retention rate of above 80%, and demonstrated that ozone can be used on polyester fabric and dye simultaneously. The aim of entering the fibre was achieved by etching the polyester and decolorisation was achieved by oxidising the chromaticity groups.
Trapped K‐feldspar phenocrysts as a signature of melt migration pathways within active high‐strain zones
Authors: Silva David , Piazolo Sandra , Daczko Nathan R.
Published: November 2022

Melt migration through high‐strain zones in the crust fundamentally influences their rheological behaviour and is important for the transfer of fluids to upper crustal regions. The inference of former melt‐present deformation, based on field observations, may be hampered if the high‐strain zone experience a low time‐integrated melt flux or high melt volume expulsion during deformation. In these cases, typical macro‐scale field evidence of former melt presence limits interpretations. In this contribution, we investigate igneous field evidence ranging from obvious to cryptic in the Gough Dam shear zone (central Australia), a 2‐ to 4‐km‐wide high‐strain zone shown to have acted as a significant melt pathway during the Alice Springs Orogeny. Within bands of the high‐strain zone, granitic lenses are easily discernible in the field and are inferred to have formed during melt present deformation. Related coarse K‐feldspar is observed in biotite‐rich (>75 vol%) schist (glimmerite) as either isolated grains, forming trails (sub)parallel to the main foliation, or in aggregates with subordinate quartz. Detailed characterization of the granitic lenses shows that pockets of phenocrysts may be entrained in the shear zone. If melt expulsion and melt‐rock interaction is severe, isolated K‐feldspar grains in glimmerite may form. These grains exhibit (i) partially preserved crystal faces; (ii) a lack of internal grain deformation; (iii) reaction textures preferentially formed along the main crystallographic axes showing dissolution of K‐feldspar and precipitation of dominantly biotite; (iv) low‐strain domains between multiple K‐feldspar grains being inferred to enclose crystallized melt pockets, with some apparently isolated grains showing connectivity in three dimensions; and (v) a weak quartz and K‐feldspar crystallographic preferred orientation. These observations suggest an igneous phenocrystic origin for the isolated K‐feldspar grains hosted in glimmerite, which is consistent with the observed REE concentration patterns with positive Eu anomaly. We propose that the K‐feldspar phenocrysts are early‐formed crystals that were entrained into the glimmerite rocks as reactive melt migrated through the actively deformatting high‐strain zone. Previously entrained K‐feldspar phenocrysts were trapped during the collapse of the melt pathway when melt flux‐related fluid pressure waned while confining pressure and tectonic stress were still significant. The active deformation facilitated expulsion or loss of the melt phase but retainment and trapping of phenocrysts. Hence, the presence of isolated or ‘trains’ of K‐feldspar phenocrysts is a cryptic signature of syndeformational melt transfer. If melt transfer occurs in an open chemical system, phenocrysts will be entrained within the reaction product of melt‐rock interaction. We suggest that these so‐called trapped phenocrysts are a viable indicator of former syntectonic melt passage through rocks.
The molecular diversity of plasticity mechanisms underlying memory: An evolutionary perspective
Authors: Zha Congyao , Sossin Wayne S.
Published: November 2022

Experience triggers molecular cascades in organisms (learning) that lead to alterations (memory) to allow the organism to change its behavior based on experience. Understanding the molecular mechanisms underlying memory, particularly in the nervous system of animals, has been an exciting scientific challenge for neuroscience. We review what is known about forms of neuronal plasticity that underlie memory highlighting important issues in the field: (1) the importance of being able to measure how neurons are activated during learning to identify the form of plasticity that underlies memory, (2) the many distinct forms of plasticity important for memories that naturally decay both within and between organisms, and (3) unifying principles underlying the formation and maintenance of long‐term memories. Overall, the diversity of molecular mechanisms underlying memories that naturally decay contrasts with more unified molecular mechanisms implicated in long‐lasting changes. Despite many advances, important questions remain as to which mechanisms of neuronal plasticity underlie memory.

image
The associated evolution among the extensive RNA editing, GC‐biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae
Authors: Kang Jong‐Soo , Yu Jigao , Zhang Xian‐Chun , Xiang Qiao‐Ping
Published: November 2022

Extensive C‐to‐U editing has been reported from plastid genomes (plastomes) and mitochondrial genomes (mitogenomes) of spikemoss. While “reverse” U‐to‐C editing was recorded in other seed‐free plants such as hornworts, quillworts, and ferns, it was not observed in spikemosses. However, no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses. Here, we report thousands of C‐to‐U editing sites from plastomes and mitogenomes of two species: 1767 and 2394 edits in Selaginella remotifolia, and 4091 and 2786 edits in Selaginella nipponica, respectively. Comparative analyses revealed two different editing frequencies among plastomes, but one similar frequency in mitogenomes. The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity. The high guanine and cytosine (GC) content caused by GC‐biased mutations in organelle genomes might be related to the absence of U‐to‐C editing in Selaginellaceae. Using RNA‐seq and whole‐genome data, we screened the pentatricopeptide repeat (PPR) family and discovered that the number of aspartic acid–tyrosine–tryptophan (DYW) domain‐containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes. Consequently, we hypothesize that associated evolution among RNA editing, GC‐biased mutation in organelle genomes, and the PPR protein family encoded in the nuclear genome, is probably triggered by the aberrant DNA repair system in Selaginellaceae. Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae, which would contribute to understanding the evolution of post‐transcriptional modifications of organelle genomes in land plants.
Landscape and evolutionary dynamics of Helitron transposons in plant genomes as well as construction of online database HelDB
Authors: Li Shu‐Fen , Zhang Xin‐Yu , Yang Long‐Long , Jia Ke‐Li , Li Jia‐Rong , Lan Li‐Na , Zhang Yu‐Lan , Li Ning , Deng Chuan‐Liang , Gao Wu‐Jun
Published: November 2022

Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high‐quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user‐friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20–30 Ma and peaking at approximately 24 Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.
Characterization of clinicopathologic and abdominal ultrasound findings in dogs with glucocorticoid deficient hypoadrenocorticism
Authors: Reagan Krystle L. , McLarty Ehren , Marks Stanley L. , Sebastian Jamie , McGill Jennifer , Gilor Chen
Published: November 2022

Background

Clinical findings of glucocorticoid‐deficient hypoadrenocorticism (GDH) can overlap with other diseases, presenting a diagnostic challenge.

Objectives

Describe clinicopathologic and ultrasonographic features of dogs with GDH and those suspected of having GDH that had the disease ruled out.

Animals

Six hundred twenty‐three dogs.

Methods

Records from dogs with suspected GDH between 2003 and 2018 were reviewed. Dogs with hyperkalemia or hyponatremia were excluded. Dogs were categorized as controls when the resting serum cortisol or post‐ACTH cortisol concentration were > 2 μg/dL. Clinicopathologic and ultrasonographic features were compared between groups. The optimal cut‐point, area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were calculated for individual features used to detect GDH.

Results

Dogs were categorized as GDH (n = 29) or controls (n = 594). Lymphocyte count (>1750 cells/L; sensitivity, 96.6%; 95% confidence interval [CI], 82.8%‐99.8%; specificity, 60.3%; 95% CI, 56.3%‐64.1%; AUC, 0.828; 95% CI, 0.762‐0.894) and albumin/globulin ratio (<1.081; sensitivity, 86.2%; 95% CI, 69.4%‐94.5%; specificity, 78.8%; 95% CI, 75.3%‐81.9%; AUC, 0.886; 95% CI, 0.827‐0.944) had the highest discriminatory power between groups. Left adrenal gland width <0.39 cm was 80% (95% CI, 58.4%‐91.9%) sensitive and 82.4% (95% CI, 74.2‐88.4) specific for GDH. Serum cobalamin concentrations and ultrasonographic abnormalities of the GI tract were not different between groups.

Conclusion and Clinical Importance

No single variable could be used to confidently rule out GDH and obviate the need for cortisol testing in dogs with a clinical presentation consistent with GDH.
Canine and feline P‐glycoprotein deficiency: What we know and where we need to go
Authors: Mealey Katrina L. , Owens Jane G. , Freeman Elaine
Published: November 2022

In 2001 the molecular genetic basis of so‐called “ivermectin sensitivity” in herding breed dogs was determined to be a P‐glycoprotein deficiency caused by a genetic variant of the MDR1 (ABCB1) gene often called “the MDR1 mutation.” We have learned a great deal about P‐glycoprotein's role in drug disposition since that discovery, namely that P‐glycoprotein transports many more drugs than just macrocyclic lactones that P‐glycoprotein mediated drug transport is present in more places than just the blood brain barrier, that some cats have a genetic variant of MDR1 that results in P‐glycoprotein deficiency, that P‐glycoprotein dysfunction can occur as a result of drug–drug interactions in any dog or cat, and that the concept of P‐glycoprotein “inhibitors” versus P‐glycoprotein substrates is somewhat arbitrary and artificial. This paper will review these discoveries and discuss how they impact drug selection and dosing in dogs and cats with genetically mediated P‐glycoprotein deficiency or P‐glycoprotein dysfunction resulting from drug–drug interactions.
Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community
Authors: Srivathsan Amrita , Loh Rebecca Ker , Ong Elliott James , Lee Leshon , Ang Yuchen , Kutty Sujatha Narayanan , Meier Rudolf
Published: November 2022

DNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. However, little attention has been paid to the interaction between the invertebrate and vertebrate species. Here, we tested for specialization by sampling the dung and carrion fly community of a swamp forest remnant along a disturbance gradient (10 sites: 80–310 m from a road). Approximately, 60% of the baited 407 flies yielded 294 vertebrate identifications based on two COI fragments and 16S. A bipartite network analysis found no statistically significant specialization in the interactions between fly and vertebrate species, but uncommon fly species can carry the signal for vertebrate species that are otherwise difficult to detect with iDNA. A spatial analysis revealed that most of the 20 vertebrate species reported in this study could be detected within 150 m of the road (18 spp.) and that the fly community sourced for iDNA was unexpectedly rich (24 species, 3 families). They carried DNA for rare and common species inhabiting different layers of the forest (ground‐dwelling: wild boar, Sunda pangolin, skinks, rats; arboreal: long‐tailed macaque, Raffles' banded langur; flying: pin‐striped tit‐babbler, olive‐winged bulbul). All our results were obtained with a new, greatly simplified iDNA protocol that eliminates DNA extraction by obtaining template directly through dissolving fly faeces and regurgitates with water. Lastly, we show that MinION‐ and Illumina‐based metabarcoding yield similar results. We conclude by urging more studies that use different baits and involve experiments that are capable of revealing the dispersal capabilities of the flies carrying the iDNA.
Parents' Separation: What is the Effect on Parents' and Children's Time Investments?*
Authors: Le Forner Hélène
Published: November 2022

This paper investigates the effect of parental separation on children's allocation of their time and on the time spent with their parents. Based on detailed time‐use diaries from the Panel Study of Income Dynamics – Child Development Supplement, I estimate an individual fixed‐effect model and find that being in a single‐parent family decreases time with a parent accessible by 18% of a standard deviation (3 hours 30 minutes per week). Time spent with both parents together and alone with the non‐custodial parent is greatly affected, but the custodial parent partially compensates for this decrease. The decrease in time with a parent actively engaged in activities is, however, not statistically significant. Younger children continue spending as much time with their parents after separation. Effects on boys and girls differ, but this difference depends on the type of parental time investment we consider. Time spent with a grandparent acts as a recovery channel in single‐mother families. Time with a step‐parent increases but does not lead to an accumulation of parental time.
Phenotypic variability in LAMA3‐associated amelogenesis imperfecta
Authors: Wang Shih‐Kai , Zhang Hong , Wang Yin‐Lin , Seymen Figen , Koruyucu Mine , Simmer James P. , Hu Jan C.‐C.
Published: November 2022

Objective

Amelogenesis imperfecta (AI) is defined as inherited enamel malformations. LAMA3 (laminin alpha‐3) encodes a critical protein component of the basement membrane (laminin‐332). Individuals carrying heterozygous LAMA3 mutations have previously been shown to have localized enamel defects. This study aimed to define clinical phenotypes and to discern the genetic etiology for four AI kindreds.

Materials and Methods

Whole‐exome analyses were conducted to search for sequence variants associated with the disorder, and micro‐computed tomography (μCT) to characterize the enamel defects.

Results

The predominant enamel phenotype was generalized thin enamel with defective pits and grooves. Horizonal bands of hypoplastic enamel with chalky‐white discoloration and enamel hypomineralization were also observed and demonstrated by μCT analyses of affected teeth. Four disease‐causing LAMA3 mutations (NM_198129.4:c.3712dup; c.5891dup; c.7367del; c.9400G > C) were identified. Compound heterozygous MMP20 mutations (NM_004771.4:c.539A > G; c.692C > T) were also found in one proband with more severe enamel defects, suggesting a mutational synergism on disease phenotypes. Further analyses of the AI‐causing mutations suggested that both α3A (short) and α3B (long) isoforms of LAMA3 are essential for enamel formation.

Conclusions

Heterozygous LAMA3 mutations can cause generalized enamel defects (AI1A) with variable expressivity. Laminin‐332 is critical not only for appositional growth but also enamel maturation.
Implication of Changes in the Imaging Measurements after Mechanically Aligned Total Knee Arthroplasty
Authors: Cheng Long , Ren Peng , Zheng Qingyuan , Ni Ming , Geng Lei , Wang Yi‐Ming , Zhang Guo‐Qiang
Published: November 2022

Objective

Imaging measurements allow assessment of the mechanical alignment before and after total knee arthroplasty (TKA). The changes in radiographic parameters in each period of time within 1 year after TKA has been poorly understood. The purpose of this study was to examine the timing and causes of imaging changes in lower extremity force lines after total knee arthroplasty with mechanical alignment.

Methods

A total of 93 mechanically‐aligned TKA were radiographically examined before, 3 days, 3 months, and 1 year after surgery. Radiographic parameters included hip‐knee angle (HKA), lateral distal femoral angle (LDFA), medial proximal tibial angle (MPTA), knee joint line orientation (KJLO), ankle joint line orientation (AJLO), the knee joint line relative to ankle joint line angle (KJLTA) and midpoints of the ankle distance (MAD). Paired t‐test were used to analyze the changes of these imaging parameters, By establishing a simple tibial model, the time points of changes in the imaging parameters after TKA was determined, with an attempt to understand the post‐TKA changes in these imaging parameters.

Results

Statistically significant differences were found between the preoperative data and the data measured 3 days after surgery in HKA, LDFA, MPTA, MAD, KJLTA, AJLO (P < 0.05) while KJLO exhibited no significant difference (P = 0.089). There existed significant differences between the data measured 3 days and the measurements taken 3 months after operation in HKA, MPTA, KJLTA, KJLO, AJLO (P < 0.05), whereas LDFA and MAD showed no significant difference (P > 0.05). Significant differences were revealed between the data measured 3 months and those collected 1 year after surgery in LDFA, MPTA, AJLO, KJLTA (P < 0.05) but HKA, KJLO, AJLO showed no significant differences (P > 0.05). The tibial model was made to look into the changes in postoperative imaging parameters. ΔMAD and postoperative AJLO were calculated to verify the model and hypothesis.

Conclusions

Postoperative changes in radiographic parameters and tibial models showed that the lower extremities were in an unnatural state within 1 year after TKA. The changes in the lower extremities force line were the results of the gradual adaptation of the lower extremities to TKA and the lateral swing of the extremities (3°) after surgery. Imaging data 1 year after surgery should be taken into account in the explanation of post‐TKA changes in lower limb force lines.
Correctly responding to reasons while being means‐end incoherent
Authors: Schneider Leonhard
Published: November 2022

This paper argues that Reason Responsiveness (RR) accounts of rationality, proposed for example by Benjamin Kiesewetter and Error Lord, fail to explain structural irrationality (i.e., the irrationality involved in holding incoherent attitudes). Proponents of RR hold that rationality consists in correctly responding to available reasons. Structural irrationality, they argue, is just a “by‐product” of incorrect reason‐responding. Applying this idea to cases of means–end incoherence, this paper shows that RR accounts must rely on a certain transmission principle. Roughly, this amounts to the principle that necessarily, if (1) A has decisive available reason to intend to E and (2) A has decisive available reason to believe that intending to M is necessary for E‐ing, it follows that (3) A has decisive available reason to intend to M. By considering an example, this paper argues that even the most plausible version of this transmission principle does not hold true. It follows that one can correctly respond to one's available reasons while being means–end incoherent.
Changes in occupational class differences in leisure‐time physical activity and the contribution of retirement
Authors: Karjala Anni , Pietiläinen Olli , Salonsalmi Aino , Lahti Jouni , Lallukka Tea , Rahkonen Ossi
Published: November 2022

Occupational class differences in leisure‐time physical activity (LTPA) are well recognized. Less is known about how these differences develop as individuals age, and how retirement is associated with this change. We investigated how occupational class differences in LTPA change in a cohort over a 15–17 years follow‐up. We further examined, how the transition into mandatory or disability retirement contributed to the change in LTPA levels and occupational class differences. We used the data from the Helsinki Health Study surveying the aging City of Helsinki employees. In all, 8773 individuals were included in the analyses. We evaluated LTPA levels using weekly metabolic equivalent task (MET) hours and used generalized linear mixed effect models (GLMM) to estimate the development of LTPA levels. Commuting was included in the LTPA measure. Occupational class differences in LTPA emerged and widened during the follow‐up. The physical activity levels decreased in the lower occupational class and slightly increased in the higher occupational class, resulting in a difference of 4.3 MET‐hours at the end of follow‐up, accounting for 50 min of brisk walking per week. The occupational class differences emerged during transition into mandatory retirement and persisted after this. Transition into disability retirement temporarily widened the occupational class differences in LTPA levels, but the differences diminished during the follow‐up. Research on interventions to counteract the declining LTPA is needed to discover ways to prevent the widening of occupational health disparities during aging. The transition into old‐age retirement could be an optimal period for focusing these interventions.
Characterization of the novel HLA‐C*05:01:72 allele by next generation sequencing
Authors: Peters Lindsey , Mancini Shannon , Gravante Christopher , Persidsky Yuri , Liacini Abdelhamid
Published: November 2022

Full‐length sequence of HLA‐C*05:01:72 covers the 5′‐untranslated region (UTR), all introns and exons and the 3′ UTR.
Special IMM groups
Authors: Groves Daniel , Manning Jason Fox
Published: November 2022

Italiano–Martelli–Migliorini recently constructed hyperbolic groups which have non‐hyperbolic subgroups of finite type. Using a closely related construction, Llosa Isenrich–Martelli–Py constructed hyperbolic groups with subgroups of type but not . We observe that these hyperbolic groups can be chosen to be special in the sense of Haglund–Wise.
Spatiotemporal modelling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology
Authors: Bell Miriam K. , Lee Christopher T. , Rangamani Padmini
Published: November 2022

The modification of neural circuits depends on the strengthening and weakening of synaptic connections. Synaptic strength is often correlated to the density of the ionotropic, glutamatergic receptors, AMPARs, (α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptors) at the postsynaptic density (PSD). While AMPAR density is known to change based on complex biological signalling cascades, the effect of geometric factors such as dendritic spine shape, size and curvature remain poorly understood. In this work, we developed a deterministic, spatiotemporal model to study the dynamics of AMPARs during long‐term potentiation (LTP). This model includes a minimal set of biochemical events that represent the upstream signalling events, trafficking of AMPARs to and from the PSD, lateral diffusion in the plane of the spine membrane, and the presence of an extrasynaptic AMPAR pool. Using idealized and realistic spine geometries, we show that the dynamics and increase of bound AMPARs at the PSD depends on a combination of endo‐ and exocytosis, membrane diffusion, the availability of free AMPARs and intracellular signalling interactions. We also found non‐monotonic relationships between spine volume and the change in AMPARs at the PSD, suggesting that spines restrict changes in AMPARs to optimize resources and prevent runaway potentiation.

image

Key points

Synaptic plasticity involves dynamic biochemical and physical remodelling of small protrusions called dendritic spines along the dendrites of neurons.

Proper synaptic functionality within these spines requires changes in receptor number at the synapse, which has implications for downstream neural functions, such as learning and memory formation.

In addition to being signalling subcompartments, spines also have unique morphological features that can play a role in regulating receptor dynamics on the synaptic surface.

We have developed a spatiotemporal model that couples biochemical signalling and receptor trafficking modalities in idealized and realistic spine geometries to investigate the role of biochemical and biophysical factors in synaptic plasticity.

Using this model, we highlight the importance of spine size and shape in regulating bound AMPA receptor dynamics that govern synaptic plasticity, and predict how spine shape might act to reset synaptic plasticity as a built‐in resource optimization and regulation tool.