bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of productive qualities of rabbits when creating a new breeding group
Authors: Kosovsky G Yu , Karelina T K , Shumilina A R , Golovanova E V 
Published: September 2021

Abstract
Many branches of animal husbandry in our country are in need of domestic highly productive breeds and types of animals. Along with other problems – the lack of domestic developments in the field of animal housing and feeding systems that ensure high production efficiency, the lack of high-quality breeding resources is the most important factor hindering the development of the population’s own food production. Technologies and breeding resources of animals borrowed from other countries lead to short-term effects of the development of livestock industries. Rabbit breeding is no exception – the branch of animal husbandry that allows you to get dietary meat at a fast pace. Since the 1940s of the XX century, NIIPZK has been providing scientific support for the formation and development of the rabbit breeding industry. In particular, the scientists of the institute carried out work on breeding. With the participation of the Institute’s employees, the Soviet Chinchilla rabbit breed was created and the White Giant breed was significantly improved. To increase the efficiency of rabbit breeding, different two- and three-breed crosses were tested. Since the 1970s of the last century, no work has been carried out to create new crosses of meat-skin and meat breeds of rabbits. The last rabbit breed approved by the Ministry of Agriculture of Russia (2014) was a decorative breed-the Russian dwarf Angora. Currently, rabbit breeding uses breeding resources imported from abroad, which makes the farms dependent and leads to serious financial costs. Therefore, the actual directions in the selection of domestic rabbit breeding are the creation of new domestic highly productive breeds, types, and crosses. The article presents the results of the creation of a breeding group of rabbits to obtain a new breed. The breeding group was created using at the first stage animals of the parental form of the three-breed cross of Spring rabbits, conducting further breeding "in itself" and selecting from the offspring from the best pairs of individuals that meet the target criteria.
Effect of genotype on the development pattern of muscles and muscle groups in steers at the age of 18 months
Authors: Zhaimysheva S S , Kosilov V I , Voroshilova L N , Gerasimova T G , Klyukvina Ye Yu 
Published: September 2021

Abstract
The development patterns of carcass muscles were studied on Simmental and Black-Spotted steers and their hybrids of the 1st generation. At the age of 18 months, a control slaughter of 3 steers of different genotypes was carried out: Group I - purebred Simmental steers; Group II - hybrids of ½ Simmentals x ½ Red Steppe steers; Group III - hybrids of ½ Simmentals x ½ Black-Spotted steers. To study the muscle groups and individual muscles development according to anatomical regions, the left half-carcasses were prepared, taking into account the methodological instructions, and to facilitate the analysis of the material, the muscles were grouped according to the joints associated with them and the topographic location, using the generally accepted scheme. The muscles development was studied on the basis of the absolute mass indices of individual muscles and muscle groups. It was established that steers of Group III had the following advantages over the animals of the same age in Groups I and II: in the total muscle mass of the spinal column the advantage was 217-772 g (1.43 - 18.30%), in the total muscle mass of the shoulder girdle - 1.45-0.51 kg (9.78-3.51 %), the thoracic limb - 231-660g (14.37-41.04%), the pelvic limb - 3.16-1.11 kg (9.78-3.45%) and in general for the entire half-carcass of the recorded muscles - 6.62-2.33 kg (9.79-3.44 %).
Integrating terrestrial laser scanning with functional–structural plant models to investigate ecological and evolutionary processes of forest communities
Authors: O’Sullivan Hannah , Raumonen Pasi , Kaitaniemi Pekka , Perttunen Jari , Sievänen Risto 
Published: September 2021

AbstractBackgroundWoody plants (trees and shrubs) play an important role in terrestrial ecosystems, but their size and longevity make them difficult subjects for traditional experiments. In the last 20 years functional–structural plant models (FSPMs) have evolved: they consider the interplay between plant modular structure, the immediate environment and internal functioning. However, computational constraints and data deficiency have long been limiting factors in a broader application of FSPMs, particularly at the scale of forest communities. Recently, terrestrial laser scanning (TLS), has emerged as an invaluable tool for capturing the 3-D structure of forest communities, thus opening up exciting opportunities to explore and predict forest dynamics with FSPMs.ScopeThe potential synergies between TLS-derived data and FSPMs have yet to be fully explored. Here, we summarize recent developments in FSPM and TLS research, with a specific focus on woody plants. We then evaluate the emerging opportunities for applying FSPMs in an ecological and evolutionary context, in light of TLS-derived data, with particular consideration of the challenges posed by scaling up from individual trees to whole forests. Finally, we propose guidelines for incorporating TLS data into the FSPM workflow to encourage overlap of practice amongst researchers.ConclusionsWe conclude that TLS is a feasible tool to help shift FSPMs from an individual-level modelling technique to a community-level one. The ability to scan multiple trees, of multiple species, in a short amount of time, is paramount to gathering the detailed structural information required for parameterizing FSPMs for forest communities. Conventional techniques, such as repeated manual forest surveys, have their limitations in explaining the driving mechanisms behind observed patterns in 3-D forest structure and dynamics. Therefore, other techniques are valuable to explore how forests might respond to environmental change. A robust synthesis between TLS and FSPMs provides the opportunity to virtually explore the spatial and temporal dynamics of forest communities.
Into Collabs: Public Applied Linguistics and Hip Hop Language Technicians
Authors: Williams Quentin 
Published: September 2021

Abstract
In this article, I propose the idea of public applied linguistics: that is, a type of applied linguistics that sees applied linguists doing the work of activism, with language activists, in the public, are (i) invested in the artistic representation of linkages between language reinvention and new relationalities, and (ii) highlighting, documenting and framing interventionist debates around language. Public applied linguists encounter, discourse with ‘language technicians’, expert-like language activists working with new visions of language on the periphery of post-apartheid South Africa, to think language otherwise and as a critical historical process, continually reinvented through the unique, creative, and dynamic practices of multilingualism to attain linguistic justice.
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data
Authors: Wong Christina , Li Bo 
Published: September 2021

AbstractSummaryT cells participate directly in the body's immune response to cancer, allowing immunotherapy treatments to effectively recognize and target cancer cells. We previously developed DeepCAT to demonstrate that T cells serve as a biomarker of immune response in cancer patients and can be utilized as a diagnostic tool to differentiate healthy and cancer patient samples. However, DeepCAT’s reliance on tumor bulk RNA-seq samples as training data limited its further performance improvement. Here, we benchmarked a new approach, AutoCAT, to predict tumor-associated TCRs from targeted TCR-seq data as a new form of input for DeepCAT, and observed the same level of predictive accuracy.Availability and implementationSource code is freely available at https://github.com/cew88/AutoCAT, and data is available at 10.5281/zenodo.5176884.Supplementary informationSupplementary data are available at Bioinformatics online.
Translating genetic and functional data into clinical practice: a series of 223 families with myotonia
Authors: Suetterlin Karen , Matthews Emma , Sud Richa , McCall Samuel , Fialho Doreen , Burge James , Jayaseelan Dipa , Haworth Andrea , Sweeney Mary G , Kullmann Dimitri M , Schorge Stephanie , Hanna Michael G , Männikkö Roope 
Published: September 2021

Abstract
High-throughput DNA sequencing is increasingly employed to diagnose single gene neurological and neuromuscular disorders. Large volumes of data present new challenges in data interpretation and its useful translation into clinical and genetic counselling for families. Even when a plausible gene is identified with confidence, interpretation of the clinical significance and inheritance pattern of variants can be challenging. We report our approach to evaluating variants in the skeletal muscle chloride channel ClC-1 identified in 223 probands with myotonia congenita as an example of these challenges. Sequencing of CLCN1, the gene that encodes CLC-1, is central to the diagnosis of myotonia congenita. However, interpreting the pathogenicity and inheritance pattern of novel variants is notoriously difficult as both dominant and recessive mutations are reported throughout the channel sequence, ClC-1 structure-function is poorly understood and significant intra- and interfamilial variability in phenotype is reported.
Heterologous expression systems to study functional consequences of CIC-1 variants are widely reported to aid the assessment of pathogenicity and inheritance pattern. However, heterogeneity of reported analyses does not allow for the systematic correlation of available functional and genetic data. We report the systematic evaluation of 95 CIC-1 variants in 223 probands, the largest reported patient cohort, in which we apply standardized functional analyses and correlate this with clinical assessment and inheritance pattern. Such correlation is important to determine whether functional data improves the accuracy of variant interpretation and likely mode of inheritance.
Our data provide an evidence-based approach that functional characterization of ClC-1 variants improves clinical interpretation of their pathogenicity and inheritance pattern, and serve as reference for 34 previously unreported and 28 previously uncharacterized CLCN1 variants. In addition, we identify novel pathogenic mechanisms and find that variants that alter voltage dependence of activation cluster in the first half of the transmembrane domains and variants that yield no currents cluster in the second half of the transmembrane domain. None of the variants in the intracellular domains were associated with dominant functional features or dominant inheritance pattern of myotonia congenita.
Our data help provide an initial estimate of the anticipated inheritance pattern based on the location of a novel variant and shows that systematic functional characterization can significantly refine the assessment of risk of an associated inheritance pattern and consequently the clinical and genetic counselling.
Are cognition and personality related in budgerigars?
Authors: Chen Jiani , Chen Lu , Yan Chuan , Yu Zibo , Zou Yuqi , Sun Yue-Hua 
Published: September 2021

AbstractIn recent years, researchers have been attempting to relate differences in personality (e.g., boldness, aggressiveness, exploration tendency) to variation in cognition (performances in tasks that require learning, reasoning, attention, or memory, etc.) both theoretically and empirically. However, it is unclear on what basis personality and cognition might be associated with each other. Previous theory suggests a connection between fast–slow personality types and cognitive speed–accuracy tradeoffs. In this study, we tested this hypothesis in budgerigars and found that, in their 1st associative learning, birds with fast personality (less fearful of handling stress) were fast learners in the beginning, while slow personality individuals improved faster, but both types of birds did not differ in accuracy. However, these relationships were context-dependent. No significant relationship was found in subsequent learning tasks (reversal learning and a 2nd associative learning) in the familiar context (task setup and apparatus similar to the 1st associative learning). We then conducted a problem-solving experiment with novel setup and apparatus to test 1 possible explanation that the association between personality and cognition in the 1st associative learning might be caused by noncognitive constraint, such as fearfulness when facing novel task setup and apparatus. We found that fast individuals interacted more with the problem box and solved it, whereas the slow birds were not. We suggest that personalities can influence cognitive performances and trigger a cognitive speed-improvement tradeoff under the novel context. However, there are no consistent cognitive styles that co-varied with different personalities.
Pyk2 suppresses contextual fear memory in an autophosphorylation-independent manner
Authors: Zheng Jin , Suo Lun , Zhou Yuxiao , Jia Liling , Li Jingwei , Kuang Yanping , Cui Donghong , Zhang Xuehong , Wu Qiang 
Published: September 2021

Abstract
Clustered protocadherins (Pcdhs) are a large family of cadherin-like cell adhesion proteins that are central for neurite self-avoidance and neuronal connectivity in the brain. Their downstream nonreceptor tyrosine kinase Pyk2 (proline-rich tyrosine kinase 2, also known as Ptk2b, Cakb, Raftk, Fak2, and Cadtk) is predominantly expressed in the hippocampus. We constructed Pyk2-null mouse lines and found that these mutant mice showed enhancement in contextual fear memory, without significant change in auditory-cued and spatial-referenced learning and memory. In addition, by preparing Y402F mutant mice, we observed that Pyk2 suppressed contextual fear memory in an autophosphorylation-independent manner. Moreover, using high-throughput RNA sequencing, we found that immediate early genes, such as Npas4, cFos, Zif268/Egr1, Arc, and Nr4a1, were enhanced in Pyk2-null mice. We further showed that Pyk2 disruption affected pyramidal neuronal complexity and spine dynamics. Thus, we demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2-null mice provide a model for understanding fear-related disorders. These findings have interesting implications regarding dysregulation of the Pcdh‒Pyk2 axis in neuropsychiatric disorders.
‘Capitalism: what has gone wrong?’: Who went wrong? Capitalism? The market economy? Governments? ‘Neoliberal’ economics?
Authors: Hellwig Martin 
Published: September 2021

AbstractThe paper contributes to a symposium of the Oxford Review of Economic Policy on ‘Capitalism: What has Gone Wrong, What Needs to Change, and How can it be Fixed?’. The analysis starts from the observation that, in the United States, the United Kingdom, and continental Europe, widespread discontent has become an important political force. I attribute this discontent to a sense of unfairness in developments of the past few decades. I relate this sense of unfairness to: (i) negative effects of structural change, including joblessness and regional decline, (ii) the observation of extraordinary growth in executive remuneration and financial-sector remuneration, coupled with government bailouts in the global financial crisis, and (iii) changes in public policy and public discourse, with a retrenchment of public services and public investment, except for bailouts and a focus on ‘efficiency’, the meaning of which is driven by the perceptions of corporate executives rather than standard welfare economics. To capture these developments, one needs to think about ‘capitalism’ in the sense of French capitalisme or German Kapitalismus, with a focus on the symbiosis of wealth and power, including the elimination of competition, rather than merely another term for the market economy.
Long-term improvements in sleep, pain, depression, and fatigue in older adults with comorbid osteoarthritis pain and insomnia
Authors: Vitiello Michael V , Zhu Weiwei , Von Korff Michael , Wellman Robert , Morin Charles M , Yeung Kai , McCurry Susan M 
Published: September 2021

AbstractIn a primary care population of 327 older adults (age 60+) with chronic osteoarthritis (OA) pain and insomnia, we examined the relationship between short-term improvement in sleep or pain and long-term sleep, pain, depression, and fatigue by secondary analyses of randomized controlled trial data. Study participants, regardless of trial arm, were classified as Sleep or Pain Improvers with ≥30% baseline to 2-month reduction on the Insomnia Severity Index or the Brief Pain Inventory, respectively, or Sleep or Pain Non-Improvers. After controlling for trial arm and potential confounders, both Sleep and Pain Improvers showed significant (p &lt; .01) sustained improvements across 12 months compared to respective Non-Improvers for the Insomnia Severity Index (ISI), Pittsburgh Sleep Quality Index, Brief Pain Inventory-short form (total, Interference, and Severity subscales), Patient Health Questionnaire, and Flinders Fatigue Scale. The effect sizes (Cohen’s f2) for the sustained benefits in both Sleep and Pain Improvers compared to their respective Non-Improvers for all variables were small (&lt;0.15) with the exception of medium effect size for sustained reduction in insomnia symptoms for the Sleep Improvers. We conclude that short-term sleep improvements in pain populations with comorbid insomnia precede benefits not only for long-term improvement in sleep but also for reduced pain over the long-term, along with associated improvements in depression and fatigue. Short-term improvements in pain appear to have similar long-term sequelae. Successfully improving sleep in pain populations with comorbid insomnia may have the additional benefits of improving both short- and long-term pain, depression, and fatigue.Trial Registration: OsteoArthritis and Therapy for Sleep (OATS) NCT02946957: https://clinicaltrials.gov/ct2/show/NCT02946957.
Comparative Internal Market Law: The UK and the EU
Authors: Weatherill Stephen 
Published: September 2021

Abstract
The United Kingdom Internal Market Act 2020 introduces a new field of enquiry for scholars. It allows reflection on the model of an internal market chosen by the United Kingdom to regulate relations between its four constituent elements now that, after Brexit, the authority of the EU’s common rules has come to an end. It allows comparison and contrasts between the UK’s chosen model and the longer established patterns of the EU internal market. It is an invitation to develop a comparative study of the law of internal markets.
The overall structure of the UK internal market envisaged by the 2020 Act is readily compared to that which exists in the EU, but there are also points of contrast. The most significant is that the UK model is less tolerant of regulatory diversity among its constituent elements than applies under EU free movement law. The scope to justify rules that obstruct trade within the UK is less generous than in the EU, with the consequence that the UK’s internal market has a more deregulatory flavour than the EU’s. This model of limited availability to protect local regulatory autonomy over unrestricted intra-UK trade pays little regard to sensitivities in Scotland and Wales, while the position of Northern Ireland, locked into the Protocol attached to the EU–UK Withdrawal Agreement, is different but also fragile. Internal markets possess economic motivations and they are built on legal rules, but they involve political choices and they have political implications. The UK Internal Market Act presents challenges to the stability of the United Kingdom itself.
Accordingly the ambition of this paper is to explain the shape of the UK internal market and to compare and contrast it with the EU’s internal market. It also aims to demonstrate the political sensitivity of the choices that need to be made in designing an internal market against the background competing tensions of unhindered market access, on the one hand, and, on the other, respect for the regulatory autonomy enjoyed by the constituent units.
One-Year Functional, Cognitive, and Psychological Outcomes Following the Use of Extracorporeal Membrane Oxygenation in Coronavirus Disease 2019: A Prospective Study
Authors: Rajajee Venkatakrishna , Fung Christopher Mon-Chee , Seagly Katharine Surella , Park Pauline Kyonsook , Raghavendran Krishnan , Machado-Aranda David Antonio , Scott Jonathan William , Delano Matthew Joseph , Abou El Ela Ashraf Shaaban Abdel Aziz , Haft Jonathan William , Williamson Craig Andrew , McSparron Jakob Israel , Blank Ross , Napolitano Lena Marie 
Published: September 2021

Objectives:
To prospectively describe 1-year outcomes, with a focus on functional outcome, cognitive outcome, and the burden of anxiety, depression, and post-traumatic stress disorder, in coronavirus disease 2019 patients managed with extracorporeal membrane oxygenation.

Design:
Prospective case series.

Setting:
Tertiary extracorporeal membrane oxygenation center in the United States.

Patients:
Adult coronavirus disease 2019 acute respiratory distress syndrome patients managed with extracorporeal membrane oxygenation March 1, 2020, to July 31, 2020.

Interventions:
Baseline variables, treatment measures, and short-term outcomes were obtained from the medical record. Survivors were interviewed by telephone, a year following the index intensive care admission. Functional outcome was assessed using the modified Rankin Scale and the World Health Organization Disability Assessment Scale 2.0. Cognitive status was assessed with the 5-minute Montreal Cognitive Assessment. The Hospital Anxiety and Depression Scale was used to screen for anxiety and depression. Screening for post-traumatic stress disorder was performed with the Posttraumatic Stress Disorder Checklist 5 instrument.

Measurements and Main Results:
Twenty-three patients were managed with extracorporeal membrane oxygenation, 14 (61%) survived to hospital discharge. Thirteen (57%) were alive at 1 year. One patient was dependent on mechanical ventilation, another intermittently required supplemental oxygen at 1 year. The median modified Rankin Scale score was 2 (interquartile range, 1–2), median World Health Organization Disability Assessment Scale 2.0 impairment score was 21% (interquartile range, 6–42%). Six of 12 previously employed individuals (50%) had returned to work, and 10 of 12 (83%) were entirely independent in activities of daily living. The median Montreal Cognitive Assessment score was 14 (interquartile range, 13–14). Of 10 patients assessed with Hospital Anxiety and Depression Scale, 4 (40%) screened positive for depression and 6 (60%) for anxiety. Four of 10 (40%) screened positive for post-traumatic stress disorder.

Conclusions:
Functional impairment was common a year following the use of extracorporeal membrane oxygenation in coronavirus disease 2019, although the majority achieved independence in daily living and about half returned to work. Long-term anxiety, depression, and post-traumatic stress disorder were common, but cognitive impairment was not.