bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carcass cutting yields and meat quality of market gilts managed with immunological suppression of ovarian function and estrus
Authors: Bohrer Benjamin M , Edler Roy , Galina Pantoja Lucina , Amodie Deborah , Mellencamp Martha A , Vonnahme Kimberly A 
Published: October 2024

Abstract
The objective of this study was to analyze the effects of immunological suppression of ovarian function and estrus (Improvest®; Zoetis Inc.) on carcass cutting yields and meat quality. A total of 1,080 gilts were allocated by weight and assigned to pens of 27 pigs/pen. Pens were then randomly selected to be managed with or without immunological suppression of ovarian function and estrus (IMP vs. CON). Improvest was administered to each IMP gilt on days 7 and 67 of the study. Pigs were marketed on day 89 (n = 8 heaviest gilts per pen), 103 (n = 8 next heaviest gilts per pen), and 117 (remaining pigs/pen) of the study. The heaviest 47 to 50 carcasses for each treatment from each marketing group were selected for carcass cutting tests and evaluation of meat quality the day following slaughter (approximately 32-h postmortem). A smaller subset of 18 to 20 pork loins per treatment from each marketing group were selected for meat quality evaluation following 14 d of postmortem storage. Carcasses were fabricated according to institutional meat purchase specifications (IMPS) and meat quality analyses included pH and instrumental color at 32-h postmortem and purge loss, pH, instrumental color, intramuscular fat (IMF), cooking loss, and star probe following 14 d of postmortem storage. Live performance data were analyzed using the pen as the experimental unit, while carcass data were analyzed using the individual carcass as the experimental unit. During the post-second dose period (measured from days 70 to 85), IMP gilts consumed 10.8% more feed (P &lt; 0.01) and grew 13.5% faster (P &lt; 0.01) compared with CON gilts. Hot carcass weight (HCW), and the weights of many cuts, were significantly influenced by the interaction of Improvest management and marketing group. Therefore, the focus was directed toward primal weights and merchandized cut weights when expressed as a percentage of HCW. When expressed as a percentage of HCW, primal-cut yield and merchandized-cut yield calculations were not different (P = 0.33 and P = 0.65, respectively) between CON and IMP gilts. Meat quality traits did not differ (P &gt; 0.05) between CON and IMP gilts, with the exception of instrumental a* at 32-h postmortem which was 0.32 units greater for CON gilts compared with IMP gilts. In summary, managing market gilts with immunological suppression of ovarian function and estrus improves the rate of weight gain through increased feed intake; however, carcass-cutting yields were not significantly changed.
Validity of Myobradypterygius hauthali von Huene, 1927 (Ichthyosauria: Ophthalmosauria) from the Early Cretaceous of Chile and Argentina
Authors: Pardo-Pérez Judith , Zambrano Patricio , Malkowski Matthew , Lomax Dean , Villa-Martínez Rodrigo , Stinnesbeck Wolfgang , Frey Eberhard , Scapini Francisca , Gascó Cristina , Maxwell Erin E 
Published: October 2024

Abstract
Early Cretaceous ichthyosaurs were globally distributed pelagic marine reptiles, but many remains are fragmentary, creating a Northern Hemisphere diversity bias. A rich Hauterivian locality near the Tyndall Glacier inside Torres del Paine National Park in southern Chile yields important new data regarding ichthyosaurian diversity along the Pacific margin of Gondwana. These new data will contribute to clarifying questions regarding ichthyosaur taxonomy and the palaeobiogeographical relationships between the southern Gondwanan and Northern Hemisphere ichthyosaur groups during the Early Cretaceous. Here, we describe three new ichthyosaur specimens from this locality. Two of them are referred to Myobradypterygius hauthali, expanding the distribution of this species from the Barremian of Argentina to the Hauterivian of the Chilean Patagonia. This material shows that M. hauthali differs from Platypterygius platydactylus in forefin construction and scapular morphology, supporting its classification as a separate genus within Platypterygiinae. The third specimen is a large-bodied indeterminate ophthalmosaurine ichthyosaur. This record represents the southernmost record of Ophthalmosaurinae and the first occurrence of this group from the Cretaceous of the Southern Hemisphere. These discoveries show that ophthalmosaurines and platypterygiines continued to occur sympatrically in southernmost Gondwana during the Early Cretaceous, expanding the pattern documented in Europe to the Pacific region.
High retention rates of custom 3D printed titanium implants in complex pelvic reconstruction, a report on 106 consecutive cases over 10 years
Authors: Boyle Richard , Scholes Corey , Franks Daniel , Lodhia Amish , Harrison-Brown Meredith , Ebrahimi Milad , Guzman Maurice , Stalley Paul 
Published: October 2024

AbstractBackgroundAccess to custom 3D printed pelvic implants (3DPI) is improving for application in both arthroplasty revision and tumour reconstruction. There is limited evidence regarding the safety and outcomes of such implants for large bony defects of the pelvis.PurposeTo report the incidence of complications, patient mortality and implant survival following pelvic reconstruction using custom 3Dprinted prostheses in the setting of extensive pelvic bone defects following pelvic tumour resection or failure of total hip arthroplasty (THA)MethodsPatients who underwent reconstruction with a custom 3D printed pelvic prosthesis (3DPI) were identified from our clinical outcomes registry (Complex Reconstruction and Sarcoma Surgical Outcomes Registry; ANZCTRN 12621001421820). Indications for surgery, adverse events, reoperations and rates and modes of failure were recorded. Kaplan-Meier and multistate survival curves were generated for cumulative survival based on indication.ResultsOne hundred and six procedures were completed(RevisionTHA = 33; TumourPelvis = 73) with a median follow up of 4.1 years, ranging from 0.6 to 10 years. Acetabular loosening was the most frequent indication for the RevisionTHA cohort, while indications for tumour varied across primary presentations, metastases and failures of previous resection/reconstruction. Intraoperative complications were observed in 4.1% (95%CI 1.1 - 12.3) of TumourPelvis cases. Overall implant retention was 96% (90 - 99). No mortality events were observed in the RevisionTHA cohort, with 5-year patient survival 79% (70-90) in the TumourPelvis cohort. Procedure-survival free from periprosthetic infection was 86% (74-100) in the RevisionTHA cohort and 85% (76 - 95) in the TumourPelvisCohort. Modelling adverse events using multistate survival models in both cohorts revealed complex time-varying presentation of adverse events, with a significant burden of reoperations and local tumour recurrence in the TumourPelvis cohort.Conclusion3DPIs are a safe and viable option for complex reconstruction of the pelvis across a range of oncological and non-oncological indications. The initial results of the present study provide important information to aid in counselling patients about such procedures and allocating healthcare resources for ongoing care. Further work is required to document functional and biomechanical outcomes in these patient populations.
ASSOCIATIONS OF AUTISTIC TRAITS AND AUTISM WITH INCONTINENCE AND CONSTIPATION IN A UK BIRTH COHORT
Authors: Gyamenah Prince , Burrows Kimberley , Rai Dheeraj , Joinson Carol 
Published: October 2024

ABSTRACTBackgroundThere is evidence that children with autism/autistic traits have higher risks of incontinence and constipation, but no studies have examined this in a large community-based cohort.Aim/Research questionare autistic traits and diagnosed autism prospectively associated with increased odds of incontinence and constipation in children and adolescents?MethodsThis was a population-based cohort study based on data from the Avon Longitudinal Study of Parents and Children (n=4233-4490 at age 9 years; n=3403-3697 at age 14). We used multivariable logistic regression to examine associations of parent-reported autistic traits (sociability, repetitive behaviours, social-communication, coherence) (at ages 3-9 years) and autism with incontinence (bedwetting, daytime-wetting, soiling) and constipation (parent-reported at age 9, self-reported at age 14). We adjusted for parity, maternal age at delivery, child’s sex and developmental level, maternal depression, and anxiety (antenatal and postnatal), and indicators of family socioeconomic status.ResultsSocial-communication and speech coherence difficulties showed the strongest associations with incontinence, e.g. adjusted odds ratio (OR) and 95% confidence interval (CI) for the association between social-communication difficulties and daytime-wetting was 2.21 (1.47-3.32) and for coherence was 2.34 (1.60-3.43). The odds of soiling were also higher in children with social-communication (OR:1.88, 95%CI:1.28-2.75) and coherence difficulties (OR:2.04, 95%CI:1.43-2.93). Diagnosed autism was only associated with an increase in the odds of daytime-wetting (OR:3.18, 95%CI:1.44-7.02). At 14 years, there was less evidence of associations between autistic traits and incontinence but there was evidence of associations between autistic traits and constipation: social-communication (OR:1.68, 95%CI:1.13-2.49), coherence difficulties (OR:1.64, 95%CI:1.11-2.41). 5ConclusionsEarly assessment and treatment of incontinence/constipation should be considered for children with autistic traits.
Computational design of developable therapeutic antibodies: efficient traversal of binder landscapes and rescue of escape mutations
Authors: Dreyer Frédéric A. , Schneider Constantin , Kovaltsuk Aleksandr , Cutting Daniel , Byrne Matthew J. , Nissley Daniel A. , Wahome Newton , Kenlay Henry , Marks Claire , Errington David , Gildea Richard J. , Damerell David , Tizei Pedro , Bunjobpol Wilawan , Darby John F. , Drulyte Ieva , Hurdiss Daniel L. , Surade Sachin , Pires Douglas E. V. , Deane Charlotte M. 
Published: October 2024

AbstractDeveloping therapeutic antibodies is a challenging endeavour, often requiring large-scale screening to produce initial binders, that still often require optimisation for developability. We present a computational pipeline for the discovery and design of therapeutic antibody candidates, which incorporates physics- and AI-based methods for the generation, assessment, and validation of developable candidate antibodies against diverse epitopes, via efficient few-shot experimental screens. We demonstrate that these orthogonal methods can lead to promising designs. We evaluated our approach by experimentally testing a small number of candidates against multiple SARS-CoV-2 variants in three different tasks: (i) traversing sequence landscapes of binders, we identify highly sequence dissimilar antibodies that retain binding to the Wuhan strain, (ii) rescuing binding from escape mutations, we show up to 54% of designs gain binding affinity to a new subvariant and (iii) improving developability characteristics of antibodies while retaining binding properties. These results together demonstrate an end-to-end antibody design pipeline with applicability across a wide range of antibody design tasks. We experimentally characterised binding against different antigen targets, developability profiles, and cryo-EM structures of designed antibodies. Our work demonstrates how combined AI and physics computational methods improve productivity and viability of antibody designs.
A curve fitting method for analysing starch granule size distributions in cereals
Authors: McNelly Rose , Briffa Amy , Yiasoumi Georgia , Uauy Cristobal , Matsushima Ryo , Seung David 
Published: October 2024

AbstractBackground and ObjectivesThe size distribution of starch granules is an important factor determining functional and nutritional properties of starch. However, a simple, standardised method for their analysis is lacking. Here, we developed an approach for estimating granule size parameters using a Python script that fits curves to volumetric granule size distributions generated using a Coulter counter.FindingsThe bimodal size distribution of starch from most wheat and barley cultivars could be best described with a mixed distribution curve. A log-normal distribution was fitted to the small B-type granules, and a normal distribution was fitted to the large A-type granules, allowing estimation of their relative abundance and size parameters, despite their overlapping size distributions. However, the optimal fitting is altered in wheat mutants with large perturbations in B-type granule content. In maize and rice, which have unimodal granule size distributions, size parameters were calculated by fitting a single normal distribution.ConclusionsCurve fitting is an effective approach for estimating starch granule size parameters in diverse cereals, particularly the Triticeae with A- and B-type granules.Significance and noveltyWe provide new tools and guidelines for the quantitative analysis of granule size in cereals.
Aperiodic neural excitation of the prefrontal cortex offsets age-related decrease in hippocampal theta activity for spatial memory maintenance
Authors: Park Sang-Eon , Donoghue Thomas , Jacobs Joshua , Lee Sang Ah 
Published: October 2024

AbstractCurrently, there is a critical gap in age-related electrophysiological changes in the human brain and how they are correlated with individual decline and maintenance of spatial cognitive function. To characterize these complex neurocognitive changes using direct intracranial recordings, we isolated periodic band power from the aperiodic spectral slope from iEEG power spectra of 69 presurgical epilepsy patients between 19 and 61 years of age while they performed a virtual spatial navigation task. We found a flattening of aperiodic spectral slope in the prefrontal cortex, but also observed a steepening in the hippocampus, suggestive of region-specific changes in excitatory/inhibitory balance across aging. The hippocampus showed pronounced changes in periodic (oscillatory) activity, including a decrease in theta power that correlated with impaired spatial memory, potentially due to changes in the cholinergic system. Interestingly, individuals with the flatter spectral slope in DLPFC showed preserved performance despite lower hippocampal theta, indicating a potential compensatory mechanism for cognitive maintenance. These findings provide new evidence that individual age-related cognitive decline can be predicted by changes in hippocampal theta oscillation, in combination with concomitant prefrontal compensatory mechanisms.
Bilateral Symmetry and Asymmetry in the C. elegans Connectome: A Graph-Theoretic Analysis based on Redundancy Measures
Authors: Kim Pyeong Soo , Song Youngjo , Kralik Jerald D. , Jeong Jaeseung 
Published: October 2024

AbstractUnderstanding the balance between symmetry and asymmetry in animal nervous systems is crucial for unraveling the complexities of neural architectures and their functions. Previous studies have primarily focused on morphological symmetry, such as neuron placement, leaving the symmetry in the functional architecture largely unexplored. The current study investigates this aspect within theCaenorhabditis elegansconnectomes by introducing a graph-theoretic approach. By defining a ‘mirror-symmetry index,’ we quantitatively assess the symmetry in these connectomes, revealing a significant level of bilateral symmetry alongside notable asymmetry. Our approach also incorporates measures including connectivity similarity, motif-fingerprint differences, and path-compensation index to evaluate the network’s functional redundancy and its capacity to compensate for unilateral disturbances. Here we show the C. elegans connectomes’ robust bilateral symmetry, which not only facilitates similar functions across neuron pairs but also ensures resilience against disruptions. This redundancy is not confined to symmetrical connections; it also includes asymmetric ones, adding to the neural network’s complexity. An in-depth analysis into different neuron types shows varied redundancy levels: high in interneurons, moderate in motor neurons, and low in sensory neurons. This pattern suggests a strategic neural design where diverse inputs from sensory neurons, coupled with the stable integration by interneurons, lead to coordinated actions through motor neurons. This study advances our understanding of neural connectomes, offering insights into the intricate balance of symmetry and asymmetry in neural systems and their implications for complex, adaptive behaviors.
Reducing spatial heterogeneity in coverage improves the effectiveness of dog vaccination campaigns against rabies
Authors: Ferguson Elaine A , Lugelo Ahmed , Czupryna Anna , Anderson Danni , Lankester Felix , Sikana Lwitiko , Dushoff Jonathan , Hampson Katie 
Published: October 2024

AbstractVaccination programs are the mainstay of control for many infectious diseases. Heterogeneous coverage is hypothesised to reduce vaccination programme effectiveness, but this impact has not been quantified in real systems. We address this gap using fine-scale data from two decades of rabies contact tracing and dog vaccination campaigns in Serengeti district, Tanzania. We also aimed to identify drivers of continued circulation of rabies in the district despite annual vaccination campaigns. Using generalised linear mixed models, we find that current focal (village-level) dog rabies incidence decreases with increasing recent focal vaccination coverage. However, current focal incidence depends most on recent incidence, both focally and in the wider district, consistent with high population connectivity. Removing the masking effects of prior non-focal incidence shows that, for the same average prior non-focal (wider-district) vaccination coverage, increased heterogeneity in coverage among the non-focal villages leads to increased focal incidence. These effects led to outbreaks following years when vaccination campaigns missed many villages, whereas when heterogeneity in coverage was reduced, incidence declined to low levels (<0.4 cases/1,000 dogs annually and no human deaths) and short vaccination lapses thereafter did not lead to resurgence. Through transmission-tree reconstruction, we inferred frequent incursions into the district each year (mean of 7). Inferred incursions substantially increased as a percentage of all cases in recent years, reaching 50% in 2022, suggesting regional connectivity is driving residual transmission. Overall, we empirically demonstrate how population connectivity and spatial heterogeneity in vaccination can impact disease outcomes, highlighting the importance of fine-scale monitoring in managing vaccination programs.
k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance
Authors: Jaegle Benjamin , Voicheck Yoav , Haupt Max , Sotiropoulos Alexandros G. , Gauthier Kevin , Heuberger Matthias , Jung Esther , Herren Gerhard , Widrig Victoria , Leber Rebecca , Li Yipu , Schierscher Beate , Serex Sarah , Boczkowska Maja , Jasińska Marta-Puchta , Bolc Paulina , Chalhoub Boulos , Stein Nils , Keller Beat , Sanchez Martin Javier 
Published: October 2024

AbstractBackgroundWheat landraces and cultivars stored in gene banks worldwide represent a valuable source of genetic diversity for discovering genes critical for agriculture, which is increasingly constrained by climate change and inputs reduction. We assembled and genotyped, using DArTseq technology, a panel of 461 accessions representative of the genetic diversity of Swiss wheat material. The collection was evaluated for powdery mildew resistance under field conditions for two consecutive years and at the seedling stage with 10 different wheat powdery mildew isolates.ResultsTo identify the genetic basis of mildew resistance in wheat, we developed ak-mer-based GWAS approach using multiple fully-assembled genomes includingTriticum aestivumas well as four progenitor genomes. Compared to approaches based on single reference genomes, we unambiguously mapped an additional 25% resistance-associatedk-mers. Our approach outperformed SNP-based GWAS in terms of number of loci identified and precision of mapping. In total, we detected 34 (Pm) powdery mildew resistance loci, including seven previously-described and more importantly 27 novel loci active at the seedling stage. Furthermore, we identified a region associated with adult plant resistance, which was not detected with SNP-based approaches.ConclusionsThe described non-reference-based approach highlights the potential of integrating multiple wheat reference genomes withk-mer GWAS to harness the untapped genetic diversity present in germplasm collections.
Conserved chromatin regulators control the transcriptional immune response to intracellular pathogens inCaenorhabditis elegans
Authors: Tecle Eillen , Li Samuel , Blanchard Michael J. , Bui Theresa , Chhan Crystal B. , Underwood Ryan S. , Bakowski Malina A. , Troemel Emily R. , Lažetić Vladimir 
Published: October 2024

ABSTRACTRobust transcriptional responses are critical for defense against infection. However, unrestrained immune responses can cause negative impacts such as damaging inflammation and slowed development. Here we find that a class of transcriptional regulators previously associated with regulation of development inCaenorhabditis elegans, is also involved in immune responses. Specifically, through forward genetics, we find that loss oflin-15Bleads to constitutive expression of Intracellular Pathogen Response (IPR) genes.lin-15Bencodes a transcriptional repressor with a conserved THAP domain that is associated with the DRM chromatin remodeling complex that regulatesC. elegansdevelopment. We show thatlin-15Bmutants have increased resistance to natural intracellular pathogens, and the induction of IPR genes inlin-15Bmutants relies on the MES-4 histone methyltransferase. We extend our analyses to other DRM and NuRD chromatin remodeling factors, as well as SUMOylation histone modifiers, showing that a broad range of chromatin-related factors can repress IPR gene expression. Altogether these findings suggest that conserved chromatin regulators may facilitate development in part by repressing damaging immune responses against intracellular pathogens.AUTHOR SUMMARYIn this study, we show that transcriptional regulators, previously linked to development inC. elegans, also control immune responses. Through forward genetic screens, we found that loss of LIN-15B leads to constitutive activation of Intracellular Pathogen Response (IPR) genes. LIN-15B is part of the DREAM chromatin remodeling complex, and its loss enhances resistance to intracellular pathogens. This immune response depends on the MES-4 histone methyltransferase. We also discovered that other chromatin regulators, including NuRD and SUMOylation factors, similarly repress IPR gene expression, highlighting a new role in immunity for these conserved regulators of development.