bluuebunny/crossref_metadata_2025 huggingface dataset:
EVALUATION OF THE OBSERVANCE OF RADIATION PROTECTION PRINCIPLES IN KERMANSHAH PROVINCE (WEST OF IRAN) 2020: CROSS-SECTIONAL STUDY
Authors: Tohidinia M R , Talaee O , Amiri F , Khateri H , Mohseni H
Published: December 2022

In this descriptive cross-sectional study by census method, the performance of 116 radiographers in the target centers was evaluated in relation to the observance of radiation protection principles with respect to patients, patient companion and radiographers. The data collection tool was a checklist containing 34 principles of radiation protection that were used after confirmation of its continuity and justifiability. The results showed that only in (39.2%) 45 radiographers the observance rate of the principles of radiation protection was acceptable. The highest and lowest levels in which radiographers observed protective principles were observance of protective principles with respect to themselves (60.8%) and protective principles respect of the patient companion (6.3%), respectively. According to the findings, radiation protection principles are not systematically designed, implemented, controlled and monitored by radiographers, and less than half of the radiographers observe the protection principles at the optimal level.
Impact of dietary supplementation of l-Arginine, l-Glutamine, and the combination of both on nursing performance of multiparous sows
Authors: Wessels Anna G , Simongiovanni Aude , Zentek Jürgen
Published: December 2022

Dietary supplementation with arginine (Arg) or glutamine (Gln) has been considered as an option to improve nursing performance in reproductive sows. This study investigated whether a low-level supplementation of Arg or Gln or a blend of both could modify milk nutrients and improve piglets’ growth beyond weaning. Seventy-two multiparous sows were assigned to four groups: one group fed a control diet, three treatment groups fed the control diet supplemented with either 0.35% Arg, 0.35% Gln, or both, from day 108 of gestation until weaning at day 26 of lactation. Immediately after birth, the litters were cross fostered to 13 piglets and monitored until 2 wk after weaning. Sows body condition and litter growth were assessed. Colostrum and milk samples were collected for nutrient analyses. Plasma concentrations of insulin-like growth factor 1 (IGF-1) around weaning were determined in sows and two representative piglets per litter. Supplementing Gln or the combination of Arg and Gln had no effect on the parameters studied. Arg supplementation increased weaning weight, while decreasing the variation of piglet weights 2 wk after weaning. There was no correlation with plasma IGF-1 since the hormone was not altered in sows or piglets. The colostral concentration of fat tended to increase in the Arg-group, whereas protein, lactose, energy, and polyamine concentrations remained unaffected. Milk samples obtained on day 12 and 25 of lactation were not influenced by dietary treatment. The data indicate that there might be a window of opportunity, explicitly at the onset of lactation, for dietary intervention by maternal dietary Arg supplementation.
Expression of emotion in the British South Asian Diaspora: A Qualitative Study
Authors: Sharif Hira Salman , Miah Syed K , Ramanathan Amrita , Glover Naomi , Shaikh Madiha
Published: December 2022

Background

‘Expressed Emotion (EE)’ captures ways in which emotions are expressed within a family environment. Research has found that EE in families has an impact on psychiatric illness, in particular psychosis, such that it increases risk of relapse. EE was conceptualised by research conducted in the UK. Thus, behaviours defined as pathological were largely based on Caucasian samples adhering to UK norms. Cross-cultural variations have been found in the expression of EE and its relationship with clinical outcomes. A more culturally appropriate understanding of norms surrounding the expression of emotion across cultures is required.

Aims

This study aims to use a bottom-up approach to provide a culturally specific understanding of family relationships and the expression of emotion across ‘non-clinical’ UK-based South Asian families.

Methods

Semi-structured interviews were conducted with 18 South Asian participants to explore their relationships with a significant other. Interviews were analysed using thematic analysis.

Results

Four main themes were generated: expression of love, setting boundaries, inter-generational differences and acceptance.

Conclusion

The findings indicate considerable cultural variability within emotional expression and highlight the need to interpret EE in the context of socio-cultural norms. Whilst certain expressions of emotion that are considered pathological in Western contexts are present in the UK-based South Asian diaspora, these are perceived as less problematic, indicative of varying cultural norms.
NEK10 tyrosine phosphorylates β-catenin to regulate its cytoplasmic turnover
Authors: Dutt Previn , Haider Nasir , Mouaaz Samar , Podmore Lauren , Stambolic Vuk
Published: December 2022

Nek kinases are involved in regulating several different elements of the centrosomal cycle, primary cilia function, and DNA damage responses. Unlike the other members of the Nek family, which are serine-threonine kinases, Nek10 preferentially targets tyrosines. Nek10 appears to have a broad role in DNA damage responses, regulating a MAPK-activated G2/M checkpoint following UV irradiation and influencing the p53-mediated activation induced by genotoxicity. In an attempt to identify additional Nek10 functions, we characterized the effect of Nek10 deletion in lung cancer cells, where it is relatively highly expressed. Nek10 absence led to an increase in both the signaling and adherens junctions pools of β-catenin. Mechanistically, Nek10 associates with the Axin complex where it phosphorylates β-catenin at Tyr30, located within the regulatory region governing β-catenin turnover. In the absence of Nek10 phosphorylation, GSK3-mediated phosphorylation of β-catenin, a prerequisite for its turnover, was significantly impaired. Stabilization of β-catenin driven by Nek10 loss diminished the ability of cells to form tumorspheres in suspension, grow in soft agar, and colonize mouse lung tissue following tail vein injections.
Oxytocin enhances the triangular association among behavioral performance, resting state, and task-state functional connectivity
Authors: Zhang Haoming , Chen Kun , Bao Jin , Wu Haiyan
Published: December 2022

The role of oxytocin (OT) in social behavior and social brain networks has been widely documented. However, the effect of OT on the association between social behavior and brain functional connectivity (FC) is yet to be comprehensively explored. In this study, using a face-perception task and multiple connectome-based predictive (CPM) models, we aimed to: 1) determine whether OT could enhance the association between task behavioral performance, resting-state functional connectivity (rsFC), and task-state functional connectivity (tsFC), and 2) if so, determine the role of OT in enhancing this triangular association. We found that both rsFC and tsFC could independently and significantly predict task performance in the OT group, but not in the placebo (PL) group. In addition, the correlation coefficient between rsFC and tsFC was substantially higher in the OT group than in the PL group. The strength of these associations could be partly explained by OT altering the brain’s FCs related to social cognition and face-perception in both resting and task states, mainly in brain regions such as the limbic system, prefrontal cortex (PFC), temporal poles (TP), and temporoparietal junction (TPJ). Together, these results suggest that neuropeptides can increase the consistency of individual differences in different modalities (e.g., behavioral and brain level data).
Development of an amplicon-based high throughput sequencing method for genotypic characterisation of norovirus in oysters
Authors: Fitzpatrick Amy H , Rupnik Agnieszka , O’Shea Helen , Crispie Fiona , Cotter Paul D. , Keaveney Sinéad
Published: December 2022

Norovirus is a highly diverse RNA virus often implicated in food-borne outbreaks, particularly shellfish. Shellfish are filter feeders, and when harvested in bays exposed to wastewater overflow or storm overflows, they can harbour various pathogens, including human pathogenic viruses. The application of Sanger or amplicon-based High Throughput Sequencing (HTS) technologies to identify human pathogens in shellfish faces two main challenges i) distinguishing multiple genotypes/variants in a single sample and ii) low concentrations of norovirus RNA. Here we have assessed the performance of a novel norovirus capsid amplicon HTS method. We generated a panel of spiked oysters containing various norovirus concentrations with different genotypic compositions. Several DNA polymerase and Reverse Transcriptase (RT) enzymes were compared, and performance was evaluated based on i) the number of reads passing quality filters per sample, ii) the number of correct genotypes identified, and iii) the sequence identity of outputs compared to Sanger-derived sequences. A combination of the reverse transcriptase LunaScript and the DNA polymerase AmpliTaq Gold provided the best results. The method was then employed, and compared with Sanger sequencing, to characterise norovirus populations in naturally contaminated oysters.

Importance

While foodborne outbreaks account for approximately 14% of norovirus cases (Verhoef L, Hewitt J, Barclay L, Ahmed S, Lake R, Hall AJ, Lopman B, Kroneman A, Vennema H, Vinjé J, Koopmans M. 2015. 1999-2012. Emerg Infect Dis 21:592–599), we do not have standardised high-throughput sequencing methods for genotypic characterisation in foodstuffs. Here we present an optimised amplicon high- throughput sequencing method for the genotypic characterisation of norovirus in oysters. This method can accurately detect and characterise norovirus at concentrations typically detected in oysters. It will permit the investigation of norovirus genetic diversity in complex matrices and contribute to ongoing surveillance of norovirus in the environment.
Individual Astrocyte Morphology in the Collagenous Lamina Cribrosa Revealed by Multicolor DiOlistic Labeling
Authors: Waxman Susannah , Quinn Marissa , Donahue Cara , Falo Louis D. , Sun Daniel , Jakobs Tatjana C. , Sigal Ian A.
Published: December 2022

Astrocytes in the lamina region of the optic nerve head play vital roles in supporting retinal ganglion cell axon health. In glaucoma, these astrocytes are implicated as early responders to stressors, undergoing characteristic changes in cell function as well as cell morphology. Much of what is currently known about individual lamina astrocyte morphology has been learned from rodent models which lack a defining feature of the human optic nerve head, the collagenous lamina cribrosa (LC). Current methods available for evaluation of collagenous LC astrocyte morphology have significant shortcomings. We aimed to evaluate Multicolor DiOlistic labeling (MuDi) as an approach to reveal individual astrocyte morphologies across the collagenous LC.

Gold microcarriers were coated with all combinations of three fluorescent cell membrane dyes, DiI, DiD, and DiO, for a total of seven dye combinations. Microcarriers were delivered to 150μm-thick coronal vibratome slices through the LC of pig, sheep, goat, and monkey eyes via MuDi. Labeled tissues were imaged with confocal and second harmonic generation microscopy to visualize dyed cells and LC collagenous beams, respectively. GFAP labeling of DiOlistically-labeled cells with astrocyte morphologies was used to investigate cell identity. 3D models of astrocytes were created from confocal image stacks for quantification of morphological features.

DiOlistic labeling revealed fine details of LC astrocyte morphologies including somas, primary branches, higher-order branches, and end-feet. Labeled cells with astrocyte morphologies were GFAP+. Astrocytes were visible across seven distinct color channels, allowing high labeling density while still distinguishing individual cells from their neighbors. MuDi was capable of revealing tens to hundreds of collagenous LC astrocytes, in situ, with a single application. 3D astrocyte models allowed automated quantification of morphological features including branch number, length, thickness, hierarchy, and straightness as well as Sholl analysis.

MuDi labeling provides an opportunity to investigate morphologies of collagenous LC astrocytes, providing both qualitative and quantitative detail, in healthy tissues. This approach may open doors for research of glaucoma, where astrocyte morphological alterations are thought to coincide with key functional changes related to disease progression.
Reach corrections toward moving objects are faster than reach corrections toward jumping targets
Authors: Reschechtko Sasha , Gnanaseelan Cynthiya , Pruszynski J. Andrew
Published: December 2022

Visually guided reaching is a common motor behavior that engages subcortical circuits to mediate rapid corrections. These circuits help us successfully grasp objects we see, even if those objects move during the reach. Although these neural mechanisms have evolved for interaction with the physical world, they are almost always studied in the context of reaching toward virtual targets displayed on a computer or projection screen. Virtual targets are unrealistic both because they cannot be physically grasped and because they generally move by “jumping” from one place to another instantaneously. Recent work has indicated that various aspects of “real” visual stimuli, including proximity and graspability, elicit distinct neural activity. In this study, we instructed participants to perform rapid reaches to physical objects. On some trials, these objects either moved realistically (continuously from one position to another) or unrealistically (jumping instantaneously to an equivalent position). Participants were consistently faster in correcting their reach trajectories when the object moved continuously.
Mapping whole brain effects of infrared neural stimulation with positron emission tomography
Authors: Meneghetti Marcello , Gudmundsen Frederik , Jessen Naja S. , Sui Kunyang , Baun Christina , Palner Mikael , Markos Christos
Published: December 2022

The combination of neuroimaging and targeted neuromodulation is a crucial tool to gain a deeper understanding of neural networks at a circuit level. Infrared neurostimulation (INS) is a promising optical modality that allows to evoke neuronal activity with high spatial resolution without need for the introduction of exogenous substances in the brain. Here, we report the use of whole-brain functional [18F]fluorodeoxyglucose positron emission tomography (FDG-PET) imaging during INS in the dorsal striatum, performed using a multifunctional soft neural probe. We demonstrate the possibility to identify multi-circuit connection patterns in both cortical and subcortical brain regions within a single scan. By using a bolus plus infusion FDG-PET scanning protocol, we were able to observe the metabolic rate evolution in these regions during the experiments and correlate its variation with the onset of the INS stimulus. Due to the focality of INS and the large amount of viable molecular targets for PET, this novel approach to simultaneous imaging and stimulation is highly versatile. This pilot study can pave the way to further understand the brain connectivity on a global scale.
Significant SAR11 removal by a hard-bottom community
Authors: Dadon-Pilosof Ayelet , Conley Keats , Suzuki Marcelino T.
Published: December 2022

Microorganisms are a key component of the marine food webs through the microbial loop. In previous work, we have shown that some bacteria, including CandidatusPelagibacterspp (SAR11)—the most abundant bacterium in the ocean—can evade filtration by benthic and planktonic tunicates. Here we tested whether differential removal of microbial taxa by benthic filter-feeders can be observed in the distribution and abundance of microbial taxa from hard-bottom subtidal communities, a common coastal habitat in the Eastern Mediterranean Sea towards the open sea. The abundance of microbial groups along crosss-hore transects was measured based on combined flow cytometry and SSU rRNA gene metabarcoding. Our results show that most groups were depleted (up to 50%) over the hard-bottom compared to the open sea, but unexpectedly we did not observe a clear differential removal of different taxa, SAR 11 notably. This study indicates a strong top-down control of the abundance of pelagic microorganisms over shallow hard-bottom where suspension feeders are common.
Polymer folding through active processes recreates features of genome organization
Authors: Goychuk Andriy , Kannan Deepti , Chakraborty Arup K. , Kardar Mehran
Published: December 2022

From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate (ATP). Moreover, chromatin motion varies with genomic coordinate, pointing towards a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers non-equilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward disentangling active and passive mechanisms of folding, we discuss a data-driven approach to discern if and how active processes affect genome organization.
Recurrent evolution of small body size and loss of the sword ornament in Northern Swordtail fish
Authors: Preising Gabriel A. , Gunn Theresa , Baczenas John J. , Pollock Alexa , Powell Daniel L. , Dodge Tristram O. , Machin Kairuz Jose Angel , Savage Markita , Lu Yuan , Fitschen-Brown Meredith , Cummings Molly , Thakur Sunishka , Tobler Michael , Ríos-Cardenas Oscar , Morris Molly , Schumer Molly
Published: December 2022

Across the tree of life, species have repeatedly evolved similar phenotypes. While well-studied for ecological traits, there is also evidence for convergent evolution of sexually selected traits. Swordtail fish (Xiphophorus) are a classic model system for studying sexual selection, and femaleXiphophorusexhibit strong mate preferences for large male body size and a range of sexually dimorphic ornaments. However, sexually selected traits have been lost multiple times in the genus. Phylogenetic relationships between species in this group have historically been controversial, likely as a result of prevalent gene flow, resulting in uncertainty over the number of losses of ornamentation and large body size. Here, we use whole-genome sequencing approaches to re-examine phylogenetic relationships within aXiphophorusclade that varies in the presence and absence of sexually selected traits. Using wild-caught individuals, we determine the phylogenetic placement of a small, unornamented species,X. continens, confirming an additional loss of ornamentation and large body size in the clade. With these revised phylogenetic relationships, we analyze evidence for coevolution between body size and other sexually selected traits using a phylogenetically independent contrasts approach. These results provide insights into the evolutionary pressures driving the recurrent loss of suites of sexually selected traits.
Adaptation of the binding domain ofLactobacillus acidophilusS-layer protein as a molecular tag for affinity chromatography development
Authors: Muruaga Emanuel J. , Uriza Paula J. , Eckert Gonzalo A. K. , Pepe María V. , Duarte Cecilia M. , Roset Mara S. , Briones Gabriel
Published: December 2022

The SLAPTAGis a novel molecular TAG derived from a protein domain present in the sequence ofLactobacillus acidophilusSlpA (SlpA284–444). Proteins from different biological sources, with different molecular weights or biochemical functions, can be fused in frame to the SLAPTAGand efficiently purified by the specific binding to a bacterial-derived chromatographic matrix named here Bio-Matrix (BM). Different binding and elution conditions were evaluated to set an optimized protocol for the SLAPTAG-based affinity chromatography (SAC). The binding equilibrium between SLAPTAGand BM was reached after a few minutes at 4°C, being the apparent dissociation constant (KD) of 4.3 µM, a value which is similar to different Kd determined for other S-layer proteins and their respective bacterial cell walls. A reporter protein was generated (H6-GFP-SLAPTAG) to compare the efficiency of the SAC against a commercial system based on a Ni2+-charged agarose matrix, observing no differences in the H6-GFP-SLAPTAGpurification performance. The stability and reusability of the BM were evaluated, and it was determined that the matrix was stable for more than a year, being possible to reuse it five times without a significant loss in the efficiency for protein purification. Alternatively, we explored the recovery of bound SLAP-tagged proteins by proteolysis using the SLAPASE(a SLAP-tagged version of the HRV-3c protease) that released a tag-less GFP (SLAPTAG-less). Additionally, iron nanoparticles were linked to the BM and the resulting BMmagwas successfully adapted for a magnetic SAC, a technique that can be potentially applied for high-throughput-out protein production and purification.
Rhythmic oscillations in the midbrain dopaminergic nuclei in mice
Authors: Oberto Virginie , Matsumoto Jumpei , Pompili Marco , Todorova Ralitsa , Papaleo Francesco , Nishijo Hisao , Venance Laurent , Vandecasteele Marie , Wiener Sidney
Published: December 2022

Dopamine release in the forebrain by midbrain ventral tegmental nucleus (VTA) and substantia nigra pars compacta (SNpc) neurons is implicated in reward processing, goal-directed learning, and decision-making. Rhythmic oscillations of neural excitability underlie coordination of network processing, and have been reported in these dopaminergic nuclei at several frequency bands. This paper provides a comparative characterization of several frequencies of oscillations of local field potential and single unit activity, highlighting some behavioral correlates. We recorded from optogenetically identified dopaminergic sites in mice training in operant olfactory and visual discrimination tasks. Rayleigh and Pairwise Phase Consistency (PPC) analyses revealed some VTA/SNc neurons phase-locked to each frequency range, with fast spiking interneurons (FSIs) prevalent at 1-2.5 Hz (slow) and 4 Hz bands, and dopaminergic neurons predominant in the theta band. More FSIs than dopaminergic neurons were phase-locked in the slow and 4 Hz bands during many task events. The highest incidence of phase-locking in neurons was in the slow and 4 Hz bands, and occurred during the delay between the operant choice and trial outcome (reward or punishment) signals. These data provide a basis for further examination of rhythmic coordination of activity of dopaminergic nuclei with other brain structures, and its impact for adaptive behavior.
Opioid receptor architecture for the modulation of brainstem functions
Authors: Hug Nicholas F. , Lindsay Nicole Mercer , McCallum William M. , Bryan Justin , Huang Karen , Ochandarena Nicole , Tassou Adrien , Scherrer Grégory
Published: December 2022

Opioids produce profound and diverse effects on a range of behaviors, many driven by brainstem activity; however, the presence of opioid and opioid-like receptors at this level has been poorly studied outside of nociceptive structures and components of respiratory circuitry. While previous studies identified expression of µ, δ, κ, and nociceptin opioid and opioid-like receptors in the brainstem, patterns have not been fully delineated, and neither has receptor coexpression nor the behavioral implications of their expression in most structures. We aimed to elucidate expression patterns for all four receptors across somatosensory-motor, auditory, and respiratory brainstem circuits; identify recurring themes to provide insight into the mechanisms by which exogenous opioids affect broader brainstem circuits; and characterize the function of endogenous opioids in subcortical processing and behavior modulation. Using a fluorescent reporter mouse line for each receptor, we created a comprehensive atlas of brainstem receptor distribution and identified novel expression patterns in modality-specific circuits. Each receptor showed unique expression patterns across the brainstem with minimal correlation between receptors. Orofacial somatosensory-motor circuits expressed all four receptors, though generally in distinct regions, suggesting differential opiate modulation of afferent and efferent trigeminal signaling. Within the auditory circuits, receptors segregated along the vertical and horizontal processing pathways with minimal colocalization. Finally, the respiratory circuit strongly expressed the µ opioid receptor in multiple crucial structures with minimal presence of the other three receptors. We further assessed the functional significance of these expression patterns, using the respiratory circuitry as an example, by characterizing respiratory responses to selective opioid agonists, finding that each agonist caused unique alterations in breathing pattern and/or breath shape. Together, these results establish a comprehensive atlas of opioid and opioid-like receptor expression throughout the brainstem, laying the essential groundwork for further evaluation of opioid neuromodulation across the broad spectrum of behaviors.
Phenotypic plasticity during diel cycling hypoxia in Arctic char (Salvelinus alpinus)
Authors: Ducros Loïck , Touaibia Mohamed , Pichaud Nicolas , Lamarre Simon G.
Published: December 2022

Oxygen concentration naturally fluctuates in aquatic environments. Due to increased eutrophication caused by anthropic activities, this phenomenon could be amplified and result in a daily cycle of alternating normoxic and hypoxic conditions. At the metabolic level, lack of oxygen and reoxygenation can both have serious repercussions on fish due to fluctuations in ATP supply and demand and an elevated risk of oxidative burst. Thus, fish must adjust their phenotype to survive and equilibrate their energetic budget. However, their energy allocation strategy could imply a reduction in growth which could be deleterious for their fitness. Although the impact of cyclic hypoxia is a major issue for ecosystems and fisheries worldwide, our knowledge remains however limited. Our objective was to characterise the effects of cyclic hypoxia on growth and metabolism in fish. We monitored growth parameters (specific growth rate, condition factor), hepatosomatic and visceral indexes, relative heart mass and hematocrit of Arctic char (Salvelinus alpinus) exposed to thirty days of cyclic hypoxia. We also measured the hepatic protein synthesis rate, hepatic triglycerides as well as muscle glucose, glycogen and lactate, and quantified hepatic metabolites during this treatment. Arctic char appeared to acclimate well to oxygen fluctuations. The first days of cyclic hypoxia induced a profound metabolome reorganisation in the liver. However, fish rebalanced their metabolic activities and successfully maintained their growth and energetic reserves after one month of cyclic hypoxia. These results demonstrate the impressive ability of fish to cope with their changing environment.

Summary statement

This study characterizes the metabolic adjustments performed by Arctic char when coping with one month of cyclic hypoxia. Fish reached a new phenotype by defending their growth and energy stores.
GWAS meta-analysis of resistance against Piscirickettsia salmonis in Atlantic salmon
Authors: Rodrigo Marín-Nahuelpi , Garcia Baltasar F. , Piña-Elgueda Agustin , Gallardo-Garrido Jousepth , López Paulina , Cichero Daniela , Moen Thomas , Ødegård Jørgen , Yáñez José M.
Published: December 2022

Salmonid rickettsial syndrome (SRS) remains as one of the most important pathogens for salmon farming. Genetic improvement has proven to be a viable alternative to reduce mortality in breeding stock. Understanding the genetic architecture of resistance has been a matter of ongoing research aimed at establishing the most appropriate method by which genomic information can be incorporated into breeding programs. However, the genetic architecture of complex traits such as SRS resistance may vary due to genetic and environmental background. In this work, we used the genotypes of a total of 5839 Atlantic salmon from 4 different experimental challenges againstPiscirickttsia salmonis, which were imputed high density (∼930K SNP) to perform within-population genomic-association analyses, followed by a meta-analysis of resistance to SRS defined as binary survival and day of death. The objectives of this study were to i) uncover the genomic regions associated with resistance to SRS among multiple populations; and ii) identify candidate genes associated with each trait definition. SNP-based meta-analysis revealed a clear QTL onSsa02for both traits while gene-based meta-analysis revealed 16 genes in common for both traits. Our results suggest a polygenic genetic architecture and provide novel insights into the candidate genes underpinning resistance toP. salmonisinSalmo salar.
Identification of Disease Modules Using Higher-Order Network Structure
Authors: Singh Pramesh , Kuder Hannah , Ritz Anna
Published: December 2022

Motivation

Higher-order interaction patterns among proteins have the potential to reveal mechanisms behind molecular processes and diseases. While clustering methods are used to identify functional groups within molecular interaction networks, these methods largely focus on edge density and do not explicitly take into consideration higher-order interactions. Disease genes in these networks have been shown to exhibit rich higher-order structure in their vicinity, and considering these higher-order interaction patterns in network clustering have the potential to reveal new disease-associated modules.

Results

We propose a higher-order community detection method which identifies community structure in networks with respect to specific higher-order connectivity patterns beyond edges. Higher-order community detection on four different protein-protein interaction networks identifies biologically significant modules and disease modules that conventional edge-based clustering methods fail to discover. Higher-order clusters also identify disease modules from GWAS data, including new modules that were not discovered by top-performing approaches in a Disease Module DREAM Challenge. Our approach provides a more comprehensive view of community structure that enables us to predict new disease-gene associations.

Availability

https://github.com/Reed-CompBio/graphlet-clustering
DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis
Authors: Liu Yi , Yang Yun , Chen Wendong , Shen Feng , Xie Linhai , Zhang Yingying , Zhai Yuanjun , He Fuchu , Zhu Yunping , Chang Cheng
Published: December 2022

Retention time (RT) alignment is one of the crucial steps in liquid chromatography-mass spectrometry (LC-MS)-based proteomic and metabolomic experiments, especially for large cohort studies, and it can be achieved using computational methods; the most popular methods are the warping function method and the direct matching method. However, the existing tools can hardly handle monotonic and non-monotonic RT shifts simultaneously. To overcome this, we developed a deep learning-based RT alignment tool, DeepRTAlign, for large cohort LC-MS data analysis. It first performs a coarse alignment by calculating the average time shift between any two samples and then uses RT and m/z as the main features to train its deep learning-based model. We demonstrate that DeepRTAlign has improved performances, especially when handling complex samples, by benchmarking it against current state-of-the-art approaches on 19 real-world proteomic and metabolomic datasets and the corresponding simulated datasets. Benchmarked on a dataset with known fold changes, the results showed that DeepRTAlign can improve the identification sensitivity of MS data without compromising the quantitative accuracy. Furthermore, using the MS features aligned by DeepRTAlign in a large cohort, we trained a classifier of 15 features to predict the early recurrence of hepatocellular carcinoma. The features were validated on an independent cohort using targeted proteomics with an AUC of 0.833. Being flexible and robust with four different feature extraction tools, DeepRTAlign provides an advanced solution to RT alignment in large cohort LC-MS data, which is currently one of the bottlenecks in proteomics and metabolomics research, especially for clinical applications.
Employing active learning in the optimization of culture medium for mammalian cells
Authors: Hashizume Takamasa , Ozawa Yuki , Ying Bei-Wen
Published: December 2022

Medium optimization is a crucial step of cell culture for biopharmaceutics and regeneration medicine. It remains challenging, as both media and cells are highly complex systems. To address the issue, we tried active learning to fine-tune the culture medium by combining the high-throughput assay and machine learning. As a pilot study, the cell line HeLa-S3 and the gradient-boosting decision tree algorithm were used. The regular and time-saving approaches were developed, and both successfully fine-tuned 29 components to achieve improved cell culture than the original medium. The fine-tuned media showed a significant decrease in fetal bovine serum and the differentiation in vitamins and amino acids. Unexpectedly, the medium optimization raised the cellular NAD(P)H abundance but not the cell concentration owing to the conventional method used for cell culture assay. Our study demonstrated the efficiency of active learning for medium optimization and provided valuable hints for employing machine learning in cell culture.
The multiple lncRNAs encodinghsrω gene is essential for oogenesis inDrosophila
Authors: Saha Rima , Lakhotia Subhash C.
Published: December 2022

In the background of limited studies on noncoding RNAs inDrosophilaoogenesis, we show developmentally activehsrω lncRNA gene to be essential in oogenesis and ovulation. The near-nullhsrω66females, and ovaries with down- or up-regulatedhsrω display varyingly perturbed oogenesis including fewer ovarioles, high apoptosis, poor actin nuclear-cage (stage 10), low Cut levels in late chambers and, finally ovulation block. Restoration of normal oogenesis following targeted expression ofhsrω-RH transcript inhsrω66confirmedhsrω mis-function to underlie these defects. Genetic interaction studies showed varying modulation of ovarian defects following mis-expression of Cut, and TBPH/TDP-43 or Caz/dFUS hnRNPs by alteredhsrω transcript levels. Dietary supplement of ecdysone tohsrω66females, which have reduced ecdysone titer, substantially restored normal oogenesis. Our results show for the first time that the multiple lncRNA producinghsrω gene, which interacts with diverse hnRNPs and other regulatory molecules, As expected of a gene with key roles in dynamics of various hnRNPs, interactions between down or upregulatedhsrω transcripts and various oogenesis regulators are not linear.

Summary Statement

The multiple lncRNA producinghsrω gene critically impactsDrosophilaoogenesis at multiple steps through intra- and inter-organ signaling.
Niche partitioning and coexistence of sympatric macaques in a fragmented habitat of the Upper Brahmaputra Valley, northeastern India
Authors: Sharma Narayan , Sinha Anindya
Published: December 2022

How closely related species co-exist, especially under conditions of resource limitation remains an intriguing problem in ecology. Having to share space and resources, such species are expected to have evolved a variety of behavioural mechanisms to reduce competition. Understanding such adaptation could also provide clues to designing effective conservation strategies for these species. In this chapter, I examine the niche partitioning and co-existence of three congeneric species, the rhesus macaqueMacaca mulatta, northern pig-tailed macaqueMacaca leoninaand stump-tailed macaqueMacaca arctoides, in a fragment of less than 20 km2, the Hollongapar Gibbon Sanctuary, which still harbours a significant proportion of original species pool. An intensive observational study was conducted on two troops each of the three species over a period of 23 months from March 2008 to January 2010. We examined niche partitioning among the macaques along two major axes—space and food. Our results found significant interspecific differences among macaques in their utilisation of both horizontal and vertical space, as well as in their utilisation of food resources. The differential utilisation of space and food has enabled the continued co-existence of the three macaque species in this fragment. At the fragment level and over proximate time scales, our results explain why primates, particularly the three species of macaques, are able to thrive even after being isolated for over one hundred years. Ecological and behavioural insights gleaned from this fragment will help us understand and promote the co-existence of primates in other habitat fragments of the Upper Brahmaputra Valley.
A contribution to the variability ofPrunus spinosaL. in the vicinity of the mediaeval Castle Kolno, near Brzeg, S-W Poland
Authors: Kosina Romuald
Published: December 2022

In the present work, the variability of stone characteristics of mediaeval fossil forms and modern ones from a small blackthorn population in the vicinity of Castle Kolno was analysed. A modern hybrid form obtained from crossing with cultivated plums and appropriate fossil morphotypes were discovered. The analysis of the correlation of features indicated developmental relationships between them. The pattern of variability of the examined stones in the ordination space confirmed the development of thePrunus spinosa-Prunus domesticacomplex as an element of the dynamic syngameon. The population also showed variations in leaf morphotypes, which may be used in taxonomic analysis.
Invasive species modulate the structure and stability of a multilayer mutualistic network
Authors: Vitali Agustin , Ruiz-Suarez Sofía , Vázquez Diego P. , Schleuning Matthias , Rodríguez-Cabal Mariano A. , Sasal Yamila , Pilosof Shai
Published: December 2022

Species interactions are the backbone of the structure and dynamics of communities. The extensive research into the link between structure and stability has been primarily theoretical and focused on monotrophic networks. Therefore, how the disruption of multitrophic interactions alters communities’ response to perturbations in nature remains an open question. Here, we explored how non-native ungulates affect pollination-seed dispersal multilayer networks in Patagonia, Argentina. Ungulates disrupt a hummingbird-mistletoe-marsupial keystone interaction, which alters community composition. We calculated interlayer connectivity, modularity, and species’ roles in connecting modules for intact vs. invaded networks. To link structural changes to stability, we quantified network tolerance to a single random species removal (disturbance propagation) and sequential species removal (robustness) using a stochastic coextinction model. Non-native ungulates reduced the connectivity between pollination and seed dispersal and produced fewer modules with a skewed size distribution. Moreover, species shifted their structural role, primarily from connectors to peripherals, thereby fragmenting the network by reducing the “bridges” among modules. These structural changes altered the dynamics of cascading effects in the community, increasing disturbance propagation and reducing network robustness. Our results highlight the importance of understanding the mechanisms that alter the structure and subsequent stability of multitrophic communities in nature.
From where do legislators draw scientific knowledge? Organizations as scientific authorities in four countries' parliamentary debates
Authors: Syväterä Jukka , Rautalin Marjaana , Magyari Attila Kustán
Published: December 2022

Organizations far beyond traditional academic institutions have become prolific science producers, with many now providing evidence‐based advice for national governments and policy‐makers. Neo‐institutional sociology explains organizations' growing investment in research activities and research‐based policy advice by the all‐embracing scientization and the expansion of the educated population, phenomena observable throughout the world. There is, however, considerably less knowledge about how the organizations' increased knowledge production and the supply of science‐based policy advice are reflected in national policy‐making, including the legislative work of parliaments, and to what extent distinct organizations are deemed authoritative in different countries. In this paper, we examine how different organizations are used as scientific authorities in parliamentary debates over new legislation. Drawing on analyses of 576 parliamentary debates from Australia, Finland, Kenya, and the United Kingdom, we study what organizations are acknowledged as scientific authorities and the relative weight of different organization types in the context of political debates over new legislation. The results reveal that while organizations in general are frequently evoked as scientific authorities in all four countries, there is remarkable variation in the types of organizations considered authoritative in different national contexts. We elaborate these findings by analysing ways in which politicians evaluate organizations as sources of scientific authority. While the same set of evaluative schemas are used in all four countries, each is typically applied to certain types of organization. The results suggest that both the supply of scientific policy advice and political culture shape legislators' rhetorical practices when drawing on organizations' scientific authority.
Modified chest wall lateral intercostal artery perforator (MCW‐LICAP) flap: a versatile flap in the era of oncoplastic breast surgery
Authors: Yee Francis Zheng Yi , Lim Ee Wen , Seet Yert Li Melissa , Hing Jun Xian , Mok Chi Wei
Published: December 2022

Background

Breast reconstruction following oncological resection is becoming more common in recent years. In some ladies, implant reconstruction is not ideal due to significant implant visibility or palpability. Autologous reconstruction addresses the limitations of implant reconstruction but results in potential donor site morbidities. To date, there is no clear advantage ascribed to any technique. With appropriate selection, patients with adequate lateral mammary fold have the option of reconstruction with MCW‐LICAP flap. We present our techniques and outcomes from a series of 29 patients who underwent MCW‐LICAP flap.

Methods

A retrospective review of consecutive patients who underwent curative resection for breast cancer with immediate MCW‐LICAP flap reconstruction, between July 2018 to April 2022 was conducted. The techniques used with its variations along with video demonstrations are presented.

Results

A total of 29 patients underwent 34 procedures. Nineteen breast conserving surgeries and 15 mastectomies were completed, and immediate reconstruction performed in all cases. Twenty‐three patients had MCW‐LICAP, 1 with a Stacked intercostal artery perforator (STICAP) flap, and 5 had MCW‐LICAP combined with a Goldilocks mastectomy. There were no cases of complications requiring re‐operation. All patients had acceptable time to adjuvant therapy with a median of 36 days. Learning curve analysis showed a significant reduction in operative time after the 6th case.

Conclusion

In our preliminary experience, MCW‐LICAP flap is a safe, reliable, and versatile oncoplastic reconstruction option.
Improved prediction of 10‐year risk of severe liver disease in the general population using commonly available biomarkers
Authors: Hagström Hannes , Yan Jacinth , Talbäck Mats , Andreasson Anna , Walldius Göran , Bottai Matteo , Hammar Niklas
Published: December 2022

Background

Estimating the risk for cirrhosis in the general population is complex. Existing prediction tools are in general unsatisfactory.

Aims

To explore if using commonly available biomarkers can improve the commonly used FIB‐4 score in the identification of subgroups at risk of cirrhosis.

Methods

We used laboratory and clinical data on 126,925 individuals aged 35–79 years in Stockholm, Sweden, undergoing health examinations from 1985 to 1996. We used Swedish nationwide registries to ascertain 10‐year cumulative incidence of severe liver disease, a composite of diagnoses corresponding to cirrhosis and its complications. We considered combinations of biomarkers associated with severe liver disease to identify subgroups with different risk profiles.

Results

During an average follow‐up of 9.3 years, we ascertained 630 incident cases of severe liver disease (0.5%). Age, the FIB‐4 score, diabetes or impaired glucose and gamma‐glutamyl transferase (gGT) were the most relevant characteristics for classifying risk profiles. Using these factors, we identified 24 groups with a cumulative incidence of severe liver disease at 10 years ranging from 0.2% (age 35–65, low FIB‐4, no diabetes or impaired glucose and normal gGT) to 32.1% (age 35–65, high FIB‐4, diabetes or impaired glucose and high gGT).

Conclusions

Identification of subjects at increased risk of severe liver disease in the general population using the FIB‐4 score can be substantially improved by adding age and specific biomarkers commonly available in the primary care setting. These parameters should be considered for inclusion in the development of future risk prediction models.
The impact of Phelan–McDermid syndrome on the child and family
Authors: Phelan Katy
Published: December 2022

This commentary is on the original articles by García‐Bravo et al. and Dille et al. on pages 908–916 and 917–925 of this issue.
Complexities of psychosocial late effects of childhood and adolescent brain tumors
Authors: Mucci Grace A.
Published: December 2022

This commentary is on the original article by Pickering et al. on pages 942–952 of this issue.