bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retinal, Optic Nerve, and Cerebral Infarction in Odontogenic Lemierre Syndrome
Authors: Halawa Ahmad , Kim John , Trobe Jonathan D. 
Published: August 2021

Abstract:
A 61-year-old healthy woman developed congestive orbitopathy, and bilateral retinal, optic nerve, and cerebral infarctions after removal of a chipped molar tooth. Ophthalmoscopy disclosed multiple retinal arteriolar occlusions and pallid swelling of both optic discs. Imaging revealed ipsilateral masticator and pterygoid muscle abscesses, and thrombosis of the right internal jugular vein and sigmoid sinus, both cavernous sinuses and superior ophthalmic veins, and restricted diffusion of both optic nerves and corona radiata. Blood cultures were positive for Streptococcus anginosus. Despite aggressive medical and surgical treatment, the patient remained unresponsive and presumptively blind. This case is an example of a catastrophic form of odontogenic Lemierre syndrome. Blindness, attributable to venous hypertension and vasculitis, has been rarely reported. Early recognition and treatment are critical to avoid such dire consequences.
Failure to Obtain Urgent Arterial Imaging in Acute Third Nerve Palsies
Authors: Chung Jennifer E. , Schroeder Richard M. , Wilson Bradley , Van Stavern Gregory P. , Stunkel Leanne 
Published: August 2021

Background:
Isolated third nerve palsy may indicate an expanding posterior communicating artery aneurysm, thus necessitating urgent arterial imaging. This study aims to assess the rate and duration of delays in arterial imaging for new isolated third nerve palsies, identify potential causes of delay, and evaluate instances of delay-related patient harm.

Methods:
In this cross-sectional study, we retrospectively reviewed 110 patient charts (aged 18 years and older) seen between November 2012 and June 2020 at the neuro-ophthalmology clinic and by the inpatient ophthalmology consultation service at a tertiary institution. All patients were referred for suspicion of or had a final diagnosis of third nerve palsy. Demographics, referral encounter details, physical examination findings, final diagnoses, timing of arterial imaging, etiologies of third nerve palsy, and details of patient harm were collected.

Results:
Of the 110 included patients, 62 (56.4%) were women, 88 (80%) were white, and the mean age was 61.8 ± 14.6 years. Forty (36.4%) patients received arterial imaging urgently. Patients suspected of third nerve palsy were not more likely to be sent for urgent evaluation (P = 0.29) or arterial imaging (P = 0.082) than patients in whom the referring doctor did not suspect palsy. Seventy-eight of 95 (82%) patients with a final diagnosis of third nerve palsy were correctly identified by referring providers. Of the 20 patients without any arterial imaging before neuro-ophthalmology consultation, there was a median delay of 24 days from symptom onset to imaging, and a median delay of 12.5 days between first medical contact for their symptoms and imaging. One patient was harmed as a result of delayed imaging.

Conclusions:
Third nerve palsies were typically identified correctly, but referring providers failed to recognize the urgency of arterial imaging to rule out an aneurysmal etiology. Raising awareness of the urgency of arterial imaging may improve patient safety.
Sustainability in wood materials science: an opinion about current material development techniques and the end of lifetime perspectives
Authors: Goldhahn Christian , Cabane Etienne , Chanana Munish 
Published: August 2021

Wood is considered the most important renewable resource for a future sustainable bioeconomy. It is traditionally used in the building sector, where it has gained importance in recent years as a sustainable alternative to steel and concrete. Additionally, it is the basis for the development of novel bio-based functional materials. However, wood's sustainability as a green resource is often diminished by unsustainable processing and modification techniques. They mostly rely on fossil-based precursors and yield inseparable hybrids and composites that cannot be reused or recycled. In this article, we discuss the state of the art of environmental sustainability in wood science and technology. We give an overview of established and upcoming approaches for the sustainable production of wood-based materials. This comprises wood protection and adhesion for the building sector, as well as the production of sustainable wood-based functional materials. Moreover, we elaborate on the end of lifetime perspective of wood products. The concept of wood cascading is presented as a possibility for a more efficient use of the resource to increase its beneficial impact on climate change mitigation. We advocate for a holistic approach in wood science and technology that not only focuses on the material's development and production but also considers recycling and end of lifetime perspectives of the products.This article is part of the theme issue ‘Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)’.
Using attentive gated neural networks to quantify the impact of non-coding variants on transcription factor binding affinity
Authors: Patel Neel , Bai Haimeng , Bush William S. 
Published: August 2021

AbstractA large proportion of non-coding variants are present within binding sites of transcription factors(TFs), which play a significant role in gene regulation. Thus, deriving the impact of non-coding variants on TF binding is the first step towards unravelling their regulatory roles within their associated disease traits. Most of the modern algorithms used for this purpose are based on convolutional neural network(CNN) architectures. However, these models are incapable of capturing the positional effect of different sub-sequences within the TF binding sites on the binding affinity. In this paper, we utilize the attentive gated neural network(AGNet) architecture to build a set of TF-AGNet models for predicting in vivo TF binding intensities in the GM12878 lymphoblastoid cells. These models have novel layers capable of deriving the impact of relative positions of different DNA sub-sequences, within a binding site, on TF binding affinity, and of extracting the most relevant prediction features. We show that the TF-AGNet models are able to outperform conventional CNNs for predicting continuous values of TF binding affinity. We also train additional TF-AGNet models for 20 TFs using data from 4 other cell-lines to assess the generalizability of their prediction accuracy. Lastly, we show that the TF-AGNet based models more accurately classify non-coding variants that significantly affect TF binding compared to models based on 7 variant annotation tools. This accuracy can be leveraged to derive gene regulatory roles of millions of non-coding variants across the genome to further examine their mechanistic associations with complex disease traits.
Evolution of gene expression across species and specialized zooids in Siphonophora
Authors: Munro Catriona , Zapata Felipe , Howison Mark , Siebert Stefan , Dunn Casey W. 
Published: August 2021

AbstractBackgroundSiphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework.ResultsWithin and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression.ConclusionsOur findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.
From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)
Authors: Ruiz José L. , Reimering Susanne , Escobar-Prieto Juan David , Brancucci Nicolas M. B. , Echeverry Diego F. , Abdi Abdirahman I. , Marti Matthias , Gómez-Díaz Elena , Otto Thomas D. 
Published: August 2021

ABSTRACTRecent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Although there is a promise of long read technologies to obtain “perfect genomes”, the number of contigs often exceeds the number of chromosomes by far, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented the ILRA pipeline to correct long read-based assemblies, so contigs are reordered, renamed, merged, circularized, or filtered if erroneous or contaminated, and Illumina reads are used to correct homopolymer errors. We successfully tested our approach by improving the genomes ofTrypanosoma bruceiandLeptosphaeriaspp, and generated four novelPlasmodium falciparumassemblies from field samples. We found that correcting homopolymer tracks reduced the number of genes incorrectly annotated as pseudogenes, but an iterative correction seems to be required to correct larger numbers of sequencing errors. In summary, we described and compared the performance of our new tool, which improved the quality of novel long read assemblies of genomes up to 1Gbp.AvailabilityThe tool is available at GitHub:https://github.com/ThomasDOtto/ILRA.
Changes in movement characteristics in response to private and social information acquisition of socially foraging fish
Authors: Mazué Geoffrey P. F. , Adams Maxim W. D. , Seebacher Frank , Ward Ashley J. W. 
Published: August 2021

ABSTRACTTo overcome the cost of competition resulting from foraging in a group, individuals may balance their use of private (i.e., acquired from personal sampling) and social (i.e., acquired by watching other individuals) information to adjust their foraging strategy accordingly. Reliability of private information about environmental characteristics, such as the spatial distribution of prey, is thus likely to affect individual movement and social interactions during foraging. Our aim was to investigate how movement characteristics of foraging individuals changed as they acquired reliable private information about the spatial occurrence of prey in a foraging context. We allowed guppies (Poecilia reticulata) to develop the reliability of their private knowledge about prey spatial occurrence by repeatedly testing shoals in a foraging task under three experimental distributions of prey: 1) aggregated prey forming three patches located in fixed locations, 2) scattered distribution of prey with random locations, or 3) no prey (used as control). We then applied tracking methods to obtain individual time series of spatial coordinates from which we computed a suite of movement variables reflecting search effort, social proximity and locomotion characteristics during foraging, to examine changes occurring over repeated trials and to investigate which best explained foraging success. We show that foraging shoals became more efficient at finding and consuming food over the first three days by increasing their time spent active. Over time, individuals foraging on either scattered or aggregated prey travelled greater distances, showed an increasing distance to their closest neighbour and became slightly more stochastic in their acceleration profile, compared to control individuals. We found that behaviour changed as private information increased over time, with a clear behavioural shift occurring on the third testing day. Social proximity was the major predictor of foraging success in the absence of prior foraging information, while search effort became the most important predictors of foraging success as information increased. In conclusion, we show that individual movement patterns changed as they acquired private information. Contrary to our predictions, the spatial distribution of prey did not affect any of the movement variables of interest. Our results emphasise the importance of information in shaping movement behaviour in animals.
Brain structure and function predict adherence to an exercise intervention in older adults
Authors: Morris Timothy P. , Burzynska Agnieszka , Voss Michelle , Fanning Jason , Salerno Elizabeth A. , Prakash Ruchika , Gothe Neha P. , Whitfield-Gabrieli Susan , Hillman Charles H. , McAuley Edward , Kramer Arthur F. 
Published: August 2021

AbstractIndividualized and precision medicine approaches to exercise for cognitive and brain health in aging have the potential to improve intervention efficacy. Predicting adherence to an exercise intervention in older adults prior to its commencement will allow for adaptive and optimized approaches that could save time (no need to demonstrate failure before changing course) and money (cost of de-implementing approaches that do not work for certain individuals) which ultimately could improve health outcomes (e.g., preventative medicine approaches prior to the onset of symptoms). Individual differences in brain structure and function in older adults are potential proxies of brain and brain reserve or maintenance and may provide strong predictions of adherence. We hypothesized that brain-based measures would predict adherence to a six-month randomized controlled trial of exercise in older adults, alone and in combination with psychosocial, cognitive and health measures. In 131 older adults (aged 65.79 ± 4.65 years, 63% female) we found, using regularized elastic net regression within a nested cross-validation framework, that brain structure (cortical thickness and cortical surface area) in somatosensory, inferior temporal, and inferior frontal regions and functional connectivity (degree count) in primary information processing (somatosensory, visual), executive control, default, and attentional networks, predicted exercise adherence (R2 = 0.15, p < 0.001). Traditional survey and clinical measures such as gait and walking self-efficacy, biological sex and perceived stress also predicted adherence (R2 = 0.06, p = 0.001) but a combined multimodal model achieved the highest predictive strength (R2 = 0.22, p <0.001). Neuroimaging features alone can predict adherence to a structured group-based exercise intervention in older adults which suggests there is substantial utility of these measures for future research into precision medicine approaches. The best performing model contained multimodal features suggesting that each modality provided independent relevant information in the prediction of exercise adherence.
A model of photosynthetic CO2assimilation in C3leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway
Authors: Wieloch Thomas , Augusti Angela , Schleucher Jürgen 
Published: August 2021

Summary-Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin-Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate actual flux at low atmospheric CO2concentration (Ca).-Since the OPPP releases CO2and reduces NADP+, it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer-Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously.-We found that flux through the plastidial OPPP increases both above and belowCa≈ 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at lowCa.-We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2mesophyll conductance, and the contribution of day respiration to theA/Cicurve drop at highCa. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies.
Molecular docking and molecular dynamics simulation of the anticancer active ligand from Mimosa pudica to the Fibronectin Extra Domain A (EDA)
Authors: Kohli Mayank , Kamatchi C , Kumar Kiran , Bole Shivaji 
Published: August 2021

AbstractMimosa pudica was observed to have many useful characters the main aim of the experiment is to strengthen the multiple potential value of M. Pudica L. To study its secondary metabolites antioxidant, anti-cancerous, GCMS and in-silico studies. In general, the methanol method is employed for obtaining leaf extracts. The preliminary phytochemical screening of the M. pudica leaf extract showed the presence of bioactive components such as terpenoids, flavonoids, glycosides, alkaloids, quinines, phenols, tannins, saponins, and coumarins. An attempt is made to check the anticancer activity towards the cancer cell line A549 (Lung cancer cells) by MTT assay. For the identification of the compounds and to obtain its structure the crude extract is analyzed by GC-MS technique. The result of the GC-MS is analyzed using bioinformatics tool for in-silico docking to find out its targets against lung cancer receptors and PDB ID is obtained from the RCBS PDB database. The affinity of the identified ligand molecules to bind to the active site of the protein was studied through docking. And the effectiveness of the ligand molecules was obtained through molecular dynamics for longer simulation. The RMSD, RMSF and RG interaction were studied to the screened compounds. Further, MMPBSA analysis was carried out for the selected and standard drug like irigenin compounds. These selected lead molecules shown the better binding energy compare to irigenin drug in MMPBSA. The lead derivatives have shown potential results against lung cancer cell lines.
How do King Cobras move across a major highway? Unintentional wildlife crossing structures may facilitate movement
Authors: Jones Max Dolton , Marshall Benjamin Michael , Smith Samantha Nicole , Crane Matt , Silva Inês , Artchawakom Taksin , Suwanwaree Pongthep , Waengsothorn Surachit , Wüster Wolfgang , Goode Matt , Strine Colin Thomas 
Published: August 2021

AbstractGlobal road networks continue to expand, and the wildlife responses to these landscape-level changes need to be understood to advise long-term management decisions. Roads have high mortality risk to snakes because snakes typically move slowly and can be intentionally targeted by drivers.We investigated how radio-tracked King Cobras (Ophiophagus hannah) traverse a major highway in northeast Thailand, and if reproductive cycles were associated with road hazards.We surveyed a 15.3km stretch of Highway 304 to determine if there were any locations where snakes, and other wildlife, could safely move across the road (e.g., culverts, bridges). We used recurse analysis to detect possible road-crossing events, and used subsets of King Cobra movement data to create dynamic Brownian Bridge Movement Models (dBBMM) in an attempt to show movement pathways association with possible unintentional crossing structures. We further used Integrated Step Selection Functions (ISSF) to assess seasonal differences in avoidance of major roads for adult King Cobras in relation to reproductive state.We discovered 32 unintentional wildlife crossing locations capable of facilitating King Cobra movement across the highway. Our dBBMMs failed to show if underpasses were being used by telemetered individuals; however, the tracking locations pre- and post-crossing provided strong evidence of underpass use. Our ISSF suggested a lower avoidance of roads during the breeding season, though the results were inconclusive. With the high volume of traffic, large size of King Cobras and a 98.8% success rate of crossing the road in our study, we strongly suspect that individuals are using the unintentional crossing structures to safely traverse the road.Further research is needed to determine the extent of wildlife underpass use at our study site and globally, alongside using previously proven fencing to facilitate their use. We propose that more consistent integration of drainage culverts and bridges could help mitigate the impacts of roads on some terrestrial wildlife, particularly in areas where roads fragment forests and wildlife corridors.
Studying magnetic susceptibility, microstructural compartmentalisation and chemical exchange in a formalin-fixed ex vivo human brain specimen
Authors: Chan Kwok-Shing , Hédouin Renaud , Mollink Jeroen , Schulz Jenni , Walsum Anne-Marie van Cappellen van , Marques José P. 
Published: August 2021

AbstractPurposeEx vivo imaging is a preferable method to study the biophysical mechanism of white matter orientation-dependent signal phase evolution. Yet, how formalin fixation, commonly used for tissue preservation, affects the phase measurement is not fully known. We, therefore, study the impacts of formalin fixation on magnetic susceptibility, microstructural compartmentalisation and chemical exchange measurement on human brain tissue.MethodsA formalin-fixed, post-mortem human brain specimen was scanned with multiple orientations with respect to the main magnetic field direction for robust bulk magnetic susceptibility measurement with conventional quantitative susceptibility imaging models. Homogeneous white matter tissues were subsequently excised from the whole-brain specimen and scanned in multiple rotations on an MRI scanner to measure the anisotropic magnetic susceptibility and microstructure-related contributions in the signal phase. Electron microscopy was used to validate the MRI findings.ResultsThe bulk isotropic magnetic susceptibility of ex vivo whole-brain imaging is comparable to in vivo imaging, with noticeable enhanced non-susceptibility contributions. The excised specimen experiment reveals that anisotropic magnetic susceptibility and compartmentalisation phase effect were considerably reduced in formalin-fixed white matter tissue.ConclusionsDespite formalin-fixed white matter tissue has comparable bulk isotropic magnetic susceptibility to those measured via in vivo imaging, its orientation-dependent components in the signal phase related to the tissue microstructure is substantially weaker, making it less favourable in white matter microstructure studies using phase imaging.