bluuebunny/crossref_metadata_2025 huggingface dataset:
Incidence and Risk Factors for Diaphragmatic Herniation Following Esophagectomy for Cancer
Authors: Hertault Hugo , Gandon Anne , Behal Hélène , Legault Gaëtan , Degisors Sébastien , Martin Louis , Messier Marguerite , Noiret Barbara , Vermersch Mathilde , Nuytens Frederiek , Eveno Clarisse , Piessen Guillaume
Published: August 2021

Objective:

To evaluate the incidence and risk factors of diaphragmatic herniation following esophagectomy for cancer (DHEC), and assess the results of surgical repair.

Summary Background data:

The current incidence of DHEC is discussed with conflicting data regarding its treatment and natural course.

Methods:

Monocentric retrospective cohort study (2009–2018). From 902 patients, 719 patients with a complete follow-up of CT scans after transthoracic esophagectomy for cancer were reexamined to identify the occurrence of a DHEC. The incidence of DHEC was estimated using Kalbfleisch and Prentice method and risk factors of DHEC were studied using the Fine and Gray competitive risk regression model by treating death as a competing event. Survival was analyzed.

Results:

Five-year DHEC incidence was 10.3% [95% CI, 7.8%–13.2%] (n = 59), asymptomatic in 54.2% of cases. In the multivariable analysis, the risk factors for DHEC were: presence of hiatal hernia on preoperative CT scan (HR = 1.72 [1.01–2.94], P = 0.046), previous hiatus surgery (HR = 3.68 [1.61–8.45], P = 0.002), gastroesophageal junction tumor location (HR = 3.51 [1.91–6.45], P < 0.001), neoadjuvant chemoradiotherapy (HR = 4.27 [1.70–10.76], P < 0.001), and minimally invasive abdominal phase (HR = 2.98 [1.60–5.55], P < 0.001). A cure for DHEC was achieved in 55.9%. The postoperative mortality rate was nil, the overall morbidity rate was 12.1%, and the DHEC recurrence rate was 30.3%. Occurrence of DHEC was significantly associated with a lower hazard rate of death in a time-varying Cox's regression analysis (HR = 0.43[0.23–0.81], P = 0.010).

Conclusions:

The 5-year incidence of DHEC is 10.3% and is associated with a favorable prognosis. Surgical repair of symptomatic or progressive DHEC is associated with an acceptable morbidity. However, the optimal surgical repair technique remains to be determined in view of the large number of recurrences.
The Impact of Cold Ischaemia Time on Outcomes of Living Donor Kidney Transplantation in the UK Living Kidney Sharing Scheme
Authors: van de Laar Stijn C. , Robb Matthew L. , Hogg Rachel , Burnapp Lisa , Papalois Vassilios E. , Dor Frank J. M. F.
Published: August 2021

Objective:

To assess the impact of CIT on living donor kidney transplantation (LDKT) outcomes in the UKLKSS versus outside the scheme.

Background:

LDKT provides the best treatment option for end-stage kidney disease patients. end-stage kidney disease patients with an incompatible living donor still have an opportunity to be transplanted through Kidney Exchange Programmes (KEP). In KEPs where kidneys travel rather than donors, cold ischaemia time (CIT) can be prolonged.

Methods:

Data from all UK adult LDKT between 2007 and 2018 were analysed.

Results:

9969 LDKT were performed during this period, of which 1396 (14%) were transplanted through the UKLKSS, which we refer to as KEP. Median CIT was significantly different for KEP versus non-KEP (339 versus 182 minutes,P< 0.001). KEP LDKT had a higher incidence of delayed graft function (DGF) (2.91% versus 5.73%,P< 0.0001), lower 1-year (estimated Glomerular Filtration Rate (eGFR) 57.90 versus 55.25 ml/min,P= 0.04) and 5-year graft function (eGFR 55.62 versus 53.09 ml/min,P= 0.01) compared to the non-KEP group, but 1- and 5-year graft survival were similar. Within KEP, a prolonged CIT was associated with more DGF (3.47% versus 1.95%,P= 0.03), and lower graft function at 1 and 5-years (eGFR = 55 vs 50 ml/min,P= 0.02), but had no impact on graft survival.

Conclusion:

Whilst CIT was longer in KEP, associated with more DGF and lower graft function, excellent 5-year graft survival similar to non-KEP was found.
Population-Based Evaluation of Indirect Signs of Increased Intracranial Pressure
Authors: Witsberger Emily M. , Huston John , Cutsforth-Gregory Jeremy K. , Johnson Patrick W. , Bhatti M. Tariq , Chen John J.
Published: August 2021

Background:

The Mayo Clinic Study of Aging (MCSA) is a unique prospective study that systematically evaluates the normal aging population and includes many participants undergoing both MRI and lumbar puncture (LP). Using MCSA date, we aimed to determine the prevalence of indirect signs of raised intracranial pressure (ICP) on MRI and whether these correlate with LP opening pressure (OP). This is a large-scale study that evaluates how often indirect signs of increased ICP occur in a normal population.

Methods:

MCSA participants who had an MRI within 3 months of an LP with recorded OP were included in the study. MRIs were reviewed for indirect signs of raised ICP, including pituitary to sella (P/S) ratio, cerebellar tonsillar ectopia, and optic nerve sheath diameter (ONSD). These signs were evaluated for correlations with OP and influences from body mass index (BMI) and obstructive sleep apnea (OSA).

Results:

Five hundred ninety-seven MCSA patients were identified who underwent both LP and MRI. Two hundred sixty (43.6%) were women. The median age was 70.7 years (range 32.6–92.7). Median OP was 152 mm H2O (range 60–314 mm H2O), with 91 (15.2%) participants having an OP ≥ 200 mm H2O. Empty or partially empty sella was seen in 81 (12.8%) of the cohort. The P/S ratio decreased with increasing OP (r = −0.3, P < 0.001). There was a weak correlation between OP and average ONSD (r = 0.184, P = 0.01), which was no longer significant when accounting for age, gender, and BMI (partial r2 = 0.014, P = 0.097). There was no correlation between OP and cerebellar tonsillar ectopia. OSA was associated with increased ONSD (P = 0.004), but this did not remain statistically significant after accounting for age, gender, and BMI (P = 0.085).

Conclusion:

Smaller pituitary gland size correlated with increasing OP. This suggests that ICP is a continuum with some normal individuals demonstrating asymptomatic radiologic signs of raised ICP.
Retinal, Optic Nerve, and Cerebral Infarction in Odontogenic Lemierre Syndrome
Authors: Halawa Ahmad , Kim John , Trobe Jonathan D.
Published: August 2021

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.
Understanding the structural diversity of chitins as a versatile biomaterial
Authors: Hou Jiaxin , Aydemir Berk Emre , Dumanli Ahu Gümrah
Published: August 2021

Chitin is one of the most abundant biopolymers, and it has adopted many different structural conformations using a combination of different natural processes like biopolymerization, crystallization and non-equilibrium self-assembly. This leads to a number of striking physical effects like complex light scattering and polarization as well as unique mechanical properties. In doing so, chitin uses a fine balance between the highly ordered chain conformations in the nanofibrils and random disordered structures. In this opinion piece, we discuss the structural hierarchy of chitin, its crystalline states and the natural biosynthesis processes to create such specific structures and diversity. Among the examples we explored, the unified question arises from the generation of completely different bioarchitectures like the Christmas tree-like nanostructures, gyroids or helicoidal geometries using similar dynamic non-equilibrium growth processes. Understanding the
in vivo
development of such structures from gene expressions, enzymatic activities as well as the chemical matrix employed in different stages of the biosynthesis will allow us to shift the material design paradigms. Certainly, the complexity of the biology requires a collaborative and multi-disciplinary research effort. For the future's advanced technologies, using chitin will ultimately drive many innovations and alternatives using biomimicry in materials science.

This article is part of the theme issue ‘Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.
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)’.
Corynebacterium hindlerae sp. nov., derived from a human granuloma, which forms black colonies and black halos on modified Tinsdale medium but is not closely related to Corynebacterium diphtheriae and related taxa
Authors: Bernard Kathryn A. , Burdz Tamara , Pacheco Ana Luisa , Wiebe Deborah , Bernier Anne-Marie
Published: August 2021

Corynebacterium diphtheriae

,

Corynebacterium belfantii

,

Corynebacterium rouxii

,

Corynebacterium ulcerans

,

Corynebacterium pseudotuberculosis

and

Corynebacterium silvaticum

are the only taxa from among ~121

Corynebacterium

species deemed potentially able to harbour diphtheria tox genes. Subsequently tox-gene bearing species may potentially produce diphtheria toxin, which is linked to fatal respiratory distress if a pharyngeal pseudomembrane is formed or toxaemia develops in those unimmunized or under-immunized. Detection of diphtheria toxin-producing species may also invoke a public health response and contact tracing. Recovery of such species from the respiratory tract or other contaminated sources such as non-healing ulcerative wounds are expedited by use of differential and selective media such as modified Tinsdale medium (MTM). This medium is supplemented with potassium tellurite, which supresses most normal flora present in contaminated specimens, as well as l-cystine and thiosulphate. Most diphtheria-tox-gene bearing species grow well on MTM, producing black colonies with a black halo around each colony. This is due to an ability to produce cystinase in the presence of tellurite, cystine and thiosulphate, resulting in black tellurium deposits being observed in the agar. Other

Corynebacterium

species may/may not be able to grow at all in the presence of tellurite but if able to grow, will have small beige or brownish colonies which do not exhibit black halos. We describe here an unusual non-tox-gene-bearing isolate, NML 93-0612T, recovered from a human wrist granuloma, which produced black colonies with black halos on MTM agar but was otherwise distinguishable from

Corynebacterium

species which can bear tox genes. Distinctive features included its unusual colony morphology on MTM and sheep blood agar, by proteomic, biochemical and chemotaxonomic properties and by molecular methods. Its genome contained 2 680 694 bytes, a G+C content of 60.65 mol% with features consistent with the genus

Corynebacterium

and so represents a new species for which we propose the name Corynebacterium hindlerae sp. nov.
Increased biofilm formation by Staphylococcus aureus clinical isolates on surfaces covered with plasma proteins
Authors: Cardoso Guimarães Lorrayne , Marques de Souza Bruna , de Oliveira Whitaker Carolina , Abreu Fernanda , Barreto Rocha Ferreira Rosana , dos Santos Kátia Regina Netto
Published: August 2021

Introduction. Biofilm formation is a major virulence factor associated with

Staphylococcus aureus

infections. However, the influence of plasma proteins on biofilm formation of clinical isolates in vitro remains unclear.

Hypotheses. We hypothesized that coating surfaces with plasma proteins might induce biofilm formation by

S. aureus

of different clonal lineages.

Aim. To evaluate biofilm production by clinical

S. aureus

isolates of different clonal lineages isolated in Rio de Janeiro hospitals and investigated the presence of biofilm-associated genes.

Methodology. This study assessed biofilm production of 60

S. aureus

isolates in polystyrene microtitre plates with and without fibrinogen or fibronectin. The biochemical composition of the biofilm matrices was determined and the biofilm formation on fibrinogen-coated surfaces was also evaluated by confocal laser scanning microscopy. The presence of biofilm-related genes was detected by PCR, and the typing and functionality of agr operon was also evaluated.

Results. Most of the isolates (45 %) were weak biofilm producers or non-producers. However, most of them presented a significant increase in biofilm production on plates covered with plasma proteins. There was no significant difference in biofilm formation between methicillin-resistant and -susceptible

S. aureus

isolates, or between different clonal lineages, except for ST30-IV (weak producers) and ST239-III (strong producers). The fnbB gene was associated with higher biofilm production.

Conclusion. An increase in biofilm production in the presence of plasma proteins highlights the importance of investigating biofilm formation by

S. aureus

clinical isolates under different conditions since this virulence factor contributes to persistent infections and increased resistance to antimicrobials.
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

A 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

Background

Siphonophores 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.

Results

Within 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.

Conclusions

Our 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

Recent 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.

Availability

The 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

To 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

Individualized 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

-

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

Mimosa 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

Global 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

Purpose

Ex 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.

Methods

A 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.

Results

The 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.

Conclusions

Despite 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.
Comparable neutralization of SARS-CoV-2 Delta AY.1 and Delta in individuals sera vaccinated with BBV152
Authors: Yadav Pragya D. , Sahay Rima R , Sapkal Gajanan , Nyayanit Dimpal , Shete Anita M. , Deshpande Gururaj , Patil Deepak Y. , Gupta Nivedita , Kumar Sanjay , Abraham Priya , Panda Samiran , Bhargava Balram
Published: August 2021

The recent emergence of the SARS-CoV-2 Variant of Concern, B.1.617.2 (Delta) variant and its high transmissibility has led to the second wave in India. BBV152, a whole-virion inactivated SARS-CoV-2 vaccine used for mass immunization in India, showed a 65.2% protection against the Delta variant in a double-blind, randomized, multicentre, phase 3 clinical trial. Subsequently, Delta has been further mutated to Delta AY.1, AY.2, and AY.3. Of these, AY.1 variant was first detected in India in April 2021 and subsequently from twenty other countries as well. Here, we have evaluated the IgG antibody titer and neutralizing potential of sera of COVID-19 naive individual’s full doses of BBV152 vaccine, COVID-19 recovered cases with full dose vaccines and breakthrough cases post-immunization BBV152 vaccines against Delta, Delta AY.1 and B.1.617.3. A reduction in neutralizing activity was observed with the COVID-19 naive individuals full vaccinated (1.3, 1.5, 1.9-fold), COVID-19 recovered cases with full BBV152 immunization (2.5, 3.5, 3.8-fold) and breakthrough cases post-immunization (1.9, 2.8, 3.5-fold) against Delta, Delta AY.1 and B.1.617.3 respectively compared to B.1 variant. A minor reduction was observed in the neutralizing antibody titer in COVID-19 recovered cases full BBV152 vaccinated and post immunized infected cases compared to COVID-19 naive vaccinated individuals. However, with the observed high titers, the sera of individuals belonging to all the aforementioned groups they would still neutralize the Delta, Delta AY.1 and B.1.617.3 variants effectively.
Neuronal correlates of attentional selectivity and intensity in visual area V4 are invariant of motivational context
Authors: Ghosh Supriya , Maunsell John H.R.
Published: August 2021

Flexibly switching attentional strategies is crucial for adaptive behavior in changing environments. Depending on the context, task demand employs different degrees of the two fundamental components of attention– attentional selectivity (preferentially attending to one location in visual space) and effort (the total non-selective intensity of attention). Neuronal responses in the visual cortex that show modulation with changes in either selective attention or effort are reported to partially represent motivational aspect of the task context. The relative contributions and interactions of these two components of attention to modulate neuronal signals and their sensitivity to distinct motivational drives are poorly understood. To address this question, we independently controlled monkeys’ spatially selective attention and non-selective attentional intensity in the same experimental session during a novel visual orientation change detection task. Attention was controlled either by adjusting the relative difficulty of the orientation changes at the two locations or by the reward associated with stimuli at two locations while simultaneously recording spikes from populations of neurons in area V4. We found that V4 neurons are robustly modulated by either selective attention or attentional intensity. Notably, as attentional selectivity for a neuron’s receptive field location decreased, its responses became weaker, despite an increase in the animal’s overall attentional intensity. This strong interaction between attentional selectivity and intensity could be identified in single trial spike trains. A simple divisive normalization of spatially distributed attention performances can explain the interaction between attention components well at the single neuron level. The effects of attentional selectivity and attentional intensity on neuronal responses were the same regardless of whether the changes were motivated by reward or task difficulty. These results provide a detailed cellular-level mechanism of how fundamental components of attention integrate and affect sensory processing in varying motivational and stimulus contexts.
The Effects of Posture on the Three-Dimensional Gait Mechanics of Human Walking in Comparison to Bipedal Chimpanzees
Authors: Johnson Russell T. , O’Neill Matthew C. , Umberger Brian R.
Published: August 2021

Humans walk with an upright posture on extended limbs during stance and with a double-peaked vertical ground reaction force. Our closest living relatives, chimpanzees, are facultative bipeds that walk with a crouched posture on flexed, abducted hind limbs and with a single-peaked vertical ground reaction force. Differences in human and bipedal chimpanzee three-dimensional kinematics have been well quantified; however, it is unclear what the independent effects of using a crouched posture are on three-dimensional gait mechanics for humans, and how they compare with chimpanzees. Understanding the relationships between posture and gait mechanics, with known differences in morphology between species, can help researchers better interpret the effects of trait evolution on bipedal walking. We quantified pelvis and lower limb three-dimensional kinematics and ground reaction forces as humans adopted a series of upright and crouched postures and compared them with data from bipedal chimpanzee walking. Human crouched posture gait mechanics were more similar to bipedal chimpanzee gait than normal human walking, especially in sagittal plane hip and knee angles. However, there were persistent differences between species, as humans walked with less transverse plane pelvis rotation, less hip abduction, and greater peak horizontal ground reaction force in late stance than chimpanzees. Our results suggest that human crouched posture walking reproduces only a small subset of the characteristics of three-dimensional kinematics and ground reaction forces of chimpanzee walking, with the remaining differences likely due in large part to the distinct musculoskeletal morphologies of humans and chimpanzees.

Summary Statement

Differences between human crouched posture gait and bipedal chimpanzee gait illustrate the limitations of using modern day humans to infer the evolution of hominin bipedalism.
Quantitative traits under selection: derivations of distributions, higher moments, and the effects of recombination
Authors: Smith Reginald D.
Published: August 2021

The mathematical theory of quantitative traits is over one hundred years old but it is still a fertile area for research and analysis. However, the effects of selection on a quantitative trait, while well understood for the effects on the mean and variance, have traditionally been difficult to attack from the perspective of analyzing the probability density of the breeding values and deriving higher (third and fourth) moments as well as analyzing the impact of recombination. In this paper, the exact formula for the breeding value distribution after selection is derived and, using new integral tables, the first four moments are given exact expressions for the first time. In addition, the effects of recombination on the full distribution of breeding values are demonstrated. Finally, the changes of GXE covariance in the selected parent population caused by factors similar to the Bulmer Effect are also investigated in detail.

Mathematics Subject Classification (2020)

MSC code 92D10 · MSC code 92D15
Recombinant single-cycle influenza virus as a new tool to augment antitumour immunity with immune checkpoint inhibitors
Authors: Kandasamy Matheswaran , Gileadi Uzi , Rijal Pramila , Tan Tiong Kit , Lee Lian Ni , Chen Jili , Prota Gennaro , Zhang Jing , Rabbitts Terence , Townsend Alain , Cerundolo Vincenzo
Published: August 2021

Virus-based tumour vaccines offer many advantages compared to other antigen delivering systems. They generate concerted innate and adaptive immune response, and robust CD8+T cell responses. We engineered a non-replicating pseudotyped influenza virus (S-FLU) to deliver the well-known cancer testis antigen, NY-ESO-1 (S-NY-ESO-1 FLU). Intranasal or intramuscular immunization of NY-ESO-1 S-FLU virus in mice elicited a strong NY-ESO-1 specific CD8+T cell response in lungs and spleen that resulted in the regression of NY-ESO-1 expressing lung tumour and subcutaneous tumour respectively. Combined administration with anti PD-1 antibody, NY-ESO-1 S-FLU virus augmented the tumour protection by reducing the tumour metastasis. We propose that the antigen delivery through S-FLU is highly efficient in inducing antigen specific CD8+T cell response and protection against tumour development in combination with PD-1 blockade.
Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae
Authors: Dorrell Richard G. , Kuo Alan , Füssy Zoltan , Richardson Elisabeth , Salamov Asaf , Zarevski Nikola , Freyria Nastasia J. , Ibarbalz Federico M. , Jenkins Jerry , Karlusich Juan Jose Pierella , Steindorff Andrei Stecca , Edgar Robyn E. , Handley Lori , Lail Kathleen , Lipzen Anna , Lombard Vincent , McFarlane John , Nef Charlotte , Novák Vanclová Anna M.G. , Peng Yi , Plott Chris , Potvin Marianne , Vieira Fabio Rocha Jimenez , Barry Kerrie , Dacks Joel B. , de Vargas Colomban , Henrissat Bernard , Pelletier Eric , Schmutz Jeremy , Wincker Patrick , Bowler Chris , Grigoriev Igor V. , Lovejoy Connie
Published: August 2021

The Arctic Ocean is being impacted by warming temperatures, increasing freshwater and highly variable ice conditions. The microalgal communities underpinning Arctic marine food webs, once thought to be dominated by diatoms, include a phylogenetically diverse range of small algal species, whose biology remains poorly understood. Here, we present genome sequences of a cryptomonad, a haptophyte, a chrysophyte, and a pelagophyte, isolated from the Arctic water column and ice. Comparing protein family distributions and sequence similarity across a densely-sampled set of algal genomes and transcriptomes, we note striking convergences in the biology of distantly related small Arctic algae, compared to non-Arctic relatives; although this convergence is largely exclusive of Arctic diatoms. Using high-throughput phylogenetic approaches, incorporating environmental sequence data from Tara Oceans, we demonstrate that this convergence was partly explained by horizontal gene transfers (HGT) between Arctic species, in over at least 30 other discrete gene families, and most notably in ice-binding domains (IBD). These Arctic-specific genes have been repeatedly transferred between Arctic algae, and are independent of equivalent HGTs in the Antarctic Southern Ocean. Our data provide insights into the specialized Arctic marine microbiome, and underlines the role of geographically-limited HGT as a driver of environmental adaptation in eukaryotic algae.