bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Paramedian Pedicle Forehead and Free Medial Sural Artery Perforator Flap Reconstruction of a Composite Nasal Defect: A Case Report
Authors: Liao Kuan-Hao , Yen Cheng-I , Chang Chun-Shin , Hsiao Yen-Chang 
Published: February 2022

Background
Extensive nasal defects after resection of a malignancy are a challenge for all plastic surgeons. Nasal composite tissue defects have to be reconstructed with multiple staging surgeries. A paramedian pedicled forehead flap and free tissue transfer can be used for lining and skin replacement at different stages. In general, free tissue transfer is used for nasal lining and nasal floor reconstruction at the preliminary stage. Several weeks or months later, a paramedian pedicled forehead flap is used to replace the skin. Intermediate stages will also be necessary, and therefore the total therapeutic course is very long.

Aim and Objectives
The aim of this study was to report the simultaneous use of a paramedian pedicle forehead flap and a free medial sural artery perforator (MSAP) flap to reconstruct a composite nasal defect after wide excision of squamous cell carcinoma.

Patient
In 2015, a 57-year-old woman with squamous cell carcinoma of the nose underwent tumor wide excision, which caused a composite defect involving multiple nasal subunits (partial tip, dorsum, right sidewall, right ala subunits). She received both a pedicled paramedian forehead flap to replace the skin and an MSAP flap to reconstruct the lining during the same procedure. At the intermediate stage 4 weeks later, the pedicled forehead flap was elevated and tailored. Then, a further 4 weeks later, flap division was performed.

Results
The patient received a total of 3 surgical procedures to reconstruct the composite defects of multiple nasal subunits. Nasal reconstruction was done within 2 months. The patient was satisfied with the aesthetic appearance and functional outcome.

Conclusions
Simultaneous paramedian pedicle forehead and free flap reconstruction can provide an effective solution for composite nasal defects. Satisfactory functional and aesthetic results can be achieved.
Distributed renewable energy systems for resilient and sustainable development of remote and vulnerable communities
Authors: Ahmad Tanvir , Ali Saddam , Basit Abdul 
Published: February 2022

More than 940 million people (13% of the world population) do not have any access to electricity. Most of these people live in rural and remote areas, where the lack of electricity access is significantly damaging the quality of life, economic development and the environment. Distributed energy systems (DESs) (based on clean energy technologies) for energy access offer a potentially important strategy for pursuing environment-friendly sustainable development and poverty alleviation; especially in rural and remote communities. DESs are also helpful in reducing deforestation and greenhouse gas (GHG) emissions as the fossil fuel-based energy production is among the largest contributors to GHG emissions. This paper presents the importance of energy access through DESs for resilient and sustainable development using two projects case studies from Pakistan. The first project case study is based on the Afghan refugee villages, where, currently, there is no electricity access. A baseline survey was conducted to assess the socio-economic conditions and energy demand of the refugees. This assessment is then used to devise clean energy solutions as per the local context. This project aims to improve the quality of life of the refugees by providing energy access. In the second case study, electricity access was provided to the local communities a few years ago. Analyses of primary data collected in this case study show that DES integrated with socio-economic and cultural systems can bring a significantly positive impact on the local communities, advancing all the sustainability development goals. This work concludes that DES can be significantly generative, if effectively integrated into socio-economic processes.
This article is part of the theme issue ‘Developing resilient energy systems’.
On the potential of pristine
Cocos nucifera L
. tissues for green desalination
Authors: Adelodun Adedeji A. 
Published: February 2022

Coconut palm tree (
Cocos nucifera L
.) tissues were used as a readily available, low-cost and green adsorbent to desalinate seawater. The tree bark (CB), husk (CH), leaves (CL) and roots (CR) were examined in their fresh (F) and dry (D) forms. The salinity removal (adsorption) efficiency followed the trend: F_CB ≈ F_CR > F_CL > D_CR > F_CL > D_CR. The sorbents from the coastal region desalinated more efficiently than those from a non-coastal region. Also, the fresh tissues were more effective and efficient than the dry parts. The salinity retention ability (desalination : desorption) follows the trend: F_CR (22.2) > F_CB (19.0) ≫ D_CR (12.3) > D_CB (11.0) > D_CL (6.14) ≈ F_CL (6.10) > F_CH (4.3) > D_CH (2.1). Moreover, the desalination fitted the pseudo-second-order kinetics than the pseudo-first-order, suggesting the predominance of chemisorption over physical removal. Overall, water pH, conductivity, total dissolved solids and dissolved oxygen (DO) correlated positively and strongly with desalination. By contrast, the density and redox potential correlated negatively, whereas temperature and DO showed no definite influence. Conclusively, F_CR and F_CB are the most suitable coconut palm tree tissues for desalination. Future studies should include chemical characterization of the tissues and system optimization for upscaling.

This article is part of the theme issue ‘Developing resilient energy systems’.
When the whole is less than the sum of its parts: maximum object category information and behavioral prediction in multiscale activation patterns
Authors: Karimi-Rouzbahani Hamid , Woolgar Alexandra 
Published: February 2022

AbstractNeural codes are reflected in complex, temporally and spatially specific patterns of activation. One popular approach to decode neural codes in electroencephalography (EEG) is multivariate decoding. This approach examines the discriminability of activity patterns across experimental conditions to test if EEG contains information about those conditions. However, conventional decoding analyses ignore aspects of neural activity which are informative. Specifically, EEG data can be decomposed into a large number of mathematically distinct features (e.g., entropy, Fourier and Wavelet coefficients) which can reflect different aspects of neural activity. We previously compared 30 such features of EEG data, and found that visual category, and participant behavior, can be more accurately predicted using multiscale spatiotemporally sensitive Wavelet coefficients than mean amplitude (Karimi-Rouzbahani et al., 2021b). Here, we considered that even this larger set of features may only partially capture the underlying neural code, because the brain could use a combination of encoding protocols within a single trial which is not reflected in any one mathematical feature alone. To check, we combined those mathematical features using state-of-the-art supervised and unsupervised feature selection procedures (n = 17). Across 3 datasets, we compared decoding of visual object category between these 17 sets of combined features, and between combined and individual features. Object category could be robustly decoded using the combined features from all of the 17 algorithms. However, the combination of features, which were equalized in dimension to the individual features, were outperformed in most of the time points by the most informative individual feature (Wavelet coefficients). Moreover, the Wavelet coefficients also explained the behavioral performance more accurately than the combined features. These results suggest that a single but multiscale encoding protocol may capture the neural code better than any combination of features. Our findings put new constraints on the models of neural information encoding in EEG.
Identification of novel leaf rust seedling resistance loci in Iranian bread wheat germplasm using genome-wide association mapping
Authors: Delfan Saba , Bihamta Mohammad Reza , Dadrezaei Seyed Taha , Abbasi Alireza , Alipour Hadi , Imani Jafargholi , Kogel Karl-Heinz 
Published: February 2022

AbstractLeaf or brown rust caused by Puccinia triticina Eriks. (Pt) is a major biotic constraint threatening bread wheat production worldwide. The continued evolution of new races of Pt necessitates a constant search for the identification of new resistance genes, or QTLs, to enhance the resistance durability of bread varieties. On a panel of 320 bread wheat accessions, we used a genome-wide association study (GWAS) technique to map loci associated with Pt resistance using single-nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). The panel was tested with five Pt races gathered from different regions of IRAN to identify loci associated with seedling resistance. After estimating genetic relatedness and population structure among accessions, GWAS discovered a total of 19 SNPs on chromosomes 1B, 2B, 3A, 3B, 4A, 5B, 5D, 6A, 6B, 6D, 7B, and 7D that were significantly associated with seedling stage resistance. The three SNP markers rs12954, rs34220, and rs42447 on chromosomes 5D, 6A, and 7D, respectively, associated with resistance to Pt race PKTTS expressing potential new loci for leaf rust resistance. Overall, this research gives an integrated perspective of leaf rust resistance resources in Iranian bread wheat and recognizes new resistance loci that will be valuable to expand the set of resistance genes available to control this serious disease.
Rapid estimation of cryptic adult abundance and breeding dynamics in a critically endangered elasmobranch from close-kin mark recapture
Authors: Patterson TA , Hillary R , Feutry P , Gunasakera R , Marthick J , Pillans RD 
Published: February 2022

AbstractElasmobranchs are one of the most highly-threatened vertebrate taxa. Estimating abundance of spawning adults is often extremely challenging, yet crucial for prioritization of conservation measures. Emblematic of these challenges, the speartooth shark (Glyphis glyphis, Müller and Henle, 1839) was initially known only from rare specimens collected in a few tropical regions river systems of Australia and Papua New Guinea. Listed as critically endangered in Australia (where only six adults have ever been recorded) and endangered by the IUCN, such scarcity and limited distribution prevent direct assessments of abundance or reproductive biology. We used close-kin mark-recapture to estimate the abundance of matureG. glyphisin a genetically isolated population in the Wenlock River, Queensland, Australia. From 224 juvenile/sub-adults and 2 adult samples taken over three years (2013-2016), 46 half-sibling and 33 full-sibling pairs were found. The adult population was estimated at 897 (80% Credible interval 531 – 1684) with a sex ratio (based on mitochondrial DNA) highly skewed to males (females – 0.09: males – 0.91). Based on juveniles sampled in different years that shared a mother, 71% of females were estimated to skip-spawn. In an average year we estimate 44 breeding females occupy the system. Importantly, these methods constitute a viable and relatively rapid approach to obtain robust estimates of absolute abundance and other key population parameters for similar rare species.
Polyelectrolyte brush bilayers at thermal equilibrium: Density functional theory and molecular dynamic simulations
Authors: Edwards Mike J. 
Published: February 2022

ABSTRACTIn this article, the equilibrium properties of Polyelectrolyte brush bilayers is studied. The density functional theory framework as well as the benchmark molecular dynamic simulations are employed to indicate the correct equation of state. Both techniques turn out that the equation of state neutral polymer brush bilayers scales with the wall distance asD−4. Additionally, it turns out that the electrostatic interactions does not change the universal power laws. The only difference is that the charged systems posses larger pressure due to stored electrostatic energy.SIGNIFICANCEStudying Polyelectrolyte brush bilayers is important because it exists widely in nature, biology and industry. In biology, they could be found in mammalian synivial joints as well as in the cellular structures.
Basolateral amygdala to insular cortex activity makes sign-tracking behavior insensitive to outcome value
Authors: Keefer Sara E. , Kochli Daniel E. , Calu Donna J. 
Published: February 2022

AbstractGoal-tracking rats are sensitive to Pavlovian outcome devaluation while sign-tracking rats are devaluation insensitive. During outcome devaluation, goal-tracking (GT) rats flexibly modify responding to cues based on the current value of the associated outcome. However, sign-tracking (ST) rats rigidly respond to cues regardless of the current outcome value. Our prior study demonstrated disconnection of the basolateral amygdala (BLA) and anterior insular cortex (aIC) decreased both goal- and sign-tracking behaviors. Given the role of these regions in appetitive motivation and behavioral flexibility we predicted that disrupting BLA to aIC pathway during outcome devaluation would reduce flexibility in GT rats and reduce rigid appetitive motivation in ST rats. We inhibited the BLA to aIC pathway by infusing inhibitory DREADDs (hM4Di-mcherry) or control (mCherry) virus into the BLA and implanted cannulae into the aIC to inhibit BLA terminals using intracranial injections of clozapine N-oxide (CNO). After training, we used a within subject satiety-induced outcome devaluation procedure in which we sated rats on training pellets (devalued condition) or homecage chow (valued condition). All rats received bilateral CNO infusions into the aIC prior to brief non-reinforced test sessions. Contrary to our hypothesis, BLA-IC inhibition did not interfere with devaluation sensitivity in GT rats but did make ST behaviors sensitive to devaluation. Intermediate rats showed the opposite effect, showing rigid in responding to cues with BLA-aIC pathway inactivation. Together, these results demonstrate BLA-IC projections mediate tracking-specific Pavlovian devaluation sensitivity and highlights the importance of considering individual differences in Pavlovian approach when evaluating circuitry contributions to behavioral flexibility.
The comparison of Post-Operative Complications pre Covid era versus during Covid-Era based on Clavien-Dindo-classification: A Systematic Review and Meta-Analysis
Authors: Farsi Yeganeh , Shojaeian Fatemeh , Ahmad Safavi-Naini Seyed Amir , Honarvar Mohammadjavad , Mohammadzadeh Benyamin , Nasiri Mohammad Javad 
Published: February 2022

AbstractIntroductionCoronavirus Disease 2019 (COVID -19) pandemic challenged the healthcare system drastically, and it was concomitant with a remarkable decline in surgeries and modified routine care of patients worldwide. This systematic review and meta-analysis aimed to compare the surgical complications before COVID -19 (Pre-COVID) and after COVID -19 (post-COVID) appearance using the Clavien-Dindo classification (CDC).Methodsbetween January 1, 2019, to November 3, 2021, we performed a comprehensive search in PubMed/Medline and Scopus for studies reporting the postoperative complications based on/transformable to CDC.ResultFrom 909 screened articles, 34 studies were included for systematic review. Among included articles, 11 were eligible for meta-analysis. Nineteen thousand one hundred thirty-seven patients (pre-COVID: 3522, post-COVID: 15615) were included, mostly undergoing elective surgeries (86.32%). According to CDC classification, there were no significant change between pre-COVID and post-COVID for grade 1 (Odds ratio (OR) and 95% confidence interval (95-CI): 0.99, 0.60-1.63, p=0.96), grade 2 (OR and 95-CI: 0.65, 0.42-1.01, p = 0.055), grade 3 (OR and 95-CI: 0.86, 0.48-1.57, p=0.64), grade 4 (OR and 95-CI: 0.85, 0.46-1.57, p =0.60). However, the postoperative mortality was lower before the COVID -19 outbreak (OR and 95-CI: 0.51, 0.27-0.95, p= 0.035). The included studies for systematic review and meta-analysis had a low risk of bias and unsignificant publication bias.ConclusionAlthough delivering routine surgery was challenging, the postoperative complications during the pandemic remained identical to the pre-pandemic era. The stricter patient selection tending to choose more critical states and more advanced clinical stages of the operated patients may explain some extent of higher mortality during the pandemic. Adopting preventive strategies helped deliver surgeries during the outbreak of COVID -19 while limiting the capacity of operations and admissions.
Protein-protein interaction prediction for targeted protein degradation
Authors: Orasch O. , Weber N. , Müller M. , Amanzadi A. , Gasbarri C. , Trummer C. 
Published: February 2022

AbstractProtein-protein interactions (PPIs) play a fundamental role in various biological functions; thus, detecting PPI sites is essential for understanding diseases and developing new drugs. PPI prediction is of particular relevance for the development of drugs employing targeted protein degradation, as their efficacy relies on the formation of a stable ternary complex involving two proteins. However, experimental methods to detect PPI sites are both costly and time-intensive. In recent years, computer-aided approaches have been developed as screening tools, but these tools are primarily based on sequence information and are therefore limited in their ability to address spatial requirements and have thus far not been applied to targeted protein degradation.Here, we present a new deep learning architecture based on the concept of graph representation learning that can predict interaction sites and interactions of proteins based on their surface representations. We demonstrate that our model reaches state-of-the-art performance using AUROC scores on the established MaSIF dataset. We furthermore introduce a new dataset with more diverse protein interactions and show that our model generalizes well to this new data. These generalization capabilities allow our model to predict the PPIs relevant for targeted protein degradation, which we show by demonstrating the high accuracy of our model for PPI prediction on the available ternary complex data. Our results suggest that PPI prediction models can be a valuable tool for screening protein pairs while developing new drugs for targeted protein degradation.
Modulation of nuclear and cytoplasmic mRNA fluctuations by time-dependent stimuli: analytical distributions
Authors: Filatova Tatiana , Popović Nikola , Grima Ramon 
Published: February 2022

AbstractTemporal variation of environmental stimuli leads to changes in gene expression. Since the latter is noisy and since many reaction events occur between the birth and death of an mRNA molecule, it is of interest to understand how a stimulus affects the transcript numbers measured at various sub-cellular locations. Here, we construct a stochastic model describing the dynamics of signal-dependent gene expression and its propagation downstream of transcription. For any time-dependent stimulus and assuming bursty gene expression, we devise a procedure which allows us to obtain time-dependent distributions of mRNA numbers at various stages of its life-cycle, e.g. in its nascent form at the transcription site, post-splicing in the nucleus, and after it is exported to the cytoplasm. We also derive an expression for the error in the approximation whose accuracy is verified via stochastic simulation. We find that, depending on the frequency of oscillation and the time of measurement, a stimulus can lead to cytoplasmic amplification or attenuation of transcriptional noise.
Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters
Authors: Forquet Raphaël , Nasser William , Reverchon Sylvie , Meyer Sam 
Published: February 2022

AbstractDNA supercoiling acts as a global transcriptional regulator in bacteria, but the promoter sequence or structural determinants controlling its effect remain unclear. It was previously proposed to modulate the torsional angle between the -10 and -35 hexamers, and thereby regulate the formation of the closed-complex depending on the length of the “spacer” between them. Here, we develop a ther-modynamic model of this notion based on DNA elasticity, providing quantitative and parameter-free predictions on the relative activation of promoters containing a short vs long spacer when the DNA supercoiling level is varied. The model is tested through an analysis of in vitro and in vivo expression assays of mutant promoters with variable spacer lengths, confirming its accuracy for spacers ranging from 15 to 19 nucleotides, except those of 16 nucleotides where other regulatory mechanisms likely overcome the effect of this specific step. An analysis at the whole-genome scale in E. coli then demonstrates a significant effect of the spacer length on the genomic expression after transient or inheritable superhelical variations, validating the model’s predictions. Altogether, this study shows that the torsional constraints associated to promoter binding by RNA Polymerase underpin a basal and global regulatory mechanism independent of specific transcription factors.
Distinct subpopulations of DN1 thymocytes exhibit preferential γδ T lineage potential
Authors: Oh Seungyoul , Liu Xin , Tomei Sara , Luo Mengxiao , Skinner Jarrod P. , Berzins Stuart P. , Naik Shalin H. , Gray Daniel H.D. , Chong Mark M.W. 
Published: February 2022

AbstractThe αβ and γδ T cell lineages are both are thought to differentiate in the thymus from common uncommitted progenitors. The earliest stage of T cell development is known as known as CD4-CD8-double negative 1 (DN1). These thymocytes have previously been revealed to be a heterogenous mixture of cells, which of only the CD117+fraction have been proposed to be true T cell progenitors that progress to the DN2 and DN3 thymocyte stages, at which point the development of the αβ and γδ T cell lineages diverge. However, recently, it has been shown that at least some γδ T cells are actually derived from a subset of CD117-DN thymocytes. Along with other ambiguities, this suggests that T cell development may not be as straightforward as previously thought. To better understand early T cell development, particularly the heterogeneity of DN1 thymocytes, we performed single cell RNA sequence (scRNAseq) of mouse DN and γδ thymocytes and show that the various DN stages are indeed comprised of transcriptionally diverse subpopulations of cells. We also show that multiple subpopulations of DN1 thymocytes exhibit preferential development towards the γδ lineage. Furthermore, specific γδ-primed DN1 subpopulations preferentially develop into IL-17 or IFNγ-producing γδ T cells. We show that DN1 subpopulations that only give rise to IL-17-producing γδ T cells already express many of the transcription factors associated with type 17 immune cell differentiation, while the DN1 subpopulations that can give rise to IFNγ-producing γδ T cell already express transcription factors associated with type 1 immune cell differentiation.