bluuebunny/crossref_metadata_2025_split huggingface dataset:
Working Memory and Processing Speed Predict Math Skills in Pediatric Brain Tumor Survivors
Authors: Peterson Rachel K. , Ng Rowena , Ludwig Natasha N. , Jacobson Lisa A. 
Published: October 2022

Objective:
Childhood brain tumor (BT) survivors are at risk for working memory (WM) and processing speed (PS) deficits, which impact other cognitive domains. This study aimed to characterize WM, PS, and untimed mathematics calculation performance in pediatric BT survivors at least 2 years post-diagnosis, identify medical factors associated with deficits in mathematics, and examine whether WM and/or PS predict mathematics performance in this clinical sample.

Methods:
Retrospective data were gathered from 72 BT survivors between 7 and 21 years of age (M=13.64 y, SD=4.01 y) for a clinical neuropsychologic evaluation. All participants completed Wechsler measures of WM and PS and a measure of untimed mathematics calculation.

Results:
WM, PS, and the mathematics calculation were significantly lower than the normative mean. Math scores were not correlated with any of the examined medical factors. PS was negatively correlated with the Neurological Predictor Scale and positively correlated with age at diagnosis. Both WM and PS were associated with math outcomes and accounted for 30.4% and 19.2% of the variance, respectively.

Conclusions:
The findings indicate that WM and PS contribute to mathematics performance in pediatric BT survivors. Examining mathematics performance should be a part of clinical neuropsychological evaluations. Interventions to improve mathematics performance in this population should also focus on WM and compensatory strategies for slowed PS.
The Midfacial Soft Tissue Changes After Anterior Maxillary Segmental Distraction Osteogenesis in Patients With Cleft: A 3-Dimensional Volumetric-Based Subunit Analysis
Authors: Wan Teng , Sun Hao , Jiang Tengfei , Zhu Min , Wang Xudong 
Published: October 2022

Background:
Maxillary hypoplasia is common in patients with cleft lip and palate. In this study, the authors investigated the soft tissue changes in midfacial regions after anterior maxillary segmental distraction osteogenesis (AMSDO) in patients with cleft.

Methods:
Eight patients with cleft lip and palate who underwent AMSDO were enrolled in this study. Spiral computed tomographic images were taken before surgery and 6–12 months after surgery to evaluate soft tissue changes after AMSDO. The midfacial area was divided into 6 regions of interest according to anatomical subunits. The average movements of each region were calculated using volumetric changes and preoperative region surface areas.

Results:
The upper lip on both sides has the most anterior movement (5.22±0.86 and 5.14±0.84 mm), supracommissural regions have a little less movement (4.11±0.55 and 3.81±0.67 mm), paranasal regions have the least movement (3.37±0.47 and 3.15±0.36 mm). The corresponding regions of interest showed no significant difference on the cleft side versus the noncleft side.

Conclusions:
Anterior maxillary segmental distraction osteogenesis can improve the soft tissue profile in patients with cleft, and there was no significant difference in soft tissue changes between the cleft side and the noncleft side.
PD-L1 activity is associated with partial EMT and metabolic reprogramming in carcinomas
Authors: Muralidharan Srinath , Sehgal Manas , Soundharya R , Mandal Susmita , Majumdar Sauma Suvra , Yeshwanth M , Saha Aryamaan , Jolly Mohit Kumar 
Published: October 2022

AbstractImmune evasion and metabolic reprogramming are hallmarks of cancer progression often associated with a poor prognosis and frequently present significant challenge for cancer therapies. Recent studies have emphasized on the dynamic interaction between immunosuppression and the dysregulation of energy metabolism in modulating the tumor microenvironment to promote cancer aggressiveness. However, a pan-cancer association among these two hallmarks, and a potent common driver for them – Epithelial-Mesenchymal Transition (EMT) – remains to be done. Here, our meta-analysis across 184 publicly available transcriptomic datasets as well as The Cancer Genome Atlas (TCGA) data reveals that an enhanced PD-L1 activity signature along with other immune checkpoint markers correlate positively with a partial EMT and elevated glycolysis signature but a reduced OXPHOS signature in many carcinomas. These trends were also recapitulated in single-cell RNA-seq time-course EMT induction data across cell lines. Furthermore, across multiple cancer types, concurrent enrichment of glycolysis and PD-L1 results in worse outcomes in terms of overall survival as compared to enrichment for only PD-L1 activity or expression. Our results highlight potential functional synergy among these interconnected axes of cellular plasticity in enabling metastasis and/or multi-drug resistance in cancer.
Engineering Nanowires in Bacteria to Elucidate Electron Transport Structural-Functional Relationships
Authors: Myers Ben , Catrambone Francesco , Allen Stephanie , Hill Phil J , Kovacs Katalin , Rawson Frankie J 
Published: October 2022

AbstractBacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells’ bioenergetic programming. Their role is thought to be linked to facilitating electron transfer with the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineeredCupriavidus necatorH16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achievedviaa combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells for the first time. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using aCNchassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.Abstract FigureGraphical abstract displaying theoretical PilA monomer models (left), PeakForce TUNA atomic force microscopy contact current images (right) of wild-type (top) and modified with increased tyrosine content (bottom) PilA filaments expressed byCupriavidus necatorH16 cells.
Towards modelling cold-water coral reef-scale crumbling: Including morphological variability in mechanical surrogate models
Authors: Fernández Marta Peña , Williams Josh , Büscher Janina V. , Titschack Jürgen , Roberts J Murray , Henninge Sebastian , Wolfram Uwe 
Published: October 2022

AbstractThe structural complexity of cold-water corals is threatened by ocean acidification. Increased porosity and weakening of structurally critical parts of the reef framework may lead to rapid physical collapse on an ecosystem scale, reducing their potential for biodiversity support. We can use computational models to describe the mechanisms leading to reef-crumbling. How-ever, the implementation of such models into an efficient predictive tool that allows us to determine risk and timescales of reef collapse is missing. Here, we identified possible surrogate models to represent the branching architecture of the cold-water coral speciesLophelia pertusa. For length scales greater than 13 cm, a continuum finite element mechanical approach can be used to analyse mechanical competence whereas at smaller length scales, mechanical surrogate models need to explicitly account for the statistical differences in the structure. We showed large morphological variations betweenL. pertusacolonies and branches, as well asdeadandliveskeletal structures, which need to be considered for the development of rapid monitoring tools for predicting risk of cold-water coral reefs crumbling. This will allow us to investigate timescales of changes, including the impact of exposure times to acidified waters on reef-crumbling.
canaper: Categorical analysis of neo- and paleo-endemism in R
Authors: Nitta Joel H. , Laffan Shawn W. , Mishler Brent D. , Iwasaki Wataru 
Published: October 2022

AbstractBiodiversity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of biodiversity. CANAPE (categorical analysis of neo- and paleo-endemism) is one such method that can provide insight into the evolutionary processes generating biodiversity. The only currently available software implementing CANAPE is Biodiverse, which is written in Perl and can be used either through a graphical user interface (GUI) or user-developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses.Here, we present canaper, a new R package that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility; CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code.Our case study shows that canaper produces equivalent results to Biodiverse and can complete computations on moderately sized datasets quickly (< 10 min to reproduce a canonical study).canaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby averting the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing biodiversity in R.
PointedSDMs– an R package to help facilitate the construction of integrated species distribution models
Authors: Mostert Philip S. , O’Hara Robert B. 
Published: October 2022

1AbstractIntegration of disparate datasets is a rapidly growing area in quantitative ecology, and is subsequently becoming a major asset in understanding the shifts and trends in species’ distributions.However, the tools and software available to construct statistical models to integrate these disparate datasets into a unified framework is lacking, stagnating the growth of data integration in applications.This paper presentsPointedSDMs: an easy to useRpackage used to construct integrated species distribution models using the integrated nested Laplace Approximation methodology.The package is presented in this paper through an illustrative example for a selection of species found across Pennsylvania state.
Streetlights affect moth orientation beyond flight-to-light behaviour
Authors: Degen Jacqueline , Storms Mona , Lee Chengfa Benjamin , Jechow Andreas , Stöckl Anna Lisa , Hölker Franz , Jakhar Aryan , Walter Thomas , Walter Stefan , Mitesser Oliver , Hovestadt Thomas , Degen Tobias 
Published: October 2022

SummaryOne of the most dramatic changes occurring on our planet in recent decades is the ever-increasing extensive use of artificial light at night, which drastically altered the environment nocturnal animals are adapted to 1,2. One nocturnal species group experiencing marked declines are moths, which are not only of great importance for species conservation, but also for their key role in food webs and in ecosystem services such as nocturnal plant pollination 3,4. Light pollution has been identified as a driver in the dramatic insect decline of the past years 5–7, yet little is known about its impact on natural insect orientation behaviour. Using harmonic radar tracking, we show that the orientation of several species of moths is significantly affected by streetlights, although only 4 % of individuals showed flight-to-light behaviour. We reveal a species-specific barrier effect of streetlights on lappet moths whenever the moon was not available as a natural celestial cue. Furthermore, streetlights increased the tortuosity of flight trajectories for both hawk moths and lappet moths. Our results provide the first spatially resolved experimental evidence for the fragmentation of landscapes by streetlights and demonstrate that light pollution affects movement patterns of moths beyond previously assumed extend, potentially affecting their reproductive success and hampering a vital ecosystem service.
Structural analysis and ensemble docking revealed the binding modes of selected progesterone receptor modulators
Authors: Saritha F. , Aiswarya N. , Kumar R. Aswath , Dileep K.V. 
Published: October 2022

AbstractUterine fibroids (UF) are benign smooth muscle neoplasm of uterus that have a significant impact on a woman’s quality of life as they perturb hormonal homeostasis resulting in heavy menstrual bleeding, impaired fertility, pregnancy complications and loss. UF can be surgically removed through invasive procedures, but their recurrence rate is often high. Progesterone receptor (PR) has an imperative role in UF management. Mifepristone, ulipristal acetate (UPA) and asoprisnil (ASO) are some promising selective progesterone receptor modulators (SPRMs), acts on PR, but due to their side effects in long term use, they were withdrawn from the market. Hence, there is a dire need for novel, highly efficient with least side effects, therapeutics for the treatment of UF. To contribute towards the drug discovery for UF, we made an extensive structural comparison of reported PR crystal structures, also elucidated the binding modes of four existing SPRMs against human PR through ensemble docking approach. Our studies revealed the presence of 5 highly repeating water molecules that has an important role in ligand binding and structural stability. Our ensemble docking and MD simulation revealed that studied ligands have preferential selectivity towards the specific conformation of PR. It is anticipated that our study will be a useful resource to all the drug discovery scientists who are engaged in the identification of lead molecules against UF.
Inbreeding depression in polyploid species: a meta-analysis
Authors: Clo Josselin , Kolář Filip 
Published: October 2022

AbstractWhole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects, the resulting morphological and fitness consequences and how they affect the survival of polyploid lineages are intensively studied. Another important factor may also determine the probability of establishment and success of polyploid lineages: inbreeding depression. Inbreeding depression is expected to play an important role in the establishment of neopolyploid lineages, their capacity to colonize new environments, and in the simultaneous evolution of ploidy and other life-history traits such as self-fertilization. Both theoretically and empirically, there is no consensus on the consequences of polyploidy on inbreeding depression. In this meta-analysis, we investigated the effect of polyploidy on the evolution of inbreeding depression, by performing a meta-analysis within angiosperm species. The main results of our study are that the consequences of polyploidy on inbreeding depression are complex and depend on the time since polyploidization. We found that young polyploid lineages have a much lower amount of inbreeding depression than their diploid relatives and their established counterparts. Natural polyploid lineages are intermediate, and have a higher amount of inbreeding depression than synthetic neopolyploids, and a smaller amount than diploids, suggesting that the negative effect of polyploidy on inbreeding depression decrease with time since polyploidization.
Multi range ERK responses shape the proliferative trajectory of single cells following oncogene induced senescence
Authors: Chen Jia-Yun , Hug Clemens , Reyes José , Tian Chengzhe , Gerosa Luca , Fröhlich Fabian , Ponsioen Bas , Snippert Hugo J G , Spencer Sabrina L. , Jambhekar Ashwini , Sorger Peter K. , Lahav Galit 
Published: October 2022

SUMMARYOncogene-induced senescence (OIS) is a phenomenon in which aberrant oncogene expression causes non-transformed cells to enter a non-proliferative state. Cells undergoing OIS display phenotypic heterogeneity, with some cells senescing and others remaining proliferative. The causes of the heterogeneity remain poorly understood. We studied the sources of heterogeneity in the responses of human epithelial cells to oncogenic BRAFV600E expression. We found that a narrow expression range of BRAFV600E generated a wide range of activities of its downstream effector ERK. In population-level and single cell assays, ERK activity displayed a non-monotonic relationship to proliferation, with intermediate ERK activities leading to maximal proliferation. We profiled gene expression across a range of ERK activities over time and characterized four distinct ERK response classes, which we propose act in concert to generate the unique ERK-proliferation response. Altogether, our studies mapped the input-output relationships between ERK activity and proliferation providing important insights into how heterogeneity can be generated during OIS.
Fast computation of principal components of genomic similarity matrices
Authors: Hahn Georg , Lutz Sharon M. , Hecker Julian , Prokopenko Dmitry , Cho Michael H. , Silverman Edwin K. , Weiss Scott T. , Lange Christoph 
Published: October 2022

AbstractThe computation of a similarity measure for genomic data, for instance using the (genomic) covariance matrix, the Jaccard matrix, or the genomic relationship matrix (GRM), is a standard tool in computational genetics. The principal components of such matrices are routinely used to correct for biases in, for instance, linear regressions. However, the calculation of both a similarity matrix and its singular value decomposition (SVD) are computationally intensive. The contribution of this article is threefold. First, we demonstrate that the calculation of three matrices (the genomic covariance matrix, the weighted Jaccard matrix, and the genomic relationship matrix) can be reformulated in a unified way which allows for an exact, faster SVD computation. An exception is the Jaccard matrix, which does not have a structure applicable for the fast SVD computation. An exact algorithm is proposed to compute the principal components of the genomic covariance, weighted Jaccard, and genomic relationship matrices. The algorithm is adapted from an existing randomized SVD algorithm and ensures that all computations are carried out in sparse matrix algebra. Second, an approximate Jaccard matrix is introduced to which the fast SVD computation is applicable. Third, we establish guaranteed theoretical bounds on the distance (in L2 norm and angle) between the principal components of the Jaccard matrix and the ones of our proposed approximation, thus putting the proposed Jaccard approximation on a solid mathematical foundation. We illustrate all computations on both simulated data and data of the 1000 Genome Project, showing that the approximation error is very low in practice.
A SI3-σ arch stabilizes cyanobacteria transcription initiation complex
Authors: Shen Liqiang , Lai Giorgio , You Linlin , Shi Jing , Wu Xiaoxian , Puiu Maria , Gu Zhanxi , Feng Yu , Yuzenkova Yulia , Zhang Yu 
Published: October 2022

SUMMARYMulti-subunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all bacterial RNAPs. Here, we report two cryo-EM structures of cyanobacterial transcription initiation complexes at near-atomic resolutions. The structures show that cyanobacterial RNAP forms an ‘SI3-σ’ arch interaction between domain 2 of σA (σ2) and the sequence insertion 3 (SI3) in the mobile catalytic domain Trigger Loop (TL). The ‘SI3-σ’ arch facilitates transcription initiation from promoters of different classes through sealing the main cleft and thereby stabilizing RNAP-promoter DNA open complex. Disruption of the ‘SI3-σ’ arch disturbs cyanobacteria growth and stress response. Our study reports the structure of cyanobacterial RNAP and unique mechanism for its transcription initiation. Our data suggest functional plasticity of SI3 and provide foundation for further research into cyanobacteria and chloroplasts transcription.
Arabidopsis CPK6 regulates drought tolerance under high nitrogen by the phosphorylation of NRT1.1
Authors: Ma Qijun , Zhao Chunyan , Hu Shi , Zuo Kaijing 
Published: October 2022

AbstractNitrogen is an essential macronutrient for plant growth and development, and its availability to some extent is regulated by drought stress. Calcium-dependent protein kinases (CPKs) are a unique family of Ca2+ sensors with diverse functions in nitrogen and drought signaling pathways. However, which and how CPKs involve in the crosstalk between drought stress and nitrogen transportation remains largely unknown. Here we identified the drought tolerant function of Arabidopsis CPK6 under high nitrogen condition. The CPK6 expression is induced by the treatments of ABA and drought. The mutant cpk6 is insensitive to the ABA treatment, but sensitive to drought only under high nitrogen condition. CPK6 interacts with and phosphorylates the Thr571 in NRT1.1 protein, and thus represses its NO3− transporting activity under drought stress. Taken together, we showed the evidences that CPK6 regulates Arabidopsis drought tolerance through the phosphorylation of NRT1.1, and that enriches the knowledge of nitrogen uptake in plants during drought stress.
A Multi-Granular Stacked Regression for Forecasting Long-Term Demand in Emergency Departments
Authors: James Charlotte , Wood Richard , Denholm Rachel 
Published: October 2022

AbstractBackgroundIn the United Kingdom, Emergency Departments (EDs) are under significant pressure due to an ever-increasing number of attendances. Understanding how the capacity of other urgent care services and the health of a population may influence ED attendances is imperative for commissioners and policy makers to develop long-term strategies for reducing this pressure and improving quality and safety.MethodsWe developed a novel Multi-Granular Stacked Regression (MGSR) model using publicly available data to predict future mean monthly ED attendances within Clinical Commissioning Group regions in England. The MGSR combines measures of population health and health service capacity in other related settings. We assessed model performance using the R-squared statistic, measuring variance explained, and the Mean Absolute Percentage Error (MAPE), measuring forecasting accuracy. We used the MGSR to forecast ED demand over a 4-year period under hypothetical scenarios where service capacity is increased, or population health is improved.ResultsMeasures of service capacity explain 41 ± 4% of the variance in monthly ED attendances and measures of population health explain 61 ± 25%. The MGSR leads to an overall improvement in performance, with an R-squared of 0.75 ± 0.03 and MAPE of 4% when forecasting mean monthly ED attendances per CCG. Using the MGSR to forecast long-term demand under different scenarios, we found improving population health would reduce peak ED attendances per CCG by approximately 600 per month after 2 years.ConclusionsCombining models of population health and wider urgent care service capacity for predicting monthly ED attendances leads to an improved performance compared to each model individually. Policies designed to improve population health will reduce ED attendances and enhance quality and safety in the long-term.