bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different Tendencies in Muscle Ultrasound Characteristic in Amyotrophic Lateral Sclerosis and Chronic Inflammatory Demyelinating Polyradiculoneuropathy
Authors: Hokkoku Keiichi , Tsukamoto Hiroshi , Uchida Yudai , Gatto Dario M. , Sonoo Masahiro 
Published: October 2021

Introduction:
The difference in muscle ultrasound (MUS) characteristics in primary axonal degeneration and demyelination has not been well established. The authors aimed to investigate the subject based on the correlation between MUS findings (echo intensity and muscle thickness) and compound muscle action potential (CMAP) amplitude in amyotrophic lateral sclerosis (ALS) and chronic inflammatory demyelinating polyradiculoneuropathy.

Methods:
Fifteen patients with ALS and 16 patients with chronic inflammatory demyelinating polyradiculoneuropathy were examined. For each patient, echo intensity and muscle thickness of the abductor pollicis brevis, abductor digiti minimi, and first dorsal interosseous muscles were investigated. Compound muscle action potential amplitudes were measured by median and ulnar nerve conduction studies.

Results:
In total, 45 muscles were evaluated in each group. The ALS group showed a linear correlation between the MUS finding and CMAP amplitude (rs = −0.70 and 0.59 for echo intensity and muscle thickness, respectively), whereas the chronic inflammatory demyelinating polyradiculoneuropathy group showed a weaker correlation than the ALS group (rs = −0.32 for echo intensity and rs = 0.34 for muscle thickness).

Conclusions:
The relationship between MUS abnormalities and CMAP amplitude showed different tendencies in ALS and chronic inflammatory demyelinating polyradiculoneuropathy. The results suggested that MUS abnormalities substantially reflect the muscle function in primary axonal degeneration, whereas a discrepancy between MUS findings and muscle function can be frequently seen in demyelination; specifically, MUS findings tend to be normal even though CMAP showed a reduction. These tendencies originating from underlying pathophysiology should be considered when MUS findings are used as biomarkers of disease severity.
TIME-Seq Enables Scalable and Inexpensive Epigenetic Age Predictions
Authors: Griffin Patrick T , Kane Alice E , Trapp Alexandre , Li Jien , Arnold Matthew , Poganik Jesse R , McNamara Maeve S , Meer Margarita V , Hoffman Noah , Amorim João , Tian Xiao , MacArthur Michael R , Mitchell Sarah J , Mueller Amber L , Carmody Colleen , Vera Daniel L , Kerepesi Csaba , Hooten Nicole Noren , Mitchell James R , Evans Michele K , Gladyshev Vadim N , Sinclair David A 
Published: October 2021

AbstractEpigenetic “clocks” based on DNA methylation (DNAme) have emerged as the most robust and widely employed aging biomarkers, but conventional methods for applying them are expensive and laborious. Here, we developTagmentation-based Indexing forMethylationSequencing (TIME-Seq), a highly multiplexed and scalable method for low-cost epigenetic clocks. Using TIME-Seq, we applied multi-tissue and tissue-specific epigenetic clocks to over 1,600 mouse DNA samples. We also discovered a novel approach for age prediction from shallow sequencing (e.g., 10,000 reads) by adaptingscAgefor bulk measurements. In benchmarking experiments, TIME-Seq performed favorably against prevailing methods and could quantify the effects of interventions thought to accelerate, slow, and reverse aging in mice. Finally, we built and validated a highly accurate human blood clock from 1,056 demographically representative individuals. Our methods increase the scalability and reduce the cost of epigenetic age predictions by more than 100-fold, enabling accurate aging biomarkers to be applied in more large-scale animal and human studies.
European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci
Authors: Blanca Jose , Pons Clara , Montero-Pau Javier , Sanchez-Matarredona David , Ziarsolo Peio , Fontanet Lilian , Fisher Josef , Plazas Mariola , Casals Joan , Rambla Jose Luis , Riccini Alessandro , Pombarelli Samuela , Ruggiero Alessandra , Sulli Maria , Grillo Stephania , Kanellis Angelos , Giuliano Giovanni , Finkers Richard , Cammareri Maria , Grandillo Silvana , Mazzucato Andrea , Causse Mathilde , Díez Maria José , Prohens Jaime , Zamir Dani , Cañizares Joaquin , Monforte Antonio Jose , Granell Antonio 
Published: October 2021

AbstractA comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types.HighlightThe high phenotypic diversity observed among European vintage varieties was created by traditional farmers by combining very few polymorphic loci subjected to balancing selection.
Cognitive and affective Theory of Mind double dissociation after parietal and temporal lobe tumors
Authors: Campanella Fabio , West Thomas , Corradi Dell’Acqua Corrado , Skrap Miran 
Published: October 2021

ABSTRACTExtensive neuroimaging literature suggests that understanding others’ thoughts and emotions engages a wide network encompassing parietal, temporal and medial frontal brain areas. However, the causal role played by these regions in social inferential abilities is still unclear. Moreover very little is known about ToM deficits in brain tumours and whether potential anatomical substrates are comparable to those identified in fMRI literature. This study evaluated the performance of 105 tumour patients, before and immediately after brain surgery, on a cartoon-based non-verbal task evaluating Cognitive (Intention Attribution) and Affective (Emotion Attribution) ToM, as well as a non-social control condition (Causal Inference). Across multiple analyses, we found converging evidence of a double dissociation between patients with right superior parietal damage, selectively impaired in Intention Attribution, and those with right antero-medial temporal lesion, exhibiting deficits only in Emotion attribution. Instead, patients with damage to the frontal cortex were impaired in all kinds of inferential processes, including those from the non-social control conditions. Overall, our data provides novel reliable causal evidence of segregation between different aspects of the ToM network from both the cognitive and also the anatomical point of view.
High spatial resolution analysis using indentation mapping differentiates biomechanical properties of normal vs. degenerated mouse articular cartilage
Authors: Masson Anand O. , Besler Bryce A. , Edwards W. Brent , Krawetz Roman J 
Published: October 2021

AbstractCharacterizing the biomechanical properties of articular cartilage is crucial to understanding processes of tissue homeostasis vs. degeneration. In mouse models, however, limitations are imposed by their small joint size and thin cartilage surfaces. Here we present a 3D automated surface mapping system and methodology that allows for mechanical characterization of mouse cartilage with high spatial resolution. We performed repeated indentation mappings, followed by cartilage thickness measurement via needle probing, at 31 predefined positions distributed over the medial and lateral femoral condyles of healthy mice. High-resolution 3D x-ray microscopy (XRM) imaging was used to validate tissue thickness measurements. The automated indentation mapping was reproducible, and needle probing yielded cartilage thicknesses comparable to XRM imaging. When comparing healthy vs. degenerated cartilage, topographical variations in biomechanics were identified, with altered thickness and stiffness (instantaneous modulus) across condyles and within anteroposterior sub-regions. This quantitative technique comprehensively characterized cartilage function in mice femoral condyle cartilage. Hence, it has the potential to improve our understanding of tissue structure-function interplay in mouse models of repair and disease.
Relative importance of region, seasonality and weed management practices effects on the functional structure of weed communities in French vineyards
Authors: Bopp Marie-Charlotte , Kazakou Elena , Metay Aurélie , Fried Guillaume 
Published: October 2021

AbstractWinegrowers have diversified their weed management practices over the last two decades changing the structure and the composition of weed communities. Complementary to taxonomic studies, trait-based approaches are promising ways for a better understanding of weed communities’ responses to environmental and agronomic filters. In the present study, the impact of climate, soil characteristics, seasons and weed management practices (chemical weeding, tillage and mowing) were assessed on weed communities in three French wine-growing regions (Champagne, Languedoc and Rhône valley). These agro-environmental gradients structuring weed communities according to their combination of traits were highlighted using multivariate analysis (RLQ). The impacts of these filters on Community Weighted Means (CWM) and the Community Weighted Variance (CWV) of weed communities were analysed using mixed and null modelling. Our results showed that spatio-temporal and weed management practices variables explained from 13% to 48% of the total variance of CWM (specific leaf area, maximum height, seed mass, flowering onset and duration and lateral spread). Region, seasonality and management practices explained 53%, 28% and 19% of CWM marginal variance, respectively. Weed management impacted CWM and CWV through two main gradients: (i) a soil disturbance gradient with high mechanical disturbance of soil in tilled plots and low mechanical disturbance in chemically weeded plots and (ii) a vegetation cover gradient with high vegetation abundance in mowed plots compared to more bare soils in tilled and chemically weeded plots. Chemically weeded communities showed trait values of ruderal strategies (low seed mass, small-stature) in Languedoc. Mowed plots were associated with more competitive strategies (higher seed mass, higher stature and lower SLA) in Languedoc. Tillage favoured communities with high seed mass that increases the viability of buried seeds and high lateral spread values associated to the ability to resprout after tillage in Languedoc and Champagne. This study demonstrated that trait-based approach can be successfully applied to perennial cropping systems such as vineyards, in order to understand community assembly to better guide weed management practices.
Effects of perfluoroalkyl and polyfluoroalkyl substances on soil structure and function
Authors: Xu Baile , Yang Gaowen , Lehmann Anika , Riedel Sebastian , Rillig Matthias C. 
Published: October 2021

AbstractSoils are impacted at a global scale by several anthropogenic factors, including chemical pollutants. Among those, perfluoroalkyl and polyfluoroalkyl substances (PFAS) are of concern due to their high environmental persistence, and as they might affect soil health and functions. However, data on impacts of PFASs on soil structure and microbially-driven processes are currently lacking. This study explored the effects of perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorobutanesulfonic acid (PFBS) at environmental-relevant nominal concentrations (1 ~ 1000 ng g−1) on soil functions, using a 6-week microcosm experiment. We measured soil respiration, litter decomposition, enzyme and microbial activities, soil aggregates, and bacterial abundance. PFAS (even at 1 ng g−1 for PFBS) significantly increased litter decomposition, associated with positive effects on bacterial abundance, and β-glucosidase activities. This effect increased with PFAS concentrations. Soil respiration was significantly inhibited by PFAS in the 3rd week, while this effect was more variable in week 6. Water-stable aggregates were negatively affected by PFOS and PFOA, possibly related to microbial shifts. The general microbial activities and β-D-cellobiosidase and phosphatase activities were barely affected by PFAS treatments. Our work highlights the potential effects of PFAS on soil health, and we argue that this substance class could be a factor of environmental change of potentially broad relevance in terrestrial ecosystem functioning.SynopsisPFAS are likely to affect soil health.Abstract Art
Functional and historical drivers of leaf shape evolution in Palms (Arecaceae)
Authors: Jimenez Maria Fernanda Torres , Chazot Nicolas , Emilio Thaise , Fredin Johan Uddling , Antonelli Alexandre , Faurby Soren , Bacon Christine D 
Published: October 2021

AbstractAimLeaves display a remarkable variety of shapes, each with potential ecological advantages in specific climates. While relations between leaf shape and either climate or height has been relatively well studied in eudicots, the macroecological drivers of shape remain poorly known in monocots. Here, we investigated associations between climate and plant height with the evolution of leaf shape in a clade with high species and morphological diversity.LocationGlobal.Time periodCretaceous to contemporary.Major taxa studiedPalms (Arecaceae).MethodsWe apply a Bayesian phylogenetic mixed model to test for associations between climate and leaf shape (all entire-leaved, pinnate-dissected, palmate-dissected, and costapalmate). We further reconstruct the ancestral leaf shape using multistate speciation and extinction models and compare the frequency of shapes with global temperatures through time.ResultsWe find that plant height associates with dissected leaves and that annual precipitation associates with pinnate shapes. The ancestral leaf shape is unclear but early diversification was dominated by pinnate-dissected palms, which has remained the most species-rich form of leaves throughout palm history.Main conclusionsPalms that are tall and live in humid regions are more likely to have pinnate leaves. Through geological time scales, temperature did not play an obvious role in determining leaf shapes. This study contributes to our understanding of how the diversity of leaf shapes is linked to biological and climatic factors.
Actinosomes: condensate-templated proteinaceous containers for engineering synthetic cells
Authors: Ganar Ketan A. , Leijten Liza , Deshpande Siddharth 
Published: October 2021

AbstractEngineering synthetic cells has a broad appeal, from understanding living cells to designing novel biomaterials for therapeutics, biosensing, and hybrid interfaces. A key prerequisite to creating synthetic cells is a functional three-dimensional container capable of orchestrating biochemical reactions. In this study, we present an easy and effective technique to make cell-sized porous containers crafted using the interactions between biomolecular condensates and actin cytoskeleton - we coin them actinosomes. This approach uses polypeptide/nucleoside triphosphate condensates and localizes actin monomers on their surface. By triggering actin polymerization at the expense of sequestered ATP and using osmotic gradients, the condensates are structurally transformed into containers with the boundary made up of actin filaments and polylysine polymers. We show that the GTP-to-ATP ratio is a crucial parameter for forming actinosomes: insufficient ATP prevents condensate dissolution while excess ATP leads to undesired crumpling. The surface of actinosomes lacks any structural order and is porous. We show the functionality of the actinosomes by using them as bioreactors capable of protein synthesis. Actinosomes are a handy addition to the synthetic cell platform, with appealing properties like ease-of-production, inherent encapsulation capacity, and an active surface which holds the potential to trigger signaling cascades and form multicellular assemblies, with potential for medical and biotechnological applications.
Whole-genome sequencing of Vero E6 (C1008) and comparative analysis of four Vero cell sublines
Authors: Konishi Kazuhiro , Yamaji Toshiyuki , Sakuma Chisato , Kasai Fumio , Endo Toshinori , Kohara Arihiro , Hanada Kentaro , Osada Naoki 
Published: October 2021

AbstractThe Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of sublines have been established from the original cell line, which display different characteristics. In this study, we determined the whole-genome sequence of Vero E6 (C1008) and performed comparative analysis among Vero JCRB 0111, Vero CCL-81, Vero 76 and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that all sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and CDKN2 gene clusters. We identified a substantial number of genetic differences among the sublines including single nucleotide variants, indels, and copy number variations. The spectrum of single nucleotide variants indicated a close genetic relationship between Vero JCRB0111 and Vero CCL-81, and between Vero 76 and Vero E6, and a considerable genetic gap between the former two and the latter two lines. In contrast, we confirmed the pattern of genomic integration sites of simian endogenous retroviral sequences, which was consistent among the sublines. We identified subline-specific/enriched loss of function and missense variants, which potentially contribute to the differences in response to viral infection among the Vero sublines. In particular, we focused on Vero E6-specific/enriched variants and identified four genes (IL1RAP, TRIM25, RB1CC1, and ATG2A) that contained missense variants specific or enriched in Vero E6. In addition, we found that V739I variants of ACE2, which functions as the receptor for SARS-CoV-2, were heterozygous in Vero JCRB0111, Vero CCL-81, and Vero 76; however, Vero E6 contained the allele with isoleucine, resulting from the loss of one of the X chromosomes.
Kinetics of immune responses to the AZD1222/Covishield vaccine with varying dose intervals in Sri Lankan individuals
Authors: Jeewandara Chandima , Aberathna Inoka Sepali , Gomes Laksiri , Pushpakumara Pradeep Darshana , Danasekara Saubhagya , Guruge Dinuka , Ranasinghe Thushali , Gunasekera Banuri , Kamaladasa Achala , Kuruppu Heshan , Somathilake Gayasha , Dissanayake Osanda , Gamalath Nayanathara , Ekanayake Dinithi , Jayamali Jeewantha , Jayathilaka Deshni , Mudunkotuwa Anushika , Harvie Michael , Nimasha Thashmi , Wijayamuni Ruwan , Schimanski Lisa , Rijal Pramila , Tan Tiong K. , Dong Tao , Townsend Alain , Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: October 2021

AbstractBackgroundTo understand the kinetics of immune responses with different dosing gaps of the AZD1222 vaccine, we compared antibody and T cell responses in two cohorts with two different dosing gaps.MethodsAntibodies to the SARS-CoV-2 virus were assessed in 297 individuals with a dosing gap of 12 weeks, sampled at 12 weeks post second dose (cohort 1) and in 77 individuals with a median dosing gap of 21.4 weeks (cohort 2) sampled 6 weeks post second dose. ACE2 receptor blocking antibodies (ACE2R-Abs), antibodies to the receptor binding domain (RBD) of the virus and variants of concern (VOC) and ex vivo T cell responses were assessed in a sub cohort.ResultsAll individuals (100%) had SARS-CoV-2 specific total antibodies and 94.2% of cohort 1 and 97.1% of cohort 2 had ACE2R-blocking Abs. There was no difference in antibody titres or positivity rates in different age groups in both cohorts. The ACE2R-blocking Abs (p<0.0001) and antibodies to the RBD of the VOCs were significantly higher in cohort 2, compared to cohort 1. 41.2% to 65.8% of different age groups gave a positive response by the haemagglutination assay to the RBD of the ancestral virus and VOCs in cohort 1, while 53.6% to 90% gave a positive response in cohort 2. 17/57 (29.8%) of cohort 1 and 17/29 (58.6%) of cohort 2 had ex vivo IFNγ ELISpot responses above the positive threshold. The ACE2R-blocking antibodies and ex vivo IFNγ ELISpot responses at 12 weeks post-first dose, significantly correlated with levels 12 weeks post second dose (Spearman’s r=0.46, p=0.008) and (Spearman’s r=0.71, p<0.0001) respectively.ConclusionsBoth dosing schedules resulted in high levels of antibody and T cell responses post vaccination, although those with a longer dosing gap had a higher magnitude of responses, possibly as immune responses were measured 6 weeks post second dose compared to 12 weeks post second dose.
Computational analysis reveals similarities and differences between SCLC subtypes
Authors: Singh Abhay , Desai Parth , Pillai Maalavika , Agarwal Nilay , Takahashi Nobuyuki , Thomas Anish , Jolly Mohit Kumar 
Published: October 2021

AbstractSmall cell lung cancer (SCLC) is a neuroendocrine malignancy with dismal survival rates. Previous studies have revealed inter and intra tumoral heterogeneity of SCLC driven by neuroendocrine differentiation and multiple gene expression signatures have been proposed to classify the distinct SCLC molecular subtypes However, few questions remain unanswered: a) how many SCLC subtypes exist? b) how similar or different are these subtypes?, c) which gene list(s) can be used to identify those specific subtypes? Here, we show that irrespective of the three gene sets (33 genes, 50 genes, 105 genes) proposed in different studies to classify SCLC into different subtypes, the markers of phenotypic heterogeneity in SCLC form a “teams” like pattern of co-expressed modules. Moreover, the 105 geneset could classify SCLC cell lines into five clusters, three of which can be distinctly mapped to the SCLC-A, SCLC-N and SCLC-Y subtypes. Intriguingly, we noticed a high degree of similarity in the transcriptional landscape of two non-neuroendocrine subtypes: SCLC-Y and SCLC-I*, as well as in their enrichment of EMT. Thus, our analysis elucidates the landscape of phenotypic heterogeneity enabling diverse SCLC subtypes.