bluuebunny/crossref_metadata_2025_split huggingface dataset:
Up-regulation of SLC27A2 suppresses the proliferation and invasion of renal cancer by down-regulating CDK3-mediated EMT
Authors: Xu Ning , Xiao Wen , Meng Xiangui , Li Weiquan , Wang Xuegang , Zhang Xiaoping , Yang Hongmei 
Published: August 2022

AbstractClear cell renal cell carcinoma (ccRCC) is one of the most common malignant tumors of the urinary system. Distant metastasis is the leading cause of poor prognosis in ccRCC. However, ccRCC is found poorly responsitive to radiotherapy and chemotherapy. Effective therapeutic strategies for its metastasis remain scarce. We analyzed clinical samples and public database, for differential expression of SLC27A2 and further explored its relationship with clinical prognosis. Biochemistry and functional experiments were carried out to study the potential mechanisms of SLC27A2, CDK3, and EMT. SLC27A2 was significantly downregulated in clinical specimens and renal cancer cell lines and predicted poor prognosis. We found that specific upregulation of SLC27A2 could significantly inhibited the proliferation, migration, and invasion of renal cancer cell lines. SLC27A2 could also influence the Epithelial-mesenchymal transition (EMT) signaling pathway, linked to the progression and metastasis of renal cancer. Using whole transcriptome sequencing of SLC27A2, CDK3 was identified as a regulatory SLC27A2 target. In terms of mechanism, SLC27A2 may further inhibit the epithelial-to-mesenchymal transition by negatively regulating CDK3. Our work suggests that functional inhibition of SLC27A2-CDK3-EMT axis may be an attractive therapeutic target for metastasis of ccRCC.
A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4
Authors: Sadée Christoph , Hagler Lauren D. , Becker Winston R. , Jarmoskaite Inga , Vaidyanathan Pavanapuresan P. , Denny Sarah K. , Greenleaf William J. , Herschlag Daniel 
Published: August 2022

AbstractGenomic methods have been valuable for identifying RNA-binding proteins (RBPs) and the genes, pathways, and processes they regulate. Nevertheless, standard motif descriptions cannot be used to predict all RNA targets or test quantitative models for cellular interactions and regulation. We present a complete thermodynamic model for RNA binding to the S. cerevisiae Pumilio protein PUF4 derived from direct binding data for 6180 RNAs measured using the RNA on a massively parallel array (RNA-MaP) platform. The PUF4 model is highly similar to that of the related RBPs, human PUM2 and PUM1, with one marked exception: a single favorable site of base flipping for PUF4, such that PUF4 preferentially binds to a non-contiguous series of residues. These results are foundational for developing and testing cellular models of RNA-RBP interactions and function, for engineering RBPs, for understanding the biophysical nature of RBP binding and the evolutionary landscape of RNAs and RBPs.
Homotypic and heterotypic immune responses to Omicron variant in immunocompromised patients in diverse clinical settings
Authors: Ferreira Victor H. , Solera Javier T. , Hu Queenie , Hall Victoria G. , Arbol Berta G. , Rod Hardy W. , Samson Reuben , Marinelli Tina , Ierullo Matthew , Virk Avneet Kaur , Kurtesi Alexandra , Mavandadnejad Faranak , Majchrzak-Kita Beata , Kulasingam Vathany , Gingras Anne-Claude , Kumar Deepali , Humar Atul 
Published: August 2022

AbstractImmunocompromised patients are predisposed to severe COVID-19. Here we compare homotypic and heterotypic humoral and cellular immune responses to Omicron BA.1 in organ transplant patients across a diverse clinical spectrum. We perform variant-specific pseudovirus neutralization assays for D614G, and Omicron-BA.1, -BA.2, and Delta variants. We also measure poly-and monofunctional T-cell responses to BA.1 and ancestral SARS-CoV-2 peptide pools. We identify that partially or fully-vaccinated transplant recipients after infection with Omicron BA.1 have the greatest BA.1 neutralizing antibody and BA.1-specific polyfunctional CD4+and CD8+T-cell responses, with potent cross-neutralization against BA.2. In these patients, the magnitude of the BA.1-directed response is comparable to immunocompetent triple-vaccinated controls. A subset of patients with pre-Omicron infection have heterotypic responses to BA.1 and BA.2, whereas uninfected transplant patients with three doses of vaccine demonstrate the weakest comparative responses. These results have implications for risk of infection, re-infection, and disease severity among immune compromised hosts with Omicron infection.
TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening
Authors: Álvarez Miguel M. , Biayna Josep , Supek Fran 
Published: August 2022

AbstractCRISPR/Cas9 gene editing can inactivate genes in a precise manner. This process involves DNA double-strand breaks (DSB), which may incur a loss of cell fitness. We hypothesize that DSB toxicity may be variable depending on the chromatin environment in the targeted locus. Here, by analyzing isogenic cell line pair CRISPR experiments jointly with previous screening data from across ~900 cell lines, we show that TP53-associated break toxicity is higher in genomic regions that harbor active chromatin, such as gene regulatory elements or transcription elongation histone marks. DSB repair pathway choice and DNA sequence context also associate with toxicity. We also show that, due to noise introduced by differential toxicity of sgRNA-targeted sites, the power of genetic screens to detect conditional essentiality is reduced in TP53 wild-type cells. Understanding the determinants of Cas9 cut toxicity will help improve design of CRISPR reagents to avoid incidental selection of TP53-deficient and/or DNA repair deficient cells.
Ligand-specific conformational change drives interdomain allostery in Pin1
Authors: Born Alexandra , Soetbeer Janne , Henen Morkos A. , Breitgoff Frauke , Polyhach Yevhen , Jeschke Gunnar , Vögeli Beat 
Published: August 2022

AbstractPin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations, but the conformational changes that lead to the altered domain sampling were unknown. Prior evidence has supported an interdomain allosteric mechanism. We recently introduced a magnetic resonance-based protocol that allowed us to determine the coupling of intra- and interdomain structural sampling in apo Pin1. Here, we describe ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.
Impact of adjuvants on the biophysical and functional characteristics of HIV vaccine-elicited antibodies in humans
Authors: Xu Shiwei , Carpenter Margaret C. , Spreng Rachel L. , Neidich Scott D. , Sarkar Sharanya , Tenney DeAnna , Goodman Derrick , Sawant Sheetal , Jha Shalini , Dunn Brooke , Juliana McElrath M. , Bekker Valerie , Mudrak Sarah V. , Flinko Robin , Lewis George K. , Ferrari Guido , Tomaras Georgia D. , Shen Xiaoying , Ackerman Margaret E. 
Published: August 2022

AbstractAdjuvants can alter the magnitude, characteristics, and persistence of the humoral response to protein vaccination. HIV vaccination might benefit from tailored adjuvant choice as raising a durable and protective response to vaccination has been exceptionally challenging. Analysis of trials of partially effective HIV vaccines have identified features of the immune response that correlate with decreased risk, including high titers of V1V2-binding IgG and IgG3 responses with low titers of V1V2-binding IgA responses and enhanced Fc effector functions, notably antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). However, there has been limited opportunity to compare the effect of different adjuvants on these activities in humans. Here, samples from the AVEG015 study, a phase 1 trial in which participants (n = 112) were immunized with gp120SF-2and one of six different adjuvants or combinations thereof were assessed for antibody titer, biophysical features, and diverse effector functions. Three adjuvants, MF59 + MTP-PE, SAF/2, and SAF/2 + MDP, increased the peak magnitude and durability of antigen-specific IgG3, IgA, FcγR-binding responses and ADCP activity, as compared to alum. While multiple adjuvants increased the titer of IgG, IgG3, and IgA responses, none consistently altered the balance of IgG to IgA or IgG3 to IgA. Linear regression analysis identified biophysical features including gp120-specific IgG and FcγR-binding responses that could predict functional activity, and network analysis identified coordinated aspects of the humoral response. These analyses reveal the ability of adjuvants to drive the character and function of the humoral response despite limitations of small sample size and immune variability in this human clinical trial.
Single mutation makes Escherichia coli an insect mutualist
Authors: Koga Ryuichi , Moriyama Minoru , Onodera-Tanifuji Naoko , Ishii Yoshiko , Takai Hiroki , Mizutani Masaki , Oguchi Kohei , Okura Reiko , Suzuki Shingo , Gotoh Yasuhiro , Hayashi Tetsuya , Seki Masahide , Suzuki Yutaka , Nishide Yudai , Hosokawa Takahiro , Wakamoto Yuichi , Furusawa Chikara , Fukatsu Takema 
Published: August 2022

AbstractMicroorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host’s high adult emergence and improved body colour; these were called ‘mutualistic’ E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of ‘mutualistic’ E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host–microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.
Near-real-time MODIS-derived vegetation index data products and online services for CONUS based on NASA LANCE
Authors: Zhang Chen , Yang Zhengwei , Di Liping , Yu Eugene G. , Zhang Bei , Han Weiguo , Lin Li , Guo Liying 
Published: August 2022

AbstractThis paper describes a set of Near-Real-Time (NRT) Vegetation Index (VI) data products for the Conterminous United States (CONUS) based on Moderate Resolution Imaging Spectroradiometer (MODIS) data from Land, Atmosphere Near-real-time Capability for EOS (LANCE), an openly accessible NASA NRT Earth observation data repository. The data set offers a variety of commonly used VIs, including Normalized Difference Vegetation Index (NDVI), Vegetation Condition Index (VCI), Mean-referenced Vegetation Condition Index (MVCI), Ratio to Median Vegetation Condition Index (RMVCI), and Ratio to previous-year Vegetation Condition Index (RVCI). LANCE enables the NRT monitoring of U.S. cropland vegetation conditions within 24 hours of observation. With more than 20 years of observations, this continuous data set enables geospatial time series analysis and change detection in many research fields such as agricultural monitoring, natural resource conservation, environmental modeling, and Earth system science. The complete set of VI data products described in the paper is openly distributed via Web Map Service (WMS) and Web Coverage Service (WCS) as well as the VegScape web application (https://nassgeodata.gmu.edu/VegScape/).
Childhood individual and family modifiable risk factors for criminal conviction: a 7-year cohort study from Brazil
Authors: Ziebold Carolina , Evans-Lacko Sara , Andrade Mário César Rezende , Hoffmann Maurício Scopel , Fonseca Lais , Barbosa Matheus Ghossain , Pan Pedro Mario , Miguel Euripedes , Bressan Rodrigo Affonseca , Rohde Luis Augusto , Salum Giovanni Abrahão , de Jesus Mari Jair , Gadelha Ary 
Published: August 2022

AbstractCrime is a major public problem in low- and middle-income countries (LMICs) and its preventive measures could have great social impact. The extent to which multiple modifiable risk factors among children and families influence juvenile criminal conviction in an LMIC remains unexplored; however, it is necessary to identify prevention targets. This study examined the association between 22 modifiable individual and family exposures assessed in childhood (5–14 years, n = 2511) and criminal conviction at a 7-year follow-up (13–21 years, n = 1905, 76% retention rate) in a cohort of young people in Brazil. Population attributable risk fraction (PARF) was computed for significant risk factors. Criminal convictions were reported for 81 (4.3%) youths. Although most children living in poverty did not present criminal conviction (89%), poverty at baseline was the only modifiable risk factor significantly associated with crime (OR 4.14, 99.8% CI 1.38–12.46) with a PARF of 22.5% (95% CI 5.9–36.1%). It suggests that preventing children’s exposure to poverty would reduce nearly a quarter of subsequent criminal convictions. These findings highlight the importance of poverty in criminal conviction, as it includes several deprivations and suggest that poverty eradication interventions during childhood may be crucial for reducing crime among Brazilian youth.
Consistent trait-temperature interactions drive butterfly phenology in both incidental and survey data
Authors: Larsen Elise A. , Belitz Michael W. , Guralnick Robert P. , Ries Leslie 
Published: August 2022

AbstractData availability limits phenological research at broad temporal and spatial extents. Butterflies are among the few taxa with broad-scale occurrence data, from both incidental reports and formal surveys. Incidental reports have biases that are challenging to address, but structured surveys are often limited seasonally and may not span full flight phenologies. Thus, how these data source compare in phenological analyses is unclear. We modeled butterfly phenology in relation to traits and climate using parallel analyses of incidental and survey data, to explore their shared utility and potential for analytical integration. One workflow aggregated “Pollard” surveys, where sites are visited multiple times per year; the other aggregated incidental data from online portals: iNaturalist and eButterfly. For 40 species, we estimated early (10%) and mid (50%) flight period metrics, and compared the spatiotemporal patterns and drivers of phenology across species and between datasets. For both datasets, inter-annual variability was best explained by temperature, and seasonal emergence was earlier for resident species overwintering at more advanced stages. Other traits related to habitat, feeding, dispersal, and voltinism had mixed or no impacts. Our results suggest that data integration can improve phenological research, and leveraging traits may predict phenology in poorly studied species.
Distributed encoding of curvilinear self-motion across spiral optic flow patterns
Authors: Layton Oliver W. , Fajen Brett R. 
Published: August 2022

AbstractSelf-motion along linear paths without eye movements creates optic flow that radiates from the direction of travel (heading). Optic flow-sensitive neurons in primate brain area MSTd have been linked to linear heading perception, but the neural basis of more general curvilinear self-motion perception is unknown. The optic flow in this case is more complex and depends on the gaze direction and curvature of the path. We investigated the extent to which signals decoded from a neural model of MSTd predict the observer’s curvilinear self-motion. Specifically, we considered the contributions of MSTd-like units that were tuned to radial, spiral, and concentric optic flow patterns in “spiral space”. Self-motion estimates decoded from units tuned to the full set of spiral space patterns were substantially more accurate and precise than those decoded from units tuned to radial expansion. Decoding only from units tuned to spiral subtypes closely approximated the performance of the full model. Only the full decoding model could account for human judgments when path curvature and gaze covaried in self-motion stimuli. The most predictive units exhibited bias in center-of-motion tuning toward the periphery, consistent with neurophysiology and prior modeling. Together, findings support a distributed encoding of curvilinear self-motion across spiral space.
EKF-SIRD model algorithm for predicting the coronavirus (COVID-19) spreading dynamics
Authors: Sebbagh Abdennour , Kechida Sihem 
Published: August 2022

AbstractIn this paper, we study the Covid 19 disease profile in the Algerian territory since February 25, 2020 to February 13, 2021. The idea is to develop a decision support system allowing public health decision and policy-makers to have future statistics (the daily prediction of parameters) of the pandemic; and also encourage citizens for conducting health protocols. Many studies applied traditional epidemic models or machine learning models to forecast the evolution of coronavirus epidemic, but the use of such models alone to make the prediction will be less precise. For this purpose, we assume that the spread of the coronavirus is a moving target described by an epidemic model. On the basis of a SIRD model (Susceptible-Infection-Recovery- Death), we applied the EKF algorithm to predict daily all parameters. These predicted parameters will be much beneficial to hospital managers for updating the available means of hospitalization (beds, oxygen concentrator, etc.) in order to reduce the mortality rate and the infected. Simulations carried out reveal that the EKF seems to be more efficient according to the obtained results.
Effects of landscape structure on restoration success in tropical premontane forest
Authors: San-José Miriam , Werden Leland K. , Joyce Francis H. , Reid J. Leighton , Holl Karen D. , Zahawi Rakan A. 
Published: August 2022

AbstractReversing large-scale habitat degradation and deforestation goes beyond what can be achieved by site-level ecological restoration and a landscape ecology perspective is fundamental. Here we assess the relative importance of tree cover and its configuration on forest-dependent birds and late-successional tree seedlings in restoration sites in southern Costa Rica. The abundance and species richness of birds increased in landscapes with more corridors, higher tree cover, and lower levels of fragmentation, highlighting the importance of riparian corridors for connectivity, and continuous tree cover as suitable habitat. Landscape variables affected abundance and species richness of seedlings similarly, but effects were weaker, possibly because seedlings face establishment limitation in addition to dispersal limitation. Moreover, the scale of landscape effects on seedlings was small, likely because proximal individual trees can significantly influence recruitment in restoration plots. Results underscore the importance of incorporating landscape-level metrics to restoration projects, as knowing the extent, and how the landscape may affect restoration outcomes can help to infer what kind of species will arrive to restoration plots.
A new marsh beetle from mid-Cretaceous amber of northern Myanmar (Coleoptera: Scirtidae)
Authors: Li Yan-Da , Ruta Rafał , Tihelka Erik , Liu Zhen-Hua , Huang Di-Ying , Cai Chen-Yang 
Published: August 2022

AbstractAs one of the earliest-diverging lineage of the megadiverse beetle suborder Polyphaga, marsh beetles (Scirtidae) are crucial for reconstructing the ancestor of all polyphagan beetles and the ecomorphological underpinnings of their remarkable evolutionary success. The phylogeny of marsh beetles has nonetheless remained challenging to infer, not least because of their fragmentary Mesozoic fossil record. Here we describe a new scirtid beetle genus and species,Varcalium lawrenceigen. et sp. nov., preserving internal tissue, from Albian–Cenomanian Kachin amber (ca99 Ma), representing the second member of this family known from the deposit. Based on a formal morphological phylogenetic analysis,Varcaliumis recovered within the crown-group of Scirtinae, forming a clade with other genera that possess subocular carinae. The finding suggests that the crown-group of Scirtinae has already diversified by the mid-Cretaceous.
Including state-of-the-art physical understanding of thermal vacancies in Calphad models
Authors: Obaied A. , Roslyakova I. , To Baben M. 
Published: August 2022

AbstractA physically sound thermochemical model accounting for explicit thermal vacancies in elements and alloys is presented. The model transfers the latest theoretical understanding of vacancy formation into the Calphad formalism where it can extend currently available thermodynamic databases to cover vacancy concentrations without a complete re-assessment. The parametrization of the model is based on ab initio-calculated enthalpy of vacancy formation and two model parameters describing the excess heat capacity of vacancy formation. Excellent agreement is obtained with temperature-dependent vacancy concentrations and elemental heat capacities while reasonable extrapolation of phase stability to high temperatures is ensured. Extrapolation to multicomponent systems is reasonable and the long-standing Neumann–Kopp related problem in the Calphad community is solved since multicomponent solid solutions will no longer show fingerprints of elemental heat capacity peaks at their melting points. FCC-Ag, FCC-Al and FCC-Cu, FCC-Zn, FCC-Ni, BCC-Ti, and BCC-W are used as a demonstration, along with the Cu–Zn binary system.