bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in spectral signature of leaves after desiccation: Implications for the prediction of leaf traits and plant-soil interaction in herbarium samples
Authors: Quinteros Casaverde Natalia L. , Serbin Shawn P. , Daly Douglas C. 
Published: January 2024

SummaryThe study investigated the impact of specimen desiccation on spectral signatures of plant tissue and its influence on models predicting biochemical and physiological traits, as well as ecosystem function.Analyzing 56 species, this study quantified the impact of leaf desiccation on: (1) the degree of change in the reflectance intensity, and its first and second derivatives within the visible - shortwave infrared spectrum, (2) the difference in change between wavebands used by Radiative Transfer Models (RTMs) for predicting traits in fresh leaves, (3) the prediction of leaf traits using PROSPECT RTM, and (4) the prediction of soil nutrient components from the leaf.Comparing desiccated specimens to fresh leaves, this study found the highest degree of change within the near infrared for the reflectance intensity, its first and second derivatives. Specific wavebands used for the prediction of leaf traits changed less that others in the VIS-SWIR. The prediction uncertainty for PROSPECT RTM differed for various leaf traits, showing an increase for equivalent water thickness, and carotene content, and a decrease in brown pigments and dry mass. Leaf traits predicted from desiccated leaves were better at predicting relationships with soil components, such as soil chemical properties and macro and micronutrients than fresh leaves.Desiccated leaves preserve and improves the capacity to inform us about important aspects of ecosystem functioning, particularly nutrient transfer between leaf and soil.
STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads
Authors: Asiimwe Rebecca , Alexander Dobin 
Published: January 2024

AbstractSummaryAllele-specific expression (ASE) is an important genetic phenomenon that impacts an individual’s phenotype and is relevant in various biological and medical contexts. Next-generation RNA sequencing technologies provide an unprecedented opportunity to measure ASE genome-wide across all heterozygous alleles expressed in a given sample. One of the major obstacles to the accurate calculation of ASE from RNA-seq data is the reference mapping bias, i.e., the preferential misalignment of the reads to the reference allele. Here, we present STAR+WASP, our reimplementation of WASP, a highly accurate algorithm for reducing the reference bias (Van De Geijnet al. 2015). We show that STAR+WASP is an order of magnitude faster than WASP while significantly reducing reference bias and providing ASE estimations similar to the original WASP algorithm.Availability and ImplementationSTAR+WASP is implemented within STAR as an integrated C++ module. STAR+WASP is open-source software, freely accessible at:http://code.google.com/p/rna-star/.Contactdobin@cshl.eduSupplementary informationSupplementary data are available at Bioinformatics online.
The Notch1/Delta-like-4 axis is crucial for the initiation and progression of oral squamous cell carcinoma
Authors: Meisel Christian T. , Destefani Riccardo , Valookkaran Ilaria J. , Batavia Aashil , Rupp Niels , Porcheri Cristina , Mitsiadis Thimios A. 
Published: January 2024

AbstractThe Notch signaling pathway is frequently altered in oral squamous cell carcinoma (OSCC), the most common malignant neoplasm of the oral mucosa. This study aimed to elucidate the functional role of this pathway in both the initiation and progression of OSCC. Using transgenic animal models, advanced imaging, and next-generation-sequencing techniques, we analyzed Notch-dependent changes driving OSCC. We found specific expression patterns of Notch1 and Delta-like-4 confined to the malignant tissue, while Jagged1 was downregulated in OSCC. This mutually exclusive expression of Delta-like-4 and Jagged1 occurs at the early hyperplastic stage and persists until more advanced stages of the developing tumor. Transcriptomic analyses confirmed the dysregulation of the Notch pathway circuitry and of the genes associated with the undifferentiated state of OSCC cells. Furthermore, pharmacological Notch inhibition significantly impaired cancer cell motility. Taken together, these results reveal the pivotal importance of the Notch1/Delta-like-4 signaling axis as a central oncogenic driver in OSCC.Graphical Abstract
New peptides against B16F10 interfere in cell cycle of melanoma cells
Authors: Xavier Eric Almeida 
Published: January 2024

AbstractPeptides have fantastic functions, they can act interfering in various cellular mechanisms such as the cell cycle. Furthermore, because of their high specificity, peptides can be used in antitumor therapy against specific targets. In this work we describe thein vitroaction of four antitumor peptide against B16F10 melanoma cells, obtained from immunoglobulin genes. As a result, we show that peptides interfered in the cell cycle of B16F10 cells. In conclusion the present article describes a molecule from immunoglobulin with future potential forin vivotherapeutic test.
REPrise:de novointerspersed repeat detection using inexact seeding
Authors: Takeda Atsushi , Nonaka Daisuke , Imazu Yuta , Fukunaga Tsukasa , Hamada Michiaki 
Published: January 2024

AbstractMotivationInterspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-freede novorepeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have sufficient repeat detection performance.ResultsIn this study, we developed REPrise, ade novointerspersed repeat detection software program based on a seed-and-extension method. Although the algorithm of REPrise is similar to that of RepeatScout, which is currently the de facto standard tool, we incorporated three unique techniques into REPrise: inexact seeding, affine gap scoring and loose masking. Analyses of rice and simulation genome datasets showed that REPrise outperformed RepeatScout in terms of sensitivity, especially when the repeat sequences contained many mutations. Furthermore, when applied to the complete human genome dataset T2T-CHM13, REPrise demonstrated the potential to detect novel repeat sequence families.AvailabilityThe source code of REPrise is freely available athttps://github.com/hmdlab/REPrise. Repeat annotations predicted for the T2T genome using REPrise are also available athttps://waseda.box.com/v/REPrise-data.Contactfukunaga@aoni.waseda.jpandmhamada@waseda.jp
Parental migration, socioeconomic deprivation and hospital admissions in preschool children: national cohort study
Authors: Lewis Kate M , Burns Rachel , Cortina-Borja Mario , Heilmann Anja , Macfarlane Alison , Nath Selina , Salway Sarah , Saxena Sonia , Villarroel-Williams Nazmy , Viner Russell , Hardelid Pia 
Published: January 2024

AbstractBackgroundA third of children born in England have at least one parent born outside the UK, yet family migration history is infrequently studied as a social determinant of child health. We describe differences in rates of hospital admissions in children aged up to five years by parental migration and socioeconomic group.MethodsBirth registrations linked to Hospital Episode Statistics were used to derive a cohort of 4,174,596 children born in state-funded hospitals in England between 2008 and 2014, with follow-up until age five years. We looked at eight maternal regions of birth, maternal country of birth for the 6 most populous groups and parental migration status for the mother and second parent (UK-born/non-UK-born). We used Index of Multiple Deprivation (IMD) quintiles to indicate socioeconomic deprivation. We fitted negative binomial/Poisson regression models to model associations between parental migration groups and the risk of hospital admissions, including interactions with IMD group.FindingsChildren of UK-born (73.6% of the cohort) mothers had the highest rates of emergency admissions (171.6 per 1000 child-years, 95% confidence interval (CI) 171.4-171.9), followed by South Asia-born mothers (155.9 per 1000, 95% CI 155.1-156.7). The high rates estimated in the South Asia group were driven by children of women born in Pakistan (186.8 per 1000, 95% CI 185.4, 188.2). A socioeconomic gradient in emergency admissions was present across all maternal region of birth groups, but most pronounced among children of UK-born mothers (incidence rate ratio 1.43, 95% CI 1.42-1.44, high vs. low IMD group). Overall, children whose parents were both born abroad had lower emergency admission rates than children whose parents were both born in the UK. Patterns of planned admissions followed a similar socioeconomic gradient and were highest among children with mothers born in Middle East and North Africa, and South Asia.InterpretationThis research indicates that children whose parents who have migrated to the UK generally have lower overall usage of NHS emergency inpatient services than children of UK-born parents. Our study revealed a socioeconomically graded patterns of hospital admissions for all children born in England, which were highest amongst those with mothers born in the UK, South Asia, and the Middle East and North Africa. Future research using linked primary and secondary care datasets will improve understanding on whether healthcare use is proportionate to need.FundingNational Institute for Health Research.
Mortality according to gender identity and sexual orientation: Data relationship strategies for Rio de Janeiro, Brazil
Authors: Rafael Ricardo de Mattos Russo , Silva Kleison Pereira da , Santos Helena Gonçalves de Souza , Depret Davi Gomes , Caravaca-Morera Jaime Alonso , Breda Karen Marie Lucas 
Published: January 2024

SUMMARYObjectiveTo evaluate the accuracy, potential, and limits of probabilistic data relationships to yield information on deaths according to sex identity and sexual orientation in the state of Rio de Janeiro.MethodsThis study evaluated the accuracy of the probabilistic relationship of data to obtain information on deaths according to gender and sexual orientation. Data from two information systems were used from June 15, 2015 to December 31, 2020. We constructed nine probabilistic data relationship strategies and identified the performance and cutoff points of the best strategy.ResultsThe best data blocking strategy was established through logical blocks with the first and last names, birthdate, and mother’s name in the pairing strategy. With a population base of 80,178 records, 1556 deaths were retrieved. With an area under the curve of 0.979, this strategy presented 93.26% accuracy, 98.46% sensitivity, and 90.04% specificity for the cutoff point ≥ 17.9 of the data relationship score. The adoption of the cutoff point optimized the manual review phase, identifying 2259 (90.04%) of the 2509 false pairs and identifying 1532 (98.46%) of the 1556 true pairs. A crude mortality rate of 19.11 deaths per 1,000 people was observed, where women who had sex with women, transvestites, and transgender women had higher mortality rates than heterosexual cisgender women. Neither men nor men with gender markers had higher mortality rates than heterosexual cisgender women.ConclusionWith the identification of possible strategies for determining probabilistic data relationships, the retrieval of information on mortality according to sexual and sex markers has become feasible. Based on information from the daily routine of health services, the formulation of public policies that consider the LGBT+ population more closely reflects the reality experienced by these population groups.
The changes of BMI in prediction of 10-year-hypertension risk in United States population- a historical cohort study
Authors: Zou Haoxuan , Wang Chumeng , Sun Wei , Kong Xiangqing , Jiang Ming , Zou Huayiyang 
Published: January 2024

AbstractBACKGROUNDThis is a historical cohort study, utilizing data from the US National Health and Nutrition Examination Survey (NHANES) 2007-2018 to predict 10-year- hypertension-risk based on body mass index (BMI) variations.METHODParticipants aged 40-79 without a hypertension diagnosis 10 years before the baseline interview were included. Subjects were categorized based on five major BMI variation patterns. Various statistical analyses, including Chi-square test, T test, univariate and multivariate logistic regression, and P-trend analysis, were employed to assess hypertension incidence among groups. Restricted cubic splines (RCS) were used to examine the age-hypertension correlation.RESULTSAmong 13,287 participants, Stable-Norm (maintaining normal BMI) exhibited the lowest 10-year hypertension risk. Other patterns—Max-OW (maximum BMI in overweight), OB-nOB (obese to non-obese), nOB-OB (non-obese to obese), and Stable-OB (maintaining obese)—showed increasing risks. Hypertension risk correlated quasi-linearly with age. Subgroups analysis suggested certain specific BMI variation modes and absolute weight change groups demonstrated equivalent risks to stable normal/weight groups, while others presented higher risks.CONCLUSIONMaintaining normal BMI had the lowest 10-year hypertension risk, and returning to normal BMI showed equivalent risk. Weight gain remained a significant hypertension risk factor in US adults, particularly with advancing age.
IL-17A/IFN-γ producing γδ T cell functional dichotomy impacts cutaneous leishmaniasis in mice
Authors: dos-Santos Júlio Souza , Firmino-Cruz Luan , Oliveira-Maciel Diogo , da Fonseca-Martins Alessandra Marcia , Ramos Tadeu Diniz , Nunes-Souza Letícia , Soares Rodrigo Pedro , Gomes Daniel Claudio Oliveira , Mengel José , Silva-Santos Bruno , de Matos Guedes Herbert Leonel 
Published: January 2024

Abstractγδ T cells are innate-like lymphocytes with pleiotropic roles in immune responses to pathogens, often ascribed to their IL-17A-producing or IFN-γ-producing γδ T cell subsets. Here we investigated the impact of this functional dichotomy on cutaneous leishmaniasis, a set of neglected diseases caused by parasites of theLeishmaniagenus. We demonstrate that in Sv129 mice susceptible toLeishmania amazonensis, Vγ4+γδ T cells are the main source of IL-17A. Furthermore, in type 1 interferon receptor-deficient (A129) mice presenting increased susceptibility to infection, there is a higher frequency of IL-17A-producing γδ T cells when compared to wild-type mice. Mechanistically, we demonstrate that lipophosphoglycan (LPG) ofL. amazonensisinduces IL-17A-producing γδ T cells. Importantly, C57Bl/6 mice deficient in γδ T cells or in IL-17 receptor (IL-17RA) show reduced lesion sizes, consistent with a pathogenic role of IL-17A-producing γδ T cells in cutaneous leishmaniasis. Conversely, the adoptive transfer of FACS-sorted γδ T cells led to an accumulation of IFN-γ-producing γδ T cells in various susceptible strains of mice which associated with control of lesion development. These data demonstrate a pathophysiological dichotomy in which IL-17A-producing γδ T cells promote pathogenesis, whereas IFN-γ-producing γδ T cells display therapeutic potential in cutaneous leishmaniasis.
Genome-informed trophic classification and functional characterization of virulence proteins from the maize tar spot pathogenPhyllachora maydis
Authors: Rogers Abigail , Jaiswal Namrata , Roggenkamp Emily , Kim Hye-Seon , MacCready Joshua S. , Chilvers Martin I. , Scofield Steven R. , Iyer-Pascuzzi Anjali S. , Helm Matthew 
Published: January 2024

ABSTRACTPhyllachora maydisis an ascomycete foliar fungal pathogen and the causal agent of tar spot in maize. ThoughP. maydisis considered one of the most economically important foliar pathogens of maize, our general knowledge of the trophic lifestyle and functional role of effector proteins from this fungal pathogen remains limited. Here, we utilized a genome-informed approach to predict the trophic lifestyle ofP. maydisand functionally characterized a subset of candidate effectors from this fungal pathogen. Leveraging the most recentP. maydisgenome annotation and the CATAStrophy pipeline, we show this fungal pathogen encodes a predicted Carbohydrate-active enzymes (CAZymes) repertoire consistent with that of biotrophs (monomertrophs). To investigate fungal pathogenicity, we selected eighteen candidate effector proteins that were previously shown to be expressed during primary disease development. We assessed whether these putative effectors share predicted structural similarity with other characterized fungal effectors and determined whether any suppress plant immune responses. Using AlphaFold2 and Foldseek, we showed one candidate effector, PM02_g1115, adopts a predicted protein structure similar to that of an effector fromVerticillium dahlia. Furthermore, transient expression of candidate effector-fluorescent protein fusions inNicotiana benthamianarevealed that most effector proteins localize to both the nucleus and the cytosol. Importantly, three candidate effectors consistently attenuated chitin-mediated reactive oxygen species production inN. benthamiana. Collectively, these results presented herein provide valuable insights into the predicted trophic lifestyle and putative functions of effectors fromP. maydisand will likely stimulate continued research to elucidate the molecular mechanisms used byP. maydisto induce tar spot.
Treatment effects in epilepsy: a mathematical framework for understanding response over time
Authors: Harrington Gwen , Kissack Peter , Terry John R. , Woldman Wessel , Junges Leandro 
Published: January 2024

AbstractEpilepsy is a neurological disorder characterized by recurrent seizures, affecting over 65 million people worldwide. Treatment typically commences with the use of anti-seizure medications, both mono- and poly-therapy. However more invasive therapies such as surgery, electrical stimulation and focal drug delivery may also be considered in an attempt to render the person seizure free. Although a significant portion ultimately benefit from these treatment options, treatment responses often fluctuate over time.The physiological mechanisms underlying these temporal variations are poorly understood, making prognosis one of the biggest challenges for treating epilepsy. In this work, we use a dynamic network model of seizure transition to understand how seizure propensity may vary over time as a consequence of changes in excitability. Through computer simulations, we explore the relationship between the impact of treatment on dynamic network properties and their vulnerability over time that permit a return to states of high seizure propensity. We show that, for small networks, vulnerability can be fully characterised by the size of the first transitive component (FTC). For larger networks, we find measures of network efficiency, incoherence and heterogeneity (degree variance) correlate with robustness of networks to increasing excitability. These results provide a set of potential prognostic markers for therapeutic interventions in epilepsy. Such markers could be used to support the development of personalized treatment strategies, ultimately contributing to understanding of long-term seizure freedom.
Identification of a Binding Site for Small Molecule Inhibitors Targeting Human TRPM4
Authors: Ekundayo Babatunde , Arullampalam Prakash , Gerber Christian E. , Hämmerli Anne-Flore , Guichard Sabrina , Boukenna Mey , Ross-Kaschitza Daniela , Lochner Martin , Rougier Jean-Sebastien , Stahlberg Henning , Abriel Hugues , Ni Dongchun 
Published: January 2024

AbstractTransient receptor potential (TRP) melastatin 4 (TRPM4) protein is a calcium-activated monovalent cation channel associated with various genetic and cardiovascular disorders. The anthranilic acid derivative NBA is a potent and specific TRPM4 inhibitor, but its binding site in TRPM4 has been unknown, although this information is crucial for drug development targeting TRPM4. We determined three cryo-EM structures of full-length human TRPM4 embedded in native lipid nanodiscs without inhibitor, bound to NBA, and a new anthranilic acid derivative, IBA. We found that the small molecules NBA and IBA were bound in a pocket formed between the S3, S4, and TRP helices and the S4-S5 linker of TRPM4. Our structural data and results from patch clamp experiments enable validation of a binding site for small molecule inhibitors, paving the way for further drug development targeting TRPM4.
Redox-dependent formation of a viral amyloid and functional impact
Authors: Gondelaud Frank , Lalande Alexandre , Pesce Giulia , Bignon Christophe , Fourquet Patrick , Ptchelkine Denis , Brouilly Nicolas , Lozach Pierre-Yves , Gerlier Denis , Mathieu Cyrille , Longhi Sonia 
Published: January 2024

AbstractThe Hendra and Nipah viruses (HeV and NiV) are zoonotic biosafety level-4 pathogens within theParamyxoviridaefamily. We previously showed that their W proteins form amyloid-like fibrilsin vitro. Here, we demonstrate that W also forms fibrilsin cellulaand that cysteine residues are crucial in dictating the ability of W proteins to fibrillate. The cysteine oxidation state acts as a switch to generate either amorphous aggregates or flexible fibrils. Ectopic expression of WHeVinduces an oxidative stress and WHeVfibrils were observed in the nuclei of different cell lines, with fibrillation being impaired by cysteine substitutions. Finally, nuclear fibrils are associated with an impairment of the NF-κB pathway in WHeVtransfected cells. This work provides experimental evidence for the ability ofHenipavirusW proteins to fibrillate in transfected cells and the first clues on their functional impact.Significance StatementNipah and Hendra viruses are severe pathogens infecting humans and livestock, classified among the 8 highest priorities for research by the WHO. The W protein, along with the V protein, is a virulence factor responsible for antiviral response inhibition and we demonstrate here that its fibrillation into amyloid-like fibrils occurs in the nucleus of transfected cells, with their formation being dependent of the redox state of the W cysteine residues. The sole transfection of W provokes the production of reactive oxygen species, creating a suitable environment for the fibrils to form. Finally, we show that W fibrils enhance the repression of the antiviral response, thus pointing to W fibrillation as a new promising antiviral target.
Molecular mechanism of β-arrestin-2 interaction with phosphatidylinositol 4,5-bisphosphate
Authors: Kim Kiae , Chung Ka Young 
Published: January 2024

AbstractPhosphorylated residues of G protein-coupled receptors bind to the N-domain of arrestin, resulting in βXX release. This induces further allosteric conformational changes, such as polar core disruption, alteration of interdomain loops, and domain rotation, which transform arrestins into the active state. It is widely accepted that arrestin activation occurs by conformational changes propagated from the N-to the C-domain. However, recent studies have revealed that binding of phosphatidylinositol 4,5-bisphosphate (PIP2) to the C-domain transforms arrestins into an active state. In this study, we aimed to elucidate the mechanisms underlying PIP2-induced arrestin activation. We compared the conformational changes of β-arrestin-2 upon binding of PIP2or phosphorylated C-tail peptide of vasopressin receptor type 2 using hydrogen/deuterium exchange mass spectrometry (HDX-MS). Introducing point mutations on the potential routes of the allosteric conformational changes and analyzing these mutant constructs with HDX-MS revealed that PIP2-binding at the C-domain affects the back loop, which destabilizes the gate loop and βXX to transform β-arrestin-2 into the pre-active state.