bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new approach for incorporating sea-level rise in hybrid 2D/one-line shoreline models
Authors: Seenath Avidesh 
Published: October 2022

AbstractHybrid 2D/one-line shoreline models, which typically apply a finite volume approach to simulate sediment transport and the one-line theory to update the shoreline morphology, are being increasingly applied over meso timescales (101 to 102 years) to inform coastal management. The one-line theory assumption of a constant closure depth prevents these models from considering the effects of sea-level rise in the shoreline morphology update. Sea-level rise, an endogenous driving factor of meso timescale coastal behaviour, influences the closure depth through its effects on the wave climate. This paper presents a new hybrid 2D/one-line approach that enables a time-varying closure depth in response to annual variations in wave climate as a solution for mirroring the effects of sea-level rise on the coastal profile and associated shoreline evolution. This new hybrid approach is applied to hindcast meso timescale shoreline evolution in a sandy coastal system and compared against the traditional hybrid 2D/one-line approach. Results show that the traditional hybrid approach gives the most accurate predictions whereas the new hybrid approach overpredicts shoreline erosion. However, this overprediction is attributed to net closure depth overestimation. This attribution gives confidence that the shoreline response to the time-varying closure depth specified is within expectations since closure depth overestimation increases offshore sediment transport in shoreline models. Therefore, it is likely that enabling a time-varying closure depth in hybrid 2D/one-line models may improve meso timescale shoreline predictions under sea-level rise if closure depths can be accurately prescribed over time.
Effects of mesenchymal stem cells in renovascular disease of preclinical and clinical studies: a systematic review and meta-analysis
Authors: Wang Hong-Shen , Yi Ming-Yu , Wu Xi , Liu Qian , Deng Ying-Hao , Wu Ting , Wang Lin , Kang Yi-Xin , Luo Xiao-Qin , Yan Ping , Wang Mei , Duan Shao-Bin 
Published: October 2022

AbstractRenal artery stenosis (RAS) causes severe renovascular hypertension, worsening kidney function, and increased cardiovascular morbidity. According to recent studies, mesenchymal stem cells (MSCs) administration is a promising therapy for the improvement of RAS outcomes. The meta-analysis aims to evaluate the therapeutic effects of MSC therapy on RAS. We performed a search in MEDLINE, Web of Science, Embase, and Cochrane Library from inception to 5, October 2022. We included 16 preclinical and 3 clinical studies in this meta-analysis. In preclinical studies, the pooled results indicated that animals treated with MSCs had lower levels of systolic blood pressure (SBP) (SMD = − 1.019, 95% CI − 1.434 to − 0.604, I2 = 37.2%, P = 0.000), serum creatinine (Scr) (SMD = − 1.112, 95% CI − 1.932 to − 0.293, I2 = 72.0%, P = 0.008), and plasma renin activity (PRA) (SMD = − 0.477, 95% CI − 0.913 to 0.042, I2 = 43.4%, P = 0.032). The studies also revealed increased levels of renal blood flow (RBF) in stenotic kidney (STK) (SMD = 0.774, 95% CI − 0.351 to 1.197, I2 = 0%, P = 0.000) and the glomerular filtration rate (GFR) of STK (SMD = 1.825, 95% CI 0.963 to 2.688, I2 = 72.6%, P = 0.000). In clinical studies, the cortical perfusion and fractional hypoxia of the contralateral kidney (CLK) were alleviated by MSC therapy. Taken together, this meta-analysis revealed that MSCs therapy might be a promising treatment for RAS. However, due to the discrepancy between preclinical studies and early clinical trials outcomes, MSC therapy couldn’t be recommended in clinical care for the moment, more high-quality randomized controlled clinical trials are needed to validate our conclusions and standardize MSCs protocols.
Relating individual cell division events to single-cell ERK and Akt activity time courses
Authors: Stern Alan D. , Smith Gregory R. , Santos Luis C. , Sarmah Deepraj , Zhang Xiang , Lu Xiaoming , Iuricich Federico , Pandey Gaurav , Iyengar Ravi , Birtwistle Marc R. 
Published: October 2022

AbstractBiochemical correlates of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to division events in the same single cells using the non-transformed MCF10A epithelial line. Following growth factor treatment, in cells that divide both ERK and Akt activities are significantly higher within the S-G2 time window (~ 8.5–40 h). Such differences were much smaller in the pre-S-phase, restriction point window which is traditionally associated with ERK and Akt activity dependence, suggesting unappreciated roles for ERK and Akt in S through G2. Simple metrics of central tendency in this time window are associated with subsequent cell division fates. ERK activity was more strongly associated with division fates than Akt activity, suggesting Akt activity dynamics may contribute less to the decision driving cell division in this context. We also find that ERK and Akt activities are less correlated with each other in cells that divide. Network reconstruction experiments demonstrated that this correlation behavior was likely not due to crosstalk, as ERK and Akt do not interact in this context, in contrast to other transformed cell types. Overall, our findings support roles for ERK and Akt activity throughout the cell cycle as opposed to just before the restriction point, and suggest ERK activity dynamics may be more important than Akt activity dynamics for driving cell division in this non-transformed context.
Exceptional preservation of internal organs in a new fossil species of freshwater shrimp (Caridea: Palaemonoidea) from the Eocene of Messel (Germany)
Authors: de Mazancourt Valentin , Wappler Torsten , Wedmann Sonja 
Published: October 2022

AbstractA new species of extinct freshwater shrimp was discovered in the Eocene deposit of the Messel Pit Konservat-Lagerstätte. This rare find is represented by only a few specimens, one of which showing exceptionally preserved soft tissues and other internal parts like the stomach with possibly gastric ossicles in place, branchiae, the ovary, and the left mandible, never described in a fossil shrimp. The new species Bechleja brevirostris n. sp. is characterized by a short rostrum bearing 6–8 dorsal spines and one ventral tooth, and long second pereiopods with strong chelae. One additional specimen shows a slightly different morphology and might belong to a different species. The systematic position of the species among the superfamily Palaemonoidea is discussed, as well as implications for the knowledge of the paleoenvironment of Lake Messel and the paleobiogeography of the Eocene.
Evolution of naturally arising SARS-CoV-2 defective interfering particles
Authors: Girgis Samer , Xu Zaikun , Oikonomopoulos Spyros , Fedorova Alla D. , Tchesnokov Egor P. , Gordon Calvin J. , Schmeing T. Martin , Götte Matthias , Sonenberg Nahum , Baranov Pavel V. , Ragoussis Jiannis , Hobman Tom C. , Pelletier Jerry 
Published: October 2022

AbstractDefective interfering (DI) particles arise during virus propagation, are conditional on parental virus for replication and packaging, and interfere with viral expansion. There is much interest in developing DIs as anti-viral agents. Here we characterize DI particles that arose following serial passaging of SARS-CoV-2 at high multiplicity of infection. The prominent DIs identified have lost ~84% of the SARS-CoV-2 genome and are capable of attenuating parental viral titers. Synthetic variants of the DI genomes also interfere with infection and can be used as conditional, gene delivery vehicles. In addition, the DI genomes encode an Nsp1-10 fusion protein capable of attenuating viral replication. These results identify naturally selected defective viral genomes that emerged and stably propagated in the presence of parental virus.
Fate mapping reveals mixed embryonic origin and unique developmental codes of mouse forebrain septal neurons
Authors: Magno Lorenza , Asgarian Zeinab , Apanaviciute Migle , Milner Yasmin , Bengoa-Vergniory Nora , Rubin Anna Noren , Kessaris Nicoletta 
Published: October 2022

AbstractThe septum is a key structure at the core of the forebrain that integrates inputs and relays information to other brain areas to support cognition and behaviours such as feeding and locomotion. Underlying these functions is a rich diversity of neuronal types and an intricate complexity of wiring across and within the septal region. We currently have very little understanding of how septal neuronal diversity emerges during development. Using transgenic mice expressing Cre in different subsets of telencephalic precursors we explored the origins of the three main neuronal types of the septal complex: GABAergic, cholinergic and glutamatergic neurons. We find that septal neurons originate from distinct neuroepithelial domains of the developing septum and are born at different embryonic time points. An exception to this is the GABAergic medial septal Parvalbumin-expressing population which is generated outside the septum from surrounding germinal zones. We identify the transcription factor BSX as being expressed in the developing glutamatergic neuron population. Embryonic elimination of BSX in the septum results in a reduction of septal glutamatergic cell numbers and a consequent deficit in locomotion. Further refinement of septal neuron diversity is needed to understand the multiple roles of septal neurons and their contribution to distinct behaviours.
Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis
Authors: Kaiser Marco S. , Milan Giulia , Ham Daniel J. , Lin Shuo , Oliveri Filippo , Chojnowska Kathrin , Tintignac Lionel A. , Mittal Nitish , Zimmerli Christian E. , Glass David J. , Zavolan Mihaela , Rüegg Markus A. 
Published: October 2022

AbstractMuscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced muscle hypertrophy, its constant activation alone induces muscle atrophy. Here we show that this paradox is based on mTORC1 activity promoting protein breakdown through the ubiquitin-proteasome system (UPS) by simultaneously inducing ubiquitin E3 ligase expression via feedback inhibition of PKB/Akt and proteasome biogenesis via Nuclear Factor Erythroid 2-Like 1 (Nrf1). Muscle growth was restored by reactivation of PKB/Akt, but not by Nrf1 knockdown, implicating ubiquitination as the limiting step. However, both PKB/Akt activation and proteasome depletion by Nrf1 knockdown led to an immediate disruption of proteome integrity with rapid accumulation of damaged material. These data highlight the physiological importance of mTORC1-mediated PKB/Akt inhibition and point to juxtaposed roles of the UPS in atrophy and proteome integrity.
Three-dimensional characterization of developing and adult ocular vasculature in mice using in toto clearing
Authors: Darche Marie , Verschueren Anna , Belle Morgane , Boucherit Leyna , Fouquet Stéphane , Sahel José Alain , Chédotal Alain , Cascone Ilaria , Paques Michel 
Published: October 2022

AbstractThe ocular vasculature is critically involved in many blinding diseases and is also a popular research model for the exploration of developmental and pathological angiogenesis. The development of ocular vessels is a complex, finely orchestrated sequence of events, involving spatial and temporal coordination of hyaloid, choroidal and retinal networks. Comprehensive studies of the tridimensional dynamics of microvascular remodeling are limited by the fact that preserving the spatial disposition of ocular vascular networks is cumbersome using classical histological procedures. Here, we demonstrate that light-sheet fluorescence microscopy (LFSM) of cleared mouse eyes followed by extensive virtual dissection offers a solution to this problem. To the best of our knowledge, this is the first 3D quantification of the evolution of the hyaloid vasculature and of post-occlusive venous remodeling together with the characterization of spatial distribution of various cell populations in ocular compartments, including the vitreous. These techniques will prove interesting to obtain other insights in scientific questions addressing organ-wide cell interactions.
An open-source molecular builder and free energy preparation workflow
Authors: Bieniek Mateusz K. , Cree Ben , Pirie Rachael , Horton Joshua T. , Tatum Natalie J. , Cole Daniel J. 
Published: October 2022

AbstractAutomated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity, but building reliable initial binding poses for the ligands is challenging. Here, we introduce the open-source FEgrow workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations. For a given ligand core and receptor structure, FEgrow enumerates and optimises the bioactive conformations of the grown functional group(s), making use of hybrid machine learning/molecular mechanics potential energy functions where possible. Low energy structures are optionally scored using the gnina convolutional neural network scoring function, and output for more rigorous protein–ligand binding free energy predictions. We illustrate use of the workflow by building and scoring binding poses for ten congeneric series of ligands bound to targets from a standard, high quality dataset of protein–ligand complexes. Furthermore, we build a set of 13 inhibitors of the SARS-CoV-2 main protease from the literature, and use free energy calculations to retrospectively compute their relative binding free energies. FEgrow is freely available athttps://github.com/cole-group/FEgrow, along with a tutorial.
Artificial intelligence and machine learning in cancer imaging
Authors: Koh Dow-Mu , Papanikolaou Nickolas , Bick Ulrich , Illing Rowland , Kahn Charles E. , Kalpathi-Cramer Jayshree , Matos Celso , Martí-Bonmatí Luis , Miles Anne , Mun Seong Ki , Napel Sandy , Rockall Andrea , Sala Evis , Strickland Nicola , Prior Fred 
Published: October 2022

AbstractAn increasing array of tools is being developed using artificial intelligence (AI) and machine learning (ML) for cancer imaging. The development of an optimal tool requires multidisciplinary engagement to ensure that the appropriate use case is met, as well as to undertake robust development and testing prior to its adoption into healthcare systems. This multidisciplinary review highlights key developments in the field. We discuss the challenges and opportunities of AI and ML in cancer imaging; considerations for the development of algorithms into tools that can be widely used and disseminated; and the development of the ecosystem needed to promote growth of AI and ML in cancer imaging.
A Brønsted acid-catalyzed thioacid addition toin situ-generated aldimine for the synthesis of isoindolinones with theN,S-acetal framework
Authors: Sadhu Milon M. , Khajuria Chhavi , Singh Vinod K. 
Published: October 2022

A Brønsted acid catalyzed three-component reaction has been developed for the synthesis of isoindolinones containing N,S-acetal framework.
Stuttering Behavior in a National Age Cohort of Norwegian First-Graders With Down Syndrome
Authors: Hokstad Silje , Næss Kari-Anne B. , Yaruss J. Scott , Hoff Karoline , Melle Ane H. , Lervåg Arne Ola 
Published: October 2022

Purpose:
The aims of this study were to investigate the occurrence of stuttering behavior across time and to evaluate the relationship between stuttering behavior and language ability in children with Down syndrome.

Method:

A national age cohort of Norwegian first graders with Down syndrome (
N
= 75) participated in the study. Speech samples from a story-retelling task and a picture book dialogue as well as standardized measures of vocabulary, grammar, and nonverbal mental ability were collected at two time points approximately 5 months apart. Stuttering behavior was evaluated through counting stuttering-like disfluencies and stuttering severity ratings. The relationship between stuttering behavior and language ability was investigated through hierarchical regression analysis.

Results:
The participants had stuttering severity ratings ranging from no stuttering behavior to severe and displayed all types of stuttering-like disfluencies. There were significant relationships between stuttering behavior and language ability at the first time point, whereas the relationships were not significant at the second time point. The stuttering severity ratings were significantly predicted by language ability across time, whereas the frequency of stuttering-like disfluencies was not.

Conclusions:
The occurrence of stuttering behavior was high across the measures and time points; however, the relationship between stuttering behavior and language ability varied across these variables. Thus, the nature of the relationship does not seem to follow a strict pattern that can be generalized to all children across time.
Statistical Errors in “How Graduate Students With Vocal Fry Are Perceived by Speech-Language Pathologists”
Authors: Theodore Rachel M. 
Published: October 2022

Purpose:

Perspectives of the ASHA Special Interest Groups
recently published a study (Gallena & Pinto, 2021) that investigated how graduate students with vocal fry are perceived by speech-language pathologists. The statistical analysis of the data presented in this study contains errors. The purpose of this letter is to describe these errors, outline practices that may facilitate error detection prior to publication, and position these errors in the broader context of vocal quality biases that may influence hiring and supervision decisions among speech-language pathologists.

Conclusions:
The statistical errors in Gallena and Pinto (2021) reflected a violation of the assumption of independence required by the employed statistical tests and inaccurate calculation of effect size measures. The severity of these errors makes it difficult to determine whether the reported results would hold if the correct statistical analyses were applied to the data and, thus, challenge an understanding of the degree to which vocal quality may influence perceived speaker traits and hiring or supervision decisions. Open science practices, including the Registered Report model of publication and open access to data and analysis pipelines during the review process, provide mechanisms to support error detection prior to publication.
State vulnerability assessment against false data injection attacks in AC state estimators
Authors: Khare Gaurav , Mohapatra Abheejeet , Singh Sri Niwas 
Published: October 2022

AbstractThe transformation of the conventional power grid into a smart grid has revolutionised the power industry. However, this has also made the power grid vulnerable to various cyberattacks. This study evaluates the vulnerability of system states, which act as crucial inputs to other essential grid monitoring and control functions, against credible false data injection attacks on nonlinear AC state estimators. Accordingly, two approaches are proposed. The first maximises the yield of the attack, and the second reduces the number of physical meters to be manipulated to launch an attack. This study also develops an attack feasibility index, which can assist in quantifying the feasibility of an false data injection attack while considering various characteristics of a cyberattack. The attack feasibility index also aids in simultaneously comparing the effects of both approaches and assessing the vulnerability of the estimated states. The effectiveness of the proposed methods and the index are established by calculating the state vulnerability of the IEEE 39 bus and IEEE 118 bus test systems.
Constraints on planetary tidal dissipation from a detailed study of Kepler 91b
Authors: Fellay L. , Pezzotti C. , Buldgen G. , Eggenberger P. , Bolmont E. 
Published: October 2022

Context. With the detection of thousands of exoplanets, characterising their dynamical evolution in detail represents a key step in the understanding of their formation. Studying the dissipation of tides occurring both in the host star and in the planets is of great relevance in order to investigate the distribution of the angular momentum occurring among the objects populating the system and to studying the evolution of the orbital parameters. From a theoretical point of view, the dissipation of tides throughout a body may be studied by relying on the so-called phase or time-lag equilibrium tides model in which the reduced tidal quality factor Q′p, or equivalently the product between the love number and the time lag (k2,pΔtp), describe how efficiently tides are dissipated within the perturbed body. Constraining these factors by looking at the current configuration of the exoplanetary system is extremely challenging, and simulations accounting for the evolution of the system as a whole might help to shed some light on the mechanisms governing this process.
Aims. We aim to constrain the tidal dissipation factors of hot-Jupiter-like planets by studying the orbital evolution of Kepler-91b.
Methods. We firstly carried out a detailed asteroseismc characterisation of Kepler-91 and computed a dedicated stellar model using both classical and astereoseismic constraints. We then coupled the evolution of the star to the one of the planets by means of our orbital evolution code and studied the evolution of the system by accounting for tides dissipated both in the planet and in the host star.
Results. We found that the maximum value for k2,pΔtp (or equivalently the minimum value for Q′p) determining the efficiency of equilibrium tides dissipation occurring within Kepler-91b is 0.4 ± 0.25 s (4.5−1.5+5.8 × 105). We constrained these factors by computing the evolution of the planetary orbit and by reproducing the current properties of the Kepler-91 system.
Conclusions. We developed a new method to constrain the tidal dissipation factors using the observed eccentricity of a given planet. Our new approach showed that Kepler 91b has dissipation coefficients compatible with colder Jupiter-like planets. When applied to other targets, our new method could potentially give more precise boundary values to the tidal dissipation factors, and determine whether planetary tides dominate the dissipation during the stellar main sequence.