bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low atmospheric CO2 levels before the rise of forested ecosystems
Authors: Dahl Tais W. , Harding Magnus A. R. , Brugger Julia , Feulner Georg , Norrman Kion , Lomax Barry H. , Junium Christopher K. 
Published: December 2022

AbstractThe emergence of forests on Earth (~385 million years ago, Ma)1has been linked to an order-of-magnitude decline in atmospheric CO2levels and global climatic cooling by altering continental weathering processes, but observational constraints on atmospheric CO2before the rise of forests carry large, often unbound, uncertainties. Here, we calibrate a mechanistic model for gas exchange in modern lycophytes and constrain atmospheric CO2levels 410–380 Ma from related fossilized plants with bound uncertainties of approximately ±100 ppm (1 sd). We find that the atmosphere contained ~525–715 ppm CO2before continents were afforested, and that Earth was partially glaciated according to a palaeoclimate model. A process-driven biogeochemical model (COPSE) shows the appearance of trees with deep roots did not dramatically enhance atmospheric CO2removal. Rather, shallow-rooted vascular ecosystems could have simultaneously caused abrupt atmospheric oxygenation and climatic cooling long before the rise of forests, although earlier CO2levels are still unknown.
Synthesis of macrocyclic nucleoside antibacterials and their interactions with MraY
Authors: Nakaya Takeshi , Yabe Miyuki , Mashalidis Ellene H. , Sato Toyotaka , Yamamoto Kazuki , Hikiji Yuta , Katsuyama Akira , Shinohara Motoko , Minato Yusuke , Takahashi Satoshi , Horiuchi Motohiro , Yokota Shin-ichi , Lee Seok-Yong , Ichikawa Satoshi 
Published: December 2022

AbstractThe development of new antibacterial drugs with different mechanisms of action is urgently needed to address antimicrobial resistance. MraY is an essential membrane enzyme required for bacterial cell wall synthesis. Sphaerimicins are naturally occurring macrocyclic nucleoside inhibitors of MraY and are considered a promising target in antibacterial discovery. However, developing sphaerimicins as antibacterials has been challenging due to their complex macrocyclic structures. In this study, we construct their characteristic macrocyclic skeleton via two key reactions. Having then determined the structure of a sphaerimicin analogue bound to MraY, we use a structure-guided approach to design simplified sphaerimicin analogues. These analogues retain potency against MraY and exhibit potent antibacterial activity against Gram-positive bacteria, including clinically isolated drug resistant strains of S. aureus and E. faecium. Our study combines synthetic chemistry, structural biology, and microbiology to provide a platform for the development of MraY inhibitors as antibacterials against drug-resistant bacteria.
Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing
Authors: Blair Kerry , Tehseen Muhammad , Raducanu Vlad-Stefan , Shahid Taha , Lancey Claudia , Rashid Fahad , Crehuet Ramon , Hamdan Samir M. , De Biasio Alfredo 
Published: December 2022

AbstractDuring lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIPN-term) and DNA binding domain (PIPDBD). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIPN-term is released from PCNA and only PIPDBD is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation.
BCM3D 2.0: accurate segmentation of single bacterial cells in dense biofilms using computationally generated intermediate image representations
Authors: Zhang Ji , Wang Yibo , Donarski Eric D. , Toma Tanjin T. , Miles Madeline T. , Acton Scott T. , Gahlmann Andreas 
Published: December 2022

AbstractAccurate detection and segmentation of single cells in three-dimensional (3D) fluorescence time-lapse images is essential for observing individual cell behaviors in large bacterial communities called biofilms. Recent progress in machine-learning-based image analysis is providing this capability with ever-increasing accuracy. Leveraging the capabilities of deep convolutional neural networks (CNNs), we recently developed bacterial cell morphometry in 3D (BCM3D), an integrated image analysis pipeline that combines deep learning with conventional image analysis to detect and segment single biofilm-dwelling cells in 3D fluorescence images. While the first release ofBCM3D(BCM3D 1.0) achieved state-of-the-art 3D bacterial cell segmentation accuracies, low signal-to-background ratios (SBRs) and images of very dense biofilms remained challenging. Here, we presentBCM3D 2.0to address this challenge.BCM3D 2.0is entirely complementary to the approach utilized inBCM3D 1.0. Instead of training CNNs to perform voxel classification, we trained CNNs to translate 3D fluorescence images into intermediate 3D image representations that are, when combined appropriately, more amenable to conventional mathematical image processing than a single experimental image. Using this approach, improved segmentation results are obtained even for very low SBRs and/or high cell density biofilm images. The improved cell segmentation accuracies in turn enable improved accuracies of tracking individual cells through 3D space and time. This capability opens the door to investigating time-dependent phenomena in bacterial biofilms at the cellular level.
Biogeography of Rhaponticoides, an Irano-Turanian element in the Mediterranean flora
Authors: Bozkurt Meryem , Calleja Alarcón Juan Antonio , Uysal Tuna , Garcia-Jacas Nuria , Ertuğrul Kuddisi , Susanna Alfonso 
Published: December 2022

AbstractFloristic relationships between the Irano-Turanian and Mediterranean regions have been known from old. However, only a few biogeographical analyses based on molecular data have evaluated the history of steppe plants within the Mediterranean basin. Our study aims to contribute to a better understanding of the migratory and diversification processes by reconstructing the biogeography ofRhaponticoides(Cardueae), distributed in the Mediterranean and Irano-Turanian regions. We generated nuclear and plastid sequences that were analyzed by Bayesian inference. We used the resulting phylogeny for dating the diversification of the genus and examining the dispersal pathways. Two clades were recovered, an Irano-Turanian clade and a Mediterranean clade. The origin of the genus was placed in the Anatolian plateau in the Middle Miocene. The genus experienced several diversifications and expansions correlated to the Messinian salinity crisis and the environmental changes in the Pliocene and the Quaternary.Rhaponticoidesmigrated following two routes reflecting the two souls of the genus: Irano-Turanian taxa colonized the steppes of Eurasia whilst Mediterranean species migrated via eastern and central Mediterranean and North Africa, leaving a trail of species; both pathways ended in the Iberian Peninsula. Our study also confirms that more work is needed to unravel phylogenetic relationships inRhaponticoides.
Defining the timeline of periostin upregulation in cardiac fibrosis following acute myocardial infarction in mice
Authors: Gil Hadas , Goldshtein Matan , Etzion Sharon , Elyagon Sigal , Hadad Uzi , Etzion Yoram , Cohen Smadar 
Published: December 2022

AbstractAfter myocardial infarction (MI), the heart's reparative response to the ischemic insult and the related loss of cardiomyocytes involves cardiac fibrosis, in which the damaged tissue is replaced with a fibrous scar. Although the scar is essential to prevent ventricular wall rupture in the infarction zone, it expands over time to remote, non-infarct areas, significantly increasing the extent of fibrosis and markedly altering cardiac structure. Cardiac function in this scenario deteriorates, thereby increasing the probability of heart failure and the risk of death. Recent works have suggested that the matricellular protein periostin, known to be involved in fibrosis, is a candidate therapeutic target for the regulation of MI-induced fibrosis and remodeling. Different strategies for the genetic manipulation of periostin have been proposed previously, yet those works did not properly address the time dependency between periostin activity and cardiac fibrosis. Our study aimed to fill that gap in knowledge and fully elucidate the explicit timing of cellular periostin upregulation in the infarcted heart to enable the safer and more effective post-MI targeting of periostin-producing cells. Surgical MI was performed in C57BL/6J and BALB/c mice by ligation of the left anterior descending coronary artery. Flow cytometry analyses of cells derived from the infarcted hearts and quantitative real-time PCR of the total cellular RNA revealed that periostin expression increased during days 2–7 and peaked on day 7 post-infarct, regardless of mouse strain. The established timeline for cellular periostin expression in the post-MI heart is a significant milestone toward the development of optimal periostin-targeted gene therapy.
A national, multicenter, secondary data use study evaluating efficacy and retention of first-line biologic treatment with tocilizumab in patients with rheumatoid arthritis in real-life setting: results from TURKBIO registry
Authors: Yazici Ayten , Özdemir Işık Özlem , Dalkılıç Ediz , Koca Süleyman Serdar , Pehlivan Yavuz , Şenel Soner , Inanc Nevsun , Akar Servet , Yılmaz Sema , Soysal Gündüz Özgül , Cefle Ayse , Karakaş Ömer Fatih , Onen Fatos 
Published: December 2022

AbstractTocilizumab (TCZ) is a recombinant humanized monoclonal antibody that targets the IL-6 receptor. TCZ found to be efficacious and has a good tolerated safety profile in rheumatoid arthritis (RA) patients. The aim of this study was to describe the disease activity and retention rate in Turkish RA patients who were prescribed TCZ as first-line biologic treatment in a real-world setting. Secondary data obtained from adult RA patients’ files was used in a multicenter and retrospective context. Clinical Disease Activity Index (CDAI), Disease Activity Score in 28 joints with ESR (DAS28-ESR), and retention rates of TCZ were evaluated at related time points. 130 patients (87.7% female) with a mean age of 53 years (SD; 15.0) were included in the study. Mean RA duration was 14 years and median duration of follow-up was 18.5 months. Number of patients with ongoing TCZ treatment at 6, 12, and 24 months were 121 (93%), 85 (65%), and 46 (35%), respectively. Remission rates at 6, 12, and 24 months per CDAI (< 2.8) and DAS28-ESR (< 2.6) scores were 61.5, 44.6, 30%, and 54.6, 40.8, 27.7%, respectively. Both CDAI and DAS28-ESR scores significantly improved at 6, 12 and 24 months (p < 0.001 for both). At 24 months, 23 patients (17.6%) discontinued TCZ, of whom majority (17/23) were due to unsatisfactory response. Retention rates of TCZ at 6, 12, and 24 months were 93, 84.3, and 72.2%, respectively. In this real-world study, TCZ as a first-line biologic therapy was found to be efficacious and showing high retention rates. These real-world study results are in line with previous randomized studies.
The impacts of shape factor and heat transfer on two-phase flow of nano and hybrid nanofluid in a saturated porous medium
Authors: Ananth Subray P. V. , Hanumagowda B. N. , Varma S. V. K. , Hatami Mohammad 
Published: December 2022

AbstractThe focus of this article is to obtain the effect of shape factor of the hybrid nanoparticles on the convective heat and mass transference of two immiscible fluids in an inclined duct by employing the perturbation technique. The hybrid nanoparticle of Carbon Nanotube & Sodium alginate is being used with Silicon oil as the base fluid to study the heat and mass phenomena due to the soret effect, viscous dissipation, Darcy and Thermal diffusion. The physical flow problem is then modelled into a set of differential equations. The system of equations is solved analytically to obtain various graphical and numerical results for analyzing the impact of various material parameters on velocity and thermal field. The heat transfer rate and skin friction analysis for the flow dynamics are also investigated. It is observed that the shape factor enhances the fluid flow and temperature distribution. In specific lamina shape particles have better performance comparatively, significance of the soret number can also be observed.
Design and control of soft biomimetic pangasius fish robot using fin ray effect and reinforcement learning
Authors: Youssef Samuel M. , Soliman MennaAllah , Saleh Mahmood A. , Elsayed Ahmed H. , Radwan Ahmed G. 
Published: December 2022

AbstractSoft robots provide a pathway to accurately mimic biological creatures and be integrated into their environment with minimal invasion or disruption to their ecosystem. These robots made from soft deforming materials possess structural properties and behaviors similar to the bodies and organs of living creatures. However, they are difficult to develop in terms of integrated actuation and sensing, accurate modeling, and precise control. This article presents a soft-rigid hybrid robotic fish inspired by the Pangasius fish. The robot employs a flexible fin ray tail structure driven by a servo motor, to act as the soft body of the robot and provide the undulatory motion to the caudal fin of the fish. To address the modeling and control challenges, reinforcement learning (RL) is proposed as a model-free control strategy for the robot fish to swim and reach a specified target goal. By training and investigating the RL through experiments on real hardware, we illustrate the capability of the fish to learn and achieve the required task.
Novel multimorbidity clusters in people with eczema and asthma: a population-based cluster analysis
Authors: Mulick Amy R. , Henderson Alasdair D. , Prieto-Merino David , Mansfield Kathryn E. , Matthewman Julian , Quint Jennifer K. , Lyons Ronan A. , Sheikh Aziz , McAllister David A. , Nitsch Dorothea , Langan Sinéad M. 
Published: December 2022

AbstractEczema and asthma are allergic diseases and two of the commonest chronic conditions in high-income countries. Their co-existence with other allergic conditions is common, but little research exists on wider multimorbidity with these conditions. We set out to identify and compare clusters of multimorbidity in people with eczema or asthma and people without. Using routinely-collected primary care data from the U.K. Clinical Research Practice Datalink GOLD, we identified adults ever having eczema (or asthma), and comparison groups never having eczema (or asthma). We derived clusters of multimorbidity from hierarchical cluster analysis of Jaccard distances between pairs of diagnostic categories estimated from mixed-effects logistic regressions. We analysed 434,422 individuals with eczema (58% female, median age 47 years) and 1,333,281 individuals without (55% female, 47 years), and 517,712 individuals with asthma (53% female, 44 years) and 1,601,210 individuals without (53% female, 45 years). Age at first morbidity, sex and having eczema/asthma affected the scope of multimorbidity, with women, older age and eczema/asthma being associated with larger morbidity clusters. Injuries, digestive, nervous system and mental health disorders were more commonly seen in eczema and asthma than control clusters. People with eczema and asthma of all ages and both sexes may experience greater multimorbidity than people without eczema and asthma, including conditions not previously recognised as contributing to their disease burden. This work highlights areas where there is a critical need for research addressing the burden and drivers of multimorbidity in order to inform strategies to reduce poor health outcomes.
High-accuracy model recognition method of mobile device based on weighted feature similarity
Authors: Li Ruixiang , Wang Xiuting , Luo Xiangyang 
Published: December 2022

AbstractAccurately model recognition of mobile device is of great significance for identifying copycat device and protecting intellectual property rights. Although existing methods have realized high-accuracy recognition about device’s category and brand, the accuracy of model recognition still needs to be improved. For that, we propose Recognizer, a high-accuracy model recognition method of mobile device based on weighted feature similarity. We extract 20 features from the network traffic and physical attributes of device, and design feature similarity metric rules, and calculate inter-device similarity further. In addition, we propose feature importance evaluation strategies to assess the role of feature in recognition and determine the weight of each feature. Finally, based on all or part of 20 features, the similarity between the target device and known devices is calculated to recognize the brand and model of target device. Based on 587 models of mobile devices of 17 widely used brands such as Apple and Samsung, we carry out device recognition experiments. The results show that Recognizer can identify the device’s brand and model than existing methods more effectively. In average, the model recognition accuracy of Recognizer is 99.08% (+ 9.25%↑) when using 20 features and 92.08% (+ 29.26%↑) when using 13 features.
Oropharyngeal Dysphagia in Hospitalized Older Adults With Dementia: A Mixed-Methods Study of Care Partners
Authors: Makhnevich Alex , Marziliano Allison , Porreca Kristen , Gromova Valeria , Diefenbach Michael A. , Sinvani Liron 
Published: December 2022

Purpose:
Oropharyngeal dysphagia (OD) affects nearly 90% of hospitalized persons with dementia. Yet, little is known about the care partner experience. The purpose of our study was to describe the experience of care partners related to OD management in patients with dementia as they transition from the hospital to the community setting.

Method:
Using a mixed-methods approach, we conducted telephone interviews with care partners of recently hospitalized older adults with dementia and OD. Interviews consisted of quantitative/qualitative assessments: communication with health care team, perception about risks/benefits of dysphagia diet, and informational needs. Descriptive statistics were used for quantitative data. For the qualitative data, transcripts were independently coded by research team and categorized into themes.

Results:

Of the care partners interviewed (
N
= 24), mean age was 63.5 (
SD
= 14.9), 62.5% were female, and 66.7% were White. Nearly 60% of patients had severe dementia, and 66.7% required feeding assistance. Care partners (
n
= 18) reported moderate burden of 14.11 (
SD
= 10.03). Most care partners (83.3%) first learned about OD during hospitalization. Only 29.2% of care partners reported that they discussed OD with a physician. Care partner perception of dysphagia diet risks/benefits ranged widely: 33.3% thought dysphagia diets would promote a more enjoyable existence. Over half (54.2%) of care partners indicated no choice regarding dysphagia diets was presented to them. Two thirds (
n
= 16) of care partners were nonadherent to diet recommendations; the top reason (
n
= 13%) was diet refusal by patients. Although 83.3% of care partners wanted additional information regarding dysphagia management, only 20.8% sought any.

Conclusions:
Our findings highlight that care partners of persons with dementia face significant OD-related communication and informational gaps, which may lead to elevated burden. Future studies are needed to address unmet OD-related care partner needs.
Writing Instruction as an Authentic Context for Targeting Speech and Language Therapy Goals for Deaf and Hard of Hearing Children
Authors: Secora Kristen , Wolbers Kimberly , Dostal Hannah 
Published: December 2022

Purpose:
This tutorial describes how a speech-language pathologist (SLP) might incorporate writing-based principles into therapy sessions to target a variety of speech and language goals for deaf and hard of hearing (DHH) children in addition to writing. We present an illustrative example of one SLP's experience implementing Strategic and Interactive Writing Instruction (SIWI), an approach to writing instruction designed for DHH students, within a public elementary school setting.

Method:
We motivate this tutorial by first reviewing the literature related to the challenges for SLPs in targeting written language within therapy settings and then discuss writing and communication difficulties for DHH students. We describe the components of SIWI with illustrative examples of how one SLP applied these principles within her therapy sessions with DHH students. The SIWI instructional approach integrates well with the roles and responsibilities of an SLP in providing therapy across a variety of communication domains for the DHH students. This tutorial describes how the SLP scaffolds production of various morphological and syntactic linguistic structures as a natural part of cocreating text with her students. The highly interactive nature of SIWI allows for targeting pragmatic language goals with student–student and student–SLP interactions. Students also have opportunities for practicing articulation when generating or revising ideas for the cocreated text and when rereading the text.

Conclusions:
SIWI provides a framework to address DHH students' speech and language goals within authentic writing activities that may support increased generalization into classroom academic tasks. We provide suggestions about how an SLP can incorporate the principles of SIWI into therapy sessions to integrate writing instruction with the various speech and language goals they already target as a part of implementing a student's Individualized Education Program.
An overview of power swing detection methods in distance relays and the factors involved
Authors: Taheri Behrooz , Hosseini Seyed Amir , Salehimehr Sirus 
Published: December 2022

AbstractNowadays, due to the simplicity of operation and proper coordination characteristics, distance relays are being extensively used in the protection of power transmission lines. Despite many advantages, the distance relay is exposed to a maloperation when a power swing phenomenon occurs. Power swings may occur due to major disturbances, such as switching lines, generator interruptions, and connecting or disconnecting a large part of the loads, causing outages in healthy lines. Detecting power swing and preventing distance relay maloperation has always been a challenge. In addition, different parameters can have a great impact on the performance of power swing detection methods. In this paper, these parameters and their effects are examined along with various methods for detecting power swings. Accordingly, this comprehensive review covers all aspects of power swing phenomenon and its detection, including causes of power swings, power swing detection methods, determining threshold values in power swing methods, effecting of compensated lines and wind farms in power swing detection methods, and testing power swing function in the distance relays. It is hoped that this study will be helpful for researchers in power system protection to find relevant references and develop new methods for power swing function.