bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apomixis and the paradox of sex in plants
Authors: Hörandl Elvira 
Published: March 2024

Abstract

Background
The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species.

Scope
This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies.

Conclusions
Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis–syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle–nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.
Does stomatal patterning in amphistomatous leaves minimize the CO2 diffusion path length within leaves?
Authors: Watts Jacob L , Dow Graham J , Buckley Thomas N , Muir Christopher D 
Published: March 2024

Abstract
Photosynthesis is co-limited by multiple factors depending on the plant and its environment. These include biochemical rate limitations, internal and external water potentials, temperature, irradiance and carbon dioxide ( CO2). Amphistomatous leaves have stomata on both abaxial and adaxial leaf surfaces. This feature is considered an adaptation to alleviate CO2 diffusion limitations in productive environments as the diffusion path length from stomate to chloroplast is effectively halved in amphistomatous leaves. Plants may also reduce CO2 limitations through other aspects of optimal stomatal anatomy: stomatal density, distribution, patterning and size. Some studies have demonstrated that stomata are overdispersed compared to a random distribution on a single leaf surface; however, despite their prevalence in nature and near ubiquity among crop species, much less is known about stomatal anatomy in amphistomatous leaves, especially the coordination between leaf surfaces. Here, we use novel spatial statistics based on simulations and photosynthesis modelling to test hypotheses about how amphistomatous plants may optimize CO2 diffusion in the model angiosperm Arabidopsis thaliana grown in different light environments. We find that (i) stomata are overdispersed, but not ideally dispersed, on both leaf surfaces across all light treatments; (ii) the patterning of stomata on abaxial and adaxial leaf surfaces is independent and (iii) the theoretical improvements to photosynthesis from abaxial–adaxial stomatal coordination are miniscule (≪1%) across the range of feasible parameter space. However, we also find that (iv) stomatal size is correlated with the mesophyll volume that it supplies with CO2, suggesting that plants may optimize CO2 diffusion limitations through alternative pathways other than ideal, uniform stomatal spacing. We discuss the developmental, physical and evolutionary constraints that may prohibit plants from reaching this theoretical adaptive peak of uniform stomatal spacing and inter-surface stomatal coordination. These findings contribute to our understanding of variation in the anatomy of amphistomatous leaves.
Complications and Risks Associated With the Different Types of Abdominoplasties: An Analysis of 55,956 Patients
Authors: Chaker Sara C , Hung Ya-Ching , Saad Mariam , Perdikis Galen , Grotting James C , Higdon K Kye 
Published: March 2024

Abstract

Background
Different types of abdominoplasties have been developed to address individual patient characteristics. However, an analysis of complication rates and risk factors for different types of abdominoplasties has yet to be reported.

Objectives
The aim of this study was to evaluate the complication rates and risks associated with each type of abdominoplasty.

Methods
Utilizing the CosmetAssure database, patients undergoing an abdominoplasty from 2015 to 2022 were identified. Demographic factors and major complications were recorded and analyzed with a chi-square test or analysis of variance. A logistic regression was performed to identify the risk for developing complications associated with each type of abdominoplasty.

Results
A total of 55,596 patients underwent an abdominoplasty procedure by any method. The overall complication rate was 2.1%. There was a significant difference in the overall complication rates of all 7 types of abdominoplasties (P &lt; .05), with fleur-de-lis abdominoplasty having the highest complication rate. The year of surgery, being underweight or morbidly obese, having diabetes, and being male placed patients at a significantly higher risk for developing a postoperative complication. Over 15,000 patients (27.2%) had concurrent procedures related to breast surgery, other body contouring, liposuction, or facial surgery. When accounting for various risk factors in a regression model, there was no significant added risk for major complications after a combination procedure with an abdominoplasty compared to abdominoplasty alone.

Conclusions
Among the different types of abdominoplasties, a fleur-de-lis abdominoplasty has the highest complication rate. Concurrent cosmetic procedures with an abdominoplasty showed no added risk for major complications when compared to abdominoplasty alone.

Level of Evidence: 3
CLAUDIO: automated structural analysis of cross-linking data
Authors: Röhl Alexander , Netz Eugen , Kohlbacher Oliver , Elhabashy Hadeer 
Published: March 2024

Abstract

Motivation
Cross-linking mass spectrometry has made remarkable advancements in the high-throughput characterization of protein structures and interactions. The resulting pairs of cross-linked peptides typically require geometric assessment and validation, given the availability of their corresponding structures.

Results
CLAUDIO (Cross-linking Analysis Using Distances and Overlaps) is an open-source software tool designed for the automated analysis and validation of different varieties of large-scale cross-linking experiments. Many of the otherwise manual processes for structural validation (i.e. structure retrieval and mapping) are performed fully automatically to simplify and accelerate the data interpretation process. In addition, CLAUDIO has the ability to remap intra-protein links as inter-protein links and discover evidence for homo-multimers.

Availability and implementation
CLAUDIO is available as open-source software under the MIT license at https://github.com/KohlbacherLab/CLAUDIO.
Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction
Authors: Sun Saisai , Gao Lin 
Published: March 2024

Abstract

Motivation
The diverse structures and functions inherent in RNAs present a wealth of potential drug targets. Some small molecules are anticipated to serve as leading compounds, providing guidance for the development of novel RNA-targeted therapeutics. Consequently, the determination of RNA–small molecule binding affinity is a critical undertaking in the landscape of RNA-targeted drug discovery and development. Nevertheless, to date, only one computational method for RNA–small molecule binding affinity prediction has been proposed. The prediction of RNA–small molecule binding affinity remains a significant challenge. The development of a computational model is deemed essential to effectively extract relevant features and predict RNA–small molecule binding affinity accurately.

Results
In this study, we introduced RLaffinity, a novel deep learning model designed for the prediction of RNA–small molecule binding affinity based on 3D structures. RLaffinity integrated information from RNA pockets and small molecules, utilizing a 3D convolutional neural network (3D-CNN) coupled with a contrastive learning-based self-supervised pre-training model. To the best of our knowledge, RLaffinity was the first deep learning based method for the prediction of RNA–small molecule binding affinity. Our experimental results exhibited RLaffinity’s superior performance compared to baseline methods, revealed by all metrics. The efficacy of RLaffinity underscores the capability of 3D-CNN to accurately extract both global pocket information and local neighbor nucleotide information within RNAs. Notably, the integration of a self-supervised pre-training model significantly enhanced predictive performance. Ultimately, RLaffinity was also proved as a potential tool for RNA-targeted drugs virtual screening.

Availability and implementation
https://github.com/SaisaiSun/RLaffinity
TemStaPro: protein thermostability prediction using sequence representations from protein language models
Authors: Pudžiuvelytė Ieva , Olechnovič Kliment , Godliauskaite Egle , Sermokas Kristupas , Urbaitis Tomas , Gasiunas Giedrius , Kazlauskas Darius 
Published: March 2024

Abstract

Motivation
Reliable prediction of protein thermostability from its sequence is valuable for both academic and industrial research. This prediction problem can be tackled using machine learning and by taking advantage of the recent blossoming of deep learning methods for sequence analysis. These methods can facilitate training on more data and, possibly, enable the development of more versatile thermostability predictors for multiple ranges of temperatures.

Results
We applied the principle of transfer learning to predict protein thermostability using embeddings generated by protein language models (pLMs) from an input protein sequence. We used large pLMs that were pre-trained on hundreds of millions of known sequences. The embeddings from such models allowed us to efficiently train and validate a high-performing prediction method using over one million sequences that we collected from organisms with annotated growth temperatures. Our method, TemStaPro (Temperatures of Stability for Proteins), was used to predict thermostability of CRISPR-Cas Class II effector proteins (C2EPs). Predictions indicated sharp differences among groups of C2EPs in terms of thermostability and were largely in tune with previously published and our newly obtained experimental data.

Availability and implementation
TemStaPro software and the related data are freely available from https://github.com/ievapudz/TemStaPro and https://doi.org/10.5281/zenodo.7743637.
Unmasked and Exposed: The Impact of COVID-19 on the Youth Custodial Estate. A Compelling Case for Ideological Change
Authors: Smithson Hannah , Jump Deborah 
Published: March 2024

Abstract
The impact of the COVID-19 pandemic on custodial institutions has been the subject of intense scrutiny. During the pandemic, many international jurisdictions failed to develop clear and child-focussed plans for the management of children in custody, instead relying on strategies developed for adult populations. Presenting the findings from the United Kingdom’s (England Wales) first empirical in-depth exploration of the impacts of COVID-19 on children at each stage of the Youth Justice System, this article discusses the devastating effect on incarcerated children. The pandemic exacerbated existing failures in the children’s secure estate, eradicated children’s rights and exposed children to increased vulnerabilities. We present an urgent need for a fundamental ideological reconsideration of the purpose of custody for children.
Monopolar diathermy versus a vessel-sealing device for reducing postoperative drain output after simple mastectomy: randomized clinical trial
Authors: Keelan Stephen , Dowling Gavin P , Roche Trudi , Hegarty Aisling , Davey Matthew G , Dhannoon Amenah A , O’Grady Sorcha , Downey Eithne , Bolger Jarlath , Boland Michael , Sorensen Jan , Power Colm , Butt Abeeda , Baban Chwanrow , Hill Arnold D K 
Published: March 2024

Abstract

Background
Electrosurgical devices are commonly used during mastectomy for simultaneous dissection and haemostasis, and can provide potential benefits regarding vessel and lymphatic ligation. The aim of this prospective RCT was to assess whether using a vessel-sealing device (LigaSure™) improves perioperative outcomes compared with monopolar diathermy when performing simple mastectomy.

Methods
Patients were recruited prospectively and randomized in a 1 : 1 manner to undergo simple mastectomy using either LigaSure™ or conventional monopolar diathermy at a single centre. The primary outcome was the number of days the drain remained in situ after surgery. Secondary outcomes of interest included operating time and complications.

Results
A total of 86 patients were recruited (42 were randomized to the monopolar diathermy group and 44 were randomized to the LigaSure™ group). There was no significant difference in the mean number of days the drain remained in situ between the monopolar diathermy group and the LigaSure™ group (7.75 days versus 8.23 days; P = 0.613) and there was no significant difference in the mean total drain output between the monopolar diathermy group and the LigaSure™ group (523.50 ml versus 572.80 ml; P = 0.694). In addition, there was no significant difference in the mean operating time between the groups, for simple mastectomy alone (88.25 min for the monopolar diathermy group versus 107.20 min for the LigaSure™ group; P = 0.078) and simple mastectomy with sentinel lymph node biopsy (107.20 min for the monopolar diathermy group versus 114.40 min for the LigaSure™ group; P = 0.440).

Conclusion
In this double-blinded single-centre RCT, there was no difference in the total drain output or the number of days the drain remained in situ between the monopolar diathermy group and the LigaSure™ group.

Registration number
EudraCT 2018-003191-13 BEAUMONT HOSPITAL REC 18/66.
O77: Invasive intraductal oncocytic papillary neoplasms (IOPN) and adenocarcinomas arising from Intraductal papillary mucinous neoplasms (IPMN): adjuvant chemotherapy, patterns of recurrence and survival
Authors: Lucocq James ,   Adeno-IPMN Collaborative, Pandanaboyana Sanjay 
Published: March 2024

Abstract

Introduction
Invasive intraductal oncocytic papillary neoplasms (IOPNs) are extremely rare and are increasingly being recognised as their own entity, distinct from intraductal papilliary mucinous neoplasism subtypes (IPMN). Their clinicopathologic behaviour, recurrence patterns, response to adjuvant chemotherapy and long-term survival outcomes are unknown compared to adenocarcinomas arising from IPMN but were investigated in the present study.

Methods
Patients undergoing pancreatic resection between 2010-2020 for invasive IOPNs and adenocarcinoma arising from IPMNs were identified retrospectively from 18 academic pancreatic centers worldwide. Survival analyses were conducted to compare outcome measures between IOPNs and IPMN precursor epithelial subtypes and invasive components.

Results
Of the 459 patients with invasive IOPN/IPMNs, 20 patients had an invasive IOPN (median age,69; male,n=11), the majority of which were in the pancreatic head (75%) and underwent either a Whipples procedure (40%) or PPPD (35%). After a median follow-up of 6 years, 45% of invasive IOPNs developed recurrence (1-year,30.0%; 5-year,69.2%) and 40% survived follow-up (2-year survival 55.0%, 5-year survival, 30.8%). Recurrence rates and survival of invasive IOPNs were higher than colloid IPMNs (n=64) (p=0.031 and p=0.007) and comparable with ductal IPMNs (n=331) as well as gastric (n=54) and pancreatobiliary (n=111) IPMN subtypes. Invasive IOPN had significantly lower cancer-specific survival compared to colloid carcinomas (p&lt;0.001). Adjuvant chemotherapy did not improve rates of recurrence in invasive IOPN and IPMN subtypes (p&gt;0.05).

Conclusions
Invasive IOPNs are more aggressive than previously suspected and should be regarded as their own entity. Adjuvant chemotherapy does not reduce rates of recurrence regardless of neoplasm type.
Dynamic nonreversibility view of intrinsic brain organization and brain dynamic analysis of repetitive transcranial magnitude stimulation
Authors: Fan Liming , Li Youjun , Zhao Xingjian , Huang Zi-gang , Liu Tian , Wang Jue 
Published: March 2024

Abstract
Intrinsic neural activities are characterized as endless spontaneous fluctuation over multiple time scales. However, how the intrinsic brain organization changes over time under local perturbation remains an open question. By means of statistical physics, we proposed an approach to capture whole-brain dynamics based on estimating time-varying nonreversibility and k-means clustering of dynamic varying nonreversibility patterns. We first used synthetic fMRI to investigate the effects of window parameters on the temporal variability of varying nonreversibility. Second, using real test–retest fMRI data, we examined the reproducibility, reliability, biological, and physiological correlation of the varying nonreversibility substates. Finally, using repetitive transcranial magnetic stimulation–fMRI data, we investigated the modulation effects of repetitive transcranial magnetic stimulation on varying nonreversibility substate dynamics. The results show that: (i) as window length increased, the varying nonreversibility variance decreased, while the sliding step almost did not alter it; (ii) the global high varying nonreversibility states and low varying nonreversibility states were reproducible across multiple datasets and different window lengths; and (iii) there were increased low varying nonreversibility states and decreased high varying nonreversibility states when the left frontal lobe was stimulated, but not the occipital lobe. Taken together, these results provide a thermodynamic equilibrium perspective of intrinsic brain organization and reorganization under local perturbation.
Prediction of image interpretation cognitive ability under different mental workloads: a task-state fMRI study
Authors: Li Bao , Tong Li , Zhang Chi , Chen Panpan , Wang Linyuan , Yan Bin 
Published: March 2024

AbstractVisual imaging experts play an important role in multiple fields, and studies have shown that the combination of functional magnetic resonance imaging and machine learning techniques can predict cognitive abilities, which provides a possible method for selecting individuals with excellent image interpretation skills. We recorded behavioral data and neural activity of 64 participants during image interpretation tasks under different workloads. Based on the comprehensive image interpretation ability, participants were divided into two groups. general linear model analysis showed that during image interpretation tasks, the high-ability group exhibited higher activation in middle frontal gyrus (MFG), fusiform gyrus, inferior occipital gyrus, superior parietal gyrus, inferior parietal gyrus, and insula compared to the low-ability group. The radial basis function Support Vector Machine (SVM) algorithm shows the most excellent performance in predicting participants’ image interpretation abilities (Pearson correlation coefficient = 0.54, R2 = 0.31, MSE = 0.039, RMSE = 0.002). Variable importance analysis indicated that the activation features of the fusiform gyrus and MFG played an important role in predicting this ability. Our study revealed the neural basis related to image interpretation ability when exposed to different mental workloads. Additionally, our results demonstrated the efficacy of machine learning algorithms in extracting neural activation features to predict such ability.
In the face of ambiguity: intrinsic brain organization in development predicts one’s bias toward positivity or negativity
Authors: Harp Nicholas R , Nielsen Ashley N , Schultz Douglas H , Neta Maital 
Published: March 2024

Abstract
Exacerbated negativity bias, including in responses to ambiguity, represents a common phenotype of internalizing disorders. Individuals differ in their propensity toward positive or negative appraisals of ambiguity. This variability constitutes one’s valence bias, a stable construct linked to mental health. Evidence suggests an initial negativity in response to ambiguity that updates via regulatory processes to support a more positive bias. Previous work implicates the amygdala and prefrontal cortex, and regions of the cingulo-opercular system, in this regulatory process. Nonetheless, the neurodevelopmental origins of valence bias remain unclear. The current study tests whether intrinsic brain organization predicts valence bias among 119 children and adolescents (6 to 17 years). Using whole-brain resting-state functional connectivity, a machine-learning model predicted valence bias (r = 0.20, P = 0.03), as did a model restricted to amygdala and cingulo-opercular system features (r = 0.19, P = 0.04). Disrupting connectivity revealed additional intra-system (e.g. fronto-parietal) and inter-system (e.g. amygdala to cingulo-opercular) connectivity important for prediction. The results highlight top–down control systems and bottom–up perceptual processes that influence valence bias in development. Thus, intrinsic brain organization informs the neurodevelopmental origins of valence bias, and directs future work aimed at explicating related internalizing symptomology.
Effect of Exercise Training on Prognosis in Community-acquired Pneumonia: A Randomized Controlled Trial
Authors: Ryrsø Camilla Koch , Faurholt-Jepsen Daniel , Ritz Christian , Hegelund Maria Hein , Dungu Arnold Matovu , Pedersen Bente Klarlund , Krogh-Madsen Rikke , Lindegaard Birgitte 
Published: March 2024

Abstract

Objective
To investigate the effect of standard care (SoC) combined with supervised in-bed cycling (Bed-Cycle) or booklet exercises (Book-Exe) versus SoC in community-acquired pneumonia (CAP).

Methods
In this randomized controlled trial, 186 patients with CAP were assigned to SoC (n = 62), Bed-Cycle (n = 61), or Book-Exe (n = 63). Primary outcome length of stay (LOS) was analyzed with analysis of covariance. Secondary outcomes, 90-day readmission, and 180-day mortality were analyzed with Cox proportional hazard regression and readmission days with negative-binominal regression.

Results
LOS was −2% (95% CI: −24 to 25) and −1% (95% CI: −22 to 27) for Bed-Cycle and Book-Exe, compared with SoC. Ninety-day readmission was 35.6% for SoC, 27.6% for Bed-Cycle, and 21.3% for Book-Exe. Adjusted hazard ratio (aHR) for 90-day readmission was 0.63 (95% CI: .33–1.21) and 0.54 (95% CI: .27–1.08) for Bed-Cycle and Book-Exe compared with SoC. aHR for 90-day readmission for combined exercise was 0.59 (95% CI: .33–1.03) compared with SoC. aHR for 180-day mortality was 0.84 (95% CI: .27–2.60) and 0.82 (95% CI: .26–2.55) for Bed-Cycle and Book-Exe compared with SoC. Number of readmission days was 226 for SoC, 161 for Bed-Cycle, and 179 for Book-Exe. Incidence rate ratio for readmission days was 0.73 (95% CI: .48–1.10) and 0.77 (95% CI: .51–1.15) for Bed-Cycle and Book-Exe compared with SoC.

Conclusions
Although supervised exercise training during admission with CAP did not reduce LOS or mortality, this trial suggests its potential to reduce readmission risk and number of readmission days.

Clinical Trials Registration
NCT04094636.