bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic signatures of strawberry domestication and diversification
Authors: Fan Zhen , Whitaker Vance M 
Published: December 2023

Abstract
Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.
Cognitive reappraisal of food craving and emotions: a coordinate-based meta-analysis of fMRI studies
Authors: Gerosa Marta , Canessa Nicola , Morawetz Carmen , Mattavelli Giulia 
Published: December 2023

Abstract
Growing evidence supports the effectiveness of cognitive reappraisal in down-regulating food desire. Still, the neural bases of food craving down-regulation via reappraisal, as well as their degree of overlap vs specificity compared with emotion down-regulation, remain unclear. We addressed this gap through activation likelihood estimation meta-analyses of neuroimaging studies on the neural bases of (i) food craving down-regulation and (ii) emotion down-regulation, alongside conjunction and subtraction analyses among the resulting maps. Exploratory meta-analyses on activations related to food viewing compared with active regulation and up-regulation of food craving have also been performed. Food and emotion down-regulation via reappraisal consistently engaged overlapping activations in dorsolateral and ventrolateral prefrontal, posterior parietal, pre-supplementary motor and lateral posterior temporal cortices, mainly in the left hemisphere. Its distinctive association with the right anterior/posterior insula and left inferior frontal gyrus suggests that food craving down-regulation entails a more extensive integration of interoceptive information about bodily states and greater inhibitory control over the appetitive urge towards food compared with emotion down-regulation. This evidence is suggestive of unique interoceptive and motivational components elicited by food craving reappraisal, associated with distinctive patterns of fronto-insular activity. These results might inform theoretical models of food craving regulation and prompt novel therapeutic interventions for obesity and eating disorders.
EvoLaps 2: Advanced phylogeographic visualization
Authors: Chevenet F , Fargette D , Bastide P , Vitré T , Guindon S 
Published: December 2023

Abstract
EvoLaps is a user-friendly web application designed to visualize the spatial and temporal spread of pathogens. It takes an annotated tree as entry, such as a maximum clade credibility tree obtained through continuous phylogeographic inference. By following a ‘Top-Down’ reading of a tree recursively, transitions (latitude/longitude changes from a node to its children) are represented on a cartographic background using graphical paths. The complete set of paths forms the phylogeographic scenario. EvoLaps offers several features to analyze complex scenarios: (1) enhanced path display using multiple graphical variables with time-dependent gradients, (2) cross-highlighting and selection capabilities between the phylogeographic scenario and the phylogenetic tree, (3) production of specific spatio-temporal scales and synthetic views through dynamic and iterative clustering of localities into spatial clusters, (4) animation of the phylogeographic scenario using tree brushing, which can be done manually or automatically, gradually over time or at specific time intervals, and for the entire tree or a specific clade, and (5) an evolving library of additional tools. EvoLaps is freely available for use at evolaps.org.
Same But Different: An 18-Month Cross-Sectional Study of Cosmetic Procedures in Patients With Skin Phototype I–III Versus IV–VI in Toronto, Canada
Authors: Williams Stephen , McDonald Katherine A. , Beach Renée A. 
Published: December 2023

BACKGROUND
Patients with darker skin phototypes self-report less facial aging than their lighter-skinned counterparts. However, the association of skin phototype with the type of cosmetic procedures received, is yet to be established in a Canadian context.

OBJECTIVE
To compare the pattern of nonsurgical cosmetic procedures performed on people with different Fitzpatrick SPTs.

MATERIALS AND METHODS
Cross-sectional study of patient encounters from October 2020–April 2022. Charts and photographs were reviewed and analyzed for age, sex, SPT, and procedure type. Participants were stratified by SPT into 2 cohorts: SPT I–III and SPT IV–VI. SPTs were collapsed into groups based on definitions of “skin of color” (SPT IV–VI) in previous literature.

RESULTS
We analyzed 350 patients with mean age 43.4, of whom 320 (91%) were female and 30 (9%) were male. The SPT I–III cohort was older (mean age 45 vs 38.5 years, p < .0001) and more frequently underwent neuromodulator injection. The SPT IV–VI cohort more frequently underwent microneedling, platelet-rich plasma, or electrodessication.

CONCLUSION
There are distinct patterns of cosmetic procedures performed. The SPT I–III cohort more commonly received procedures to manage facial aging. The SPT IV–VI cohort was younger and more commonly underwent procedures to manage hyperpigmentation.
Impact of Prepectoral vs. Subpectoral Tissue Expander Placement on Post-mastectomy Radiation Therapy Delivery: A Retrospective Cohort Study
Authors: Copeland-Halperin Libby R. , Lyatskaya Yulia , Bellon Jennifer R. , Dey Tanujit , Carty Matthew J. , Barbie Thanh , Erdmann-Sager Jessica 
Published: December 2023

Background:
Implant-based reconstruction is the most common method of postmastectomy reconstruction. Many patients require postmastectomy radiation (PMRT). Tissue expanders (TEs), typically inserted as a first stage, have historically been placed subpectorally. More recently, prepectoral reconstruction has gained popularity, but its impact on PMRT is unknown. Prior studies focus on complication rates and aesthetic outcomes. This study examines whether there is a difference in radiation dosimetry among patients undergoing prepectoral versus subpectoral TE reconstruction.

Methods:
Electronic medical records and radiation plans of 50 patients (25 prepectoral, 25 subpectoral) who underwent mastectomy with immediate TE reconstruction at our institution or affiliate site were reviewed. Pectoralis major muscle and chest wall structures were contoured and mean percentage volumes of these structures receiving less than 95%, 100%, and more than 105% target radiation dose were calculated, as were heart and ipsilateral lung doses. Welch two sample t test, Fisher exact test, and Pearson chi-squared tests were performed.

Results:
The groups had comparable patient and tumor characteristics and underwent similar ablative and reconstructive procedures and radiation dosimetry. Subpectoral patients had larger mean areas receiving less than 95% target dose (“cold spots”); prepectoral patients had larger mean areas receiving greater than 105% (“hot spots”) and 100% target doses. There were no differences in chest wall, heart, and lung doses.

Conclusions:
Our results demonstrate an increased mean percentage area of pectoralis cold spots with subpectoral reconstruction and increased area of hot spots and 100% dose delivery to the pectoralis in prepectoral patients. Larger studies should analyze long-term effects of prepectoral reconstruction on radiation dosing and recurrence rates.
Free Flap Survival with External Jugular Vein as a Detour Due to Internal Jugular Vein Thrombosis
Authors: Sotsuka Yohei , Murakami Ayaka , Wakatsuki Hanako , Matsuda Ken 
Published: December 2023

Summary:
In head and neck reconstructions, venous anastomosis of the free flap to the internal jugular vein system is a common procedure. However, in some cases, postoperative complications such as internal jugular vein thrombosis can occur. In this report, we present a case where postoperative internal jugular vein thrombosis was identified after venous anastomosis of the free flap to the internal jugular vein system. In this case, preserving the external jugular vein allowed for retrograde flow of venous blood in the internal jugular vein to enter the external jugular vein, serving as an alternative drainage pathway. This finding highlights the potential benefits of preserving the external jugular vein in head and neck surgery involving free flap venous anastomosis to mitigate the adverse effects of internal jugular vein thrombosis. Further investigations are warranted to better understand the underlying mechanisms and optimize surgical approaches for improved patient outcomes.
Ensuring Intervention Fidelity of an Attention Control Arm in a Multisite Randomized Controlled Trial
Authors: Newman Amy R. , Moody Karen M. , Becktell Kerri , Connelly Erin , Holladay Cynthia , Parisio Katie , Powell Jonathan L. , Steineck Angela , Hendricks-Ferguson Verna L. 
Published: December 2023

Abstract

Background
Intervention fidelity is a critical element of randomized controlled trials, yet reporting of intervention fidelity among attention control arms is limited. Lack of fidelity to attention control procedures can affect study outcomes by either over- or underestimating the efficacy of the intervention under examination.

Objectives
This brief report describes the approach researchers took to promote fidelity to the attention control arm of a National Institutes of Health-funded pediatric palliative care randomized controlled trial.

Methods
The Informational Meetings for Planning and Coordinating Treatment trial aims to determine the efficacy of a communication intervention that uses care team dyads (i.e., physicians partnered with nurses or advanced practice providers) to engage parents of children with cancer that have a poor prognosis in structured conversations about prognostic information, goals of care, and care planning. The intervention is compared to an attention control arm, which provides parents with structured conversations on common pediatric cancer education topics, such as talking with their child about their cancer, clinical trials, cancer treatment, side effects, etc. National Institutes of Health guidelines for assessing and implementing strategies to promote intervention fidelity were used to design (a) the attention control arm of a randomized controlled trial, (b) related attention control arm training, and (c) quality assurance monitoring.

Results
Attention control study procedures were designed to mirror that of the intervention arm (i.e., same number, frequency, and time spent in study visits). Cluster randomization was used to allocate care team dyads to one arm of the randomized controlled trial. Care team dyads assigned to the attention control arm participated in online training sessions to learn attention control procedures, the different roles of research team members, and quality assurance methods. Fidelity to attention control procedures is assessed by both the interveners themselves and a quality assurance team.

Discussion
Study design, training, and delivery are all critical to attention control fidelity. Baseline training often needs to be supplemented with booster training when time gaps occur between study start-up and implementation. Quality assurance procedures are essential to determine whether interveners consistently deliver attention control procedures correctly.
Achieving Functional Goals during a Skilled Nursing Facility Stay: A National Study of Medicare Beneficiaries
Authors: Downer Brian , Wickliff Megan , Malagaris Ioannis , Li Chih-Ying , Lee Mi Jung 
Published: December 2023

Abstract

Objective
To describe the frequency that functional goals are documented on the Minimum Data Set (MDS) and identify resident characteristics associated with meeting or exceeding discharge goals.

Methods
We selected Medicare fee-for-service beneficiaries admitted to a skilled nursing facility (SNF) within three days of hospital discharge from 10/01/2018-12/31/2019 (n = 1,228,913). The admission MDS was used to describe the discharge goal scores for seven self-care and 16 mobility items. We used the eight self-care and mobility items originally included in a publicly reported quality measure to calculate total scores for discharge goals, admission performance, and discharge performance (n = 371,801).

Results
For all self-care items, over 70% of residents had a goal score of 1-6 points documented on the admission MDS. Chair/bed-to-chair transfer had the highest percentage of residents with a score of 1-6 points (77.1%) and walking up/down 12-steps had the lowest (23.2%). Approximately 44% of residents had a discharge performance score that met or exceeded their goal score. Older age, urinary incontinence, and cognitive impairment had the lowest odds of meeting or exceeding discharge goals.

Conclusions
Assessing a resident’s functional goals is important to providing patient-centered care. This information may help SNFs determine if a resident has made meaningful functional improvements.
The Efficacy of Different Exercises on Mild to Moderate Adolescent Idiopathic Scoliosis: A Systematic Review and Meta-analysis
Authors: Peng Cheng , Li Daxin , Guo Tianxiao , Li Shuairan , Chen Yonghui , Zhao Li , Mi Jing 
Published: December 2023

Abstract

Purpose
The aim of this study is to evaluate the effectiveness of different exercise interventions on patients with Adolescent Idiopathic Scoliosis (AIS) and provide evidence-based exercise prescriptions for this population.

Methods
The PubMed, Embase, The Cochrane Library, Web of Science, CNKI, Chinese Biomedical Literature Database (CBM), VIP, and Wanfang Data Knowledge Service Platform were searched until January 2023. The data were pooled and a meta-analysis was conducted.

Results
A total of 19 studies were conducted with 778 participants. The Schroth exercises group (MD = -3.48, 95% CI [-4.73, -2.23], P < 0.00001) and strength training group (MD = -3.43, 95% CI [-4.06, -2.80], P < 0.00001) had better recovery of the Cobb angle than the other groups. The Cobb angle rehabilitation effect was good in the time of less than 60 minutes group. Additionally, there was no significant difference found between the different intervention periods groups (P > 0.05).

Conclusion
Schroth exercise and strength training significantly improved Cobb angle of AIS patients; Exercising for less than 60 minutes is effective for Cobb angle rehabilitation, but prolonging exercise time cannot improve training effectiveness; 12 weeks of exercise significantly improved Cobb angle, but prolonged training periods did not have a significant impact.
A maternal germline mutator phenotype in a family affected by heritable colorectal cancer
Authors: Young Candice L. , Beichman Annabel C. , Mas-Ponte David , Hemker Shelby L. , Zhu Luke , Kitzman Jacob O. , Shirts Brian H. , Harris Kelley 
Published: December 2023

AbstractVariation in DNA repair genes can increase cancer risk by elevating the rate of oncogenic mutation. Defects in one such gene,MUTYH, are known to elevate the incidence of colorectal cancer in a recessive Mendelian manner. Recent evidence has also linkedMUTYHto a mutator phenotype affecting normal somatic cells as well as the female germline. Here, we use whole genome sequencing to measure germline de novo mutation rates in a large extended family containing both mothers and fathers who are affected by pathogenicMUTYHvariation. By developing novel methodology that uses siblings as “surrogate parents” to identify de novo mutations, we were able to include mutation data from several children whose parents were unavailable for sequencing. In the children of mothers affected by the pathogenicMUTYHgenotype p.Y179C/V234M, we identify an elevation of the C>A mutation rate that is weaker than mutator effects previously reported to be caused by other pathogenicMUTYHgenotypes, suggesting that mutation rates in normal tissues may be useful for classifying cancer-associated variation along a continuum of severity. Surprisingly, we detect no significant elevation of the C>A mutation rate in children born to a father with the sameMUTYHgenotype, and we similarly find that the mutator effect of the mouse homologMutyhappears to be localized to embryonic development, not the spermatocytes. Our results suggest that maternalMUTYHvariants can cause germline mutations by attenuating the repair of oxidative DNA damage in the early embryo.
Machine learning of brain-specific biomarkers from EEG
Authors: Bomatter Philipp , Paillard Joseph , Garces Pilar , Hipp Jörg , Engemann Denis 
Published: December 2023

AbstractElectroencephalography (EEG) has a long history as a clinical tool to study brain function, and its potential to derive biomarkers for various applications is far from exhausted. Machine learning (ML) can guide future innovation by harnessing the wealth of complex EEG signals to isolate relevant brain activity. Yet, ML studies in EEG tend to ignore physiological artifacts, which may cause problems for deriving biomarkers specific to the central nervous system (CNS). We present a framework for conceptualizing machine learning from CNS versus peripheral signals measured with EEG. A common signal representation across the frequency spectrum based on Morlet wavelets allowed us to define traditional brain activity features (e.g. log power) and alternative inputs used by state-of-the-art ML approaches (covariance matrices). Using more than 2600 EEG recordings from large public databases (TUAB, TDBRAIN), we studied the impact of peripheral signals and artifact removal techniques on ML models in exemplary age and sex prediction analyses. Across benchmarks, basic artifact rejection improved model performance whereas further removal of peripheral signals using ICA decreased performance. Our analyses revealed that peripheral signals enable age and sex prediction. However, they explained only a fraction of the performance provided by brain signals. We show that brain signals and body signals, both reflected in the EEG, allow for prediction of personal characteristics. While these results may depend on specific prediction problems, our work suggests that great care is needed to separate these signals when the goal is to develop CNS-specific biomarkers using ML.
Conformational sampling and interpolation using language-based protein folding neural networks
Authors: del Alamo Diego , Jeliazkov Jeliazko R. , Truan Daphné , Karpiak Joel D. 
Published: December 2023

AbstractProtein language models (PLMs), such ESM2, learn a rich semantic grammar of the protein sequence space. When coupled to protein folding neural networks (e.g., ESMFold), they can facilitate the prediction of tertiary and quaternary protein structures at high accuracy. However, they are limited to modeling protein structures in single states. This manuscript demonstrates that ESMFold can predict alternate conformations of some proteins, includingde novodesigned proteins. Randomly masking the sequence prior to PLM input returned alternate embeddings that ESMFold sometimes mapped to distinct physiologically relevant conformations. From there, inversion of the ESMFold trunk facilitated the generation of high-confidence interconversion paths between the two states. These paths provide a deeper glimpse of how language-based protein folding neural networks derive structural information from high-dimensional sequence representations, while exposing limitations in their general understanding of protein structure and folding.
Mitochondrial thermogenesis regulates heat-shock response in the nucleus
Authors: Lee Hee Yong , Kim Hwa-Ryeon , Kwak Chulhwan , Kang Myeong-Gyun , Roe Jae-Seok , Rhee Hyun-Woo 
Published: December 2023

AbstractMitochondrial thermogenesis is a process in which heat is generated by mitochondrial respiration. In living organisms, the thermogenic mechanisms that maintain body temperature have been studied extensively in fat cells, with little knowledge on how mitochondrial heat may act beyond energy expenditure. Here, we highlighted exothermic oxygen reduction reaction (ΔHf° = -285 kJ/mol) is the main source of the protonophore-induced mitochondrial thermogenesis and this heat was conducted to other cellular organelles, including the nuclei. As a result, mitochondrial heat that reached the nucleus initiated the classical heat shock response, including the formation of nuclear stress granules and localization of heat shock factor 1 to chromatin. Consequently, activated HSF1 increases gene expression associated with the response to thermal stress in mammalian cells. Our results illustrate heat generated within the cells as a potential source of mitochondrial-nucleus communication and expand our understanding of the biological functions of mitochondria in cell physiology.
Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis
Authors: Zheng Chao , Hervé Bastien , Meijer Mandy , Rubio Rodríguez-Kirby Leslie Ann , Guerreiro Cacais André Ortlieb , Kukanja Petra , Kabbe Mukund , Olsson Tomas , Agirre Eneritz , Castelo-Branco Gonçalo 
Published: December 2023

AbstractMultiple sclerosis (MS) is a chronic demyelinating autoimmune disease that targets mature oligodendrocytes(MOLs) and their myelin. MOLs are transcriptionally heterogeneous and can transition to immune-like states in the context of MS. However, the intricacies of their dynamics throughout disease progression remain poorly understood. Here, we employed simultaneous single-cell multiome ATAC and RNA sequencing targeting oligodendroglia (OLGs) from the experimental autoimmune encephalomyelitis (EAE) MS mouse model at different stages of the disease course. We found that the transition to immune OLG states appear already at the early stages of EAE and persist to the late stages of the disease. Interestingly, transcription factor activity suggested immunosuppression in MOLs at early stages of EAE and we also observed a transitory activation of a regenerative program in MOLs at this stage. Importantly, different MOLs exhibit a differential responsiveness to EAE, with MOL2 exhibiting a stronger transcriptional immune response than MOL5/6. Moreover, we observed divergent responses at the epigenetic level of MOL2 and MOL5/6 during disease evolution. Thus, our single-cell multiomic resource highlights dynamic and distinct responses of OLG subpopulations to the evolving environment in EAE, which might modulate their response to regenerative therapeutic interventions in MS.