bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Aesthetic Surgery Education and Research Foundation (ASERF): A 30-Year Retrospective Analysis
Authors: Gryskiewicz Joe , Slavin Blaire V , Slavin Benjamin R , Nayak Vasudev Vivekanand , Pierrot Randall G , Taghioff Susan M , Alameddine Khaled O , Singh Devinder , Chopra Karan , Coelho Paulo G 
Published: January 2024

Abstract
Federal government research grants provide limited funding to plastic surgeon-scientists, with reconstructive research taking precedence over aesthetic research. The Aesthetic Surgery Education and Research Foundation (ASERF) is a nonprofit, 501(c)(3) organization that seeks to support innovative, diverse research endeavors within aesthetic surgery. A total of 130 ASERF-funded studies and 32 non-funded applications from 1992 to 2022 were reviewed. Kruskal Wallis, Fisher's exact, and chi-squared tests were utilized to assess the potential relationship between self-identified gender, practice setting, geographical location, and study type with individual grant amounts and grant funding decision. Although significant differences were observed between male and female grant recipient h-indices (P &lt; .05), there were no differences in the amount of funding they received (P &gt; .05). Grant amounts were also consistent between study types as well as principal investigator practice settings and geographical locations (P &gt; .05). The subanalysis revealed that the practice setting of the primary investigator (PI) was the only variable to exhibit a significant association with the decision to award funding (P &lt; .05). Further, of the 61 applicants between 2017 and 2022, only 2 PIs self-identified as female. ASERF serves as an excellent funding source for global aesthetic surgery. To promote further research diversification, increased emphasis should be placed on recruiting applicants from outside academia and those who identify as female or gender nonbinary.
Pathway analysis through mutual information
Authors: Jeuken Gustavo S , Käll Lukas 
Published: January 2024

Abstract

Motivation
In pathway analysis, we aim to establish a connection between the activity of a particular biological pathway and a difference in phenotype. There are many available methods to perform pathway analysis, many of them rely on an upstream differential expression analysis, and many model the relations between the abundances of the analytes in a pathway as linear relationships.

Results
Here, we propose a new method for pathway analysis, MIPath, that relies on information theoretical principles and, therefore, does not model the association between pathway activity and phenotype, resulting in relatively few assumptions. For this, we construct a graph of the data points for each pathway using a nearest-neighbor approach and score the association between the structure of this graph and the phenotype of these same samples using Mutual Information while adjusting for the effects of random chance in each score. The initial nearest neighbor approach evades individual gene-level comparisons, hence making the method scalable and less vulnerable to missing values. These properties make our method particularly useful for single-cell data. We benchmarked our method on several single-cell datasets, comparing it to established and new methods, and found that it produces robust, reproducible, and meaningful scores.

Availability and implementation
Source code is available at https://github.com/statisticalbiotechnology/mipath, or through Python Package Index as “mipathway.”
GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks
Authors: Weidner Felix M , Ikonomi Nensi , Werle Silke D , Schwab Julian D , Kestler Hans A 
Published: January 2024

Abstract

Motivation
Boolean networks can serve as straightforward models for understanding processes such as gene regulation, and employing logical rules. These rules can either be derived from existing literature or by data-driven approaches. However, in the context of large networks, the exhaustive search for intervention targets becomes challenging due to the exponential expansion of a Boolean network’s state space and the multitude of potential target candidates, along with their various combinations. Instead, we can employ the logical rules and resultant interaction graph as a means to identify targets of specific interest within larger-scale models. This approach not only facilitates the screening process but also serves as a preliminary filtering step, enabling the focused investigation of candidates that hold promise for more profound dynamic analysis. However, applying this method requires a working knowledge of R, thus restricting the range of potential users. We, therefore, aim to provide an application that makes this method accessible to a broader scientific community.

Results
Here, we introduce GatekeepR, a graphical, web-based R Shiny application that enables scientists to screen Boolean network models for possible intervention targets whose perturbation is likely to have a large impact on the system’s dynamics. This application does not require a local installation or knowledge of R and provides the suggested targets along with additional network information and visualizations in an intuitive, easy-to-use manner. The Supplementary Material describes the underlying method for identifying these nodes along with an example application in a network modeling pancreatic cancer.

Availability and implementation
https://www.github.com/sysbio-bioinf/GatekeepR https://abel.informatik.uni-ulm.de/shiny/GatekeepR/.
Commercially available artificial intelligence tools for fracture detection: the evidence
Authors: Pauling Cato , Kanber Baris , Arthurs Owen J , Shelmerdine Susan C 
Published: January 2024

Abstract
Missed fractures are a costly healthcare issue, not only negatively impacting patient lives, leading to potential long-term disability and time off work, but also responsible for high medicolegal disbursements that could otherwise be used to improve other healthcare services. When fractures are overlooked in children, they are particularly concerning as opportunities for safeguarding may be missed. Assistance from artificial intelligence (AI) in interpreting medical images may offer a possible solution for improving patient care, and several commercial AI tools are now available for radiology workflow implementation. However, information regarding their development, evidence for performance and validation as well as the intended target population is not always clear, but vital when evaluating a potential AI solution for implementation. In this article, we review the range of available products utilizing AI for fracture detection (in both adults and children) and summarize the evidence, or lack thereof, behind their performance. This will allow others to make better informed decisions when deciding which product to procure for their specific clinical requirements.
Body weight-based iodinated contrast immersion timing for human fetal postmortem microfocus computed tomography
Authors: Simcock Ian C , Shelmerdine Susan C , Hutchinson John Ciaran , Sebire Neil J , Arthurs Owen J 
Published: January 2024

Abstract

Objectives
The aim of this study was to evaluate the length of time required to achieve full iodination using potassium tri-iodide as a contrast agent, prior to human fetal postmortem microfocus computed tomography (micro-CT) imaging.

Methods
Prospective assessment of optimal contrast iodination was conducted across 157 human fetuses (postmortem weight range 2-298 g; gestational age range 12-37 weeks), following micro-CT imaging. Simple linear regression was conducted to analyse which fetal demographic factors could produce the most accurate estimate for optimal iodination time.

Results
Postmortem body weight (r2 = 0.6435) was better correlated with iodination time than gestational age (r2 = 0.1384), producing a line of best fit, y = [0.0304 × body weight (g)] − 2.2103. This can be simplified for clinical use whereby immersion time (days) = [0.03 × body weight (g)] − 2.2. Using this formula, for example, a 100-g fetus would take 5.2 days to reach optimal contrast enhancement.

Conclusions
The simplified equation can now be used to provide estimation times for fetal contrast preparation time prior to micro-CT imaging and can be used to manage service throughput and parental expectation for return of their fetus.

Advances in knowledge
A simple equation from empirical data can now be used to estimate preparation time for human fetal postmortem micro-CT imaging.
The CT knee arthrogram revisited
Authors: Chatra Priyank 
Published: January 2024

Abstract
The CT arthrogram is an underrated diagnostic study of the joint. Although MRI is considered superior to CT in joint imaging due to its higher resolution, CT arthrograms provide unique insights into the knee joint, with simultaneous dynamic assessment and an option for management in some conditions. In this pictorial essay, I will discuss the standard techniques and various pathologies affecting the knee joint and their CT arthrography appearance.
Outreach Work in ‘Hard-to-Reach’ Communities: A Critical Analysis of Task Shifting, Contact Making, Establishing Credibility and on-the-Spot, Solution-Focused Assistance
Authors: Gonzalez Benson Odessa , Magan Ifrah Mahamud , Yu Melanie 
Published: January 2024

Abstract
Outreach—the opening up of access to social services, information and opportunities—is arguably a crucial yet understudied aspect of social work practice. This study revisits ‘outreach’ as concept, using data from ‘hard to reach’ communities, specifically refugees. Our findings illuminate ‘task-shifting’, whereby professional service providers sought the help of grassroots community leaders in reaching refugees. Findings also point to issues of bidirectionality, credibility and on-the-spot assistance as aspects of outreach work. Theoretically, we apply a structural lens to problematise ‘access’ as an individual level concept, and instead turn attention to the ‘inaccessibility’ of services instead. We problematise the ‘hard-to-reachness’ of communities, and call instead for examining our services and institutions for their limited reach.
Network dynamics underlying alterations in apparent object size
Authors: Chen Lihong , Wu Baoyu , Yu Haoyang , Sperandio Irene 
Published: January 2024

Abstract
A target circle surrounded by small circles looks larger than an identical circle surrounded by large circles (termed as the Ebbinghaus illusion). While previous research has shown that both early and high-level visual regions are involved in the generation of the illusion, it remains unclear how these regions work together to modulate the illusion effect. Here, we used functional MRI and dynamic causal modelling to investigate the neural networks underlying the illusion in conditions where the focus of attention was manipulated via participants directing their attention to and maintain fixation on only one of the two illusory configurations at a time. Behavioural findings confirmed the presence of the illusion. Accordingly, functional MRI activity in the extrastriate cortex accounted for the illusory effects: apparently larger circles elicited greater activation than apparently smaller circles. Interestingly, this spread of activity for size overestimation was accompanied by a decrease in the inhibitory self-connection in the extrastriate region, and an increase in the feedback connectivity from the precuneus to the extrastriate region. These findings demonstrate that the representation of apparent object size relies on feedback projections from higher- to lower-level visual areas, highlighting the crucial role of top-down signals in conscious visual perception.
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation
Authors: Wang Kai , Perera Bambarendage P U , Morgan Rachel K , Sala-Hamrick Kimberley , Geron Viviana , Svoboda Laurie K , Faulk Christopher , Dolinoy Dana C , Sartor Maureen A 
Published: January 2024

Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2ʹ-O-methylation signature at the 3ʹ end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and while overall expression was lower than that of the germline, unique characteristics suggested tissue-specific functions of this class. While currently available databases commonly use length and association with PIWI proteins to identify piRNA, few have included a chemical oxidation method that detects piRNA based on its 3ʹ modification. This method leads to reproducible and rigorous data processing when coupled with next-generation sequencing and bioinformatics analysis. Here, we introduce piOxi DB, a user-friendly web resource that provides a comprehensive analysis of piRNA, generated exclusively through sodium periodate treatment of small RNA. The current version of piOxi DB includes 435 749 germline and 9828 somatic piRNA sequences robustly identified from M. musculus, M. fascicularis and H. sapiens. The database provides species- and tissue-specific data that are further analyzed according to chromosome location and correspondence to gene and repetitive elements. piOxi DB is an informative tool to assist broad research applications in the fields of RNA biology, cancer biology, environmental toxicology and beyond.
Database URL: https://pioxidb.dcmb.med.umich.edu/
Baseline Data and Measurement Instruments Reported in Observational Studies in Inflammatory Bowel Disease: Results from a Systematic Review
Authors: Wong Charlotte , van Oostrom Joep , Pittet Valerie , Bossuyt Peter , Hanzel Jurij , Samaan Mark , Tripathi Monika , Czuber-Dochan Wladyslawa , Burisch Johan , Leone Salvatore , Saldaña Roberto , Baert Filip , Kopylov Uri , Jaghult Susanna , Adamina Michel , Gecse Krisztina , Arebi Naila 
Published: January 2024

Abstract

Background
Heterogeneity in demographic and outcomes data with corresponding measurement instruments [MIs] creates barriers to data pooling and analysis. Several core outcome sets have been developed in inflammatory bowel disease [IBD] to homogenize outcomes data. A parallel Minimum Data Set [MDS] for baseline characteristics is lacking. We conducted a systematic review to develop the first MDS.

Methods
A systematic review was made of observational studies from three databases [2000–2021]. Titles and abstracts were screened, full-text articles were reviewed, and data were extracted by two reviewers. Baseline data were grouped into ten domains: demographics, clinical features, disease behaviour/complications, biomarkers, endoscopy, histology, radiology, healthcare utilization and patient-reported data. Frequency of baseline data and MIs within respective domains are reported.

Results
From 315 included studies [600 552 subjects], most originated from Europe [196; 62%] and North America [59; 19%], and were published between 2011 and 2021 [251; 80%]. The most frequent domains were demographics [311; 98.7%] and clinical [289; 91.7%]; 224 [71.1%] studies reported on the triad of sex [306; 97.1%], age [289; 91.7%], and disease phenotype [231; 73.3%]. Few included baseline data for radiology [19; 6%], healthcare utilization [19; 6%], and histology [17; 5.4%]. Ethnicity [19; 6%], race [17; 5.4%], and alcohol/drug consumption [6; 1.9%] were the least reported demographics. From 25 MIs for clinical disease activity, the Harvey–Bradshaw Index [n = 53] and Mayo score [n = 37] were most frequently used.

Conclusions
Substantial variability exists in baseline population data reporting. These findings will inform a future consensus for MDS in IBD to enhance data harmonization and credibility of real-world evidence.
Neopolyploidy increases stress tolerance and reduces fitness plasticity across multiple urban pollutants: support for the “general-purpose” genotype hypothesis
Authors: Turcotte Martin M , Kaufmann Nancy , Wagner Katie L , Zallek Taylor A , Ashman Tia-Lynn 
Published: January 2024

Abstract
Whole-genome duplication is a common macromutation with extensive impacts on gene expression, cellular function, and whole-organism phenotype. As a result, it has been proposed that polyploids have “general-purpose” genotypes that perform better than their diploid progenitors under stressful conditions. Here, we test this hypothesis in the context of stresses presented by anthropogenic pollutants. Specifically, we tested how multiple neotetraploid genetic lineages of the mostly asexually reproducing greater duckweed (Spirodela polyrhiza) perform across a favorable control environment and 5 urban pollutants (iron, salt, manganese, copper, and aluminum). By quantifying the population growth rate of asexually reproducing duckweed over multiple generations, we found that across most pollutants, but not all, polyploidy decreased the growth rate of actively growing propagules but increased that of dormant ones. Yet, when considering total propagule production, polyploidy increased tolerance to most pollutants, and polyploids maintained population-level fitness across pollutants better than diploids. Furthermore, broad-sense genetic correlations in growth rate among pollutants were all positive in neopolyploids but not so for diploids. Our results provide a rare test and support for the hypothesis that polyploids are more tolerant of stressful conditions and can maintain fitness better than diploids across heterogeneous stresses. These results may help predict that polyploids may be likely to persist in stressful environments, such as those caused by urbanization and other human activities.
Plasma of COVID-19 Patients Does Not Alter Electrical Resistance of Human Endothelial Blood-Brain Barrier In Vitro
Authors: Pociūtė Agnė , Kriaučiūnaitė Karolina , Kaušylė Aida , Zablockienė Birutė , Alčauskas Tadas , Jelinskaitė Augustė , Rudėnaitė Akvilė , Jančorienė Ligita , Ročka Saulius , Verkhratsky Alexei , Pivoriūnas Augustas 
Published: January 2024

Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 instigated the most serious global health crisis. Clinical presentation of COVID-19 frequently includes severe neurological and neuropsychiatric symptoms. However, it is presently unknown whether and to which extent pathological impairment of blood-brain barrier (BBB) contributes to the development of neuropathology during COVID-19 progression. In the present study, we used human induced pluripotent stem cells-derived brain endothelial cells (iBECs) to study the effects of blood plasma derived from COVID-19 patients on the BBB integrity in vitro. We also performed a comprehensive analysis of the cytokine and chemokine profiles in the plasma of COVID-19 patients, healthy and recovered individuals. We found significantly increased levels of interferon γ-induced protein 10 kDa, hepatocyte growth factor, and interleukin-18 in the plasma of COVID-19 patients. However, blood plasma from COVID-19 patients did not affect transendothelial electrical resistance in iBEC monolayers. Our results demonstrate that COVID-19-associated blood plasma inflammatory factors do not affect BBB paracellular pathway directly and suggest that pathological remodeling (if any) of BBB during COVID-19 may occur through indirect or yet unknown mechanisms.
Genetic screens in Saccharomyces cerevisiae identify a role for 40S ribosome recycling factors Tma20 and Tma22 in nonsense-mediated decay
Authors: Pacheco Miguel , D’Orazio Karole N , Lessen Laura N , Veltri Anthony J , Neiman Zachary , Loll-Krippleber Raphael , Brown Grant W , Green Rachel 
Published: January 2024

Abstract
The decay of messenger RNA with a premature termination codon by nonsense-mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon that is aberrantly distant from the poly-A tail. Here, we use a fluorescence screen to identify factors involved in NMD in Saccharomyces cerevisiae. In addition to the known NMD factors, including the entire UPF family (UPF1, UPF2, and UPF3), as well as NMD4 and EBS1, we identify factors known to function in posttermination recycling and characterize their contribution to NMD. These observations in S. cerevisiae expand on data in mammals indicating that the 60S recycling factor ABCE1 is important for NMD by showing that perturbations in factors implicated in 40S recycling also correlate with a loss of NMD.
Associations of Lower Extremity Muscle Strength, Area, and Specific Force With Lower Urinary Tract Symptoms in Older Men: The Baltimore Longitudinal Study of Aging
Authors: Langston Marvin E , Cawthon Peggy M , Lu Kaiwei , Scherzer Rebecca , Newman John C , Covinsky Kenneth , Ferrucci Luigi , Simonsick Eleanor M , Bauer Scott R 
Published: January 2024

Abstract

Background
Lower urinary tract symptoms (LUTS) in older men are associated with an increased risk of mobility limitations. Lower extremity muscle quality may represent a novel shared mechanism of both LUTS and mobility limitations.

Methods
We evaluated associations of thigh skeletal muscle measures (strength, area, and specific force) with total LUTS severity (American Urologic Association Symptom Index; AUASI) and voiding and storage subscores among 352 men aged ≥60 years enrolled in the Baltimore Longitudinal Study of Aging. Thigh muscle strength (Nm) was defined as maximum concentric 30°/s knee extensor torque, area (cm2), and specific force (Nm/cm2) defined as strength/area. Associations with AUASI score were estimated using multivariable linear regression and linear mixed models.

Results
Mean thigh muscle strength at baseline was 139.7Nm. In cross-sectional multivariable models, each 39Nm increment in thigh muscle strength and 0.28Nm/cm2 increment in specific force was associated with −1.17 point (95% CI: −1.93 to −.41) and −0.95 point (95% CI: −1.63 to −0.27) lower AUASI score, respectively. Similar associations were observed for voiding and storage subscores, although somewhat attenuated. In longitudinal analyses, baseline muscle measures were not associated with annual change in AUASI, and current changes in muscle measures and AUASI were unrelated.

Conclusions
Cross-sectionally, higher thigh muscle strength and specific force were associated with decreased LUTS severity in older men. However, we did not observe concurrent worsening LUTS severity with declining thigh muscle strength, area, or specific force in longitudinal analyses.