bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity in Plastic Surgery Authorship: A 14-Year Analysis of 2688 Articles Published in Plastic and Reconstructive Surgery
Authors: Gunderson Kirsten A. , Edalatpour Armin , Wood Kasey Leigh , Nkana Zeeda H. , Bentz Michael L. , Afifi Ahmed M. 
Published: January 2022

Background:
Publication in peer-reviewed journals is a duty and privilege. It is essential to the advancement of evidence-based medicine and often used as a proxy for academic achievement, contributing to decisions around promotion in academia. Within plastic surgery, authors have historically been male surgeons affiliated with academic institutions, lacking representation of women, private practice, medical students, and international collaboration. This study analyzes differences in authors’ gender, practice affiliation, degree of education, and international collaboration in articles published in Plastic and Reconstructive Surgery, which was chosen as the representative journal given its high impact factor (3.946) and consistent ranking as the number one journal in plastic surgery worldwide.

Methods:
A list of Breast, Cosmetic, and Hand/Peripheral Nerve articles published between 2006 and 2019 was compiled from the online archive of Plastic and Reconstructive Surgery. Demographic author characteristics were recorded, and statistical analyses were performed to identify trends over time.

Results:
A total of 2688 articles were analyzed. The proportion of articles written by female authors in the Breast category, authors in private practice with academic affiliation in the Cosmetic section, and U.S. collaboration with other countries increased over time (p = 0.038, p = 0.029, p < 0.001, respectively). First authors with bachelor’s, master’s, and doctorate degrees have also been contributing increasingly.

Conclusions:
This analysis revealed increasing demographic heterogeneity of authors in Plastic and Reconstructive Surgery over time, with increasing contributions from women, surgeons in private practice with academic affiliation, medical students, and international collaborations. The Journal is capturing contributions from an increasingly diverse authorship, consistent with the changing demographics of plastic surgeons.
Wealth Management and Retirement
Authors: Turin Sergey Y. , Fine Peter , Fine Neil 
Published: January 2022

Summary:
The purpose of this publication is to introduce basic financial planning concepts and highlight their use in creating a retirement savings plan. These tools may help young surgeons set their financial targets and create a plan to meet them, whereas surgeons later in their careers may reflect on their choices and implement adjustments, or be inspired to pass on the lessons they learned to the next generation. This publication is limited by design and should be thought of as a primer, not a comprehensive treatise. The topic of personal financial management is as vague as it is broad, and there are many concepts and situations that are outside the scope of this publication. Unique goals, income and expense streams, and risk tolerances necessitate individualized solutions, but there are fundamental concepts listed below that are more universally applicable. The discussion is tailored to the high income stream that plastic surgeons can expect, albeit one that starts relatively late in their careers compared to nonphysician colleagues. There are three foundational principles the reader should take away: having a plan is crucial in achieving any financial goal; starting any savings/investment endeavors as early as possible is as or more important than the amount of capital committed to them; and lastly, individual investors (professional and amateur) have consistently demonstrated an inability to consistently do better than the market over the long run.
Salegentibacter lacus sp. nov. and Salegentibacter tibetensis sp. nov., isolated from hypersaline lakes on the Tibetan Plateau
Authors: Lu Huibin , Gao Peixin , Phurbu Dorji , Wu Qinglong L. , Xing Peng 
Published: January 2022

Two Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile strains (LM13ST and JZCK2T) were isolated from hypersaline lakes in China. The colonies of both strains were yellow-pigmented and convex. Both strains could grow at 4–34 °C, pH 6.5–9.0 and with 1.0–13.0 % (w/v) NaCl. Comparisons based on 16S rRNA gene sequences showed that strains LM13ST and JZCK2T share less than 98.3 % similarity with species of the genus

Salegentibacter

. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that

Salegentibacter

species are the most closely related neighbours of strains LM13ST and JZCK2T. The sequenced draft genome sizes of strains LM13ST and JZCK2T are 4.06 and 4.22 Mbp with G+C contents of 37.0 and 37.8 mol%, respectively. The phylogenomic tree reconstructed using the Up-to-date Bacterial Core Gene set pipeline also demonstrated that both strains belong to the genus

Salegentibacter

. The calculated pairwise average nucleotide identity values and digital DNA–DNA hybridization values between strains LM13ST and JZCK2T and

Salegentibacter

species were less than 86.4 and 32.0 %, respectively. The respiratory quinone in both strains was MK-6. Their major fatty acids were iso-C12 : 0, iso-C14 : 0, C15 : 1
ω10c, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C17 : 1
ω10c. Their major polar lipids included phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid, but strain LM13ST also contained one more unidentified aminolipid, one more unidentified lipid and one unidentified phospholipid. Combining the above descriptions, strains LM13ST and JZCK2T should represent two independent novel species of the genus

Salegentibacter

, for which the names Salegentibacter lacus sp. nov. (type strain LM13ST=GDMCC 1.2643T=KCTC 82861T) and Salegentibacter tibetensis sp. nov. (type strain JZCK2T=GDMCC 1.2621T=KCTC 82862T) are proposed.
Integrating Math Modeling, Coding, and Biology in a CURE Lab
Authors: Dale Renee , Craig Stewart 
Published: January 2022

AbstractThe development of mathematical and quantitative skills is increasingly critical for biology students. Literacy in coding, statistics, and mathematical modeling enables students to engage in systems-thinking and the analysis of large data sets. Here we present a flexible tool illustrating concepts in mathematical modeling, coding, and biology for integration into both traditional ‘cookbook’ and inquiry-driven labs for freshmen biology students. We developed simple and complex mathematical models of potato catechol oxidase, a popular system to teach enzyme kinetics in undergraduate biology labs. We integrated both models into a freely-available web app for simulation and parameter estimation. The models are usable even if experimental details are unknown or poorly controlled, so that even novice students can work through the problem. We illustrate this by estimating the kinetic parameters of catechol oxidase in the complex model using data obtained from two sections of a course-based undergraduate research experience (CURE) freshman biology lab. Worksheets with questions motivating model building and simulation comprehension are provided. The effect of these exercises on students’ opinions of math, biology, and coding are evaluated using pre- and post-test surveys and student feedback. Our results show that these tools illustrate enzyme kinetics mathematically, students are not intimidated by the degree of math or coding involved, and in some cases are interested to do more, despite being unaware of the focus of the lab when signing up.
miniTurbo-based interactomics of two plasma membrane-localized SNARE proteins in Marchantia polymorpha
Authors: Melkonian Katharina , Stolze Sara Christina , Harzen Anne , Nakagami Hirofumi 
Published: January 2022

SummaryMarchantia polymorpha is a model liverwort and its overall low genetic redundancy is advantageous for dissecting complex pathways. Proximity-dependent in vivo biotin-labelling methods have emerged as powerful interactomics tools in recent years. However, interactomics studies applying proximity labelling are currently limited to angiosperm species in plants.Here, we established and evaluated a miniTurbo-based interactomics method in M. polymorpha using MpSYP12A and MpSYP13B, two plasma membrane- localized SNARE proteins, as baits.We show that our method yields a manifold of potential interactors of MpSYP12A and MpSYP13B compared to a co-immunoprecipitation approach. Our method could capture specific candidates for each SNARE.We conclude that a miniTurbo-based method is a feasible tool for interactomics in M. polymorpha and potentially applicable to other model bryophytes. Our interactome dataset on MpSYP12A and MpSYP13B will be a useful resource to elucidate the evolution of SNARE functions.
T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components
Authors: Jing Lichen , Wu Xia , Krist Maxwell P. , Hsiang Tien-Ying , Campbell Victoria L. , McClurkan Christopher L. , Favors Sydney M. , Hemingway Lawrence A. , Godornes Charmie , Tong Denise Q. , Selke Stacy , LeClair Angela C. , Pyo Chu-Woo , Geraghty Daniel E. , Laing Kerry J. , Wald Anna , Gale Michael , Koelle David M. 
Published: January 2022

AbstractSARS-CoV-2 provokes a brisk T cell response. Peptide-based studies exclude antigen processing and presentation biology and may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DC to activate CD8 and CD4 T cells from convalescent persons. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the alpha, beta, gamma, and delta variant lineages.
Post-COVID-19 Memory Complaints: Prevalence and Associated Factors
Authors: Ahmed Mashrur , Roy Simanta , Chowdhury Sreshtha , Iktidar Mohammad Azmain , Akhter Sharmin , Khairul Islam A. M. , Hossain Hawlader Mohammad Delwer 
Published: January 2022

AbstractIntroductionMemory complaints resulting from COVID-19 may have a significant impact on the survivors’ quality of life. Unfortunately, there is insufficient information available on memory loss and its relationship to COVID-19. Therefore, the purpose of this research was to determine the prevalence of memory complaints in post-COVID-19 patients and to find potential contributing factors.MethodA cross-sectional survey was conducted on 401 individuals who had previously been diagnosed with COVID-19 at four COVID testing centers situated across Bangladesh. The MAC-Q questionnaire was used to evaluate memory. A binary logistic regression model was fit to study the variables related to memory complaints, with a p-value of <0.05 deemed statistically significant.ResultMemory complaints was prevalent in 19.2% of the post-COVID patients. Individual predictor analysis revealed that among the treatment modalities, steroids and antibiotics were associated with impaired memory. Multiple logistic regression showed that individuals who recovered from COVID-19 within six to twelve months were more likely to have memory deficits. Even though age, sex, oxygen demand, and hospitalization were not linked with memory complaints, rural residents exhibited more significant memory complaints than urban residents.ConclusionNearly one-fifth of the COVID-19 patients suffer from various degrees of memory complaints within one year. However, no association was found between COVID-19 severity to memory complaints.
Systemic adverse effects induced by the BNT162b2 vaccine are associated with higher antibody titers from 3 to 6 months after vaccination
Authors: Koike Ryousuke , Sawahata Michiru , Nakamura Yosikazu , Nomura Yushi , Katsube Otohiro , Hagiwara Koichi , Niho Seiji , Masuda Norihiro , Tanaka Takaaki , Sugiyama Kumiya 
Published: January 2022

ABSTRACTObjectiveWe aimed to determine the relationship between vaccine-related adverse effects and antibody (Ab) titers from 3 to 6 months after the second dose of the BNT162b2 coronavirus disease 2019 (COVID-19) mRNA vaccine (Pfizer/BioNTech) in Japan.MethodsWe enrolled 378 healthcare workers (255 women, 123 men) whose Ab titers 3 and 6 months after the second dose were analyzed in our previous study and whose characteristics and adverse effects were collected previously using a structured self-report questionnaire.ResultsMedian age was 44 years. While injection-site symptoms occurred with almost equal frequency between the first and second doses, systemic adverse effects, such as general fatigue and fever, were significantly more frequent after the second dose than after the first. Multivariate analysis showed that fever was significantly correlated with female sex for the second dose (odds ratio [OR], 2.139; 95% confidence interval [95%CI], 1.185–3.859), older age for the first dose (OR, 0.962; 95%CI, 0.931–0.994) and second dose (OR, 0.957; 95%CI, 0.936–0.979), and dyslipidemia for the first dose (OR, 8.750; 95%CI, 1.814–42.20). Age-adjusted Ab titers at 3 months after vaccination were 23.7% and 23.4% higher in patients with fever than in those without fever after first and second dose, respectively. In addition, age-adjusted Ab titers at 3 and 6 months after the second dose were respectively 21.7% and 19.3% higher in the group with anti-inflammatory agent use than in the group without anti-inflammatory agent use.ConclusionParticipants with systemic adverse effects tend to have higher Ab titers from 3 to 6 months after the second dose of the BNT162b2 vaccine. Our results may encourage vaccination, even among people with vaccine hesitancy related to relatively common systemic adverse effects.
Should healthcare workers with SARS-CoV-2 household exposures work? A Cohort Study
Authors: Quach Caroline , Blanchard Ana C. , Lamarche Josée , Audy Nathalie , Lamarre Valérie 
Published: January 2022

AbstractImportanceDue to high community transmission of the Omicron variant, healthcare workers (HCWs) have been increasingly reporting household exposures to confirmed COVID-19 cases. Quebec (Canada) provincial guidelines required to quarantine these HCWs. Facing the risk of staffing shortages, our hospital decided to allow them to work.ObjectiveTo evaluate the risk for HCWs, who were household contacts, to become positive for COVID-19 by RT-PCR and evaluate the risk of nosocomial COVID-19 transmission.DesignCohort of HCWs with a history of household exposure to a confirmed case of COVID-19.SettingCHU Sainte-Justine, a tertiary care mother and child center in Montreal (QC) CanadaParticipantsConsecutive HCWs who contacted OHS between December 20, 2021 and January 17, 2022 for a history of household exposure to COVID-19.ExposureConfirmed case of COVID-19 in the householdMain outcome and measuresThe main outcome was a positive RT-PCR for SARS-CoV-2. Outbreaks and nosocomial cases were identified through daily analysis of COVID-19 cases, by sector and part of the usual Infection Prevention and Control surveillance process.ResultsOverall, 237 of 475 (50%) HCWs who declared a known household contact with a confirmed COVID-19 case remained negative. Of those who became positive, 196 (82.4%) were positive upon initial testing and were quarantined. Only 42 (15%) of 279 HCWs who were allowed to work became positive, a median of 4 days after the initial test. The absence of symptoms at initial evaluation (OR 3.8, 95% CI 2.5-5.7) and having received a third vaccine dose more than 7 days before (OR 1.88, 95% CI 1.3 – 2.8) were associated with an increased odds of remaining negative. There was no outbreak among HCWs and no nosocomial transmission to patients from a HCW that was allowed to work, while a known household contact.Conclusion and relevanceMeasures taken to protect the health care environment from COVID-19 must be cautiously balanced with the risk of staffing shortage. Allowing vaccinated asymptomatic HCWs who are known household contacts of confirmed COVID-19 cases to work is likely a safe alternative, when staff shortage is anticipated.
Early alveolar epithelial cell necrosis is a potential driver of COVID-19-induced acute respiratory distress syndrome
Authors: Tojo Kentaro , Yamamoto Natsuhiro , Tamada Nao , Mihara Takahiro , Abe Miyo , Nishii Mototsugu , Takeuchi Ichiro , Goto Takahisa 
Published: January 2022

SummaryAcute respiratory distress syndrome (ARDS) with COVID-19 is aggravated by hyperinflammatory responses even after the peak of viral load has passed; however, its underlying mechanisms remain unclear. In the present study, analysis of the alveolar tissue injury markers and epithelial cell death markers in patients with COVID-19 revealed that COVID-19-induced ARDS was characterized by alveolar epithelial necrosis at an early disease stage. Serum levels of HMGB-1, one of DAMPs released from necrotic cells, were also significantly elevated in these patients. Further analysis using mouse model mimicking COVID-19-induced ARDS showed that the alveolar epithelial cell necrosis involved two forms of programmed necrosis, namely necroptosis and pyroptosis. Finally, the neutralization of HMGB-1 attenuated alveolar tissue injury in the mouse model. Collectively, necrosis, including necroptosis and pyroptosis, is the predominant form of alveolar epithelial cell death at an early disease stage and subsequent release of DAMPs is a potential driver of COVID-19-induced ARDS.
FMSClusterFinder: A new tool for detection and identification of clusters of sequential motifs with varying characteristics inside genomic sequences
Authors: Hejazi Mohammad Mahdi , Golabi Faegheh , Bahrami Mohsen , Kahroba Houman , Hejazi Mohammad Saeid 
Published: January 2022

AbstractThis paper describes FMSClusterFinder, a new tool and algorithm for identification and detection of clusters of sequential blocks inside the DNA and RNA subject sequences. Gene expression and genomic groups’ performance is under the control of functional elements cooperating with each other as clusters. The functional motifs or blocks are often comparably short, degenerate and are located within varying distances from each other. Since functional motifs mostly act in relation to each other as clusters, finding such clusters of blocks is an effective approach to identify functional groups and their function and structure, which represents the need for development of new corresponding tools.The presented web application finds clusters of sequential blocks, with even altering sequences and located in varying distances from each other inside the subject sequences, simultaneously. Additionally, the blocks could be searched with user defined constant or varying characteristics such as: a) different levels of similarity, b) varying minimum number of blocks required to build up the query cluster, c) different types of sequence (degenerate or standard) and d) one or multiple alternative sequences for each block. FMSClusterFinder is available freely at http://fmsclusterfinder.fmsbiog.com.
Diet outweighs genetics in shaping gut microbiomes in Asian honeybee
Authors: Su Qinzhi , Tang Min , Hu Jiahui , Tang Junbo , Zhang Xue , Li Xingan , Niu Qingsheng , Zhou Xuguo , Luo Shiqi , Zhou Xin 
Published: January 2022

AbstractBackgroundThe gut microbiome is a crucial element that facilitates a host’s adaptation to a changing environment. Host-specificity often coincides with distinctions in gut microbes, suggesting a co-evolution of the holobionts. However, it is unclear how gut microbiota shared by a common host ancestor would co-diversify with hosts and eventually become distinct among sister hosts. In this context, understanding the evolutionary pathway of gut microbiomes of the same host species could provide insight on how holobionts co-adapt along environmental gradients. Specifically, we ask which factor, nature or nurture, i.e., genetics or diets, contributes more to the shaping of gut microbiome, along with host diversification and range expansion.ResultsWe compared and analyzed the gut microbiomes of 99 Asian honeybees, Apis cerana, from genetically diverged populations covering 13 provinces across China. Bacterial composition varied significantly across populations at phylotype, sequence-discrete population (SDP), and strain levels, but with extensive overlaps, indicating the diversity of microbial community among A. cerana populations is driven by nestedness. Taken together, genetics exhibited tangential impacts, while pollen diets were significantly correlated with both the composition and function of gut microbiome. Core bacteria, Gilliamella and Lactobacillus Firm-5, showed antagonistic turnovers and contributed to the enrichment in carbohydrate transport and metabolism. By feeding and inoculation bioassays, we confirmed that the variations in pollen polysaccharide composition contributed to the trade-off of these core bacteria.ConclusionsProgressive change, i.e., nestedness, is the foundation of gut microbiome evolution in the Asian honeybee. Such a transition during the co-diversification of gut microbiomes is shaped primarily by environmental factors, diets in general, pollen polysaccharide in particular.
Relation between the number of peaks and the number of reciprocal sign epistatic interactions
Authors: Saona Raimundo , Kondrashov Fyodor A. , Khudiakova Ksenia A. 
Published: January 2022

AbstractEmpirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis ([14]). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously it has been shown ([14]) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.
Single-molecule nanopore dielectrophoretic trapping of α-Synuclein with lipid membranes
Authors: Wu Jinming , Yamashita Tohru , Hamilton Andrew D. , Thompson Sam , Luo Jinghui 
Published: January 2022

ABSTRACTThe lipid-α-Synuclein (α-Syn) interaction plays a crucial role in the pathogenesis of Parkinson’s disease. Here, we trap α-Syn at a conjunction of an α-hemolysin (αHL) single nanopore-lipid to investigate the folding and unfolding kinetics of α-Syn in a lipidic environment. The hybridized α-Syn is generated through a reaction between a 5’-thiol-modified nucleotide oligo (dC30) and the α-Syn mutant (A140C). Owing to an applied voltage, single-molecule hybridized α-Syn can be trapped at the single nanopore. The trapping events are associated with dielectrophoretic force. The folding and unfolding events of α-Syn can be observed at the pore-membrane junction through interpretation of blockade current amplitudes and dwell time. This can be related to the protein quaternary structure influenced by the α-Syn-membrane interaction, allowing further analysis of α-Syn conformational dynamics. We studied how disease associated metal ions (Cu2+, Zn2+) modulate folding and unfolding of α-Syn at the interface of the membranes and pore, and how α-helical peptidomimetics stabilize the helical conformation of α-Syn in the presence of a membrane. These studies aid our understanding of the complexity of the interaction of α-Syn, lipid membranes and metal ions, and in using peptidomimetics, a new strategy against α-Syn toxicity and aggregation is advanced.