bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prospective Cohort Study Re-examining Tissue Oximetry Monitoring in Microsurgical Breast Reconstruction
Authors: Sultan Darren L. , Atamian Elisa , Tarr Joseph , Feingold Randall , Kasabian Armen K. , Tanna Neil , Smith Mark L. , Moon Victor 
Published: May 2023

Background
The goal of inpatient monitoring after microsurgical breast reconstruction is to detect vascular compromise before flap loss. Near-infrared tissue oximetry (NITO) is commonly used for this purpose, but recent reports challenge its specificity and utility in current practice. Fifteen years after Keller published his initial study using this technology at our institution, we re-evaluate the role and limitations of this popular monitoring device.

Methods
A 1-year prospective study was performed for patients undergoing microsurgical breast reconstruction and monitored postoperatively using NITO. Alerts were evaluated, and clinical endpoints relating to an unplanned return to the operating room or flap loss were recorded.

Results
A total of 118 patients reconstructed with 225 flaps were included within the study. There were no cases of flap loss at the time of discharge. There were 71 alerts relating to a drop in oximetry saturation. Of these, 68 (95.8%) were deemed to be of no significance. In 3 cases (positive predictive value of 4.2%), the alert was significant, and there were concerning clinical signs apparent at that point. A sensor in an inframammary fold position was associated with nearly twice the average number of alerts as compared with areolar or periareolar positions (P = 0.01). In 4 patients (3.4%), a breast hematoma required operative evacuation, and these cases were detected by nursing clinical examination.

Conclusions
The monitoring of free flaps after breast reconstruction through tissue oximetry shows a poor positive predictive value for flap compromise and requires clinical corroboration of alerts but missed no pedicle-related adverse events. With a high sensitivity for pedicle-related issues, NITO may be helpful postoperatively, but the exact timeframe for use must be weighed at the institutional level.
A Systematic Review of Pediatric Nonaccidental Burns
Authors: Gasteratos Konstantinos , McCarthy Michelle , Chatziathanasiou Danai , Vradeli Georgia , Vlachopoulos Nikolaos , Voitsidis Pantelis , Goverman Jeremy 
Published: May 2023

Background
Inflicted burns on children are a particularly difficult medical and psychosocial issue. Pediatric nonaccidental burns (PNABs) are unfortunately relatively common. In our study, we aim to present the key findings on PNABs with the intention of raising awareness, improving early, and recognizing accurately by identifying red flags, developing triage tools, and establishing prevention strategies for this sensitive issue.

Methods
A computerized literature search was conducted on PubMed, Google Scholar, and Cochrane for articles published until November 2020. The online screening process was performed by 3 independent reviewers with the Covidence tool against set inclusion/exclusion criteria. The protocol was reported using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) protocol. The study was registered with the International Prospective Register of Systematic Reviews (PROSPERO).

Results
A total of 12 studies were included for analysis. Scald burns via forced immersion accounted for the majority of reported PNABs affecting both feet and hands. Complications included wound infection, sepsis, requiring systemic antibiotics, or intensive care. Abused children's parents had a history of mental illness, unemployment, substance abuse, incarceration, and/or low annual income.

Conclusions
Scalds via forced immersion remain the most common mechanism of PNABs. All health care professionals must remain vigilant, be able to recognize subtle signs of abuse, triage patients appropriately, report to police and/or social services, and ensure no further harm is made to the child or children. Repeated abuse with burns can lead to death. Prevention and education are the cornerstones for addressing this social phenomenon.
Effect of Platelet-rich Plasma on the Clinical Success of Alveolar Grafts in Patients With Cleft Lip and Palate: A Systematic Review and Meta-Analysis
Authors: Eslami Neda , Heidarian Miri Hamid , Rastegar Mozhgan , Sabzevari Berahman 
Published: May 2023

Objectives:
This study assessed the effect of platelet-rich plasma (PRP) on the clinical success of alveolar grafts in patients with cleft lip and palate.

Materials and Methods:
In this meta-analysis, a search of the literature was conducted in Medline, Scopus, ISI Web of Science, and Cochrane Central Register of Controlled Trials for randomized clinical trials using PRP or platelet-rich fibrin (PRF) along with autogenous bone for alveolar ridge grafts in patients with cleft lip and palate. The methodological quality of the studies was analyzed using Cochrane’s risk of the bias assessment tool. The extracted data underwent meta-analysis using the random-effects model.

Results:
Of a total of 2256 articles retrieved, 12 met the eligibility criteria and were enrolled; out of which 6 did not undergo meta-analysis due to heterogeneous data. The percentage of defects filled by bone graft was 0.648% (95% confidence interval: −0.15 to 1.45), which was not statistically significant (P=0.115). Subgroup analysis showed no significant difference based on the use of PRF or PRP (P=0.28), type of cleft (unilateral/bilateral; P=0.56), or type of radiographic modality (3D/2D; P=0.190). Meta-regression analysis showed that the duration of follow-up and the difference in the mean age of patients did not have a significant effect on the results (R=0, I2: high).

Conclusion:
The application of PRP/PRF in combination with autogenous bone graft did not have a significant effect on the percentage of alveolar cleft filled by a bone graft. Future clinical studies are required to further elucidate the effect of PRP in the regeneration of alveolar clefts.
From bedside to bench and back: discovery of a novel missense variant in NLRP3 causing atypical CAPS with hearing loss as the primary presentation, responsive to anti-IL-1 therapy
Authors: Birk-Bachar Merav , Cohen Hadar , Sofrin-Drucker Efrat , Kropach-Gilad Nesia , Orenstein Naama , Lidzbarsky Gabriel , Kornreich Liora , Tal Rotem , Amarilyo Gil , Levinsky Yoel , Sokolov Meirav , Raveh Eyal , Gerlic Motti , Harel Liora 
Published: May 2023

ABSTRACTCryopyrin-associated periodic syndromes (CAPS) also known as NLRP3-associated auto-inflammatory diseases, are a spectrum of rare auto-inflammatory diseases caused by gain-of-function mutations in the NLRP3 gene, resulting in inflammasome hyper-activation and dysregulated release of Interleukin-1β(IL-1β). Many patients with CAPS develop progressive sensorineural hearing loss (SNHL) due to cochlear auto-inflammation which, in rare cases, may be the sole manifestation. This study was undertaken to establish the suspected diagnosis of CAPS in a family presenting autosomal dominant progressive/acute SNHL and a novel missense variant in the NLRP3 gene of unknown significance (NM_001079821:c.1790G>A, p.Ser597Asn). To do so, we conducted an ex vivo functional assessment of the NLRP3 inflammasome in carries (n=10) and healthy family members (n=5). The assay revealed hyper-activation of the inflammasome among carriers, supporting the hypothesis that this missense variant is a pathogenic gain-of-function mutation. Administration of anti-IL-1 therapy resulted in a substantial clinical improvement among pediatric patients, who exhibited near resolution of hearing impairment within 1-3 months of treatment. Our findings highlight the crucial role of early diagnosis and treatment of hearing loss due to hyperactivation of the inflammasome with an anti-IL-1 agent in reversing cochlear damage. Furthermore, our results suggest that high and ultrahigh frequency ranges need to be included in the auditory assessment to enable early detection of subclinical SNHL. Finally, incorporating functional inflammasome assessment as part of the clinical evaluation could establish the diagnosis in inconclusive cases.
A multiadjuvant polysaccharide-amino acid-lipid (PAL) subunit nanovaccine generates robust systemic and lung-specific mucosal immune responses against SARS-CoV-2 in mice
Authors: Pandey Bhawana , Wang Zhengying , Jimenez Angela , Bhatia Eshant , Jain Ritika , Beach Alexander , Maniar Drishti , Hosten Justin , O’Farrell Laura , Vantucci Casey , Hur David , Noel Richard , Ringuist Rachel , Smith Clinton , Ochoa Miguel A. , Roy Krishnendu 
Published: May 2023

ABSTRACTExisting parenteral SARS-CoV-2 vaccines produce only limited mucosal responses, which are essential for reducing transmission and achieving sterilizing immunity. Appropriately designed mucosal boosters could overcome the shortcomings of parenteral vaccines and enhance pre- existing systemic immunity. Here we present a new protein subunit nanovaccine using multiadjuvanted (e.g. RIG-I: PUUC, TLR9: CpG) polysaccharide-amino acid-lipid nanoparticles (PAL-NPs) that can be delivered both intramuscularly (IM) and intranasally (IN) to generate balanced mucosal-systemic SARS-CoV-2 immunity. Mice receiving IM-Prime PUUC+CpG PAL- NPs, followed by an IN-Boost, developed high levels of IgA, IgG, and cellular immunity in the lung, and showed robust systemic humoral immunity. Interestingly, as a purely intranasal vaccine (IN-Prime/IN-Boost), PUUC+CpG PAL-NPs induced stronger lung-specific T cell immunity than IM-Prime/IN-Boost, and a comparable IgA and neutralizing antibodies, although with a lower systemic antibody response, indicating that a fully mucosal delivery route for SARS-CoV-2 vaccination may also be feasible. Our data suggest that PUUC+CpG PAL-NP subunit vaccine is a promising candidate for generating SARS-CoV-2 specific mucosal immunity.
Signal recovery in single cell batch integration
Authors: Zhang Zhaojun , Mathew Divij , Lim Tristan , Mason Kaishu , Martinez Clara Morral , Huang Sijia , Wherry E. John , Susztak Katalin , Minn Andy J. , Ma Zongming , Zhang Nancy R. 
Published: May 2023

AbstractData integration to align cells across batches has become a cornerstone of single cell data analysis, critically affecting downstream results. Yet, how much biological signal is erased during integration? Currently, there are no guidelines for when the biological differences between samples are separable from batch effects, and thus, data integration usually involve a lot of guesswork: Cells across batches should be aligned to be “appropriately” mixed, while preserving “main cell type clusters”. We show evidence that current paradigms for single cell data integration are unnecessarily aggressive, removing biologically meaningful variation. To remedy this, we present a novel statistical model and computationally scalable algorithm, CellANOVA, to recover biological signal that is lost during single cell data integration. CellANOVA utilizes a “pool-of-controls” design concept, applicable across diverse settings, to separate unwanted variation from biological variation of interest. When applied with existing integration methods, CellANOVA allows the recovery of subtle biological signals and corrects, to a large extent, the data distortion introduced by integration. Further, CellANOVA explicitly estimates cell- and gene-specific batch effect terms which can be used to identify the cell types and pathways exhibiting the largest batch variations, providing clarity as to which biological signals can be recovered. These concepts are illustrated on studies of diverse designs, where the biological signals that are recovered by CellANOVA are shown to be validated by orthogonal assays. In particular, we show that CellANOVA is effective in the challenging case of single-cell and single-nuclei data integration, where the recovered biological signals are replicated in an independent study.
The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated byLactobacillus inersregardless of HPV status
Authors: Vargas-Robles Daniela , Romaguera Josefina , Alvarado-Velez Ian , Tosado-Rodríguez Eduardo , Dominicci-Maura Anelisse , Sanchez Maria , Wiggin Kara J. , Gilbert Jack A. , Martinez-Ferrer Magaly , Forney Larry J. , Godoy-Vitorino Filipa 
Published: May 2023

ABSTRACTIntroductionThe cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, non-pregnant and menopausal women living in Puerto Rico with and without Human Papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota associated with variation in cervical cytology. A total of 294 women comprised of reproductive-age non-pregnant (N=196), pregnant (N=37), and menopausal (N=61) women were enrolled. The cervicovaginal bacteria was characterized by 16S rRNA amplicon sequencing, the HPV were genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated byLactobacillus iners. Pregnant women in the 2ndand 3rdtrimesters had decreased diversity and a decreased abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than pre-menopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota women living in Puerto Rican were either dominated byL. inersor diverse microbial communities regardless of a woman’s physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV, increase the risk of cervical lesions of women living in Puerto Rico.
Validation of the in-house designed one-trial inhibitory avoidance test for two strains of adult zebrafish
Authors: Ferreira Jorge M. , Silva Joana , Barros Sofia , Caetano Inês , Fernandes Pedro , Olsson Anna , Valentim Ana M. 
Published: May 2023

AbstractOpen-source validated tools are important for affordable high-quality science. Zebrafish model is often used in behavioral sciences, thus validated tools must be developed for this species. We aimed to implement the memory task one-trial inhibitory avoidance test in our laboratory by creating a custom-built 3D printed apparatus and custom-made hardware and software using microcontrollers; this decreases the costs and increases methodological flexibility. In this task, a mild electric shock (3.3 ± 0.3V and 2A for 5sec) is used as an aversive stimulus for the one-trial inhibitory avoidance task based on classical conditioning. For this study we used 72-adult zebrafish from the AB and TU strain. The aversive stimulus caused a robust and long-lasting memory that was learned in one session. The apparatus consisted in one aquarium with two compartments (white and black) where, during the conditioning session, the shock was delivered in the preferred side (black), followed by 30min of immersion in 20μM MK-801, a compound known for inducing amnesia (amnesic group, n= 20 for AB and 17 for TU), or in clean water (control, n= 20 for AB and 15 for TU). Both the AB and TU strain animals from the control group took more time to enter in the black compartment after conditioning (p≤0.039), indicating avoidance for the black side, while the latency was not altered in the MK-801 group, demonstrating impaired memory. In summary, this open-source apparatus is an affordable and validated option for memory assessment for the two most used strains of zebrafish in research.
The uniqueness of the Brazilian Yellow Fever Virus. Are the vaccines less effective against it?
Authors: Mamidi Prabhudutta , Gaur Mahendra , Mishra Baijayantimala , Subudhi Bharat Bhusan , Rath Sutapa , Mohanty Monalisa 
Published: May 2023

SummaryThe years 2016-2019 witnessed the expansion of Yellow Fever Virus (YFV) circulation area in Brazil. Deforestation and mutations in the nsp genes were presumed responsible for the reemergence of YFV in brazil. However, our data analysis involving 200 clinical isolates worldwide including vaccine strains showed two amino acids substitutions exclusively in the Brazilian strains at critical positions (V318A and I335M) in the ED III domain of E protein. Our molecular dynamics analysis involving reference and mutant structures suggests that the mutations significantly changed the conformational rearrangement and folding of the YFV-EDIII domain as revealed by RMSF, PCA, Porcupine plots and secondary structure analysis. Briefly, the regions 324-330, 339-346 and 347-359 had a higher fluctuation than the wild, while regions 313-318 and 379-384 had a lower fluctuation. As reported earlier that the residues E325 and E380 are part of vaccine epitopes and any mutations in these residues reduced the binding of vaccine generated mabs to the epitopes. Hence, it may be speculated from our porcupine plot data analysis that that the commercial YFV vaccines may not be fully effective against the Brazilian strains in particular owing to the fluctuations of these residues. However, future investigation is required to validate the observations.
SARS-COV-2 Spike Protein Fragment eases Amyloidogenesis of α-Synuclein
Authors: Chesney Andrew D. , Maiti Buddhadev , Hansmann Ulrich H. E. 
Published: May 2023

ABSTRACTParkinson’s Disease is accompanied by presence of amyloids in the brain formed of α-synuclein chains. Correlation between COVID-19 and the onset of Parkinson’s disease let to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of α-synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, shifts preferentially the ensemble of α-synuclein monomer towards rod-like fibril seeding conformations, and at the same time stabilizes differentially this polymorph over the competing twister-like structure. Our results are compared with earlier work relying on a different protein fragment that is not specific for SARS-COV-2.
Quantifying Effects of Dataset Size, Data Variability, and Data Curvature on Modelling of Simulated Age-Related Motor Development Data
Authors: Dobri Stephan C.D. , Scott Stephen H. , Davies T. Claire 
Published: May 2023

AbstractMotor development in children and youth occurs non-linearly; improvements are rapid at younger ages and decrease as they reach adulthood. There is also evidence that performance variability changes as children and youth age. Accurate models of typical performance are necessary to identify deficits in motor performance and to track the efficacy of therapies. Robotic devices have been used previously to measure motor performance in children and youth, and produce models of typical performance; however, power analyses on these models have not been explored.An algorithm was created to generate normative models of typical motor performance. The accuracy and repeatability of the algorithm were tested using simulated data that changed the number of data points, and the curvature and variability of the data. Two-hundred and eighty-eight participants who are typically developing (ages 5-18) completed a robotic point-to-point reaching task with the Kinarm Exoskeleton. Exponential curves were fit to reaction time measured by the Kinarm to model typical performance. The results of the simulations were used to generate confidence intervals on the models of typical performance.The simulations showed that number of datapoints had the largest impact on accuracy and repeatability of the models, and that repeatability was age-dependent. The simulations with the uniform and non-uniform datasets generated different confidence intervals; however, these differences were minimal when the number of datapoints at each age were matched between the two datasets.To ensure identification of deficits is accurately determined, there is a need to account for differences in repeatability when developing models of typical motor performance in children and youth. The results of our simulations can be used to assess repeatability of non-linear models of motor performance based on dataset size in the future.
The Mechanical Influence of Densification on Initial Epithelial Architecture
Authors: Cammarota Christian , Dawney Nicole S. , Bellomio Phillip M. , Jüng Maren , Fletcher Alexander G. , Finegan Tara M. , Bergstralh Dan T. 
Published: May 2023

SummaryEpithelial tissues are the most abundant tissue type in animals, lining body cavities and generating compartment barriers. The function of a monolayer epithelium – whether protective, secretory, absorptive, or filtrative –relies on regular tissue architecture with respect to the apical-basal axis. Using an unbiased 3D analysis pipeline developed in our lab, we previously showed that epithelial tissue architectures in culture can be divided into distinct developmental categories, and that these are intimately connected to cell density: at sparse densities, cultured epithelial cell layers have a squamous morphology (Immature); at intermediate densities, these layers develop lateral cell-cell borders and rounded cell apices (Intermediate); cells at the highest densities reach their full height and demonstrate flattened apices (Mature). These observations prompted us to ask whether epithelial architecture emerges from the mechanical constraints of densification, and to what extent a hallmark feature of epithelial cells, namely cell-cell adhesion, contributes. In other words, to what extent is the shape of cells in an epithelial layer a simple matter of sticky, deformable objects squeezing together? We addressed this problem using a combination of computational modeling and experimental manipulations. Our results show that the first morphological transition, from Immature to Intermediate, can be explained simply by cell crowding. Additionally, we identify a new division (and thus transition) within the Intermediate category, and find that this second morphology relies on cell-cell adhesion.
MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
Authors: Jarva Taiya , Zhang Jialin , Flynt Alex 
Published: May 2023

AbstractRNA interference (RNAi) is mediated by small (20-30 nucleotide) RNAs that are produced by complex processing pathways. In animals, three main classes are recognized: microRNAs (miRNAs), small-interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Understanding of small RNA pathways has benefited from genetic models where key enzymatic events were identified that lead to stereotypical positioning of small RNAs relative to precursor transcripts. Increasingly there is interest in using RNAi in non-model systems due to ease of generating synthetic small RNA precursors for research and biotechnology. Unfortunately, small RNAs are often rapidly evolving, requiring investigation of a species’ endogenous small RNAs prior to deploying an RNAi approach. This can be accomplished through small non-coding RNA sequencing followed by applying various computational tools; however, the complexity and separately maintained packages lead to significant challenges for annotating global small RNA populations. To address this need, we developed a simple and efficient R package (MiSiPi-Rna) which can be used to characterize pre-selected loci with plots and statistics, aiding researchers understanding RNAi biology specific to their target species. Additionally, MiSiPi-Rna pioneers several computational approaches to identifying Dicer processing to assist annotation of miRNA and siRNA.