bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rapid Scoping Review of the Dual Advocacy Model for Donation Conversations
Authors: Litsas Diana C. , Mulvania Patricia A. , Roth Stephanie , Siminoff Laura A. 
Published: August 2023

Introduction Increasing family authorization for donation is critical to address the shortage of organs for transplantation, yet there is no standardized method for leading conversations with families about donation. Objective The aim of this rapid scoping review is to identify research assessing the components of dual advocacy, a model to discuss organ donation with grieving families. Methods PubMed, Web of Science, and grey literature were searched for studies published from 2012 to the present. Data representing the various dual advocacy components that were empirically tested were extracted. Outcomes of interest were authorization for organ donation or family satisfaction with the donation conversation. Results Twenty-two articles were identified that tested at least one component of dual advocacy. The most commonly tested component was effective communication about donation ( N = 9), including explaining brain death and the donation process. The primary outcome for the majority of studies was donation authorization or conversion rates. Studies that tested all components of dual advocacy ( N = 9) had overall positive results while studies that tested a single component had mixed results. Discussion Although family authorization to donation is critical to addressing the national organ shortage, there has yet to be a standardized method for leading families in the organ donation conversation. Despite the need for organ transplantation in the United States and worldwide, few large-scale studies have rigorously tested the most effective ways to engage families of donor-eligible patients about the organ donation opportunity. There is an urgent need for further research to establish a standard of evidence-based practice.
Survivorship analysis of CAD-CAM total shoulder replacement
Authors: Nayar Sandeep Krishan , Butt David , Prinja Aditya , Rudge Will , Majed Addie , Higgs Deborah , Falworth Mark 
Published: August 2023

Background Glenoid bone loss represents a challenge in shoulder arthroplasty and often precludes standard implants. The CAD-CAM total shoulder replacement (TSR) is an option in these cases. This study aimed to assess survivorship and long-term patient outcomes of the CAD-CAM TSR. Methods Fifty-eight patients that underwent a CAD-CAM TSR by three surgeons at a single tertiary referral centre between 2009 and 2017 were reviewed. The mean follow-up was 70 months (28–130). Data was collected on survivorship, range of movement, Oxford shoulder score (OSS, 0–48), subjective shoulder value (SSV, 0–100%), pain score (0–10), and overall patient satisfaction. Results CAD-CAM TSR was undertaken as a primary procedure in 28% ( n = 16) for end-stage arthritis with severe glenoid bone loss, and as a revision procedure in 72% ( n = 42). Of the total, 17% ( n = 10) required component revision at a mean of 24 months (4x prosthesis loosening, 3x infection, 3x periprosthetic fracture). Forward elevation improved from 45° ± 27° to 59° ± 29° (P = 0.0056), abduction from 43° ± 29° to 55° ± 26° (P = 0.034) and external rotation from 8° ± 11° to 16° ± 14° (P = 0.031). OSS improved from 15 ± 8 to 29 ± 9 (P = 0.0009), SSV from 18 ± 16 to 62 ± 23 (P < 0.0001), and pain score from 8 ± 2 to 2 ± 2 (P < 0.0001). 88% of patients would undergo the procedure again. Conclusion CAD-CAM TSR is reserved for complex cases involving severe glenoid bone loss, offering significant improvements in pain and function with overall positive patient satisfaction.
Short-Term Outcomes and Long-Term Implant Survival After Inpatient Surgical Management of Geriatric Proximal Humerus Fractures
Authors: Shi Brendan Y , Upfill-Brown Alexander , Wu Shannon Y , Trikha Rishi , Ahlquist Seth , Kremen Thomas J , Lee Christopher , SooHoo Nelson F 
Published: August 2023

Introduction The most common surgical options for geriatric proximal humerus fractures are open reduction and internal fixation (ORIF), hemiarthroplasty (HA), and reverse total shoulder arthroplasty. We used a longitudinal inpatient discharge database to determine the cumulative incidence of conversion to arthroplasty after ORIF of geriatric proximal humerus fractures. The rates of short-term complications and all-cause reoperation were also compared. Patients and Methods All patients 65 or older who sustained a proximal humerus fracture and underwent either ORIF, HA, or shoulder arthroplasty (SA) as an inpatient from 2000 through 2017 were identified. Survival analysis was performed with ORIF conversion to arthroplasty and all-cause reoperation as the endpoints of interest. Rates of 30-day readmission and short-term complications were compared. Trends in procedure choice and outcomes over the study period were analyzed. Results A total of 27 102 geriatric patients that underwent inpatient surgical management of proximal humerus fractures were identified. Among geriatric patients undergoing ORIF, the cumulative incidence of conversion to arthroplasty within 10 years was 8.2%. The 10-year cumulative incidence of all-cause reoperation was 12.1% for ORIF patients and less than 4% for both HA and SA patients. Female sex was associated with increased risk of ORIF conversion and younger age was associated with higher all-cause reoperation. ORIF was associated with higher 30-day readmission and short-term complication rates. Over the study period, the proportion of patients treated with ORIF or SA increased while the proportion of patients treated with HA decreased. Short-term complication rates were similar between arthroplasty and ORIF patients in the later cohort (2015-2017). Conclusion The 10-year cumulative incidence of conversion to arthroplasty for geriatric patients undergoing proximal humerus ORIF as an inpatient was found to be 8.2%. All-cause reoperations, short-term complications, and 30-day readmissions were all significantly lower among patients undergoing arthroplasty, but the difference in complication rate between arthroplasty and ORIF was attenuated in more recent years. Younger age was a risk factor for reoperation and female sex was associated with increased risk of requiring conversion to arthroplasty after ORIF.
Republication of “Perspectives in Treatments of End-Stage Ankle Arthritis Among Orthopaedic Surgeons: Analysis of an American Orthopaedic Foot & Ankle Society (AOFAS) Member Survey”
Authors: Phisitkul Phinit , Glass Natalie , Ebeling Patrick B. , Klein Sandra E. , Johnson Jeffrey E. 
Published: August 2023

Background: This study aimed to assess the preferred operative treatment for patients over the age of 60 with end-stage ankle arthritis and perspectives on total ankle replacement (TAR) among American Orthopaedic Foot & Ankle Society (AOFAS) members. Associated factors were analyzed for potential contraindications among members with different levels of experience. Method: A questionnaire containing 6 questions was designed and sent to 2056 members of the AOFAS. Responses were received from 467 orthopaedic surgeons practicing in the United States (76%), Canada (5%), and 26 other countries (20%). Participants were grouped for response comparisons according to country as well as experience level. Differences in contraindications were compared using χ2 tests or exact tests. Results: Respondents practicing in the United States and surgeons who perform 11 or more TARs per year tended to recommend operative treatments favoring TAR and displayed recognition of its increasing role (P < .05). Overall, respondents felt that 41% of typical patients over 60 years old with end-stage arthritis would be best treated with TAR. Talus avascular necrosis, morbid obesity (body mass index >40 kg/m2), and poorly controlled diabetes with neuropathy were most recognized as the absolute contraindications to TAR. Surgeon’s experience affected the consideration of these clinical factors as contraindications. Conclusions: Total ankle replacement has a substantial and increasing role in the treatment of end-stage ankle arthritis in patients over the age of 60. Absolute and potential contraindications of the procedures were indicated from a cross-sectional survey of AOFAS members. Surgeons more experienced with total ankle replacement felt more comfortable employing it in a wider range of clinical settings. Level of Evidence: Level III, therapeutic.
Republication of “First Metatarsophalangeal Joint Arthrodesis: Functional Outcomes Using 2 Different Fixation Techniques. Is More Expensive Better?”
Authors: Filomeno Paola , López Julio 
Published: August 2023

Background: First metatarsophalangeal (MTP) joint arthrodesis can be fixed using either a dorsal plate or crossed screws. However, there is considerable difference in the cost of these implants, and it is not known if there is sufficient difference in outcome that might justify this cost difference. Our aim was to compare the functional results and patient satisfaction rates after first MTP joint arthrodesis in a group of patients using the same surgical technique except for the fixation devices. Methods: A prospective cohort of 27 patients who underwent first MTP joint fusion by the same surgeon using 2 crossed screws or a single screw with a dorsal plate was recruited over a 3-year period. Demographic information, patient satisfaction rates, complications, and union rates were evaluated. American Orthopaedic Foot & Ankle Society (AOFAS) and visual analog scale (VAS) scoring systems were used pre- and postoperatively to compare the functional outcomes. Thirty consecutive procedures (screws, n = 15; plate, n = 15) were performed. Age (55.8 ± 11.1 vs 63.3 ± 12.4 years for screws and plate respectively; P = .091) and female gender percentages (80% and 73%, P = .666) were similar between groups. Results: The overall union rate was 93% with no differences between groups. AOFAS and VAS scores improved significantly postoperatively for each technique, and no differences were found between the two in the improvement in AOFAS (42.4 ± 8.0 vs 44.3 ± 8.2, screws and plate respectively; P = .520) and VAS scores (66.0 ± 5.4 vs 69.0 ± 6.9; P = .195). The implant cost for screws was $40 and for dorsal plate, $328. Conclusions: First MTP joint fusion using either screws or plate fixation results in an improvement in AOFAS and VAS scores. Functional improvement and patient satisfaction did not differ between the 2 techniques, despite a considerable difference in cost between the two methods of fixation. Level of Evidence: Level III, prospective comparative study.
Ferriandrosite-(Ce), a new member of the epidote supergroup from Betliar, Slovakia
Authors: Števko Martin , Myšľan Pavol , Biagioni Cristian , Mauro Daniela , Mikuš Tomáš 
Published: August 2023

AbstractA new member of the epidote supergroup, ferriandrosite-(Ce), ideally MnCeFe3+AlMn2+(Si2O7)(SiO4)O(OH), was found at the Július manganese ore occurrence near Betliar, Rožňava Co., Košice Region, Slovakia. It occurs as subhedral grains and polycrystalline aggregates, up to 0.3 mm in size, enclosed in pyroxmangite. Other associated minerals are spessartine, rhodochrosite, quartz, baryte and pyrosmalite-(Mn). Ferriandrosite-(Ce) is dark brown, with a light brown streak and vitreous lustre. The Mohs hardness is ~6½ to 7 and tenacity is brittle with no observable cleavage or fracture. The calculated density is 4.321 g⋅cm–3. Ferriandrosite-(Ce) is optically biaxial (+), with weak pleochroism, high surface relief and the mean calculated refractive index is 1.832. The empirical structural formula of ferriandrosite-(Ce), based on 13 anions per formula unit, isA1(Mn2+0.63Ca0.35Ce0.02)Σ1.00A2(Ce0.53La0.27Nd0.14Pr0.05REE*0.01)Σ1.00M1(Fe3+0.41Al0.12V3+0.01Mg0.40Ti0.05)Σ0.99M2Al1.00M3(Mn2+0.75Fe2+0.22Mg0.03)Σ1.00T1–3Si3.00O11O4(O0.67F0.33)(OH), where REE* are minor rare earth elements. Ferriandrosite-(Ce) is monoclinic, space groupP21/m,a= 8.8483(4) Å,b= 5.7307(3) Åc= 10.0314(5) Å, β = 113.3659(15)°,V= 466.95(4) Å3andZ= 2. The crystal structure of ferriandrosite-(Ce) was refined to a finalR1= 0.0210 for 1910 reflections withFo> 4σ(Fo) and 127 refined parameters. Structural features of ferriandrosite-(Ce) are discussed and compared with other members of the androsite-series.
Exogenous and endogenous dsRNAs perceived by plant Dicer-like 4 protein in the RNAi-depleted cellular context
Authors: Leonetti Paola , Consiglio Arianna , Arendt Dennis , Golbik Ralph Peter , Rubino Luisa , Gursinsky Torsten , Behrens Sven-Erik , Pantaleo Vitantonio 
Published: August 2023

Abstract
Background
In plants, RNase III Dicer-like proteins (DCLs) act as sensors of dsRNAs and process them into short 21- to 24-nucleotide (nt) (s)RNAs. Plant DCL4 is involved in the biogenesis of either functional endogenous or exogenous (i.e. viral) short interfering (si)RNAs, thus playing crucial antiviral roles.

Methods
In this study we expressed plant DCL4 in Saccharomyces cerevisiae, an RNAi-depleted organism, in which we could highlight the role of dicing as neither Argonautes nor RNA-dependent RNA polymerase is present. We have therefore tested the DCL4 functionality in processing exogenous dsRNA-like substrates, such as a replicase-assisted viral replicon defective-interfering RNA and RNA hairpin substrates, or endogenous antisense transcripts.

Results
DCL4 was shown to be functional in processing dsRNA-like molecules in vitro and in vivo into 21- and 22-nt sRNAs. Conversely, DCL4 did not efficiently process a replicase-assisted viral replicon in vivo, providing evidence that viral RNAs are not accessible to DCL4 in membranes associated in active replication. Worthy of note, in yeast cells expressing DCL4, 21- and 22-nt sRNAs are associated with endogenous loci.

Conclusions
We provide new keys to interpret what was studied so far on antiviral DCL4 in the host system. The results all together confirm the role of sense/antisense RNA-based regulation of gene expression, expanding the sense/antisense atlas of S. cerevisiae. The results described herein show that S. cerevisiae can provide insights into the functionality of plant dicers and extend the S. cerevisiae tool to new biotechnological applications.
Estimation and consequences of direct-maternal genetic and environmental covariances in models for genetic evaluation in broilers
Authors: Romé Hélène , Chu Thinh T. , Marois Danye , Huang Chyong-Huoy , Madsen Per , Jensen Just 
Published: August 2023

Abstract
Background
Maternal effects influence juvenile traits such as body weight and early growth in broilers. Ignoring significant maternal effects leads to reduced accuracy and inflated predicted breeding values. Including genetic and environmental direct-maternal covariances into prediction models in broilers can increase the accuracy and limit inflation of predicted breeding values better than simply adding maternal effects to the model. To test this hypothesis, we applied a model accounting for direct-maternal genetic covariance and direct-maternal environmental covariance to estimate breeding values.

Results
This model, and simplified versions of it, were tested using simulated broiler populations and then was applied to a large broiler population for validation. The real population analyzed consisted of a commercial line of broilers, for which body weight at a common slaughter age was recorded for 41 selection rounds. The direct-maternal genetic covariance was negative whereas the direct-maternal environmental covariance was positive. Simulated populations were created to mimic the real population. The predictive ability of the models was assessed by cross-validation, where the validation birds were all from the last five selection rounds. Accuracy of prediction was defined as the correlation between the predicted breeding values estimated without the phenotypic records of the validation population and a predictor. The predictors were the breeding values estimated using all the phenotypic information and the phenotypes corrected for the fixed effects, and for the simulated data, the true breeding values. In the real data, adding the environmental covariance, with or without also adding the genetic covariance, increased the accuracy, or reduced deflation of breeding values compared with a model not including dam–offspring covariance. Nevertheless, in the simulated data, reduction in the inflation of breeding values was possible and was associated with a gain in accuracy of up to 6% compared with a model not including both forms of direct-maternal covariance.

Conclusions
In this paper, we propose a simple approach to estimate the environmental direct-maternal covariance using standard software for REML analysis. The genetic covariance between dam and offspring was negative whereas the corresponding environmental covariance was positive. Considering both covariances in models for genetic evaluation increased the accuracy of predicted breeding values.
Using residual regressions to quantify and map signal leakage in genomic prediction
Authors: Valente Bruno D. , de los Campos Gustavo , Grueneberg Alexander , Chen Ching-Yi , Ros-Freixedes Roger , Herring William O. 
Published: August 2023

Abstract
Background
Most genomic prediction applications in animal breeding use genotypes with tens of thousands of single nucleotide polymorphisms (SNPs). However, modern sequencing technologies and imputation algorithms can generate ultra-high-density genotypes (including millions of SNPs) at an affordable cost. Empirical studies have not produced clear evidence that using ultra-high-density genotypes can significantly improve prediction accuracy. However, (whole-genome) prediction accuracy is not very informative about the ability of a model to capture the genetic signals from specific genomic regions. To address this problem, we propose a simple methodology that detects chromosome regions for which a specific model (e.g., single-step genomic best linear unbiased prediction (ssGBLUP)) may fail to fully capture the genetic signal present in such segments—a phenomenon that we refer to as signal leakage. We propose to detect regions with evidence of signal leakage by testing the association of residuals from a pedigree or a genomic model with SNP genotypes. We discuss how this approach can be used to map regions with signals that are poorly captured by a model and to identify strategies to fix those problems (e.g., using a different prior or increasing marker density). Finally, we explored the proposed approach to scan for signal leakage of different models (pedigree-based, ssGBLUP, and various Bayesian models) applied to growth-related phenotypes (average daily gain and backfat thickness) in pigs.

Results
We report widespread evidence of signal leakage for pedigree-based models. Including a percentage of animals with SNP data in ssGBLUP reduced the extent of signal leakage. However, local peaks of missed signals remained in some regions, even when all animals were genotyped. Using variable selection priors solves leakage points that are caused by excessive shrinkage of marker effects. Nevertheless, these models still miss signals in some regions due to low linkage disequilibrium between the SNPs on the array used and causal variants. Thus, we discuss how such problems could be addressed by adding sequence SNPs from those regions to the prediction model.

Conclusions
Residual single-marker regression analysis is a simple approach that can be used to detect regional genomic signals that are poorly captured by a model and to indicate ways to fix such problems.
BMP9 maintains the phenotype of HTR-8/Svneo trophoblast cells by activating the SDF1/CXCR4 pathway
Authors: Yang Xue , Ren Lingling , Chen Xiang , Pang Ying , Jia Baoxia , Sun Jing , Quan Xiaofang 
Published: August 2023

Abstract
Background
Bone morphogenetic protein 9 (BMP9) has been shown to regulate processes such as angiogenesis, endothelial dysfunction, and tumorigenesis. However, the role of BMP9 in preeclampsia (PE) is unclear. The purpose of this study was to investigate the role and mechanism of BMP9 in PE.

Methods
The effects of BMP9 on the viability, migration and invasion of HTR-8/Svneo cells were investigated by CCK-8 assay, wound healing assay and Transwell invasion assay. The effect of BMP9 on apoptosis of HTR-8/Svneo cells was detected by flow cytometry. Plasma levels of BMP9, SDF1 and CXCR4 were detected by ELISA kit. qRT-PCR and Western blot were used to detect the expression levels of each gene in the cells.

Results
Overexpression of BMP9 promoted the proliferation and migration of trophoblast cells and inhibited apoptosis. Knockdown of BMP9 had the opposite effect. The levels of BMP9, SDF1 and CXCR4 in the plasma of PE patients were down-regulated, and BMP9 was positively correlated with the levels of SDF1 and CXCR4. BMP9 also significantly upregulated the mRNA and protein levels of SDF1 and CXCR4 in HTR-8/SVneo cells. Further mechanistic studies found that BMP9 promoted the migration and invasion of HTR-8/SVneo cells and inhibited apoptosis by activating the SDF1/CXCR4 pathway.

Conclusion
We demonstrate for the first time that BMP9 promoted the migration and invasion of HTR-8/SVneo cells and inhibits apoptosis by activating the SDF1/CXCR4 pathway. This suggests that BMP9 may be a biomarker molecule for PE.
Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification
Authors: Tenorio Mariela , Serwatowska Joanna , Fernandez-Valverde Selene L. , Oktaba Katarzyna , Cortez Diego 
Published: August 2023

Abstract
Background
Long non-coding RNAs (lncRNAs) are defined as transcribed molecules longer than 200 nucleotides with little to no protein-coding potential. LncRNAs can regulate gene expression of nearby genes (cis-acting) or genes located on other chromosomes (trans-acting). Several methodologies have been developed to capture lncRNAs associated with chromatin at a genome-wide level. Analysis of RNA-DNA contacts can be combined with epigenetic and RNA-seq data to define potential lncRNAs involved in the regulation of gene expression.

Results
We performed Chromatin Associated RNA sequencing (ChAR-seq) in Anolis carolinensis to obtain the genome-wide map of the associations that RNA molecules have with chromatin. We analyzed the frequency of DNA contacts for different classes of RNAs and were able to define cis- and trans-acting lncRNAs. We integrated the ChAR-seq map of RNA-DNA contacts with epigenetic data for the acetylation of lysine 16 on histone H4 (H4K16ac), a mark connected to actively transcribed chromatin in lizards. We successfully identified three trans-acting lncRNAs significantly associated with the H4K16ac signal, which are likely involved in the regulation of gene expression in A. carolinensis.

Conclusions
We show that the ChAR-seq method is a powerful tool to explore the RNA-DNA map of interactions. Moreover, in combination with epigenetic data, ChAR-seq can be applied in non-model species to establish potential roles for predicted lncRNAs that lack functional annotations.