bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of increment of emission intensity in a cold atmospheric pressure helium plasma jet using the ADAS
Authors: Behera Narayan , Veda Prakash G. 
Published: February 2023

Abstract
In this paper, the Atomic Data and Analysis Structure (ADAS) has been used to study the cold atmospheric pressure plasma jet. Variation of emission intensity pattern from glass nozzle to the plasma jet tip of a helium plasma jet in ambient air has been observed from the intensified charge-coupled device (ICCD) camera image. The increase of intensity pattern towards the plasma jet tip is an important and fundamental feature of the plasma jet in ambient air. The correlation of this observed pattern with electron impact processes has been studied by computing photon emissivity coefficients (PEC) using the ADAS. The role of various atomic processes involved in this study has also been discussed.
Metabolic Characterization and Glyceraldehyde-3-Phosphate Dehydrogenase-Dependent Regulation of Epithelial Sodium Channels in hPheo1 Wild-type andSDHBKnockdown Cells
Authors: Bala Niharika , Yu Ling , Liu Lauren P , Shelton Laura , Xu Yiling , Ghayee Hans K , Alli Abdel A 
Published: February 2023

AbstractPheochromocytomas (PCC) and paragangliomas (PGL) are rare neuroendocrine tumors with limited curative treatment options outside of surgical resection. Patients with mutations in succinate dehydrogenase subunit B (SDHB) are at an increased risk of malignant and aggressive disease. As cation channels are associated with tumorigenesis, we studied the expression and activity of cation channels from the Degenerin superfamily in a progenitor cell line derived from a human PCC. hPheo1 wild-type (WT) and SDHB knockdown (KD) cells were studied to investigate whether epithelial sodium channels (ENaC) and acid-sensing ion channels (ASIC) are regulated by the activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). First, we performed targeted metabolomic studies and quantified changes in glycolysis pathway intermediates and citric acid cycle intermediates using hPheo1 WT cells and SDHB KD cells. Next, we performed protein biochemistry and electrophysiology studies to characterize the protein expression and activity, respectively, of these ion channels. Our western blot experiments show both ENaC alpha and ASIC1/2 are expressed in both hPheo1 WT and SDHB KD cells, with lower levels of a cleaved 60 kDa form of ENaC in SDHB KD cells. Single-channel patch clamp studies corroborate these results and further indicate channel activity is decreased in SDHB KD cells. Additional experiments showed a more significant decreased membrane potential in SDHB KD cells, which were sensitive to amiloride compared to WT cells. We provide evidence for the differential expression and activity of ENaC and ASIC hybrid channels in hPheo1 WT and SDHB KD cells, providing an important area of investigation in understanding SDHB-related disease.
Validation of Automated Data Extraction From the Electronic Medical Record to Provide a Pediatric Risk Assessment Score
Authors: Valencia Eleonore , Staffa Steven J. , Aslam Yousuf , Faraoni David , DiNardo James A. , Rangel Shawn J. , Nasr Viviane G. 
Published: February 2023

BACKGROUND:
Although the rate of pediatric postoperative mortality is low, the development and validation of perioperative risk assessment models have allowed for the stratification of those at highest risk, including the Pediatric Risk Assessment (PRAm) score. The clinical application of such tools requires manual data entry, which may be inaccurate or incomplete, compromise efficiency, and increase physicians’ clerical obligations. We aimed to create an electronically derived, automated PRAm score and to evaluate its agreement with the original American College of Surgery National Surgical Quality Improvement Program (ACS NSQIP)-derived and validated score.

METHODS:
We performed a retrospective observational study of children <18 years who underwent noncardiac surgery from 2017 through 2021 at Boston Children’s Hospital (BCH). An automated PRAm score was developed via electronic derivation of International Classification of Disease (ICD)-9 and -10 codes. The primary outcome was agreement and correlation among PRAm scores obtained via automation, NSQIP data, and manual physician entry from the same BCH cohort. The secondary outcome was discriminatory ability of the 3 PRAm versions. Fleiss Kappa, Spearman correlation (rho), and intraclass correlation coefficient (ICC) and receiver operating characteristic (ROC) curve analyses with area under the curve (AUC) were applied accordingly.

RESULTS:
Of the 6014 patients with NSQIP and automated PRAm scores (manual scores: n = 5267), the rate of 30-day mortality was 0.18% (n = 11). Agreement and correlation were greater between the NSQIP and automated scores (rho = 0.78; 95% confidence interval [CI], 0.76–0.79; P <.001; ICC = 0.80; 95% CI, 0.79–0.81; Fleiss kappa = 0.66; 95% CI, 0.65–0.67) versus the NSQIP and manual scores (rho = 0.73; 95% CI, 0.71–0.74; P < .001; ICC = 0.78; 95% CI, 0.77–0.79; Fleiss kappa = 0.56; 95% CI, 0.54–0.57). ROC analysis with AUC showed the manual score to have the greatest discrimination (AUC = 0.976; 95% CI, 0.959,0.993) compared to the NSQIP (AUC = 0.904; 95% CI, 0.792–0.999) and automated (AUC = 0.880; 95% CI, 0.769–0.999) scores.

CONCLUSIONS:
Development of an electronically derived, automated PRAm score that maintains good discrimination for 30-day mortality in neonates, infants, and children after noncardiac surgery is feasible. The automated PRAm score may reduce the preoperative clerical workload and provide an efficient and accurate means by which to risk stratify neonatal and pediatric surgical patients with the goal of improving clinical outcomes and resource utilization.
Developmental trajectory of pluripotent stem cell establishment in Arabidopsis callus guided by a quiescent center-related gene network
Authors: Zhai Ning , Pan Xuan , Zeng Minhuan , Xu Lin 
Published: February 2023

ABSTRACT
In plant tissue culture, callus formation is induced by a high auxin concentration. Among the three cell layers (the outer, middle and inner cell layers) of the callus, pluripotency acquisition in the middle cell layer is required for the potential ability of the callus to regenerate organs. Here, we reveal the developmental trajectory of middle cell layer initiation and maintenance in callus tissue originating from Arabidopsis thaliana hypocotyls. The S phase of the cell cycle is essential for the expression of quiescent center-related SCARECROW (SCR), PLETHORA1 (PLT1) and WUSCHEL-RELATED HOMEOBOX5 (WOX5) genes during the division of callus founder cells to initiate the callus primordium. After callus initiation, SHOOT-ROOT (SHR) proteins move from the inner to the middle cell layer and act together with SCR to promote the expression of PLT1 and WOX5. WOX5 represses the expression of VASCULAR-RELATED NAC-DOMAIN (VND) genes, thereby preventing callus tissue from differentiating into xylem cells. PLT1 and PLT2 directly activate JACKDAW (JKD), which is necessary for pluripotency acquisition in the middle cell layer. We hypothesize that the middle cell layer could have pluripotent stem cell activity and its establishment requires the quiescent center-related SCR-SHR-WOX5-PLT1/2-JKD gene network.
In vivo profiling of the Zucchini proximal proteome in the Drosophila ovary
Authors: Nguyen Thi Thanh My , Munkhzul Choijamts , Kim Jeesoo , Kyoung Yeonju , Vianney Michele , Shin Sanghee , Ju Seonmin , Pham-Bui Hoang-Anh , Kim Junhyung , Kim Jong-Seo , Lee Mihye 
Published: February 2023

ABSTRACT
PIWI-interacting RNAs (piRNAs) are small RNAs that play a conserved role in genome defense. The piRNA processing pathway is dependent on the sequestration of RNA precursors and protein factors in specific subcellular compartments. Therefore, a highly resolved spatial proteomics approach can help identify the local interactions and elucidate the unknown aspects of piRNA biogenesis. Herein, we performed TurboID proximity labeling to investigate the interactome of Zucchini (Zuc), a key factor of piRNA biogenesis in germline cells and somatic follicle cells of the Drosophila ovary. Quantitative mass spectrometry analysis of biotinylated proteins defined the Zuc-proximal proteome, including the well-known partners of Zuc. Many of these were enriched in the outer mitochondrial membrane (OMM), where Zuc was specifically localized. The proximal proteome of Zuc showed a distinct set of proteins compared with that of Tom20, a representative OMM protein, indicating that chaperone function-related and endomembrane system/vesicle transport proteins are previously unreported interacting partners of Zuc. The functional relevance of several candidates in piRNA biogenesis was validated by derepression of transposable elements after knockdown. Our results present potential Zuc-interacting proteins, suggesting unrecognized biological processes.
Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE)
Authors: Munarko Yuda , Rampadarath Anand , Nickerson David 
Published: February 2023

The Transformer-based approaches to solving natural language processing (NLP) tasks such as BERT and GPT are gaining popularity due to their ability to achieve high performance. These approaches benefit from using enormous data sizes to create pre-trained models and the ability to understand the context of words in a sentence. Their use in the information retrieval domain is thought to increase effectiveness and efficiency. This paper demonstrates a BERT-based method (CASBERT) implementation to build a search tool over data annotated compositely using ontologies. The data was a collection of biosimulation models written using the CellML standard in the Physiome Model Repository (PMR). A biosimulation model structurally consists of basic entities of constants and variables that construct higher-level entities such as components, reactions, and the model. Finding these entities specific to their level is beneficial for various purposes regarding variable reuse, experiment setup, and model audit. Initially, we created embeddings representing compositely-annotated entities for constant and variable search (lowest level entity). Then, these low-level entity embeddings were vertically and efficiently combined to create higher-level entity embeddings to search components, models, images, and simulation setups. Our approach was general, so it can be used to create search tools with other data semantically annotated with ontologies - biosimulation models encoded in the SBML format, for example. Our tool is named Biosimulation Model Search Engine (BMSE).
Investigating ultrastructural morphology in MIRAGE syndrome (SAMD9)-derived fibroblasts using transmission electron microscopy.
Authors: Buonocore Federica , Balys Monika , Anderson Glenn , Achermann John C. 
Published: February 2023

Background: Heterozygous de novo variants in the gene SAMD9 cause the complex multisystem disorder, MIRAGE syndrome. Patients are characterised by myelodysplasia, infections, growth restriction, adrenal insufficiency, gonadal dysfunction and enteropathies. Pathogenic variants in SAMD9 are gain-of-function and enhance its role as a growth repressor, leading to growth restriction of many tissues. Two studies have reported changes in skin fibroblasts derived from MIRAGE patients, more specifically identifying enlarged endosomes. We have also previously shown subtle changes in endosome size in patients’ fibroblasts compared to controls. However, these variations in endosomes were not as marked as those described in the literature. Methods: We have performed an observational study using transmission electron microscopy (EM) in a larger number of cells derived from three patients’ fibroblasts to assess ultrastructure morphology compared to control images. Results: Consistent changes were observed in cell organelles in all patient samples. In particular, increased endosomal activity was detected, characterised by augmented pinocytosis and vesicle budding, increased endosome number, as well as by large lysosomes and endosomes. Endoplasmic reticulum was also prominent. Mitochondria appeared enlarged in selected cells, possibly due to cellular stress. Cell nuclei did not display major differences compared to controls. Conclusions: EM is a powerful tool to investigate morphological features of tissues and cell organelles, although EM data could be affected by sample preparation methodology, therefore potentially explaining the variability between independent studies, and its analysis can be dependent on the experience of the researcher. The increased endosomal activity we have observed in patients’ fibroblasts could indicate that SAMD9 regulates endocytosis of receptors, acting as an endosome fusion facilitator, or in lysosomal activation. However, the precise mechanism(s) by which SAMD9 regulates cell growth is still not fully understood, and further studies are needed to elucidate its pathogenic pathway and develop therapeutic approaches to support patients.
SILVER-COATED CUSTOM COMPONENTS FOR ACETABULAR AND HEMIPELVIS RECONSTRUCTION MITIGATE INFECTION RISK WITHOUT COMPROMISING BONE ONGROWTH
Authors: Sundaram A. , Woods J. , Clifton L. , Alt V. , Clark R.H. , Carey Smith R.L. 
Published: February 2023

Complex acetabular reconstruction for oncology and bone loss are challenging for surgeons due to their often hostile biological and mechanical environments. Titrating concentrations of silver ions on implants and alternative modes of delivery allow surgeons to exploit anti-infective properties without compromising bone on growth and thus providing a long-term stable fixation. We present a case series of 12 custom acetabular tri-flange and custom hemipelvis reconstructions (Ossis, Christchurch, New Zealand), with an ultrathin plasma coating of silver particles embedded between layers of siloxane (BioGate HyProtect™, Nuremberg, Germany).At the time of reporting no implant has been revised and no patient has required a hospital admission or debridement for a deep surgical site infection. Routine follow up x-rays were reviewed and found 2 cases with loosening, both at their respective anterior fixation. Radiographs of both cases show remodelling at the ilium indicative of stable fixation posteriorly. Both patients remain asymptomatic. 3 patients were readmitted for dislocations, 1 of whom had 5 dislocations within 3 weeks post-operatively and was immobilised in an abduction brace to address a lack of muscle tone and has not had a revision of their components.Utilising navigation with meticulous implant design and construction; augmented with an ultrathin plasma coating of silver particles embedded between layers of siloxane with controlled and long-term generation of silver ion diffusion has led to outstanding outcomes in this series of 12 custom acetabular and hemipelvis reconstructions. No patients were revised for infection and no patients show signs of failure of bone on growth and incorporation. Hip instability remains a problem in these challenging mechanical environments and we continue to reassess our approach to this multifaceted problem.
COMPARISON OF TIBIOTALOCALCANEAL ARTHRODESIS WITH BELOW-KNEE AMPUTATION WITH PROMS AND OBJECTIVE OUTCOMES
Authors: Manobianco A. , Enketan O. , Grass R. 
Published: February 2023

Tibiotalocalcaneal arthrodesis (TTCA) is a salvage procedure to functionally block the ankle and subtalar joints to treat severe ankle and hindfoot disease. Complication rates range between 20-40%, with below-knee amputation rate 1.5-19%. The heterogeneous patient cohort and indication(s) for surgery make post-operative outcomes difficult to predict. Consulting patients about potential pain and functional outcomes is difficult. When researching this area commonly, PROM data is used, less frequently functional objective measures like the 2-minute-walk-test (2MWT) are used. The aim was to compare the PROMs and objective outcomes between patients who underwent TTCA and BKA.Fifty-two patients underwent a TTCA using an intramedullary hindfoot nail. Indications for TTCA, post-traumatic OA, failed arthrodesis and malalignment. These patients were compared to 11 patients who underwent unilateral below knee amputation (BKA) due to trauma. Outcomes measures PROMs AOFAS ankle hindfoot scale and Shor-Form 36 (SF-36). Objective measures; 2MWT, Timed-up-and-go (TUG).Mean age TTCA 55.9, BKA 46.4. Average follow-up time 53 months. TTCA group had average 6.3 operations prior to arthrodesis (range 1-23). Of the TTCA group two ankles did not unite (7%), all complication rate 35%, 18% reported no pain. A significant negative correlation was demonstrated between the clinical outcome and the number of surgeries prior to the TTCA. TUG and 2MWT had significantly (p<0.05) better outcomes for the BKA group compared to TTCA. SF-36 BKA patients scored higher than the TTCA patients on physical functioning (p<0.01) and mental health (p<0.05) subscales as well as the mental component score (p<0.05).This study gives clinicians evidence about the natural history of hindfoot arthrodesis and functional outcomes from BKA. Hopefully this study will improve evidence to help patients and surgeons make decisions about expected surgical outcomes from TTCA and BKA procedures.
THE CHANGING FACE OF FEMORAL FRAGILITY FRACTURES: INCIDENCE; FRACTURE PATTERNS; AND MANAGEMENT
Authors: Gibson A. , Guest M. , Taylor T. , Gwynne Jones D. 
Published: February 2023

The purpose of this study was to determine whether there have been changes in the complexity of femoral fragility fractures presenting to our Dunedin Orthopaedic Department, New Zealand, over a period of ten years.Patients over the age of 60 presenting with femoral fragility fractures to Dunedin Hospital in 2009 −10 (335 fractures) were compared with respect to demographic data, incidence rates, fracture classification and treatment details to the period 2018-19 (311 fractures). Pathological and high velocity fractures were excluded.The gender proportion and average age (83.1 vs 83.0 years) was unchanged. The overall incidence of femoral fractures in people over 60 years in our region fell by 27% (p<0.001). Intracapsular fractures (31 B1 and B2) fell by 29% (p=0.03) and stable trochanteric fractures by 56% (p<0.001). The incidence of unstable trochanteric fractures (31A2 and 31A3) increased by 84.5% from 3.5 to 6.4/10,000 over 60 years (p = 0.04). The proportion of trochanteric fractures treated with an intramedullary (IM) nail increased from 8% to 37% (p <0.001). Fewer intracapsular fractures were treated by internal fixation (p<0.001) and the rate of acute total hip joint replacements increased from 13 to 21% (p=0.07). The incidence of femoral shaft fractures did not change significantly with periprosthetic fractures comprising 70% in both cohorts.While there has been little difference in the numbers there has been a decrease in the incidence of femoral fragility fractures likely due to the increasing use of bisphosphonates. However, the incidence of unstable trochanteric fractures is increasing. This has led to the increased use of IM nails which are increasingly used for stable fractures as well.The increasing complexity of femoral fragility fractures is likely to have an impact on implant use, theatre time and cost.
OUTPATIENT PERCUTANEOUS ULTRASOUND-GUIDED FLEXOR TENOTOMY FOR NEUROPATHIC APICAL TOE ULCERS
Authors: Weber A. , Dares M. 
Published: February 2023

Percutaneous flexor tenotomy involves cutting the flexor digitorum tendons to correct claw toe deformity to treat apical pressure areas and prevent subsequent infection in patients with peripheral neuropathy. Performing this under ultrasound guidance provides reassurance of complete release of the tendon and increases procedural safety.This study is a retrospective case series evaluating the effectiveness, safety, and patient satisfaction of performing percutaneous ultrasound-guided flexor tenotomy in an outpatient setting. People with loss of protective sensation, a digital flexion deformity, and an apical toe ulcer or pre-ulcerative lesion who presented to our institution between December 2019 and June 2022 were included in this study. Participants were followed-up at a minimum of 3 months. Time to ulcer healing, re-ulceration rate, patient satisfaction, and complications were recorded. An Australian cost analysis was performed comparing this procedure performed in rooms versus theatres.There were 28 ulcers and 41 pre-ulcerative lesions. A total of 69 tenotomy procedures were performed on 38 patients across 52 episodes of care. The mean time to ulcer healing was 22.5 +/- 6.4 days. There were 2 cases of re-ulceration. 1 patient sustained a transfer lesion. There were four toes that went onto require amputation, all in the setting of pre-existing osteomyelitis. 94% of patients strongly agreed that they were satisfied with the outcome of the procedure. Costs saved were estimated to be $1426.Flexor tenotomy is a minimally invasive procedure that can be performed in the outpatient setting, and therefore without delay to treatment, reducing risk of ulcer progression and need for subsequent amputation. This is the first study to report on flexor tenotomy under ultrasound-guidance.Ultrasound-guided percutaneous flexor tenotomy is safe and effective, with high patient satisfaction and low recurrence rates. This performance in the outpatient setting ensures significant time and cost savings for both the practitioner and patient.
FAILURE TO MEET EXPECTATIONS OF SPORT OR RECREATION FOLLOWING TOTAL HIP ARTHROPLASTY IS ASSOCIATED WITH YOUNGER AGE, HIGH BMI, AND POOR GENERAL HEALTH
Authors: Matt A. , Kemp J.L. , Mosler A.B. , Semciw A.L. , Gooden B.R. , O'Sullivan M.D. , Lyons M.C. , Salmon L. 
Published: February 2023

Total hip arthroplasty (THA) has high rates of patient satisfaction; however patient expectations for recreational and sporting activities are not always met. Our study aimed to identify preoperative factors that predict whether patient expectations for sporting or recreational activity are met 12 months following THA.Patient reported outcome measures (PROMs) were collected prospectively from 2015-2018 at one private hospital in Sydney. Age, gender, postcode, weight, and height were recorded preoperatively. Included participants underwent primary THA by one of the investigating surgeons. Univariable and multivariable analyses were performed with an expectation fulfilment score used as the primary outcome variable. Preoperative predictor variables included: age, gender, BMI, Socio-economic Indexes for Areas (SEIFA), Oxford Hip Score, Hip Osteoarthritis Outcome Score, EQ-5D-5L and EQ Visual Analogue Scale (EQ VAS).1019 participants were eligible and included. 13% reported that preoperative expectations of sport or recreation were not met at 12 months. Younger age, lower preoperative EQ VAS, and higher BMI were associated with failed expectations on multivariable analysis. Odds of failed expectations increased by 2% for every one year younger in age (OR= 0.98, 95% CI = 0.96 to 1.00, p=.048), by 2% for every one point lower on EQ VAS (OR=0.98, 95% CI = 0.98 to 0.99, p=.002), and by 4% for every one-point increase in BMI (OR = 1.04, 95% CI = 1.00 to 1.09, p=.042).Failure to have expectations met for sporting or recreational activity was associated with younger age, poorer general health, and high BMI. With a rise in younger patients who likely have higher physical demands, a tailored preoperative education is preferable to generic models to better manage patient expectations.Younger age, higher BMI, and poorer health may predict unmet expectations for sport and recreation after THA. Tailored education in these groups should be considered.