bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hardware Salvage in the Lower Extremity after Flap Coverage: 10-Year Single Center Outcomes Analysis
Authors: Mardourian Markos , Wiesemann Gayle S. , Sachse Caroline C. , Nichols David S. , Hagen Jennifer E. , Chim Harvey 
Published: July 2023

Background:
An unanswered question with open tibial fractures is whether the type of flap used affects hardware retention. Flap survival may not equate hardware retention or limb salvage. In this study, we performed a 10-year single institution review and analysis of all patients who had placement of hardware for open tibial fractures followed by flap coverage.

Methods:
Inclusion criteria consisted of patients who underwent pedicled or free flap coverage of Gustilo IIIB or IIIC tibial fractures requiring open reduction and internal fixation. Outcomes and complications were statistically analyzed based on flap type. Flap type was stratified into free versus pedicled flaps and muscle versus fasciocutaneous flaps. Primary outcome measures included hardware failure and infection requiring hardware removal. Secondary outcome measures included limb salvage, flap success, and fracture union.

Results:
Overall primary outcome measures were better for pedicled flaps (n = 31), with lower rates of hardware failure and infection (25.8%; 9.7%) compared with free flaps (n = 27) (51.9%; 37.0%). Limb salvage and flap success was not different comparing pedicled and free flaps. There was no significant difference in outcomes between muscle and fasciocutaneous flaps. Multivariable analysis showed that patients who had free versus pedicled flaps or muscle versus fasciocutaneous flaps had a higher chance of hardware failure. A formal orthoplastic team was established in the period from 2017 to 2022, after which flap numbers were higher and hardware failure less for pedicled and fasciocutaneous flaps.

Conclusions:
Pedicled flaps were associated with lower rates of hardware failure and infection requiring hardware removal. A formal orthoplastic team improves hardware-related outcomes.
Abdominal Wall Incisional Hernia Repair with the Anterior Component Separation Technique and Reinforcement with an Anterior Rectus Abdominis Sheath Flap
Authors: Ishimoto Yuki , Otsuki Yuki , Nuri Takashi , Ueda Koichi 
Published: July 2023

Summary:
Mesh repair is currently the mainstay of treatment for abdominal wall incisional hernias and is considered the standard of care. However, if radiotherapy is used, the possibility of complications such as exposure or infection of the prosthesis after the surgery as a complication of the radiotherapy is a concern. The patient was a 51-year-old woman who underwent laparotomy by a mid-abdominal incision for ovarian tumors. Approximately 2 years later, the patient presented with a hypertrophic scar of the wound and mild pain in the scar. The hypertrophic scar was improved gradually by corticosteroid injection. However, she had a bulge on the left side of the umbilicus just below the hypertrophic scar. Computed tomography showed a 65 × 69 mm2 hernial orifice on the left side of the umbilical abdominal wall, and an abdominal wall incisional hernia was diagnosed. The patient underwent closure by the ACS technique and reinforcement by unilateral inversion of the anterior rectus abdominis sheath for the abdominal wall incisional hernia. No recurrence of the hypertrophic scar or abdominal wall incisional hernia was observed during the follow-up period. In the present case, the hernial orifice was closed by a modified ACS technique that was combined with the anterior rectus abdominis sheath turnover flap. This technique is likely a less invasive and relatively simple method resulting in a tighter repair of the abdominal hernia than the ACS method alone, without prostheses.
Budget Impact of Minimally Invasive Surgical Treatments of Benign Prostatic Hyperplasia: An Analysis of 6 States With Limited New Technology Coverage
Authors: Rojanasarot Sirikan , Baxter Julie , Suzuki Emi , Bresee James , Chughtai Bilal 
Published: July 2023

Purpose:
Prostatic urethral lift (PUL) and water vapor thermal therapy (WVTT) for benign prostatic hyperplasia (BPH) differ in treatment durability and cost of disposables, possibly leading to different long-term costs. This study compares the budget impact of PUL and WVTT for US payers in 6 states (Alabama, New Jersey, New York, Oregon, Pennsylvania, and Washington) over a 5-year time horizon.

Materials and Methods:
An Excel-based budget impact model was developed to estimate average total medical costs per patient of PUL and WVTT at years 1 and 5 for men with moderate-to-severe BPH. After undergoing an index procedure, men could experience adverse events (AEs) or retreatment while accumulating costs over time. Clinical inputs were derived from PUL and WVTT clinical trials while cost inputs were derived from 2021 Medicare reimbursement rates.

Results:
At year 1, per-patient costs of PUL ranged from $5690 (Alabama) to $7323 (New Jersey) compared with year 1 costs of WVTT that ranged from $1829 (Alabama) to $2330 (New Jersey). The lower year 1 costs of WVTT stemmed from both lower procedural costs relative to PUL and better durability (lower costs associated with fewer retreatments and AEs). The cost differences between the 2 treatments continued to diverge in years 2 to 5. Through year 5, the cost savings associated with WVTT vs PUL ranged from $4383 (Alabama) to $5649 (New Jersey).

Conclusions:
Compared with PUL, the use of WVTT could potentially allow payers to cover BPH treatments for more members without compromising clinical outcomes or increasing budgets.
Personalized medicine in sarcoidosis: unravelling biomarkers for targeted care
Authors: Francesqui Joel , Marrades Pau , Sellares Jacobo 
Published: July 2023

Purpose of reviewThis review provides an assessment of biomarkers in sarcoidosis, aiming to address the need for improved diagnostic, prognostic and management tools. Sarcoidosis presents diagnostic challenges, necessitating the search for reliable biomarkers to guide clinical decisions.Recent findingsEstablished biomarkers such as serum angiotensin-converting enzyme (ACE) and serum interleukin-2 receptor (sIL-2R) have limitations in sensitivity and specificity. FDG-PET/CT imaging shows promising results in assessing disease activity and guiding immunosuppression. Gene expression profiling studies reveal potential biomarkers, particularly involving TH1 immune response and IFN-γ-driven signalling pathways. The field of omics sciences offers opportunities for novel biomarker discovery.SummaryThese findings have implications for clinical practice and research. The limitations of established biomarkers underscore the need for improved diagnostic tools in sarcoidosis. The potential of FDG-PET/CT imaging requires further exploration. Gene expression profiling and omics sciences offer avenues for discovering novel biomarkers to enhance diagnosis and predict disease progression. Such advancements can facilitate personalized treatment strategies and improve patient outcomes. Continued research is vital to validate the efficacy and clinical applicability of these biomarkers. Overall, this review emphasizes ongoing efforts to advance sarcoidosis biomarkers research and improve disease management.
Urine CXCL10 to Assess BK Polyomavirus Replication After Kidney Transplantation
Authors: Haller Jana , Diebold Matthias , Leuzinger Karoline , Wehmeier Caroline , Handschin Joelle , Amico Patrizia , Hirt-Minkowski Patricia , Steiger Jürg , Dickenmann Michael , Hirsch Hans H. , Schaub Stefan 
Published: July 2023

Background.
Urine CXCL10 is a biomarker for renal allograft inflammation induced by rejection, urinary tract infection, or BK polyomavirus (BKPyV) replication. This study aimed to compare urine CXCL10 levels in different stages of BKPyV reactivation and to investigate urine CXCL10 as a biomarker for BKPyV replication.

Methods.
We included 763 urine samples (235 patients) from an interventional, randomized trial obtained in the context of regular screening for urine CXCL10 levels. All urine samples had a complete urine sediment analysis, no rejection episode noted within 30 d before urine collection, and a urine decoy cell analysis was conducted within ±3 d.

Results.
Urine CXCL10 levels were 2.31 ng/mmol in samples without BKPyV viruria, slightly rose to 4.35 ng/mmol with BKPyV viruria, and then markedly increased to 16.42 ng/mmol when decoy cells were detectable, but still in the absence of BKPyV DNAemia (P < 0.001). The highest urine CXCL10 values were observed in samples with BKPyV DNAemia (median 42.59 ng/mmol). The area under the curve of urine CXCL10 levels to detect ≥3 decoy cells was 0.816. At a CXCL10 cutoff of 3 ng/mmol, the negative predictive value was 97%. The area under the curve of urine CXCL10 levels to detect BKPyV DNAemia was 0.882, with a negative predictive value of 99% at a CXCL10 cutoff of 3 ng/mmol.

Conclusions.
Urine CXCL10 levels are already significantly elevated in BKPyV viruria (especially with decoy cell shedding) and further increase with BKPyV DNAemia. Low urine CXCL10 values can rule out the presence of ≥3 decoy cells and BKPyV DNAemia with high certainty.
The ratio of interacting miRNAs’ expressions is a robust biomarker for disease classification in multi-center data
Authors: Zhang Yonghao , Ma Cuidie , Ding Rui , Chen Han , Xu Lida , Yu Changyuan 
Published: July 2023

AbstractBackgroundMany miRNA-based diagnostic models have been constructed to distinguish diseased individuals. However, due to the inherent differences across different platforms or within multi-center data, the models usually fail in the generalization for medical application.ResultsHere, we proposed to use the within-sample expression ratios of related miRNA pairs as markers, by utilizing the internal miRNA: miRNA interactions. The ratio of the expression values between each miRNA pair turned out to be more stable cross multiple data source. Moreover, we adopted the genetic algorithm to solve the curse of dimensions when exploring the features.ConclusionsThe application results on three example datasets demonstrated that the expression ratio of interacting miRNA pair is a promising type of biomarker, which is insensitive to batch effects and has better performance in disease classifications.
Training and testing a CNN-based engine for brain MRI scan classification and segmentation
Authors: Dhawan Kunaal , Agrawal Utkarsh 
Published: July 2023

AbstractBiomedical imaging data (from X-rays, CT scans, MRIs) is a rich and crucial source of information for diagnosing and treating patients, yet the large volume of visual data generated can be challenging even for the most experienced clinical professionals to handle and use for diagnosis with high accuracy. With the traditional diagnosis approaches, patients usually face high costs too. Sometimes, abnormalities remain unspotted, causing delays in intervention which can be the difference between saving and losing patient lives. Most traditional radiomics studies use hand-crafted feature extraction techniques, such as texture analysis, followed by conventional machine learning classifiers, such as random forests and support vector machines (SVMs). In this paper, we establish that X-ray, MRI or CT-image classification using convolutional neural networks (CNNs) could be an efficient, cost-effective and fast approach for diagnosis and interpretation. The research is focused on training a CNN algorithm to develop diagnostic analysis power using 250 brain MRI images and then testing the accuracy and predictive power of the developed CNN algorithm on 5 images. We have shown the superiority of CNN models in image classification compared to traditional ML Classifiers that used an extensive ablation study. We have then compared a selected set of existing models with the new model we have built based on the EfficientNet v2-S architecture with a high classification accuracy of 98% – showing a high predictive power to provide various differential diagnoses from the brain MRI scans.
Attitudes to phage therapy among Australian infectious diseases physicians
Authors: Plymoth Martin , Lynch Stephanie A. , Khatami Ameneh , Sinclair Holly A. , Sacher Jessica C. , Zheng Jan , Lin Ruby CY. , Iredell Jonathan R. 
Published: July 2023

AbstractDue to the rise in antimicrobial resistance (AMR), there has been an increased interest in phage therapy to treat multi-drug resistant infections. In Australia, phage therapy is predominantly used in small clinical studies or for compassionate use, however, despite its potential expansion in modern medicine, the perception of phage therapy among medical professionals remains largely unknown. Therefore, we conducted a national survey of Australian infectious diseases and clinical microbiology advanced trainees and specialists to assess their knowledge, areas of interest, and concerns around the use of phage therapy in clinical practice in Australia. Our survey received 92 responses from infectious diseases and clinical microbiology professionals across all states of Australia. The majority of those surveyed believed that the current national plan for controlling AMR is inadequate and that phage therapy may be an effective solution; with 97% of respondents indicating that they would consider using phage therapy meeting established guidelines for purity and safety (United States Food and Drug Administration and/or European Union guidelines). The respondents indicated a preference for bespoke therapy, with Gram-negative pathogens highlighted as priority targets. Alongside the phage therapy delivery protocols, therapeutic phage monitoring (TPM; like therapeutic drug monitoring (TDM)) was considered important. Cystic Fibrosis, lung-infections, prosthetic device related infections, and infections among patients following transplantation and/or immunosuppression were highly ranked in terms of priorities for clinical syndromes. Accessibility was highlighted as a barrier to phage therapy, specifically timely access (72%) and logistics of phage procurement and administration (70%). Altogether, these results suggest the support of phage therapy among infectious diseases and clinical microbiology advanced trainees and specialists in Australia, and highlights areas of focus and priority in order to advance phage therapy in modern medicine.
Genetic Susceptibility to Astrovirus Diarrhea in Bangladeshi Infants
Authors: Chen Laura , Munday Rebecca M. , Haque Rashidul , Duchen Dylan , Nayak Uma , Korpe Poonum , Mentzer Alexander J. , Kirkpatrick Beth D. , Wojcik Genevieve L. , Petri William A. , Duggal Priya 
Published: July 2023

AbstractAstroviral infections commonly cause acute nonbacterial gastroenteritis in children globally. However, these infections often go undiagnosed outside of research settings. There is no treatment available for astrovirus, and Astroviridae strain diversity presents a challenge to potential vaccine development. To address our hypothesis that host genetic risk factors are associated with astrovirus disease susceptibility, we performed a genome-wide association study (GWAS) of astrovirus infection in the first year of life from children enrolled in two Bangladeshi birth cohorts. We identified a novel region on chromosome 1 near the loricrin gene (LOR) associated with astrovirus diarrheal infection (rs75437404, meta-analysis p-value=8.82×10−9, A allele OR=2.71) and on chromosome 10 near the prolactin releasing hormone receptor gene (PRLHR) (rs75935441, meta-analysis p-value=1.33×10−8, C allele OR=4.17). The prolactin-releasing peptide has been shown to influence feeding patterns and energy balance in mice. Additionally, several SNPs in the chromosome 1 locus have previously been associated with expression of innate immune system genesPGLYRP4, S100A9, andS100A12. This study identified two significant host genetic regions that may influence astrovirus diarrhea susceptibility and should be considered in further studies.
The impact ofERP29on the progression of pharyngeal squamous cell carcinoma
Authors: Carron Juliana , Coser Lilian de Oliveira , Kelemen Andrea , Tolstonog Genrich V , Lima Carmen Silvia Passos , Lourenço Gustavo Jacob 
Published: July 2023

AbstractObjectivesWe investigatedERP29gene role on pharynx squamous cell carcinoma (PSCC) progression in cisplatin (CDDP)-sensitive (FaDu and LAU-2063), CDDP-treated (FaDu-CDDP), and CDDP-resistant (FaDu-R) cells.Materials and MethodsCells, modified to induceERP29overexpression or silencing, were mainly submitted to cell proliferation, necrosis, and migration assay. E-cadherin immunoexpression was assessed in three-dimensional spheroids. WNT, MAPK, and PI3K/AKT pathways genes’ expression were identified by PCR array and validated by qPCR. The influence of microRNA miR-4421 inhibitor onERP29expression, and its target genes, were quantified by qPCR.ResultsERP29silencing especially decreased necrotic cell death and increased migration in CDDP-sensitive, treated, and resistant cells, and decreased E-cadherin immunoexpression in CDDP-sensitive three-dimensional-spheroids. During CDDP treatment,ERP29silencing increased cell proliferation. In CDDP-sensitive cells,ERP29silencing increased the expression of several genes involved in WNT, MAPK, and PI3K/AKT pathways and decreasedCASP9expression. During CDDP treatment,ERP29silencing decreasedMDM2andCASP9expression. In CDDP-resistant cells,ERP29silencing increasedSOS1,MAPK1,AKT1,ITGAV, andCCNE1; and decreasedKRAS,JUN,MDM2, andCASP9expression. In addition, miR-4421 inhibition increasedERP29expression and decreasedMAPK1,AKT1,andJUNexpression in CDDP-sensitive cells; andSOS1,MAPK1,AKT1,andITGAVin CDDP-resistant cells, suggesting a potential therapeutic use for miR-4421 inhibitor.ConclusionsERP29silencing seems to decrease necrosis and increase migration of PSCC cells by modulating genes enrolled in WNT, MAPK, and PI3K/AKT pathways. Once validated, our data may enable target therapy development based on ensuringERP29expression that could benefit patients with CDDP-sensitive and resistant tumors.
Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure
Authors: Ishizawa Hidehiro , Tashiro Yosuke , Inoue Daisuke , Ike Michihiko , Futamata Hiroyuki 
Published: July 2023

AbstractThe way to deal with higher-order effects (i.e., modification of pairwise interactions by third-party species) has been a major consideration in community ecology. Ignoring these effects is not in line with reality, yet fully considering them make the situation overly complex. Here, we propose a simple framework incorporating higher-order effects into a bottom-up community modeling, and assessed its validity using a seven-member synthetic bacterial community on a host plant, duckweed. Our findings revealed that actual interspecies interactions in community could not be predicted from pairwise co-culturing results; however, using information from trio combinations allowed for acceptable prediction. In addition, inclusion of four-, five-, and six-member combinations did not markedly enhance the prediction accuracy from trio-based prediction, suggesting that trio combinations, the smallest unit of higher-order effects, provide a reasonable baseline to unravel complex interaction networks. Building on this finding, we developed a prediction rule to estimate the structure of 4 – 7 member communities based on information from ≤ 3-member combinations, which yielded significantly better accuracy (relative mean square percentage errors of 22.7% – 61.2%) than pairwise-based model (53.5% – 185.2%). This highlights the possibility of establishing a quantitative link between the interspecies interactions and community structure, by observing beyond-pairwise combinations.
Dearth of smoking-induced mutations in NSRO-driven non-small-cell lung cancer despite smoking exposure
Authors: Huang Chen-Yang , Jiang Nanhai , Shen Meixin , Lai Gillianne , Tan Aaron C. , Jain Amit , Saw Stephanie P. , Ang Mei-Kim , Ng Quan Sing , Lim Darren Wan-Teck , Kanesvaran Ravindran , Tan Eng-Huat , Tan Wan Ling , Ong Boon-Hean , Chua Kevin L. , Anantham Devanand , Takano Angela , Lim Tony K.H. , Tam Wai Leong , Sim Ngak Leng , Skanderup Anders J. , Tan Daniel S.W. , Rozen Steven G. 
Published: July 2023

AbstractNon-small cell lung cancers (NSCLCs) in non-smokers are mostly driven by mutations in the oncogenesEGFR, ERBB2,andMET, and fusions involvingALKandRET. We term these “non-smoking-related oncogenes” (NSROs). In addition to occurring in non-smokers, NSRO-driven tumors also occur in smokers, and the clonal architecture and genomic landscape of these tumors remain unknown. We investigated genomic and transcriptomic alterations in 173 tumor sectors from 48 patients with NSRO-driven or typical-smoking NSCLCs. NSRO-driven NSCLCs in smokers and non-smokers have similar genomic landscapes. Surprisingly, even in patients with prominent smoking histories, the mutational signature caused by tobacco smoking was essentially absent in NSRO-driven NSCLCs. However, NSRO-driven NSCLCs in smokers had higher transcriptomic activities related to regulation of the cell cycle, suggesting that smoking still affects tumor phenotype independently of genomic alterations.Statement of significanceThis study highlights the lack of genomic scars caused by smoking in NSCLCs driven by non-smoking-related oncogenes regardless of smoking history. The impact of smoking on these tumors is mainly non-genomic. The transcriptomic features of NSCLCs associated with smoking may help in the development of therapeutic approaches.
Malaria resistance-related biological adaptation and complex evolutionary footprints of Tai-Kadai people inferred from 796 genomes
Authors: Duan Shuhan , Wang Mengge , Wang Zhiyong , Liu Yan , Jiang Xiucheng , Su Haoran , Cai Yan , Sun Qiuxia , Sun Yuntao , Li Xiangping , Chen Jing , Zhang Yijiu , Yan Jiangwei , Nie Shengjie , Hu Liping , Tang Renkuan , Yun Libing , Wang Chuan-Chao , Liu Chao , Yang Junbao , He Guanglin 
Published: July 2023

ABSTRACTPathogen-host adaptative interaction and complex population demographical processes, including admixture, drift and Darwen selection, have considerably shaped the Neolithic-to-Modern Western Eurasian population structure and genetic susceptibility to modern human diseases. However, the genetic footprints of evolutionary events in East Asia keep unknown as the underrepresentation of genomic diversity and the design of large-scale population studies. We reported one aggregated database of genome-wide-SNP variations from 796 Tai-Kadai (TK) genomes, including Bouyei first reported here, to explore the genetic history, population structure and biological adaptative features of TK-speaking people from Southern China and Southeast Asia. We found geography-related population substructure among TK-speaking people using the state-of-the-art population genetic structure reconstruction techniques based on the allele frequency spectrum and haplotype-resolved phased fragments. We found that the Northern TK-speaking people from Guizhou harboured one TK-dominant ancestry maximised in Bouyei people, and the Southern one from Thailand obtained more influences from Southeast Asians and indigenous people. We reconstructed the fitted admixture models and demographic graphs, which showed that TK-speaking people received gene flow from ancient rice farmer-related lineages related to the Hmong-Mien and Austroasiatic people and Northern millet farmers associated with the Sino-Tibetan people. Biological adaptation focused on our identified unique TK lineages related to Bouyei showed many adaptive signatures conferring Malaria resistance and low-rate lipid metabolism. Further gene enrichment, the allele frequency distribution of derived alleles, and their correlation with the incidence of Malaria further confirmed thatCR1played an essential role in the resistance of Malaria in the ancient “Baiyue” tribes.