bluuebunny/crossref_metadata_2025_split huggingface dataset:
The value of surgeon’s perception during transurethral resection of bladder tumors: can we trust in our eyes and experience to predict grade and staging?
Authors: Vale Luís , Sousa José , Abreu-Mendes Pedro , Vale Pedro , Dias Nuno , Dinis Paulo , Antunes-Lopes Tiago , Silva João 
Published: September 2022

Background:
Transurethral resection of newly diagnosed bladder tumors (TURBT) is a hallmark ¡n the treatment of bladder cancer. We evaluated the surgeon capacity to predict bladder tumor stage (T), grade, and presence of muscular layer based upon cystoscopic characteristics during primary TURBT.

Methods:
Prospective study enrolling 100 consecutive patients undergoing primary TURBT for newly diagnosed bladder cancers. Cystoscop¡c tumor characteristics at the time of TURBT was evaluated by an urology senior and a resident regarding histological grade, invasion (T stage), and presence of muscular layer in the specimen. We analyzed the surgeon’s accuracy in predicting these parameters using the final histology as gold standard. In addition, the predictive capacity between seniors and residents was compared.

Results:
The resident’s arm correctly predicted tumor invasiveness in 76% of cases, while seniors correctly predicted 87% of cases. Regarding tumor grade, high grade cancer was reported in 78% of the specimens and 75% and 77% of them were correctly predicted by residents and seniors, respectively. Finally, 80% of the TURBT specimens had muscle representativeness. In nearly 75% of the cases, both resident and senior correctly predicted the TURBT resection depth (presence of detrusor muscle in the specimen). The positive predictive value for this parameter was 79% for the resident, and 81% for the senior, and the negative predictive value was 25% and 40%, respectively.

Conclusion:
The surgeon’s naked eye analysis showed a good, but limited predictive ability to detect non-muscle invasive and high-grade bladder tumors in TURBT specimens. Positive predictive value for muscle representativeness is around 80%, which reinforces the need of carrying out a careful and extensive TURBT, irrespective of the surgeon experience.
Machine Learning for Automated Calculation of Vestibular Schwannoma Volumes
Authors: Cass Nathan D. , Lindquist Nathan R. , Zhu Qibang , Li Hao , Oguz Ipek , Tawfik Kareem O. 
Published: September 2022

Hypothesis
Machine learning-derived algorithms are capable of automated calculation of vestibular schwannoma tumor volumes without operator input.

Background
Volumetric measurements are most sensitive for detection of vestibular schwannoma growth and important for patient counseling and management decisions. Yet, manually measuring volume is logistically challenging and time-consuming.

Methods
We developed a deep learning framework fusing transformers and convolutional neural networks to calculate vestibular schwannoma volumes without operator input. The algorithm was trained, validated, and tested on an external, publicly available data set consisting of magnetic resonance imaging images of medium and large tumors (178–9,598 mm3) with uniform acquisition protocols. The algorithm was then trained, validated, and tested on an internal data set of variable size tumors (5–6,126 mm3) with variable acquisition protocols.

Results
The externally trained algorithm yielded 87% voxel overlap (Dice score) with manually segmented tumors on the external data set. The same algorithm failed to translate to accurate tumor detection when tested on the internal data set, with Dice score of 36%. Retraining on the internal data set yielded Dice score of 82% when compared with manually segmented images, and 85% when only considering tumors of similar size as the external data set (>178 mm3). Manual segmentation by two experts demonstrated high intraclass correlation coefficient (0.999).

Conclusion
Sophisticated machine learning algorithms delineate vestibular schwannomas with an accuracy exceeding established norms of up to 20% error for repeated manual volumetric measurements—87% accuracy on a homogeneous data set, and 82% to 85% accuracy on a more varied data set mirroring real world neurotology practice. This technology has promise for clinical applicability and time savings.
Safety Competency
Authors: Dillon-Bleich Kimberly , Dolansky Mary A. , Burant Christopher J. , Madigan Elizabeth A. , Singh Mamta K. 
Published: September 2022

Background:
Patient safety is a priority in health care systems. Nurses' safety competence along with environmental and personal factors plays a role in patient safety.

Purpose:
The purpose of this study was to explore the relationships among safety competency, structural empowerment, systems thinking, level of education, and certification.

Methods:
A cross-sectional exploratory design was used to collect data from nurses (n = 163) practicing in a large Midwestern hospital system.

Results:
There were significant positive correlations between safety competency and (a) structural empowerment, (b) systems thinking, and (c) certification. Systems thinking explained 12.9% of the variance in the knowledge component of safety competency and 6.8% of the variance in the skill component of safety competency. Certification explained 2.4% of the variance in the skill component of safety competency.

Conclusions:
Understanding factors that affect safety competency supports the development of effective interventions that may improve safety.
Data for Equity: Creating an Antiracist, Intersectional Approach to Data in a Local Health Department
Authors: Gould L. Hannah , Farquhar Stephanie E. , Greer Sophia , Travers Madeline , Ramadhar Lisa , Tantay L. , Gurr Danielle , Baquero María , Vasquez Ayanna 
Published: September 2022

Objective:
To develop recommendations to embed equity into data work at a local health department and a framework for antiracist data praxis.

Design:
A working group comprised staff from across the agency whose positions involved data collection, analysis, interpretation, or communication met during April-July 2018 to identify and discuss successes and challenges experienced by staff and to generate recommendations for achieving equitable data practices.

Setting:
Local health department in New York City.

Results:
The recommendations encompassed 6 themes: strengthening analytic skills, communication and interpretation, data collection and aggregation, community engagement, infrastructure and capacity building, and leadership and innovation. Specific projects are underway or have been completed.

Conclusions:
Improving equity in data requires changes to data processes and commitment to racial and intersectional justice and process change at all levels of the organization and across job functions. We developed a collaborative model for how a local health department can reform data work to embed an equity lens. This framework serves as a model for jurisdictions to build upon in their own efforts to promote equitable health outcomes and become antiracist organizations.
Pausing TPN to Decrease Abnormal Newborn Screens: A NICU Quality Initiative
Authors: Wiggins Jaclyn B. , Khan Marium , Vergales Brooke D. 
Published: September 2022

Introduction:
Detection of metabolic and genetic disorders via the newborn screen (NBS) remains a great diagnostic achievement in medicine. Unfortunately, many false positives for neonates due to acute illness lead to repeat testing. For example, the rate of abnormal NBS in very low birth weight (VLBW) neonates at the University of Virginia was 66%, with 23% due to total parenteral nutrition (TPN) on the amino acid profile.

Methods:
This study describes a quality improvement (QI) initiative completed in the NICU at a quaternary care center. The primary and secondary outcomes were the percentage of abnormal NBSs in VLBWs and all admissions. The intervention required a pause in TPN, and a dextrose-containing fluid ran for 4 hours before collecting the NBS. During PDSA cycle 1, the TPN pause occurred at 1400, and the collection of the NBS occurred at 1800. During PDSA cycle 2, we aimed to decrease the number of blood draws per neonate and, thus, paused the TPN at 0000 to enable NBS collection at 0400 with routine morning laboratory work.

Results:
The rate of abnormal screens in VLBWs decreased from 66% to 49%; P < 0.006; 95% CI, 0.04–0.27, and the rate of abnormal screens in all admissions dropped from 45.2% to 28.8%; P < 0.0001; 95% CI, 0.06–0.51. Hospital costs decreased from $244.79 to $170.86 per patient in the cost of the NBS cards alone.

Conclusion:
By pausing TPN for 4 hours before drawing the NBS, we decreased the number of abnormal NBS in all admissions while also decreasing hospital costs.
The Objective Buttocks Assessment Scale (OBAS): a new and complete method to assess the gluteal region.
Authors: Roccaro Giovanni , Hersant Barbara , Pensato Rosita , Pizza Chiara , Rega Umberto , D’Andrea Francesco , Meningaud Jean Paul , La Padula Simone 
Published: September 2022

Introduction:
New treatment methods to improve and enhance buttocks appearance require globally accepted scales for aesthetic research and patient evaluation. The purpose of our study was to develop a set of grading scales for objective assessment of the gluteal region and assess their reliability and validity.

Materials and methods:
Twelve photonumeric grading scales were created. Eleven aesthetic experts rated photographs of 650 women in 2 validation sessions. Responses were analyzed to assess inter-rater and intra-rater reliability. The Rasch model was used as part of the validation process.

Results:
All the scales exceeded criteria for acceptability, reliability and validity. Overall inter-rater reliability and intra-rater reliability were both “almost perfect” (p=0.15 and p=0.16 respectively).

Conclusion:
Consistent outcomes between raters and by individual raters at 2 time points confirm the reliability of the Objective Buttocks Assessment Scale in female patients and suggest it will be a valuable tool for use in research and clinical practice.
Short-term Administration of the HIV Protease Inhibitor Saquinavir Improves Skull Bone Healing with Enhanced Osteoclastogenesis
Authors: Liu Haixia , Shen Yun , Zhao Bingkun , Poon Enoch H. , Qi Shengcai , Ker Dai Fei Elmer , Billiar Timothy R. , Cooper Gregory M. , Xu Yuanzhi , Wang Dan 
Published: September 2022

Background:Utilizing immunomodulatory methods to address the challenging issue of craniofacial bone repair may be a potentially effective approach. The protease inhibitor Saquinavir (SQV) has shown to inhibit the inflammatory response by targeting the TLR4/MyD88. Independently, inhibition of TLR4 or MyD88 led to enhanced skull bone repair. Therefore, we aimed to investigate the effects of SQV on skull bone healing.Methods:The effects of SQV on skull bone healing was assessed via gene expression, histology, immunohistochemistry and tomography in a mouse calvarial defect model. Subsequently, the role of SQV in cell viability, migration, osteogenic and osteoclastogenic differentiation was also evaluatedin vitro.Results:1-week SQV administration improved skull bone healing based on µCT and histomorphometric analyses. Compared to the vehicle control, 1-week SQV treatment (1) enhanced osteoclast infiltration (TRAP staining) at day 7, but not at days 14 and 28; (2) induced more CD206+M2 macrophage infiltration, but not F4/80+M0 macrophages at days 7, 14 and 28; and (3) elevated osteoclastogenic geneRANKL(qPCR) expression and other osteogenic and cytokine expression. Furthermore,in vitrodata showed that SQV administration did not influence MC3T3-E1 cell migration or mineralization, while higher concentrations of SQV inhibited cell viability. SQV treatment also enhanced the osteoclastic differentiation of bone marrow-derived precursors, and partially reversed HMGB1-driven osteoclastogenesis inhibition and elevated pro-inflammatory cytokine expression.Conclusions:The improved skull bone repair following short-term SQV treatment may involve enhanced osteoclastogenesis and modulated inflammatory response post-skull injury.
Transtibial prosthetic socket fitting: Australian prosthetist perspectives on primary challenges, management strategies, and opportunities for workflow and technological innovation
Authors: Armitage Lucy , McDonald Kirsty A. , Kark Lauren , Buller Angela , Ford Belinda 
Published: September 2022

Background:
Following transtibial amputation, a custom-built socket is the most common interface between the prosthesis and residual limb. Desire from both prosthetists and prosthesis users for improved socket fitting processes have been well documented. However, there is currently limited information available about prosthetists’ experiences of how prosthetic manufacturing workflow can contribute to socket fit problems.

Objectives:
This study aims to determine how socket fit problems are currently detected and managed by prosthetists and to identify challenges, management strategies, and opportunities for workflow and technological innovation during prosthesis manufacture and socket fitting.

Study design:
Mixed-method (quantitative and qualitative) survey.

Methods:
An online survey was developed and piloted in consultation with members of the Australian Orthotic Prosthetic Association. The final 25-question survey was distributed through their membership database. Mixed methods were used to analyze survey items. Qualitative items were grouped and coded under themes relating to challenges, management strategies, and opportunities. Quantitative data were analyzed using nonparametric descriptive methods.

Results:
Twenty-three respondents with a range of experience completed the survey. Seven of eight major Australian states/territories were represented. Primary workflow stages presenting challenges with limited strategies/solutions available to the prosthetists were roll-on liner selection, mold or cast modifications, communication with the client, and check socket fitting. Suggested solutions included improved socket–limb interface monitoring technology.

Conclusions:
This study provides the first insights into prosthetist-identified challenges and limitations at different stages of the socket workflow and presents a starting point for more targeted research into innovation that may assist in these processes.
The association between comorbidities and coronavirus disease 2019 hospitalization among people with HIV differs by age
Authors: Moran Caitlin A. , Oliver Nora T. , Szabo Brittany , Collins Lauren F. , Nguyen Minh Ly T. , Shah N. Sarita , Moanna Abeer , Colasanti Jonathan A. , Cantos Valeria D. , Armstrong Wendy S. , Sheth Anandi N. , Ofotokun Ighovwerha , Kelley Colleen F. , Marconi Vincent C. , Lahiri Cecile D. 
Published: September 2022

Objectives:
To determine whether factors associated with coronavirus disease 2019 (COVID-19) hospitalization among people with HIV (PWH) differ by age stratum.

Design:
Retrospective cohort study.

Methods:
All adult PWH with a positive SARS-CoV-2 PCR in a public safety-net health system between 1 March 2020 and 28 February 2021 and a Veterans Affairs Medical Center between 1 1 March 2020 and 15 November 2020 in Atlanta, Georgia were included. We performed multivariable logistic regression to determine demographic and clinical factors associated with COVID-19 hospitalization overall and stratified by age less than 50 and at least 50 years.

Results:
Three hundred and sixty-five PWH (mean age 49 years, 74% cisgender male, 82% black) were included. Ninety-six percent were on antiretroviral therapy (ART), 87% had CD4+ T-cell count at least 200 cells/μl, and 89% had HIV-1 RNA less than 200 copies/ml. Overall, age [adjusted odds ratio (aOR) 95% confidence interval (CI) 1.07 (1.04–1.10)], later date of SARS-CoV-2 infection [aOR 0.997 (0.995–1.00)], heart disease [aOR 2.27 (1.06–4.85)], and history of hepatitis C virus (HCV) [aOR 2.59 (1.13–5.89)] were associated with COVID-19 hospitalization. Age-adjusted comorbidity burden was associated with 30% increased risk of hospitalization [aOR 1.30 (1.11–1.54)]. Among 168 PWH less than 50 years old, older age [aOR 1.09 (1.01–1.18)] and no ART use [aOR 40.26 (4.12–393.62)] were associated with hospitalization; age-adjusted comorbidity burden was not (P = 0.25). Among 197 PWH at least 50, older age [aOR 1.10 (1.04–1.16)], heart disease [aOR 2.45 (1.04–5.77)], history of HCV [aOR 3.52 (1.29–9.60)], and age-adjusted comorbidity burden [aOR 1.36 (1.12–1.66)] were associated with hospitalization.

Conclusion:
Comorbidity burden is more strongly associated with COVID-19 hospitalization among older, rather than younger, PWH. These findings may have important implications for risk-stratifying COVID-19 therapies and booster recommendations in PWH.
Macrophage-mediated PDGF Activation Correlates With Regenerative Outcomes Following Musculoskeletal Trauma
Authors: Chowdary Ashish R. , Maerz Tristan , Henn Dominic , Hankenson Kurt D. , Pagani Chase A. , Marini Simone , Gallagher Katherine , Aguilar Carlos A. , Tower Robert J. , Levi Benjamin 
Published: September 2022

Objective:
Our objective was to identify macrophage subpopulations and gene signatures associated with regenerative or fibrotic healing across different musculoskeletal injury types.

Background:
Subpopulations of macrophages are hypothesized to fine tune the immune response after damage, promoting either normal regenerative, or aberrant fibrotic healing.

Methods:
Mouse single-cell RNA sequencing data before and after injury were assembled from models of musculoskeletal injury, including regenerative and fibrotic mouse volumetric muscle loss (VML), regenerative digit tip amputation, and fibrotic heterotopic ossification. R packages Harmony, MacSpectrum, and Seurat were used for data integration, analysis, and visualizations.

Results:
There was a substantial overlap between macrophages from the regenerative VML (2 mm injury) and regenerative bone models, as well as a separate overlap between the fibrotic VML (3 mm injury) and fibrotic bone (heterotopic ossification) models. We identified 2 fibrotic-like (FL 1 and FL 2) along with 3 regenerative-like (RL 1, RL 2, and RL 3) subpopulations of macrophages, each of which was transcriptionally distinct. We found that regenerative and fibrotic conditions had similar compositions of proinflammatory and anti-inflammatory macrophages, suggesting that macrophage polarization state did not correlate with healing outcomes. Receptor/ligand analysis of macrophage-to-mesenchymal progenitor cell crosstalk showed enhanced transforming growth factor β in fibrotic conditions and enhanced platelet-derived growth factor signaling in regenerative conditions.

Conclusion:
Characterization of macrophage subtypes could be used to predict fibrotic responses following injury and provide a therapeutic target to tune the healing microenvironment towards more regenerative conditions.
A Delay in Adjuvant Therapy Is Associated With Worse Prognosis Only in Patients With Transitional Circulating Tumor Cells After Resection of Pancreatic Ductal Adenocarcinoma
Authors: Javed Ammar A. , Floortje van Oosten Anne , Habib Joseph R. , Hasanain Alina , Kinny-Köster Benedict , Gemenetzis Georgios , Groot Vincent P. , Ding Ding , Cameron John L. , Lafaro Kelly J. , Burns William R. , Burkhart Richard A. , Yu Jun , He Jin , Wolfgang Christopher L. 
Published: September 2022

Objectives:
The aim of the study was to assess the association of circulating tumor cells (CTCs) with survival as a biomarker in pancreatic ductal adenocarcinoma (PDAC) within the context of a delay in the initiation of adjuvant therapy.

Background:
Outcomes in patients with PDAC remain poor and are driven by aggressive systemic disease. Although systemic therapies improve survival in resected patients, factors such as a delay in the initiation of adjuvant therapy are associated with worse outcomes. CTCs have previously been shown to be predictive of survival.

Methods:
A retrospective study was performed on PDAC patients enrolled in the prospective CircuLating tUmor cellS in pancreaTic cancER trial (NCT02974764) on CTC-dynamics at the Johns Hopkins Hospital. CTCs were isolated based on size (isolation by size of epithelial tumor cells; Rarecells) and counted and characterized by subtype using immunofluorescence. The preoperative and postoperative blood samples were used to identify 2 CTC types: epithelial CTCs (eCTCs), expressing pancytokeratin, and transitional CTCs (trCTCs), expressing both pancytokeratin and vimentin. Patients who received adjuvant therapy were compared with those who did not. A delay in the receipt of adjuvant therapy was defined as the initiation of therapy ≥8 weeks after surgical resection. Clinicopathologic features, CTCs characteristics, and outcomes were analyzed.

Results:
Of 101 patients included in the study, 43 (42.5%) experienced a delay in initiation and 20 (19.8%) did not receive adjuvant therapy. On multivariable analysis, the presence of trCTCs (P=0.002) and the absence of adjuvant therapy (P=0.032) were associated with worse recurrence-free survival (RFS). Postoperative trCTC were associated with poorer RFS, both in patients with a delay in initiation (12.4 vs 17.9 mo, P=0.004) or no administration of adjuvant chemotherapy (3.4 vs NR, P=0.016). However, it was not associated with RFS in patients with timely initiation of adjuvant chemotherapy (P=0.293).

Conclusions:
Postoperative trCTCs positivity is associated with poorer RFS only in patients who either experience a delay in initiation or no receipt of adjuvant therapy. This study suggests that a delay in the initiation of adjuvant therapy could potentially provide residual systemic disease (trCTCs) a window of opportunity to recover from the surgical insult. Future studies are required to validate these findings and explore the underlying mechanisms involved.
Oxidative Stress is Intrinsic to Staphylococcal Adaptation to Fatty Acid Synthesis Antibiotics
Authors: Wongdontree Paprapach , Millan-Oropeza Aaron , Upfold Jennifer , Lavergne Jean-Pierre , Halpern David , Lambert Clara , Page Adeline , Kénanian Gérald , Grangeasse Christophe , Henry Céline , Fouet Agnès , Gloux Karine , Anba-Mondoloni Jamila , Gruss Alexandra 
Published: September 2022

AbstractAntibiotics inhibiting the fatty acid synthesis (FASII) pathway of the major pathogenStaphylococcus aureusreach their enzyme targets, but bacteria continue growth by using environmental fatty acids (eFAs) to produce phospholipids. We assessed how extreme changes in membrane phospholipids provoked by FASII-antibiotics affect globalS. aureusphysiology. Anti-FASII provoked massive lasting expression changes without genomic rearrangements. Several regulators, rather than one master switch, contributed to the timing of anti-FASII adaptation. Numerous virulence and adhesion factors showed decreased levels and/or activity. Conversely, stress response protein levels increased, and correlated with greater tolerance to peroxides. Notably, peroxide priming stimulated eFA incorporation efficiency and facilitated adaptation to FASII inhibition. These findings establish a link between oxidative stress and FA incorporation. Consistent with major shift in protein expression, anti-FASII-adaptedS. aureuskilled an insect host more slowly but continued multiplying. Thus, while anti-FASII-adapted populations are less equipped to damage the host, they may be better fit for long term survival, and could constitute a reservoir for re-infection.