bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physics-informed sinogram completion for metal artifact reduction in CT imaging
Authors: Zhu Manman , Zhu Qisen , Song Yuyan , Guo Yi , Zeng Dong , Bian Zhaoying , Wang Yongbo , Ma Jianhua 
Published: February 2023

Abstract

Objective. Metal artifacts in the computed tomography (CT) imaging are unavoidably adverse to the clinical diagnosis and treatment outcomes. Most metal artifact reduction (MAR) methods easily result in the over-smoothing problem and loss of structure details near the metal implants, especially for these metal implants with irregular elongated shapes. To address this problem, we present the physics-informed sinogram completion (PISC) method for MAR in CT imaging, to reduce metal artifacts and recover more structural textures. Approach. Specifically, the original uncorrected sinogram is firstly completed by the normalized linear interpolation algorithm to reduce metal artifacts. Simultaneously, the uncorrected sinogram is also corrected based on the beam-hardening correction physical model, to recover the latent structure information in metal trajectory region by leveraging the attenuation characteristics of different materials. Both corrected sinograms are fused with the pixel-wise adaptive weights, which are manually designed according to the shape and material information of metal implants. To furtherly reduce artifacts and improve the CT image quality, a post-processing frequency split algorithm is adopted to yield the final corrected CT image after reconstructing the fused sinogram. Main results. We qualitatively and quantitatively evaluated the presented PISC method on two simulated datasets and three real datasets. All results demonstrate that the presented PISC method can effectively correct the metal implants with various shapes and materials, in terms of artifact suppression and structure preservation. Significance. We proposed a sinogram-domain MAR method to compensate for the over-smoothing problem existing in most MAR methods by taking advantage of the physical prior knowledge, which has the potential to improve the performance of the deep learning based MAR approaches.
Characterization of breast lesions using multi-parametric diffusion MRI and machine learning
Authors: Mehta Rahul , Bu Yangyang , Zhong Zheng , Dan Guangyu , Zhong Ping-Shou , Zhou Changyu , Hu Weihong , Zhou Xiaohong Joe , Xu Maosheng , Wang Shiwei , Karaman M Muge 
Published: February 2023

Abstract

Objective. To investigate quantitative imaging markers based on parameters from two diffusion-weighted imaging (DWI) models, continuous-time random-walk (CTRW) and intravoxel incoherent motion (IVIM) models, for characterizing malignant and benign breast lesions by using a machine learning algorithm. Approach. With IRB approval, 40 women with histologically confirmed breast lesions (16 benign, 24 malignant) underwent DWI with 11 b-values (50 to 3000 s/mm2) at 3T. Three CTRW parameters, D

m
, α, and β and three IVIM parameters D
diff, D
perf, and f were estimated from the lesions. A histogram was generated and histogram features of skewness, variance, mean, median, interquartile range; and the value of the 10%, 25% and 75% quantiles were extracted for each parameter from the regions-of-interest. Iterative feature selection was performed using the Boruta algorithm that uses the Benjamin Hochberg False Discover Rate to first determine significant features and then to apply the Bonferroni correction to further control for false positives across multiple comparisons during the iterative procedure. Predictive performance of the significant features was evaluated using Support Vector Machine, Random Forest, Naïve Bayes, Gradient Boosted Classifier (GB), Decision Trees, AdaBoost and Gaussian Process machine learning classifiers. Main Results. The 75% quantile, and median of D

m
; 75% quantile of f; mean, median, and skewness of β; kurtosis of D
perf; and 75% quantile of D
diff were the most significant features. The GB differentiated malignant and benign lesions with an accuracy of 0.833, an area-under-the-curve of 0.942, and an F1 score of 0.87 providing the best statistical performance (p-value < 0.05) compared to the other classifiers. Significance. Our study has demonstrated that GB with a set of histogram features from the CTRW and IVIM model parameters can effectively differentiate malignant and benign breast lesions.
Mesh modeling of system geometry and anatomy phantoms for realistic GATE simulations and their inclusion in SPECT reconstruction
Authors: Auer Benjamin , Könik Arda , Fromme Timothy J , De Beenhouwer Jan , Kalluri Kesava S , Lindsay Clifford , Furenlid Lars R , Kuo Philip H , King Michael A 
Published: February 2023

Abstract

Objective. Monte-Carlo simulation studies have been essential for advancing various developments in single photon emission computed tomography (SPECT) imaging, such as system design and accurate image reconstruction. Among the simulation software available, Geant4 application for tomographic emission (GATE) is one of the most used simulation toolkits in nuclear medicine, which allows building systems and attenuation phantom geometries based on the combination of idealized volumes. However, these idealized volumes are inadequate for modeling free-form shape components of such geometries. Recent GATE versions alleviate these major limitations by allowing users to import triangulated surface meshes. Approach. In this study, we describe our mesh-based simulations of a next-generation multi-pinhole SPECT system dedicated to clinical brain imaging, called AdaptiSPECT-C. To simulate realistic imaging data, we incorporated in our simulation the XCAT phantom, which provides an advanced anatomical description of the human body. An additional challenge with the AdaptiSPECT-C geometry is that the default voxelized XCAT attenuation phantom was not usable in our simulation due to intersection of objects of dissimilar materials caused by overlap of the air containing regions of the XCAT beyond the surface of the phantom and the components of the imaging system. Main results. We validated our mesh-based modeling against the one constructed by idealized volumes for a simplified single vertex configuration of AdaptiSPECT-C through simulated projection data of 123I-activity distributions. We resolved the overlap conflict by creating and incorporating a mesh-based attenuation phantom following a volume hierarchy. We then evaluated our reconstructions with attenuation and scatter correction for projections obtained from simulation consisting of mesh-based modeling of the system and the attenuation phantom for brain imaging. Our approach demonstrated similar performance as the reference scheme simulated in air for uniform and clinical-like 123I-IMP brain perfusion source distributions. Significance. This work enables the simulation of complex SPECT acquisitions and reconstructions for emulating realistic imaging data close to those of actual patients.
Outcomes of emergency surgical interventions in right-sided colonic cancer: nationwide population-based study based on Danish Colorectal Cancer Group register
Authors: El-Hussuna Alaa , Knudsen Maria , Frasson Matteo , Poulsen Laurids Østergaard 
Published: February 2023

Abstract

Aim
The aim of this study was to investigate the trends in morbidity and mortality of patients with right-sided colonic cancer who had an emergency surgical procedure in Denmark after the introduction of quality index parameters.

Methods
This was a retrospective nationwide study based on a prospectively maintained Danish Colorectal Cancer Group database focused on right-sided colonic cancer in the interval from 1 May 2001 to 30 April 2018, who underwent emergency surgical intervention (within 48 h of hospital admission). The primary objective was to investigate the trends in morbidity and mortality throughout the study years. Multivariable estimates were adjusted for age, sex, smoking status, alcohol consumption, ASA score classification, tumour localization, type of access to abdominal cavity, surgeon’s grade of specialization, and metastatic disease.

Results
Out of 2839 patients, a total of 2740 patients fulfilled the inclusion criteria, of whom 2464 underwent right or transverse colon resection (89.9 per cent). The 30-day and 90-day postoperative mortality rates were significantly reduced over the time of the study (OR 0.943, 95 per cent c.i. 0.922 to 0.965, P &lt; 0.001 and OR 0.953, 95 per cent c.i. 0.934 to 0.972, P &lt; 0.001 respectively); however, the complication rates did not follow this trend. Older patients (OR 1.032, 95 per cent c.i. 1.009 to 1.055, P = 0.005) and patients with high ASA scores (OR 1.61, 95 per cent c.i. 1.422 to 1.830, P &lt; 0.001) had higher rates of severe grade 3b postoperative complications. A stoma was constructed in 276 patients (10 per cent), whereas a stent was used in only eight patients. Defunctioning procedures, including stoma construction or colonic stenting (without oncological resection), did not reduce the risk of complications compared with that of definitive surgery.

Conclusion
The 30-day and 90-day postoperative mortality rates were significantly reduced over the time of the study. Age and ASA score were risk factors for severe postoperative complications.
Verbal fluency tests assess global cognitive status but have limited diagnostic differentiation: evidence from a large-scale examination of six neurodegenerative diseases
Authors: Henderson Shalom K , Peterson Katie A , Patterson Karalyn , Lambon Ralph Matthew A , Rowe James B 
Published: February 2023

AbstractVerbal fluency is widely used as a clinical test, but its utility in differentiating between neurodegenerative dementias and progressive aphasias, and from healthy controls, remains unclear. We assessed whether various measures of fluency performance could differentiate between Alzheimer’s disease, behavioural variant of frontotemporal dementia, non-fluent and semantic variants of primary progressive aphasia, progressive supranuclear palsy, corticobasal syndrome and healthy controls. Category and letter fluency tasks were administered to 33 controls and 139 patients at their baseline clinical visit. We assessed group differences for total number of words produced, psycholinguistic word properties and associations between production order and exemplar psycholinguistic properties. Receiver operating characteristic curves determined which measure could best discriminate patient groups and controls. The total word count distinguished controls from all patient groups, but neither this measure nor the word properties differentiated the patient groups. Receiver operating characteristic curves revealed that, when comparing controls to patients, the strongest discriminators were total word count followed by word frequency. Word frequency was the strongest discriminator for semantic variant of primary progressive aphasia versus other groups. Fluency word counts were associated with global severity as measured by Addenbrooke’s Cognitive Examination Revised. Verbal fluency is an efficient test for assessing global brain–cognitive health but has limited utility in differentiating between cognitively and anatomically disparate patient groups. This outcome is consistent with the fact that verbal fluency requires many different aspects of higher cognition and language.
Biopsy type does not affect the number of stages during Mohs micrographic surgery: a retrospective study
Authors: Araneda Paulina , Donoso Francisca , Castro Juan C , Uribe Pablo , Rossi Anthony M , Hibler Brian P , Droppelmann Katherine , Cardenas Consuelo , Navarrete-Dechent Cristian 
Published: February 2023

Abstract
Mohs micrographic surgery (MMS) is the treatment of choice for high-risk basal cell carcinoma (BCC). However, there are no evidence-based recommendations regarding which biopsy type is more appropriate to obtain tumour samples prior to MMS. Shave or punch biopsies are performed depending on the clinical characteristics of the tumour, surgeon experience and local protocols. However, biopsy type might result in difficult histopathological interpretation and influence the practical implementation of MMS. We performed a retrospective study on 208 consecutive BCCs treated with MMS. Of the 208 BCC biopsies, 42 (20.2%) were obtained by the shave method and 166 (79.8%) via punch. Those obtained with the shave technique had a mean of 1.64 stages vs. 1.69 stages with the punch technique (P = 0.130). These findings suggest biopsy type does not affect Mohs surgery performance. The biopsy type of choice is the one deemed adequate for each specific case to obtain a diagnosis and tumour subtyping.
Evaluation of QuantiFERON SARS-CoV-2 interferon-γ release assay following SARS-CoV-2 infection and vaccination
Authors: Johnson Síle A , Phillips Eloise , Adele Sandra , Longet Stephanie , Malone Tom , Mason Chris , Stafford Lizzie , Jamsen Anni , Gardiner Siobhan , Deeks Alexandra , Neo Janice , Blurton Emily J , White Jemima , Ali Muhammed , Kronsteiner Barbara , Wilson Joseph D , Skelly Dónal T , Jeffery Katie , Conlon Christopher P , Goulder Philip , Consortium PITCH , Carroll Miles , Barnes Eleanor , Klenerman Paul , Dunachie Susanna J 
Published: February 2023

Abstract
T cells are important in preventing severe disease from SARS-CoV-2, but scalable and field-adaptable alternatives to expert T-cell assays are needed. The interferon-gamma release assay QuantiFERON platform was developed to detect T-cell responses to SARS-CoV-2 from whole blood with relatively basic equipment and flexibility of processing timelines. Forty-eight participants with different infection and vaccination backgrounds were recruited. Whole blood samples were analysed using the QuantiFERON SARS-CoV-2 assay in parallel with the well-established ‘Protective Immunity from T Cells in Healthcare workers’ (PITCH) ELISpot, which can evaluate spike-specific T-cell responses. The primary aims of this cross-sectional observational cohort study were to establish if the QuantiFERON SARS-Co-V-2 assay could discern differences between specified groups and to assess the sensitivity of the assay compared with the PITCH ELISpot. The QuantiFERON SARS-CoV-2 distinguished acutely infected individuals (12–21 days post positive PCR) from naïve individuals (P &lt; 0.0001) with 100% sensitivity and specificity for SARS-CoV-2 T cells, whilst the PITCH ELISpot had reduced sensitivity (62.5%) for the acute infection group. Sensitivity with QuantiFERON for previous infection was 12.5% (172–444 days post positive test) and was inferior to the PITCH ELISpot (75%). Although the QuantiFERON assay could discern differences between unvaccinated and vaccinated individuals (55–166 days since second vaccination), the latter also had reduced sensitivity (44.4%) compared to the PITCH ELISpot (66.6%). The QuantiFERON SARS-CoV-2 assay showed potential as a T- cell evaluation tool soon after SARS-CoV-2 infection but has lower sensitivity for use in reliable evaluation of vaccination or more distant infection.
Micromechanical controls on the brittle-plastic transition in rocks
Authors: Liu Dong , Brantut Nicolas 
Published: February 2023

SUMMARYThe rheology of rocks transitions from a cataclastic brittle behaviour to plastic flow with increasing pressure and temperature. This brittle-plastic transition is empirically observed to occur when the material strength becomes lower than the confining stress, which is termed Goetze’s criterion. Such a criterion works well for most silicates but is not universal for all materials. We aim to determine the microphysical controls and stress–strain behaviour of rocks in the brittle-plastic transition. We use a micromechanical approach due to Horii and Nemat-Nasser, and consider representative volume elements containing sliding wing-cracks and plastic zones. We find solutions for frictional slip, plastic deformation and crack opening at constant confining pressure, and obtain stress–strain evolution. We show that the brittle-plastic transition depends on the confining stress, fracture toughness and plastic yield stress but also critically on the friction coefficient on pre-existing defects. Materials with low friction are expected to be more brittle, and experience transition to fully plastic flow at higher pressure than anticipated from Goetze’s criterion. The overall success of Goetze’s criterion for the brittle-plastic transition in rocks is likely arising from the low toughness, high strength and medium friction coefficient character of most rock forming minerals.
Enhancing health-promoting isothiocyanates in Chinese kale sprouts via manipulating BoESP
Authors: Miao Huiying , Xia Chuchu , Yu Shunhao , Wang Jiansheng , Zhao Yanting , Wang Qiaomei 
Published: February 2023

Abstract
Glucosinolates (GSLs) are a group of sulfur-containing secondary metabolites, which are abundant in Brassica vegetables. GSL breakdown products (GBPs), especially isothiocyanates (ITCs) benefit human health. Chinese kale is a native Brassica vegetable in China, and its sprouts are rich in GSLs and nutritional substances. ITCs are the predominant GBPs while alternative products are formed in the presence of specifier proteins. However, fewer ITCs are formed in the sprouts. Epithiospecifier (ESP) promotes the formation of epithionitriles at the expense of ITCs in Arabidopsis, but a systematic study of different isoforms of ESPs in most vegetables is still missing. In this study, changes in the content of GBPs and the precursor GSLs, as well as thiols per plant were monitored during sprout development. The proportions of epithionitriles and ITCs in total GBPs were found to be increased and decreased, respectively. RNA-seq showed enhanced expression of numerous genes involved in GSLs biosynthesis and degradation, as well as sulfur assimilation in sprouts compared to seeds. Four copies of BoESPs were isolated and BoESP2 was the most abundant isoform. Generally, transcription of BoESPs showed a strong response to abscisic acid and gibberellin, and consequently epithionitriles increased under these treatments. Knockdown of BoESP2 expression through virus-induced gene silencing system could effectively increase total ITCs and decrease total epithionitriles. Overall, dynamic GSL metabolic flux exists in the sprouting period, and the expression of BoESPs determines the pattern of GBPs, suggesting that improving the health-promoting ITCs in Chinese kale sprouts through manipulating BoESPs by metabolic engineering is feasible.
Racial Disparities in Breast Imaging Wait Times Before and After the Implementation of a Same-Day Biopsy Program
Authors: Yoon Sora C , Taylor-Cho Michael W , Charles Matthew G , Grimm Lars 
Published: February 2023

AbstractObjectiveTo examine time from screening to diagnostic workup, biopsy, and surgery for non-Hispanic White (NHW) and Black women following implementation of a same-day biopsy program.MethodsAll NHW and Black women with BI-RADS category 0 screening mammogram at Duke University Hospital were identified between August 1, 2020, and August 1, 2021. Patient characteristics were recorded. Time between screening mammogram, diagnostic workup, breast biopsy, surgical consultation, and surgery were recorded. Comparisons were made between NHW and Black women using a multivariable regression model. Diagnostic imaging to biopsy time interval was compared to historical averages before same-day biopsy implementation.ResultsThere were 2156 women: 69.9% NHW (1508/2156) and 30.1% Black (648/2156). Mean ± standard deviation time from screening to diagnostic imaging overall was 13.5 ± 32.5 days but longer for Black (18.0 ± 48.3 days) than for NHW women (11.5 ± 22.2 days) (P &lt; 0.001). The mean time from diagnostic mammogram to biopsy was 5.9 ± 18.9 days, longer for Black (9.0 ± 27.9 days) than for NHW women (4.4 ± 11.8 days) (P = 0.017). The same-day biopsy program shortened the time from diagnostic imaging to biopsy overall (12.5 ± 12.4 days vs 5.9 ± 18.9 days; P &lt; 0.001), with a significant reduction for NHW women (12.4 ± 11.7 days vs 4.4 ± 11.8 days) (P &lt; 0.001) but not Black women (11.5 ± 9.9 days vs 9.0 ± 27.9 days) (P = 0.527).ConclusionDisparities exist along the breast imaging pathway. A same-day biopsy program benefited NHW women more than Black women.
Tuberculosis Diagnosis and Preventive Monotherapy Among Children and Adolescents Exposed to Rifampicin-Resistant Tuberculosis in the Household
Authors: Apolisi Ivy , Cox Helen , Tyeku Nolitha , Daniels Johnny , Mathee Shaheed , Cariem Rabia , Douglas-Jones Bianca , Ngambu Noluvo , Mudaly Vanessa , Mohr-Holland Erika , Isaakidis Petros , Pfaff Colin , Furin Jennifer , Reuter Anja 
Published: February 2023

AbstractBackgroundChildren and adolescents with household exposure to multidrug- or rifampicin-resistant tuberculosis (MDR/RR-TB) are at high risk of developing TB disease. Tuberculosis preventive therapy (TPT) is recommended, but programmatic experience is limited, particularly for adolescents.MethodsWe conducted a prospective cohort study to describe MDR/RR-TB diagnosis and TPT provision for individuals aged &lt;18 years with MDR/RR-TB exposure. Participants were assessed for TB either in homes or health facilities, with referral for chest x-ray or specimen collection at clinician discretion. The TPT regimens included levofloxacin, isoniazid, or delamanid monotherapy for 6 months, based on source patient drug-resistance profile.ResultsBetween March 1, 2020 and July 31, 2021, 112 participants were enrolled; median age was 8.5 years, 57 (51%) were female, and 6 (5%) had human immunodeficiency virus. On screening, 11 (10%) were diagnosed with TB: 10 presumptive MDR/RR-TB and 1 drug-susceptible TB. Overall, 95 (94% of 101) participants started TPT: 79 with levofloxacin, 9 with isoniazid, and 7 with delamanid. Seventy-six (80%) completed TPT, 12 (13%) were lost to follow up, and 7 (7%) stopped TPT early due to adverse events. Potential adverse events were reported for 12 (13%) participants; none were serious. There were no further TB diagnoses (200 days median follow up).ConclusionsPost-MDR/RR-TB exposure management for children and adolescents resulted in significant MDR/RR-TB detection and both high TPT initiation and completion. Tuberculosis preventive monotherapy was well tolerated and there were no further TB diagnoses after initial assessment. Key factors supporting these outcomes included use of pediatric formulations for young children, monotherapy, and community-based options for assessment and follow up.
Invasive Mold Infections Following Hurricane Harvey—Houston, Texas
Authors: Toda Mitsuru , Williams Samantha , Jackson Brendan R , Wurster Sebastian , Serpa Jose A , Nigo Masayuki , Grimes Carolyn Z , Atmar Robert L , Chiller Tom M , Ostrosky-Zeichner Luis , Kontoyiannis Dimitrios P 
Published: February 2023

AbstractBackgroundCharacterizing invasive mold infection (IMI) epidemiology in the context of large flooding events is important for public health planning and clinical decision making.MethodsWe assessed IMI incidence (per 10 000 healthcare encounters) 1 year before and after Hurricane Harvey at 4 hospitals in Houston, Texas. Potential IMI cases were assigned as proven or probable cases using established definitions, and surveillance cases using a novel definition. We used rate ratios to describe IMI incidence and multivariable logistic regression to examine patient characteristics associated with IMI case status.ResultsIMI incidence was significantly higher posthurricane (3.69 cases) than prehurricane (2.50 cases) (rate ratio, 1.48 [95% confidence interval, 1.10–2.00]), largely driven by surveillance IMI cases. Aspergillus was the most common species cultured (33.5% prehurricane and 39.9% posthurricane). About one-quarter (25.8%) of IMI patients lacked classical IMI risk factors such as hematologic malignancy and transplantations. Overall, 45.1% of IMI patients received intensive care, and in-hospital all-cause mortality was 24.2%.ConclusionsIMI incidence likely increased following Hurricane Harvey and outcomes for IMI patients were severe. Patient and clinician education on IMI prevention and identification is warranted, particularly as the frequency of extreme weather events increases due to climate change.