bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential regional importance mapping for thyroid nodule malignancy prediction with potential to improve needle aspiration biopsy sampling reliability
Authors: Wang Liping , Wang Yuan , Lu Wenliang , Xu Dong , Yao Jincao , Wang Lijing , Xu Lei 
Published: April 2023

ObjectiveExisting guidelines for ultrasound-guided fine-needle aspiration biopsy lack specifications on sampling sites, but the number of biopsies improves diagnostic reliability. We propose the use of class activation maps (CAMs) and our modified malignancy-specific heat maps that locate important deep representations of thyroid nodules for class predictions.MethodsWe applied adversarial noise perturbations to the segmented concentric “hot” nodular regions of equal sizes to differentiate regional importance for the malignancy diagnostic performances of an accurate ultrasound-based artificial intelligence computer-aided diagnosis (AI-CADx) system using 2,602 retrospectively collected thyroid nodules with known histopathological diagnosis.ResultsThe AI system demonstrated high diagnostic performance with an area under the curve (AUC) value of 0.9302 and good nodule identification capability with a median dice coefficient &gt;0.9 when compared to radiologists’ segmentations. Experiments confirmed that the CAM-based heat maps reflect the differentiable importance of different nodular regions for an AI-CADx system to make its predictions. No less importantly, the hot regions in malignancy heat maps of ultrasound images in comparison with the inactivated regions of the same 100 malignant nodules randomly selected from the dataset had higher summed frequency-weighted feature scores of 6.04 versus 4.96 rated by radiologists with more than 15 years of ultrasound examination experience according to widely used ultrasound-based risk stratification American College of Radiology (ACR) Thyroid Imaging Reporting and Data System (TI-RADS) in terms of nodule composition, echogenicity, and echogenic foci, excluding shape and margin attributes, which could only be evaluated on the whole rather than on the sub-nodular component levels. In addition, we show examples demonstrating good spatial correspondence of highlighted regions of malignancy heat map to malignant tumor cell-rich regions in hematoxylin and eosin-stained histopathological images.ConclusionOur proposed CAM-based ultrasonographic malignancy heat map provides quantitative visualization of malignancy heterogeneity within a tumor, and it is of clinical interest to investigate in the future its usefulness to improve fine-needle aspiration biopsy (FNAB) sampling reliability by targeting potentially more suspicious sub-nodular regions.
The efficacy of dermoscopy in defining the surgical margins of cutaneous squamous cell carcinoma: a retrospective study
Authors: Liu Zhenru , Huang Shudai , Li Fang , Wang Xiaoqing , Liu Mengxi , Wong Hoi Shiwn , Jiang Jiayi , Zhou Yuan , Wang Daguang 
Published: April 2023

ObjectiveTo investigate the diagnostic value of dermoscopy in defining the tumor margin of cutaneous squamous cell carcinoma (cSCC) for the appropriate surgical margin.MethodsA total of 90 cSCC patients were enrolled in the study. All patients were recruited into two groups: those who preserved intact macroscopic features of neoplasms without or after incisional biopsy and those with uncertain residual tumors after excisional biopsy. A dermoscopy-defined surgical margin of 8mm outward was used according to the tumor boundaries observed with the naked eye and dermoscopy. All excised tumor specimens were divided into serial sections according to the four “3, 6, 9, 12” directions at every 4-mm interval from the dermoscopy-detected tumor margin. Pathological examination was performed at 0 mm, 4 mm, and 8 mm margins to confirm tumor remnants.ResultsRetrospective analysis of dermatoscopic results showed inconsistent clinical and dermatoscopic borders in 43 of 90 cases (47.8%). The ability of dermoscopy to detect tumor borders showed no statistical difference between the two groups (p &gt; 0.05). In the unbiopsy or incisional biopsy group, 66.6% of the tumors were resected with a 4-mm margin and 98.3% with an 8-mm margin, with significant differences (p = 0.047). For patients with inconspicuous clinical evidence of residual tumor after excisional biopsy, the tumor clearance rate was 53.3% at 0 mm, 93.3% at 4 mm, and 100.0% at 8 mm. Statistically significant differences were noted between 0 mm and 4 mm (p = 0.017), as well as between 0 mm and 8 mm (p = 0.043) but did not differ between 4 mm and 8 mm (p &gt; 0.05).ConclusionsDermoscopy defined the tumor margin of cSCC better than visual inspection alone. Direct dermoscopic-guided surgery with at least 8-mm expansion was recommended for high-risk cSCC. Dermoscopy also assisted in identifying surgical margins at the healing biopsy site, making 8 mm still the recommended expansion range.
Postoperative circulating tumor DNA testing based on tumor naïve strategy after liver metastasis surgery in colorectal cancer patients
Authors: Jiang Huiqin , Huang Fei , Yang Yihui , Chen Xinning , Shen Minna , Zhang Chunyan , Pan Baishen , Wang Beili , Guo Wei 
Published: April 2023

ObjectiveThere is still a lack of highly sensitive methods for monitoring recurrence of colorectal cancer patients after liver metastasis surgery. The aim of this study was to evaluate the prognostic value of tumor-naive ctDNA detection after resection of colorectal liver metastases (CRLM).MethodsPatients with resectable CRLM were prospectively enrolled. Based on the tumor-naive strategy, NGS panels containing 15 colorectal cancer hotspot mutated genes were used to detect ctDNA 3-6 weeks after surgery.ResultsA total of 67 patients were included in the study, and the positive rate of postoperative ctDNA was 77.6% (52/67). Patients with positive ctDNA had a significantly higher risk of recurrence after surgery (HR 3.596, 95% CI 1.479 to 8.744, P = 0.005), and a higher proportion relapsed within 3 months after surgery (46.7% vs 3.8%). The C-index of postoperative ctDNA in predicting recurrence was higher than that of CRS and postoperative CEA. The nomogram combining CRS and postoperative ctDNA can improve the accuracy of recurrence prediction.ConclusionTumor-naive ctDNA detection can detect molecular residual lesions in patients with colorectal cancer after liver metastasis, and its prognostic value is superior to conventional clinical factors.
Time-resolved investigation of nanometric cell membrane patches with a mid-infrared laser microscope
Authors: Intze Antonia , Temperini Maria Eleonora , Baldassarre Leonetta , Giliberti Valeria , Ortolani Michele , Polito Raffaella 
Published: April 2023

The proton pump Bacteriorhodopsin (BR) undergoes repeated photocycles including reversible conformational changes upon visible light illumination. Exploiting the sensitivity of infrared (IR) spectra to the conformation, we have determined the reaction kinetic parameters of the conductive intermediate M for the wild-type protein and for its slow mutant D96N during its photocycle. Time-resolved IR micro-spectroscopy using an in-house developed confocal laser microscope operating in the mid-IR is employed to record absorption changes of 10−4 at wavelengths λ1 = 6.08 μm and λ2 = 6.35 μm, assigned to backbone and retinal structural modifications, respectively. Protein samples were embedded in dried lipid bilayers deposited on ultraflat gold supports to enhance the surface field. The signals were analyzed according to a simplified photocycle model with only two dominant states: the dark-adapted state BR* and the intermediate M. We obtained the excitation and relaxation times of the intermediate M from exponential fits to the absorption change time traces. Our results constitute a first step towards future plasmonic-assisted nanoscale time-resolved mid-IR spectrometers for the characterization of bioelectronic and light-harvesting nanodevices based on BR.
Comparison of ventilation defects quantified by Technegas SPECT and hyperpolarized 129Xe MRI
Authors: Radadia Nisarg , Friedlander Yonni , Priel Eldar , Konyer Norman B. , Huang Chynna , Jamal Mobin , Farncombe Troy , Marriott Christopher , Finley Christian , Agzarian John , Dolovich Myrna , Noseworthy Michael D. , Nair Parameswaran , Shargall Yaron , Svenningsen Sarah 
Published: April 2023

Introduction: The ideal contrast agents for ventilation SPECT and MRI are Technegas and 129Xe gas, respectively. Despite increasing interest in the clinical utility of ventilation imaging, these modalities have not been directly compared. Therefore, our objective was to compare the ventilation defect percent (VDP) assessed by Technegas SPECT and hyperpolarized 129Xe MRI in patients scheduled to undergo lung cancer resection with and without pre-existing obstructive lung disease.Methods: Forty-one adults scheduled to undergo lung cancer resection performed same-day Technegas SPECT, hyperpolarized 129Xe MRI, spirometry, and diffusing capacity of the lung for carbon monoxide (DLCO). Ventilation abnormalities were quantified as the VDP using two different methods: adaptive thresholding (VDPT) and k-means clustering (VDPK). Correlation and agreement between VDP quantified by Technegas SPECT and 129Xe MRI were determined by Spearman correlation and Bland-Altman analysis, respectively.Results: VDP measured by Technegas SPECT and 129Xe MRI were correlated (VDPT: r = 0.48, p = 0.001; VDPK: r = 0.63, p &lt; 0.0001). A 2.0% and 1.6% bias towards higher Technegas SPECT VDP was measured using the adaptive threshold method (VDPT: 23.0% ± 14.0% vs. 21.0% ± 5.2%, p = 0.81) and k-means method (VDPK: 9.4% ± 9.4% vs. 7.8% ± 10.0%, p = 0.02), respectively. For both modalities, higher VDP was correlated with lower FEV1/FVC (SPECT VDPT: r = −0.38, p = 0.01; MRI VDPK: r = −0.46, p = 0.002) and DLCO (SPECT VDPT: r = −0.61, p &lt; 0.0001; MRI VDPK: r = −0.68, p &lt; 0.0001). Subgroup analysis revealed that VDP measured by both modalities was significantly higher for participants with COPD (n = 13) than those with asthma (n = 6; SPECT VDPT: p = 0.007, MRI VDPK: p = 0.006) and those with no history of obstructive lung disease (n = 21; SPECT VDPT: p = 0.0003, MRI VDPK: p = 0.0003).Discussion: The burden of ventilation defects quantified by Technegas SPECT and 129Xe MRI VDP was correlated and greater in participants with COPD when compared to those without. Our observations indicate that, despite substantial differences between the imaging modalities, quantitative assessment of ventilation defects by Technegas SPECT and 129Xe MRI is comparable.
Development and validation of a deep learning-based model to distinguish acetabular fractures on pelvic anteroposterior radiographs
Authors: Ye Pengyu , Li Sihe , Wang Zhongzheng , Tian Siyu , Luo Yi , Wu Zhanyong , Zhuang Yan , Zhang Yingze , Grzegorzek Marcin , Hou Zhiyong 
Published: April 2023

Objective: To develop and test a deep learning (DL) model to distinguish acetabular fractures (AFs) on pelvic anteroposterior radiographs (PARs) and compare its performance to that of clinicians.Materials and methods: A total of 1,120 patients from a big level-I trauma center were enrolled and allocated at a 3:1 ratio for the DL model’s development and internal test. Another 86 patients from two independent hospitals were collected for external validation. A DL model for identifying AFs was constructed based on DenseNet. AFs were classified into types A, B, and C according to the three-column classification theory. Ten clinicians were recruited for AF detection. A potential misdiagnosed case (PMC) was defined based on clinicians’ detection results. The detection performance of the clinicians and DL model were evaluated and compared. The detection performance of different subtypes using DL was assessed using the area under the receiver operating characteristic curve (AUC).Results: The means of 10 clinicians’ sensitivity, specificity, and accuracy to identify AFs were 0.750/0.735, 0.909/0.909, and 0.829/0.822, in the internal test/external validation set, respectively. The sensitivity, specificity, and accuracy of the DL detection model were 0.926/0.872, 0.978/0.988, and 0.952/0.930, respectively. The DL model identified type A fractures with an AUC of 0.963 [95% confidence interval (CI): 0.927–0.985]/0.950 (95% CI: 0.867–0.989); type B fractures with an AUC of 0.991 (95% CI: 0.967–0.999)/0.989 (95% CI: 0.930–1.000); and type C fractures with an AUC of 1.000 (95% CI: 0.975–1.000)/1.000 (95% CI: 0.897–1.000) in the test/validation set. The DL model correctly recognized 56.5% (26/46) of PMCs.Conclusion: A DL model for distinguishing AFs on PARs is feasible. In this study, the DL model achieved a diagnostic performance comparable to or even superior to that of clinicians.
Comparison of online and in-person cognitive behavioral therapy in individuals diagnosed with major depressive disorder: a non-randomized controlled trial
Authors: Alavi Nazanin , Moghimi Elnaz , Stephenson Callum , Gutierrez Gilmar , Jagayat Jasleen , Kumar Anchan , Shao Yijia , Miller Shadé , Yee Caitlin S. , Stefatos Anthi , Gholamzadehmir Maedeh , Abbaspour Zara , Shirazi Amirhossein , Gizzarelli Tessa , Khan Ferwa , Patel Charmy , Patel Archana , Yang Megan , Omrani Mohsen 
Published: April 2023

ObjectiveThe increased prevalence of major depressive disorder (MDD) amid the COVID-19 pandemic has resulted in substantial growth in online mental health care delivery. Compared to its in-person counterpart, online cognitive behavioral therapy (e-CBT) is a time-flexible and cost-effective method of improving MDD symptoms. However, how its efficacy compares to in-person CBT is yet to be explored. Therefore, the current study compared the efficacy of a therapist-supported, electronically delivered e-CBT program to in-person therapy in individuals diagnosed with MDD.MethodsParticipants (n = 108) diagnosed with MDD selected either a 12 week in-person CBT or an asynchronous therapist-supported e-CBT program. E-CBT participants (n = 55) completed weekly interactive online modules delivered through a secure cloud-based online platform (Online Psychotherapy Tool; OPTT). These modules were followed by homework in which participants received personalized feedback from a trained therapist. Participants in the in-person CBT group (n = 53) discussed sessions and homework with their therapists during one-hour weekly meetings. Program efficacy was evaluated using clinically validated symptomatology and quality of life questionnaires.ResultsBoth treatments yielded significant improvements in depressive symptoms and quality of life from baseline to post-treatment. Participants who opted for in-person therapy presented significantly higher baseline symptomatology scores than the e-CBT group. However, both treatments demonstrated comparable significant improvements in depressive symptoms and quality of life from baseline to post-treatment. e-CBT seems to afford higher participant compliance as dropouts in the e-CBT group completed more sessions on average than those in the in-person CBT group.ConclusionThe findings support e-CBT with therapist guidance as a suitable option to treat MDD. Future studies should investigate how treatment accessibility is related to program completion rates in the e-CBT vs. in-person group.Clinical Trial RegistrationClinicalTrials.Gov Protocol Registration and Results System (NCT04478058); clinicaltrials.gov/ct2/show/NCT04478058.
Sleep and cognition in aging dogs. A polysomnographic study
Authors: Mondino Alejandra , Catanzariti Magaly , Mateos Diego Martin , Khan Michael , Ludwig Claire , Kis Anna , Gruen Margaret E. , Olby Natasha J. 
Published: April 2023

IntroductionSleep is fundamental for cognitive homeostasis, especially in senior populations since clearance of amyloid beta (key in the pathophysiology of Alzheimer's disease) occurs during sleep. Some electroencephalographic characteristics of sleep and wakefulness have been considered a hallmark of dementia. Owners of dogs with canine cognitive dysfunction syndrome (a canine analog to Alzheimer's disease) report that their dogs suffer from difficulty sleeping. The aim of this study was to quantify age-related changes in the sleep-wakefulness cycle macrostructure and electroencephalographic features in senior dogs and to correlate them with their cognitive performance.MethodsWe performed polysomnographic recordings in 28 senior dogs during a 2 h afternoon nap. Percentage of time spent in wakefulness, drowsiness, NREM, and REM sleep, as well as latency to the three sleep states were calculated. Spectral power, coherence, and Lempel Ziv Complexity of the brain oscillations were estimated. Finally, cognitive performance was evaluated by means of the Canine Dementia Scale Questionnaire and a battery of cognitive tests. Correlations between age, cognitive performance and sleep-wakefulness cycle macrostructure and electroencephalographic features were calculated.ResultsDogs with higher dementia scores and with worse performance in a problem-solving task spent less time in NREM and REM sleep. Additionally, quantitative electroencephalographic analyses showed differences in dogs associated with age or cognitive performance, some of them reflecting shallower sleep in more affected dogs.DiscussionPolysomnographic recordings in dogs can detect sleep-wakefulness cycle changes associated with dementia. Further studies should evaluate polysomnography's potential clinical use to monitor the progression of canine cognitive dysfunction syndrome.
Helicobacter pylori Strains Isolated from Raw Poultry Meat in the Shahrekord Region, Iran: Frequency and Molecular Characteristics
Authors: Asadi Sepehr , Rahimi Ebrahim , Shakerian Amir 
Published: April 2023

Even though Helicobacter pylori (H. pylori) is a serious pathogen, its origin is unknown. Poultry (chicken, turkey, quail, goose, and ostrich) is consumed as a regular protein source by many people across the world; therefore, sanitary ways of delivering poultry for food are important for global health. As a result, the distribution of the virulence genes cagA, vacA, babA2, oipA, and iceA in H. pylori isolates in poultry meat, as well as their antibacterial resistance, was investigated. A Wilkins Chalgren anaerobic bacterial medium was used to cultivate 320 samples of raw poultry meat. Disk diffusion and multiplex-PCR were used to investigate both antimicrobial resistance and genotyping patterns. H. pylori was found in 20 of 320 (6.25 %) raw chicken meat samples. The highest incidence of H. pylori was found in chicken raw meat (15%), whereas no isolate was recovered from goose or quail raw meat (0.00%). Resistance to ampicillin (85%), tetracycline (85%), and amoxicillin (75%) were the most commonly detected in the tested H. pylori isolates. The percentage of H. pylori isolates with a multiple antibiotic resistance (MAR) index value of more than 0.2 was 17/20 (85%). The most prevalent genotypes detected were VacA (75%), m1a (75%), s2 (70%) and m2 (65%), and cagA (60%). The most typically detected genotype patterns were s1am1a (45 %), s2m1a (45 %), and s2 m2 (30%). babA2, oipA+, and oipA- genotypes were found in 40%, 30%, and 30% of the population, respectively. In summary, fresh poultry meat was polluted by H. pylori, with the babA2, vacA, and cagA genotypes being more prevalent. The simultaneous occurrence of vacA, cagA, iceA, oipA, and babA2 genotypes in antibiotic-resistant H. pylori bacteria raises a serious public health concern regarding the consumption of raw poultry. Future research should evaluate antimicrobial resistance among H. pylori isolates in Iran.
A Novel Effector FlSp1 Inhibits the Colonization of Endophytic Fusarium lateritium and Increases the Resistance to Ralstonia solanacearum in Tobacco
Authors: Huang Jianming , He Zhangjiang , Wang Jiankang , Zha Xingping , Xiao Qing , Liu Guihua , Li Yongjie , Kang Jichuan 
Published: April 2023

Effectors are crucial for the interaction between endophytes and their host plants. However, limited attention has been paid to endophyte effectors, with only a few reports published. This work focuses on an effector of Fusarium lateritium, namely FlSp1 (Fusarium-lateritium-Secreted-Protein), a typical unknown secreted protein. The transcription of FlSp1 was up-regulated after 48 h following fungal inoculation in the host plant, i.e., tobacco. The inactivation of FlSp1 with the inhibition rate decreasing by 18% (p < 0.01) resulted in a remarkable increase in the tolerance of F. lateritium to oxidative stress. The transient expression of FlSp1 stimulated the accumulation of reactive oxygen species (ROS) without causing plant necrosis. In comparison with the wild type of F. lateritium (WT), the FlSp1 mutant of the F. lateritium plant (ΔFlSp1) reduced the ROS accumulation and weakened the plant immune response, which resulted in significantly higher colonization in the host plants. Meanwhile, the resistance of the ΔFlSp1 plant to the pathogenic Ralstonia solanacearum, which causes bacterial wilt, was increased. These results suggest that the novel secreted protein FlSp1 might act as an immune-triggering effector to limit fungal proliferation by stimulating the plant immune system through ROS accumulation and thus balance the interaction between the endophytic fungi and their host plants.
Regulation of Intracellular Reactive Oxygen Species Levels after the Development of Phallus rubrovolvatus Rot Disease Due to Trichoderma koningii Mycoparasitism
Authors: Lu Meiling , Wen Tingchi , Guo Ming , Li Qihua , Peng Xingcan , Zhang Yan , Lu Zhenghua , Wang Jian , Xu Yanjun , Zhang Chao 
Published: April 2023

Phallus rubrovolvatus is a unique mushroom used for medicinal and dietary purposes in China. In recent years, however, the rot disease of P. rubrovolvatus has seriously affected its yield and quality, becoming an economically important threat. In this study, samples of symptomatic tissues were collected, isolated, and identified from five major P. rubrovolvatus production regions in Guizhou Province, China. Based on combined analyses of phylogenies (ITS and EF1-α), morphological characteristics and Koch’s postulates, Trichoderma koningiopsis and Trichoderma koningii were identified as the pathogenic fungal species. Among these, T. koningii exhibited stronger pathogenicity than the other strains; thus, T. koningii was used as the test strain in the follow-up experiments. Upon co-culturing T. koningii with P. rubrovolvatus, the hyphae of the two species were intertwined, and the color of the P. rubrovolvatus hyphae changed from white to red. Moreover, T. koningii hyphae were wrapped around P. rubrovolvatus hyphae, leading to their shortening and convolution and ultimately inhibiting their growth due to wrinkling; T. koningii penetrated the entire basidiocarp tissue of P. rubrovolvatus, causing serious damage to the host basidiocarp cells. Further analyses revealed that T. koningii infection resulted in the swelling of basidiocarps and significantly enhanced the activity of defense-related enzymes, such as malondialdehyde, manganese peroxidase, and polyphenol oxidase. These findings offer theoretical support for further research on the infection mechanisms of pathogenic fungi and the prevention of diseases caused by them.