bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiogenomic Analysis of Prediction HER2 status in Breast Cancer by Linking Ultrasound Radiomic Feature Modules with Biological Functions
Authors: Cui Hao , Sun Yue , Zhao Dantong , Zhang Xudong , Kong Hanqing , Hu Nana , Wang Panting , Zuo Xiaoxuan , Fan Wei , Yao Yuan , Fu Baiyang , Tian Jiawei , Gao Yue , Ning Shangwei , Zhang Lei 
Published: July 2022

Abstract
Background
Human epidermal growth factor receptor 2 (HER2) overexpressed associated with poor prognosis in breast cancer (BRCA) and HER2 has been defined as a therapeutic target for BRCA treatment. We aimed to exploring the molecular biological information in ultrasound radiomic features (URFs) of HER2-positive BRCA using radiogenomic analysis. Moreover, a radiomics model was developed to predict the status of HER2 in BRCA.
Methods
This retrospective study included 394 patients who were diagnosed with BRCA. URFs were extracted from a radiomics analysis set using PyRadiomics. The correlations between differential URFs and HER2-related genes were calculated using Pearson correlation analysis. Functional enrichment of the identified URFs-correlated HER2 positive-specific genes was performed. Lastly, the radiomics model was developed based on the URF-modules mined from auxiliary differential URFs to assess the HER2 status of BRCA.
Results
Eight differential URFs (P < 0.05) were identified among the 86 URFs extracted by Pyradiomics. Twenty-five genes that were found to be the most closely associated with URFs. Then, the relevant biological functions of each differential URF were obtained through functional enrichment analysis. Among them, Zone Entropy is related to immune cell activity, which regulate the generation of calcification in BRCA. The radiomics model based on the Logistic classifier and URF-modules showed good discriminative ability (AUC = 0.80, 95% CI).
Conclusion
We searched for the URFs of HER2-positive BRCA, and explore the underlying genes and biological functions of these URFs. Furthermore, the radiomics model based on the Logistic classifier and URF-modules accurately predicted the HER2 status in BRCA.
Inhaled Paraquat-Induced Lung Injury in Rat, Improved by the Extract of Zataria Multiflora boiss and PPARγ Agonist, Pioglitazone
Authors: Amin Fatemeh , Kazerani Hamid Reza , Memarzia Arghavan , Rad Hamideh Kazemi , Ghasemi Seyedeh Zahra , Boskabady Mohammad Hossein 
Published: July 2022

Abstract
The effects of a PPAR-γ agonist, pioglitazone and Zataria multiflora (Z. multiflora) on inhaled paraquat (PQ)-induced lung oxidative stress, inflammation, pathological changes and tracheal responsiveness were examined. The study was carried out in control rats exposed to normal aerosol of saline, PQl and PQh groups exposed to aerosols of 27 and 54 mg/m3 PQ, groups exposed to high PQ concentration (PQh) and treated with 200 and 800 mg/kg/day Z. multiflora, 5 and 10 mg/kg/day pioglitazone, low doses of Z. multiflora + pioglitazone, and 0.03 mg/kg/day dexamethasone. Increased tracheal responsiveness, transforming growth factor beta (TGF-ß) and lung pathological changes due to PQh were significantly improved by high doses of Z. multiflora and pioglitazone, dexamethasone and extract + pioglitazone, (p < 0.05 to p < 0.001). In group treated with low doses of the extract + pioglitazone, the improvements of most measured variables were significantly higher than the low dose of two agents alone (p < 0.05 to p < 0.001). Z. multiflora improved lung injury induced by inhaled PQ similar to dexamethasone and pioglitazone which could be mediated by PPAR-γ receptor.
Sex-Differences in COVID-19 Diagnosis, Risk Factors and Disease Comorbidities
Authors: Kharroubi Samer A , Harake Marwa El- 
Published: July 2022

Abstract
Introduction: Morbidity and mortality from COVID-19 are greater for males, however, the mechanisms for this difference are unclear. We aim to investigate sex-gender differences in COVID-19 in a large US-based cohort, namely COVID-19 Research Database. Specifically, the objectives of the present study are to explore the socio-economic characteristics of COVID-19 male and female patients and to examine potential sex differences in lifestyle factors and disease comorbidities among diagnosed patients. Methods: This is a retrospective cohort study comparing males versus females with test-confirmed COVID-19 between January 2020 and December 2021 (N=62,310). The study used secondary data, called Healthjump, which were extracted from patients’ medical claims and electronic health records (e.g., demographics, encounters, medical history, procedures, social history, and vitals). Results: Significant socio-demographic and comorbidity differences were observed between male and female patients (p<0.05). For example, a significantly higher proportion of males (vs. females) were aged ≥70-year-old (17.04% vs. 15.01%) and smokers (11.04 %vs. 9.24%, p<0.0001). In addition, multiple logistic regression showed that hypertension and diabetes were significantly more frequent in males (AOR=66.19 and AOR=22.90). Conclusions: Understanding the differences in outcomes between males and females will inform gender equity responsive policy approaches to COVID-19 and improve the effectiveness of health interventions.
Strategies for Managing Neonates with Congenital Lung Mass Presenting with Respiratory Distress
Authors: He Taozhen , Sun Xiaoyan , Luo Dengke , Dai Shiyi , Yuan Miao , Yang Gang , Cheng Kaisheng , Xu Chang 
Published: July 2022

Abstract
Background: Congenital lung mass is a group of entities which are usually prenatally diagnosed and not uncommon. However, patients that present with respiratory distress in neonatal period and require emergency intervention seem to be rare. Moreover, what is the best policy facing this condition has not reached a consensus in recent years. This study aims to evaluate the efficacy and safety of our strategies in managing neonates with congenital lung mass presenting with respiratory distress.Methods: We retrospectively reviewed the data of five congenital lung mass neonates presenting with respiratory distress from April 2020 to April 2022 for whom different strategies were adopted and favorable outcomes were obtained. The clinical presentations, complications, histological examination, and treatment were analyzed. Literature concerning neonates with respiratory distress undergoing emergency interventions due to large lung lesions was also reviewed.Results: All the neonatal patients were prenatally diagnosed with congenital lung mass, and among them, four neonates with cystic lung masses accepted percutaneous thoracic catheter drainage prior to surgery. One neonate with a cystic lung mass experienced prompt open lobectomy due to little alleviation of respiratory symptoms after two maneuvers. The other three patients obtained good drainage of the large air-filled cyst, thus gaining the opportunity for elective thoracoscopic surgery in median 48 d. The fifth case directly underwent emergency surgery due to the solid nature of the lung lesion. Four patients were diagnosed with congenital pulmonary airway malformation, and the fifth patient was diagnosed with a fetal lung interstitial tumor according to the pathological findings. There were no major complications, such as major bleeding, air leakage or death.Conclusions: For neonates with cystic lung masses presenting with respiratory distress due to mediastinal compression, percutaneous thoracic catheter drainage and subsequent elective thoracoscopic surgery were superior to emergency thoracotomy in terms of safety and parenchyma-sparing surgery based on the study and literature. For those with solid lung lesions whose CVR value is no less than 1.6, either EXIT surgery or emergency thoracotomy is a reliable strategy depending on the medical resources available.
Sequential decision making for a class of hidden Markov processes, application to medical treatment optimisation
Authors: Cleynen Alice , de Saporta Benoîte 
Published: July 2022

Abstract
Sequential decision-making under uncertainty is a difficult problem that is typically encountered in patient follow-up settings. The literature on finite states problems is well developed; however there has been very little work involving continuous time and state processes. We propose to model a disease evolution through a partially observed piecewise deterministic semi-Markov process where theinter-jump times have a general distribution. The discrete coordinate (e.g. global health state of thepatient) is not observed, the continuous one (e.g. result of some blood measurement) is observed with noise at some (possibly scarce) observation times. The objective is to optimally select the observation dates while controlling the process so that it remains close to a nominal value. Thisproblem being analytically untractable, we exhibit an explicit policy close to optimality based on discretisations of the belief process. Construction of discretisation grids with theoretical guaranteesare discussed at length. The paper is illustrated with experiments on synthetic data fitted fromthe Intergroupe Francophone du Mylome 2009 clinical trial. We provide data and codes on github.
Faunal change over three decades to reveal Rotundocollarette capoori n. gen., n.sp., a unique anisakid from Johnius dussumieri at the Central west coast of India at Goa
Authors: YADAV ANITA , MALHOTRA SANDEEP K , Kapoor Neerja 
Published: July 2022

Abstract
A unique anisakid roundworm, Rotundocollarette capoori n. gen., n.sp. infesting Johnius dussumieri from the Central West coast of India at Goa has been described. The worms are typically characterized by a cephalic collarette, a muscular collarette in post-caudal zone, intestinal caecum and a ventricular appendix. 3 pores, a part of cephalic infrastructure– a dorsal oral aperture, a dorso-laterally placed genital pore, and a sub-ventral excretory pore at the junction of the bases of the 2 ventro-lateral lips were typically unique as revealed by SEM studies. A pair of large squarish teeth flanked each of these three pores in the cephalic region, with 3-5 denticles in the median group, at the junction of the two arms of V-shaped structure, that joined 26-29 denticles on each arm of this V-shaped formation running parallel and crossed past dentigerous ridges on each lip. In addition a set of 49-50 medially organized denticles occupying the dorsal arm of V- shaped formation, in the medial space, were a conspicuous configuration, besides 40 minute triangular denticles at the junction of sub-ventral lips. A spined mucron at the tip of tail. The key provided by Moravec and Justine (2020) to segregate Porrocaecum -like nematode genera ( Porrocaecum , Pseudoterranova , Pulchrascaris , Euterranova , and Neoterranova ) has been revised to include the newly proposed genus, Rotundocollarette capoori n. gen., n.sp.
Dynamic habitat suitability and connectivity analyses to inform management of an invasive species and conservation of its native competitor
Authors: Goicolea Teresa , Lewison Rebecca L. , Mateo-Sánchez M. Cruz , Jennings Megan K. 
Published: July 2022

Abstract
Forecasting habitat suitability and connectivity can be central to both controlling invasive species expansion and promoting native species conservation, especially under changing climate conditions. This study aimed to identify and prioritize areas in Spain to control the expansion of one of the most harmful invasive species in Europe, while conserving its counterpart, the endangered European mink, under current and future conditions. We used dynamic ensemble habitat suitability and connectivity models to predict species ranges and movement routes considering likely climate change under three emission scenarios. Then, using habitat availability metrics, we prioritized areas for invasive mink control and native mink conservation and classified them into different management zones that reflected the overlap between species and threat from American to European minks. Results suggest that both species are likely to experience declines in habitat and connectivity under climate change scenarios with significantly larger declines by the end of the century for European minks (72 and 80% respectively) than for American minks (41 and 32%). Priority areas for management of both species varied over time and across emission scenarios, with a general shift in priority habitat towards the North-East of the study area. Our findings demonstrate how dynamic habitat suitability and connectivity approaches can guide long-term management strategies to control invasive species and conserve native species while accounting for likely landscape changes. The simultaneous study of both invasive and native species can support prioritized management action and inform management planning of the intensity, extent, and techniques of intervention depending on the overlap between species.
Phase separation enhanced drug delivery system for anti-cancer therapy
Authors: Bai Xun , Pei Pengfei , Duan Guangfei , Chen Long , Xue Song , Luo Shi-Zhong 
Published: July 2022

Abstract
The cellular phase-separated condensates compartmentalize and concentrate biomolecules with distinct physicochemical properties, which has great potential for therapy purposes. However, the discovered phase separation phenomena in living organisms were restricted intracellularly, which limits the biomedical application of phase separation. Here, we designed a phase separation enhanced delivery system to specifically condensate molecules on the cell surface for efficient drug delivery. As a proof of concept, we demonstrated that an anti-cancer drug conjugate can selectively co-phase separate with the targeting component on cancer cell surface and efficiently kill the cells after internalization. Both cellular and in vivo assays showed more potency with this system than traditional antibody conjugates. The method provides insights in the application of phase separation as a powerful tool for therapeutic purpose.
Label-free third harmonic generation imaging and quantification of lipid droplets in live filamentous fungi
Authors: Pajić Tanja , Todorović Nataša V. , Živić Miroslav , Nikolić Stanko N. , Rabasović Mihailo D. , Clayton Andrew H. A. , Krmpot Aleksandar J. 
Published: July 2022

Abstract
We report the utilization of the Third-Harmonic Generation (THG) microscopy, using home built nonlinear laser scanning microscope, for label-free live cell imaging of lipid droplets in the hypha of filamentous fungus Phycomyces blakesleeanus. THG microscopy images show bright spherical features dispersed throughout hypha cytoplasm in control conditions and a transient increase in the number of bright features after complete nitrogen starvation. We show that predominant source of THG signal in imaged hypha are lipid droplets and test side by side two methods for quantification of lipid droplet size and number from THG images: Particle Size Analysis (PSA) and Image Correlation Spectroscopy (ICS). The two analysis methods gave congruous results, showing expected increase of lipid droplet number after nitrogen starvation, while ICS showed somewhat lower mean diameter of lipid droplets than PSA. We conclude that THG imaging, followed by PSA and ICS, can be easily and reliably used on filamentous fungi for the in vivo quantification of lipid droplets since there is no need for sample labeling, fixation or any other specific preparation. In addition, we demonstrate that ICS is suitable for THG microscopy image analysis, although it is primarily developed and have been mostly used for fluorescence signals so far.
Dissemination and Genome Characterization of a Human Adenovirus F41 in a Patient with B-Cell Lymphoma
Authors: Fall Amary , Campodonico Victoria L. , Howard Craig , Gallagher Nicholas , Bailey Gabrielle , Kajon Adriana E. , Mostafa Heba H. 
Published: July 2022

Abstract
Adenovirus (HAdV) F41 is a common cause of gastroenteritis and has rarely been reported associated with disseminated disease. In this report, a fifty-eight-year-case with a history of ulcerative colitis, cryptogenic cirrhosis, stage III adenocarcinoma, high-grade diffuse large B-cell lymphoma on chemotherapy was diagnosed with disseminated adenovirus infection. HAdV DNA was quantified in stool, plasma, and urine with viral loads of 7, 4, and 3 log10 copies/mL, respectively. The patient’s course was rapidly progressive and he passed away 2 days after initiation of antiviral therapy. The patient’s infecting virus was characterized as HAdV-F41 by whole genome sequencing.
A deep learning-based dimensional measurement directly from limited-angle CT sinograms for Additive Manufacturing
Authors: HAN ZHENYE , HU XIAODONG , XIA XIAOQIN , PENGXIANG JI , ZHAO JINTAO , ZOU JING 
Published: July 2022

Abstract
Additive manufacturing (AM) is a layer-by-layer manufacturing method which is growing considerably in recent years. Inner dimensional measurement based on Computed Tomography (CT) image is an irreplaceable method for quality control in AM. However, for special AM components, limited-angle CT imaging is the only method because of physical limitations. CT reconstruction image with ghost artifacts through incomplete data can’t be used to implement dimensional measurement. To deal with this problem, a method based on encoder-decoder neural network is proposed and applied to characterize the dimensional parameter directly from CT sinogram without reconstruction. Experiment results showed that when characterizing AM component with length of side from 10 to 15mm, the relative accuracy is less than 18.26% and the relative accuracy is less than 10% in over 83.5% sample, which verifies the effectiveness of the method that can be applied in dimensional measurement.
Delineation of seawater intrusion and groundwater quality assessment in coastal aquifers : the Korba coastal aquifer (Northeastern Tunisia)
Authors: Ayari Jamel , Ouelhazi Hassen , Charef Abdelkarin , Barhoumi Anis 
Published: July 2022

Abstract
In semi-arid regions, a major challenge facing the coastal population is the design of sustainable aquifer protection plans which primary require a reliable understanding of groundwater. The aim of this study was to determine the general state of the Korba aquifer (northwestern Tunsia) with respect to seawater intrusion and to assess the suitability of groundwater for drinking and irrigation purposes. A total of 60 samples collected from coastal shallow aquifer are analysed for physicochemical parameters (pH, EC, TDS, Na+, K+, Ca2+, Mg2+, HCO3−, Cl−, NO3 −, SO42− and Br−). The obtained results are further interpreted using ionic ratios, geochemical modelling and Hydrochemical Facies Evolution Diagram (HFE-Diagram) coupled with a GIS‐based framework. Major ionic ratios reveal the dominance of the reverse ion exchange process triggered by the marine intrusion. Br−/Cl− ratio suggests that the irrigation with saline water and wastewater are potential additional sources of salinization. HFE-Diagram indicates that most of samples are located beneath the mixing line, showing dominant marine intrusion process with reverse ion exchange. Based on the water quality index (WQI), most of groundwater samples are unsuitable for drinking. In addition, according to high sodium adsorption ratio (SAR), the groundwater quality is limited for irrigation purposes. The results obtained can be useful in further management of the coastal aquifer by delineating the areas affected by seawater.
External and internal morphological analysis in fused-rooted mandibular second molars: a micro-computed tomographic study
Authors: Wu Weiwei , Meng Yajun , Tsauo Chialing , Chen Min , Huang Dingming , Zhou Xuedong , Zou Ling , Gao Yuan 
Published: July 2022

Abstract
Objectives
To investigate the root canal morphology of fused-rooted mandibular second molars (MSMs) based on the pulp chamber floor (PCF) and to analyze the correlation between external morphology of the radicular groove and internal morphology of the PCF and root canal configuration.
Materials and Methods
Two hundred and ninety-one fused-rooted MSM were selected from a Chinese population, and were scanned and reconstructed using micro-computed tomography. The morphology of the PCF was observed under a dental operating microscope (DOM). The classification of the PCFs and root canals configuration were identified according to modified Min’s and Gao’s classifications, respectively. A new radicular groove classification was proposed. The correlation among these morphological characteristics were investigated using the Chi-square test and Fisher’s exact test (α = 0.05).
Results
A total of 216 (74.2%) teeth had C-shaped PCFs; 61 (21.0%) had NC-shaped PCFs; and 14 (4.8%) had no PCF. The root canals were categorized as follows: 109 (37.5%) teeth were identified as merging type, 119 (40.9%) as symmetrical type; 43 (14.8%) as asymmetrical type, 6 (2.0%) exhibited taurodontism, and 14 (4.8%) had a single root canal. Statistical analysis showed a correlation between the type of PCFs and the root canals (P = 0.000). For teeth with C-shaped PCFs, the majority of the root canal was classified under merging type and symmetrical type, and asymmetrical type was not identified in NC-shaped PCFs. Besides, the results revealed a morphological association between the root canals configuration and radicular grooves types (P = 0.000).
Conclusions
The internal morphology of fused-rooted MSM is very complex. To a certain extent, it is feasible to predict the morphology of root canal by using PCF observed under a DOM.
Clinical Relevance
An understanding of the morphological aspects of the root canal based on the PCF will assist the clinician in the prediction and identification of canals below the visible orifice and further achieve more predictable clinical outcomes.
A Feedforward Network with a Few Million Neurons Learns from Images to Covertly Attend to Contextual Cues like Human and Bayesian Ideal Observers
Authors: Srivast Sudhanshu , Wang William , Eckstein Miguel 
Published: July 2022

Abstract
Human behavioral experiments with predictive cues and contexts have led to influential conceptualizations of visual attention, such as limited resource mechanisms or weighting by Bayesian priors. How brains might learn to manifest cue/context effects with simple neural architectures is not known. We show that a feedforward convolutional neural network (CNN) with a few million neurons trained on noisy images to detect targets learns to utilize predictive cues and context and predicts human performance for the three most prominent behavioral signatures of covert attention: Posner cueing, set-size effects in search, and contextual cueing. The CNN also approximates a Bayesian ideal observer that has all prior statistical representations of the noise, targets, cues, and context. A larger network pre-trained on natural images and transfer learning can also account for human performance. The findings help understand the neurobiological requirements, computations, and simple neural architectures that lead to covert attention's three landmark behavioral effects.