As one of the standard electrophysiological signals in the human body, the photoplethysmography contains detailed information about the blood microcirculation and has been commonly used in various medical scenarios, where the accurate detection of the pulse waveform and quantification of its morphological characteristics are essential steps. In this paper, a modular pulse wave preprocessing and analysis system is developed based on the principles of design patterns. The system designs each part of the preprocessing and analysis process as independent functional modules to be compatible and reusable. In addition, the detection process of the pulse waveform is improved, and a new waveform detection algorithm composed of screening-checking-deciding is proposed. It is verified that the algorithm has a practical design for each module, high accuracy of waveform recognition and high anti-interference capability. The modular pulse wave preprocessing and analysis software system developed in this paper can meet the individual preprocessing requirements for various pulse wave application studies under different platforms. The proposed novel algorithm with high accuracy also provides a new idea for the pulse wave analysis process.
Humans ; Systems Analysis ; Algorithms ; Software ; Heart Rate ; Microcirculation

Objective: To examine the application value of 3D Slicer software assisted domestic frameless stereotactic robot in biopsy of intracranial lesions. Methods: A retrospective analysis was performed on 80 patients who admitted consecutively and underwent intracerebral lesions biopsy with the domestic frameless stereotactic robot at Department of Neurosurgery, Aerospace Central Hospital from January 2019 to December 2021. There were 36 males and 44 females, with a mean age of (38.5±18.0) years (range: 6 to 71 years). Before surgery only enhanced T1-weighted three-dimensional magnetization prepared gradient echo sequences and diffusion tensor imaging scans were performed. Self-reconstruction of intracranial lesions, cerebral cortex and blood vessels was carried out using 3D Slicer software system after the DICOM format imaging data of 80 patients were collected. These imaging data were merged to the workstation of the domestic frameless stereotactic robot for preoperative surgical planning and the surgical puncture path was designed to avoid blood vessels in the brain functional area, cerebral cortex and sulcus. Results: All frameless stereotactic biopsy were successfully performed. Postoperative pathological diagnosis included 50 cases of diffuse astrocytic and oligodendroglioma, 15 cases of lymphoma, 5 cases of metastatic tumors, 5 cases of inflammatory demyelinating disease, 2 cases of inflammatory granuloma, 1 case of hemangioma, 1 case of acute lymphoblastic leukemia intracranial invasion and 1 case of seminoma. The positive diagnosis rate was 100% (80/80). Postoperative imaging confirmed that the puncture path and target were accurately implemented according to the preoperative planning, and the target error was (1.32±0.44) mm (range: 0.55 to 1.99 mm). One case of puncture-related bleeding occurred at the target after surgery and improved after treatment. Conclusion: The three-dimensional multimodal images reconstructed by the 3D Slicer software before operation could help the surgeons make the preoperative planning and reduce the risk of stereotactic brain biopsy.
Male ; Female ; Humans ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Brain Neoplasms/pathology* ; Diffusion Tensor Imaging ; Retrospective Studies ; Robotics ; Biopsy ; Software ; Stereotaxic Techniques

For the detection and identification of abnormal nodular tissues on the body surface, a microwave sensor structure loaded with a spiral resonator is proposed in this paper, a sensor simulation model is established using HFSS software, the structural parameters are optimized, and the actual sensor is fabricated. The S21 parameters of the tissue were obtained when nodules appeared by simulation, and the characteristic relationship between the difference of S21 parameters with position was analyzed and tested experimentally. The results showed that when nodules were present in normal tissues, the curve of S21 parameter difference with position change had obvious inverted bimodal characteristics, and the extreme value of S21 parameter difference appeared when the sensor was directly above the nodules, which was easy to identify the position of nodules. It provides an objective detection tool for the identification of abnormal nodular tissues on the body surface.
Microwaves ; Recognition, Psychology ; Computer Simulation ; Software

Karyotype analysis is the basic method in cytogenetics, and is also recognized as the "gold standard" for diagnosing chromosomal disorders. The teaching and training for traditional karyotyping analysis is time-consuming and even boring. The individual's ability for mastering the chromosome morphology can vary greatly. Therefore, it is necessary to improve the teaching method. On the basis of the traditional method, we have added auxiliary analysis software during the teaching. This type of splicing karyotype teaching has increased the students' interest and improved their ability for karyotyping, allowing them to quickly remember the characteristic bands of chromosomes. Through enhanced memory of a large number of karyotypic images, the students' ability to recognize individual chromosomes has improved.
Humans ; Karyotyping ; Karyotype ; Cytogenetics ; RNA Splicing ; Software

OBJECTIVE: To explore an efficient and automatic method for determining the anatomical landmarks of three-dimensional(3D) mandibular data, and to preliminarily evaluate the performance of the method. METHODS: The CT data of 40 patients with normal craniofacial morphology were collected (among them, 30 cases were used to establish the 3D mandibular average model, and 10 cases were used as test datasets to validate the performance of this method in determining the mandibular landmarks), and the 3D mandibular data were reconstructed in Mimics software. Among the 40 cases of mandibular data after the 3D reconstruction, 30 cases that were more similar to the mean value of Chinese mandibular features were selected, and the size of the mandibular data of 30 cases was normalized based on the Procrustes analysis algorithm in MATLAB software. Then, in the Geomagic Wrap software, the 3D mandibular average shape model of the above 30 mandibular data was constructed. Through symmetry processing, curvature sampling, index marking and other processing procedures, a 3D mandible structured template with 18 996 semi-landmarks and 19 indexed mandibular anatomical landmarks were constructed. The open source non-rigid registration algorithm program Meshmonk was used to match the 3D mandible template constructed above with the tested patient's 3D mandible data through non-rigid deformation, and 19 anatomical landmark positions of the patient's 3D mandible data were obtained. The accuracy of the research method was evaluated by comparing the distance error of the landmarks manually marked by stomatological experts with the landmarks marked by the method of this research. RESULTS: The method of this study was applied to the data of 10 patients with normal mandibular morphology. The average distance error of 19 landmarks was 1.42 mm, of which the minimum errors were the apex of the coracoid process [right: (1.01±0.44) mm; left: (0.56±0.14) mm] and maximum errors were the anterior edge of the lowest point of anterior ramus [right: (2.52±0.95) mm; left: (2.57±1.10) mm], the average distance error of the midline landmarks was (1.15±0.60) mm, and the average distance error of the bilateral landmarks was (1.51±0.67) mm. CONCLUSION The automatic determination method of 3D mandibular anatomical landmarks based on 3D mandibular average shape model and non-rigid registration algorithm established in this study can effectively improve the efficiency of automatic labeling of 3D mandibular data features. The automatic determination of anatomical landmarks can basically meet the needs of oral clinical applications, and the labeling effect of deformed mandible data needs to be further tested.
Humans ; Imaging, Three-Dimensional/methods* ; Mandible/diagnostic imaging* ; Software ; Algorithms ; Anatomic Landmarks/anatomy & histology*

OBJECTIVE: To screen the risk factors for death in patients with nasopharyngeal carcinoma (NPC) using artificial intelligence (AI) technology and establish a risk prediction model. METHODS: The clinical data of NPC patients obtained from SEER database (1973-2015). The patients were randomly divided into model building and verification group at a 7∶3 ratio. Based on the data in the model building group, R software was used to identify the risk factors for death in NPC patients using 4 AI algorithms, namely eXtreme Gradient Boosting (XGBoost), Decision Tree (DT), Least absolute shrinkage and selection operator (LASSO) and random forest (RF), and a risk prediction model was constructed based on the risk factor identified. The C-Index, decision curve analysis (DCA), receiver operating characteristic (ROC) curve and calibration curve (CC) were used for internal validation of the model; the data in the validation group and clinical data of 96 NPC patients (collected from First Affiliated Hospital of Bengbu Medical College) were used for internal and external validation of the model. RESULTS: The clinical data of a total of 2116 NPC patients were included (1484 in model building group and 632 in verification group). Risk factor screening showed that age, race, gender, stage M, stage T, and stage N were all risk factors of death in NPC patients. The risk prediction model for NPC-related death constructed based on these factors had a C-index of 0.76 for internal evaluation, an AUC of 0.74 and a net benefit rate of DCA of 9%-93%. The C-index of the model in internal verification was 0.740 with an AUC of 0.749 and a net benefit rate of DCA of 3%-89%, suggesting a high consistency of the two calibration curves. In external verification, the C-index of this model was 0.943 with a net benefit rate of DCA of 3%-97% and an AUC of 0.851, and the predicted value was consistent with the actual value. CONCLUSIONS Gender, age, race and TNM stage are risk factors of death of NPC patients, and the risk prediction model based on these factors can accurately predict the risks of death in NPC patients.
Humans ; Nasopharyngeal Neoplasms ; Nasopharyngeal Carcinoma ; Artificial Intelligence ; Algorithms ; Software

OBJECTIVES: This study aimed to compare the effects of virtual adjustment on occlusal interferences in mandibular posterior single crown and three-unit bridge restorations by using the mandibular movement track and the movement parameters of a virtual articulator. METHODS: Twenty-two participants were recruited. Digital casts of the maxillary and mandibular arches were obtained using an intraoral scanner, and the jaw registration system was used to record the data of the mandibular movement track and the movement parameters of the articulator. Four kinds of restorations with 0.3 mm occlusal interferences were designed with dental design software. In particular, single crowns were designed for teeth 44 and 46, whereas three-unit bridges were designed for teeth 44-46 and 45-47, and the corresponding natural teeth were virtually extracted. Virtual adjustment of the restorations was performed using two dynamic occlusal recordings, namely, the mandibular movement track and the movement parameters of the virtual articulator. A reverse-engineering software was used to measure the root-mean-square of the three-dimensional deviation of the occlusal surfaces between natural teeth and the adjusted restorations. The differences between the two methods of virtual-occlusion adjustment were compared and analyzed. RESULTS: For the same group of restorations, the three-dimensional deviation of the mandibular movement track group were lower than those of the virtual articulator group, and the differences were statistically significant (P<0.05). For the four groups of restorations adjusted by the same method, the three-dimensional deviation of the 46-tooth single crown was the largest and the smallest three-dimensional deviation was that of the 44-tooth single crown. Statistical differences existed between the 44-tooth single crown and the other groups (P<0.05). CONCLUSIONS For the occlusal design of posterior single crown and three-unit bridge, the mandibular movement track could be a more effective approach to virtual occlusal adjustment than the movement parameters of the virtual articulator.
Humans ; Mouth, Edentulous ; Occlusal Adjustment ; Jaw Relation Record ; Dental Articulators ; Software

With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.
Software ; Microbiota ; Sequence Analysis, DNA ; Language

A user-friendly teaching software for visual analysis of acupoint compatibility laws has been developed based on the principles of partial order mathematics. This software is designed to provide auxiliary teaching of structured organization and visualization of law knowledge of compatibility data of acupuncture and moxibustion prescriptions from ancient texts, textbooks, and clinical case records. The software is installed as a plugin in the Microsoft Office Excel, allowing the generation of visually appealing graphs and associated rules that align with the cognitive patterns of teachers and students majoring in acupuncture and moxibustion. Its aim is to facilitate the discovery and analysis of underlying patterns and structured knowledge embedded in acupoint compatibility data, thus contributing to the enhancement of teaching effectiveness in acupoint compatibility.
Humans ; Acupuncture Points ; Acupuncture Therapy ; Moxibustion ; Acupuncture ; Software ; Meridians

Data-independent acquisition (DIA) is a high-throughput, unbiased mass spectrometry data acquisition method which has good quantitative reproducibility and is friendly to low-abundance proteins. It becomes the preferred choice for clinical proteomic studies especially for large cohort studies in recent years. The mass-spectrometry (MS)/MS spectra generated by DIA is usually heavily mixed with fragment ion information of multiple peptides, which makes the protein identification and quantification more difficult. Currently, DIA data analysis methods fall into two main categories, namely peptide-centric and spectrum-centric. The peptide-centric strategy is more sensitive for identification and more accurate for quantification. Thus, it has become the mainstream strategy for DIA data analysis, which includes four key steps: building a spectral library, extracting ion chromatogram, feature scoring and statistical quality control. This work reviews the peptide-centric DIA data analysis procedure, introduces the corresponding algorithms and software tools, and summarizes the improvements for the existing algorithms. Finally, the future development directions are discussed.
Humans ; Proteomics/methods* ; Reproducibility of Results ; Peptides/chemistry* ; Software ; Algorithms ; Tandem Mass Spectrometry/methods* ; Proteome/analysis*