UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies

Additional file 1. Evaluation of RNA quality from the two NSM parasite samples in agarose gel (a), and a flow chart of data processing and analysis (b)

Learning Unsigned Distance Fields from Local Shape Functions for 3D Surface Reconstruction

Unsigned distance fields (UDFs) provide a versatile framework for representing a diverse array of 3D shapes, encompassing both watertight and non-watertight geometries. Traditional UDF learning methods typically require extensive training on large datasets of 3D shapes, which is costly and often necessitates hyperparameter adjustments for new datasets. This paper presents a novel neural framework, LoSF-UDF, for reconstructing surfaces from 3D point clouds by leveraging local shape functions to learn UDFs. We observe that 3D shapes manifest simple patterns within localized areas, prompting us to create a training dataset of point cloud patches characterized by mathematical functions that represent a continuum from smooth surfaces to sharp edges and corners. Our approach learns features within a specific radius around each query point and utilizes an attention mechanism to focus on the crucial features for UDF estimation. This method enables efficient and robust surface reconstruction from point clouds without the need for shape-specific training. Additionally, our method exhibits enhanced resilience to noise and outliers in point clouds compared to existing methods. We present comprehensive experiments and comparisons across various datasets, including synthetic and real-scanned point clouds, to validate our method's efficacy.Comment: 14 pages, 11 figure

Volumetric-modulated arc therapy as an alternative to intensity-modulated radiotherapy for primary tumors of advanced non–small-cell lung cancer: A multicenter retrospective analysis based on propensity score matching

Purpose: To investigate the effect of volumetric-modulated arc therapy (VMAT) versus intensity-modulated radiotherapy (IMRT) for advanced non–small-cell lung cancer (NSCLC). Methods: Cases in which the primary tumors were treated with IMRT or VMAT as initial intervention in stages III and IV NSCLC patients from September 2008 to March 2020 were retrospectively analyzed. Propensity Score Matching (PSM) was used to assess the efficacy and toxicity of the two radiotherapy techniques. Results: A total of 637 patients were included, out of which 483 cases were treated with IMRT, while 154 received VMAT. A total of 308 patients were selected after PSM. Patients who were having acute radiation esophagitis and pneumonia treated with VMAT had a lower percentage than those treated with IMRT (p < 0.05) before PSM. However, there was no significant difference in grades 3 - 4 toxicity (χ2 = 2.77, p = 0.096). There were also no significant differences in the primary endpoints between the two groups after PSM (p > 0.05), while for secondary endpoints, all lung V5, and V20, mean lung dose and heart V30, heart V40, mean heart dose in all patients and stage N2 patients in VMAT after PSM were significantly lower than those of IMRT (p < 0.05). Conclusion: Radiation therapy of A-NSCLC primary tumors using VMAT and IMRT seem to produce similar efficacy. The volume parameters of normal tissues and organs is significantly lower in VMAT, especially in patients with stage N2. Therefore, VMAT may be more beneficial for reducing radiation damage in normal tissues and organs

A novel IgE epitope-specific antibodies-based sandwich ELISA for sensitive measurement of immunoreactivity changes of peanut allergen Ara h 2 in processed foods

BackgroundPeanut is an important source of dietary protein for human beings, but it is also recognized as one of the eight major food allergens. Binding of IgE antibodies to specific epitopes in peanut allergens plays important roles in initiating peanut-allergic reactions, and Ara h 2 is widely considered as the most potent peanut allergen and the best predictor of peanut allergy. Therefore, Ara h 2 IgE epitopes can serve as useful biomarkers for prediction of IgE-binding variations of Ara h 2 and peanut in foods. This study aimed to develop and validate an IgE epitope-specific antibodies (IgE-EsAbs)-based sandwich ELISA (sELISA) for detection of Ara h 2 and measurement of Ara h 2 IgE-immunoreactivity changes in foods.MethodsDEAE-Sepharose Fast Flow anion-exchange chromatography combining with SDS-PAGE gel extraction were applied to purify Ara h 2 from raw peanut. Hybridoma and epitope vaccine techniques were employed to generate a monoclonal antibody against a major IgE epitope of Ara h 2 and a polyclonal antibody against 12 IgE epitopes of Ara h 2, respectively. ELISA was carried out to evaluate the target binding and specificity of the generated IgE-EsAbs. Subsequently, IgE-EsAbs-based sELISA was developed to detect Ara h 2 and its allergenic residues in food samples. The IgE-binding capacity of Ara h 2 and peanut in foods was determined by competitive ELISA. The dose-effect relationship between the Ara h 2 IgE epitope content and Ara h 2 (or peanut) IgE-binding ability was further established to validate the reliability of the developed sELISA in measuring IgE-binding variations of Ara h 2 and peanut in foods.ResultsThe obtained Ara h 2 had a purity of 94.44%. Antibody characterization revealed that the IgE-EsAbs recognized the target IgE epitope(s) of Ara h 2 and exhibited high specificity. Accordingly, an IgE-EsAbs-based sELISA using these antibodies was able to detect Ara h 2 and its allergenic residues in food samples, with high sensitivity (a limit of detection of 0.98 ng/mL), accuracy (a mean bias of 0.88%), precision (relative standard deviation < 16.50%), specificity, and recovery (an average recovery of 98.28%). Moreover, the developed sELISA could predict IgE-binding variations of Ara h 2 and peanut in foods, as verified by using sera IgE derived from peanut-allergic individuals.ConclusionThis novel immunoassay could be a user-friendly method to monitor low level of Ara h 2 and to preliminary predict in vitro potential allergenicity of Ara h 2 and peanut in processed foods

Spatial and Temporal Characteristics of Rural Revitalization Level and Its Influencing Factors

[Objective] The levels of rural revitalization and the development levels of its subsystems in various prefecture-level cities in Guangdong Province were evaluated comprehensively, and the spatio-temporal evolution characteristics and influencing mechanisms from 2017 to 2021 were explored, in order to provide scientific references for the continuous advancement of the rural revitalization project. [Methods] A measurement system was constructed based on five subsystems: prosperous industries, affluent livelihoods, civilized rural customs, effective governance, and eco-friendly habitation. The TOPSIS method was employed to assess the level of rural revitalization in Guangdong Province. Hot-spot analysis was used to investigate the spatio-temporal evolution characteristics of rural revitalization levels and the development levels of each subsystem in Guangdong Province. Geographical detectors were applied to clarify the main influencing factors of rural revitalization and the interaction patterns of each factor. [Results] ① During the study period, the level of rural revitalization in Guangdong Province showed a slight increase, and the evolution types of research units were predominantly characterized by grade improvement. The Pearl River Delta region consistently remained a high-value unit aggregation area. Although the development levels of each subsystem changed relatively consistently, there were notable differences in the evolution of research unit types. ② Over the study period, various attributes of research units were generally characterized by hot-spot aggregation, with high-value aggregation areas consistently located in the Pearl River delta. ③ From 2017 to 2021, the main influencing factors of rural revitalization in Guangdong Province were financial support, industrial excellence and economic foundation, and the interaction types of each factor are nonlinear or double-factor enhancement in the two study years. [Conclusion] Over the study period, the rural revitalization level in Guangdong Province displayed modest improvement, with varying evolution trends in the development levels of each subsystem. Notably, spatial heterogeneity was evident, emphasizing the multifaceted nature of factors driving rural revitalization

MRI-based radiomics to determine the role of thigh muscle quality in the development of knee osteoarthritis: A discovery and validation study

Abstract Introduction: Although the reduced muscle quality is common in elderly people, its role in the development of knee osteoarthritis (OA) remains unclear. Magnetic Resonance Imaging (MRI) is considered the gold standard imaging modality to assess muscle quality, which might holistically capture the underlying pathology. Objectives: This study aimed to apply MRI-based radiomics to assess the quality of thigh muscles comprehensively, and examine its prediction performance for incident knee OA. Methods: The participants at risk of knee OA during the 48-month visit were selected from a multicenter cohort and analyzed using a nested case-control design. Cases were matched 1:1 to controls according to age, sex, and contralateral knee status. A multitask framework was developed to comprehensively evaluate thigh muscle quality by calculating conventional quantitative markers and radiomic features. Baseline collected thigh and knee MRI scans were respectively used for discovery and validation procedures. In each procedure, three (cross-sectional area [CSA], intramuscular adipose tissue [intra-MAT] CSA, and radiomic signature score [Rad-score]) imaging models of each muscle group (extensors, flexors, and auxiliaries) were trained and tested. The prediction performance of each muscle Rad-score was compared with conventional markers respectively. Furthermore, the incremental predictive value of clinical characteristics for Rad-score model was investigated. Results: 448 participants (mean age 61 years, 63 % female) were identified and split into training (314 [70.1 %]) and testing (134 [29.9 %]) cohorts. In the discovery procedure, the extensors Rad-score provided superior prediction performance than extensors CSA and intra-MAT CSA (area under the curve [AUC] 0.832 [95 % CI 0.765–0.899] vs 0.595 [0.498–0.692] and 0.600 [0.503–0.697] in testing cohort; all p < 0.001). Contrarily, the performances of the Rad-score and conventional markers of flexors were relatively poor, as were those of the auxiliaries. Extensors Rad-score also outperformed auxiliaries Rad-score, flexors Rad-score, and the clinical model (AUC 0.832 [0.765–0.899] vs 0.687 [0.597–0.777], 0.634 [0.541–0.728], and 0.577 [0.483–0.671] in testing cohort; all p < 0.001). Unexpectedly, the integration of other radiomic signatures and clinical characteristics showed comparable net benefit in decision curve analysis when compared with extensors Rad-score alone. Similar findings were obtained in the validation procedure. Conclusion: MRI-based radiomics could enable comprehensive assessment of muscle quality and allow exact prediction of incident knee OA, which helps uncover the precursory role of reduced extensors quality in developing knee OA. The radiomic signature from extensors would be an alternative indicator for future diagnosis and treatment in knee OA.Abstract Introduction: Although the reduced muscle quality is common in elderly people, its role in the development of knee osteoarthritis (OA) remains unclear. Magnetic Resonance Imaging (MRI) is considered the gold standard imaging modality to assess muscle quality, which might holistically capture the underlying pathology. Objectives: This study aimed to apply MRI-based radiomics to assess the quality of thigh muscles comprehensively, and examine its prediction performance for incident knee OA. Methods: The participants at risk of knee OA during the 48-month visit were selected from a multicenter cohort and analyzed using a nested case-control design. Cases were matched 1:1 to controls according to age, sex, and contralateral knee status. A multitask framework was developed to comprehensively evaluate thigh muscle quality by calculating conventional quantitative markers and radiomic features. Baseline collected thigh and knee MRI scans were respectively used for discovery and validation procedures. In each procedure, three (cross-sectional area [CSA], intramuscular adipose tissue [intra-MAT] CSA, and radiomic signature score [Rad-score]) imaging models of each muscle group (extensors, flexors, and auxiliaries) were trained and tested. The prediction performance of each muscle Rad-score was compared with conventional markers respectively. Furthermore, the incremental predictive value of clinical characteristics for Rad-score model was investigated. Results: 448 participants (mean age 61 years, 63 % female) were identified and split into training (314 [70.1 %]) and testing (134 [29.9 %]) cohorts. In the discovery procedure, the extensors Rad-score provided superior prediction performance than extensors CSA and intra-MAT CSA (area under the curve [AUC] 0.832 [95 % CI 0.765–0.899] vs 0.595 [0.498–0.692] and 0.600 [0.503–0.697] in testing cohort; all p < 0.001). Contrarily, the performances of the Rad-score and conventional markers of flexors were relatively poor, as were those of the auxiliaries. Extensors Rad-score also outperformed auxiliaries Rad-score, flexors Rad-score, and the clinical model (AUC 0.832 [0.765–0.899] vs 0.687 [0.597–0.777], 0.634 [0.541–0.728], and 0.577 [0.483–0.671] in testing cohort; all p < 0.001). Unexpectedly, the integration of other radiomic signatures and clinical characteristics showed comparable net benefit in decision curve analysis when compared with extensors Rad-score alone. Similar findings were obtained in the validation procedure. Conclusion: MRI-based radiomics could enable comprehensive assessment of muscle quality and allow exact prediction of incident knee OA, which helps uncover the precursory role of reduced extensors quality in developing knee OA. The radiomic signature from extensors would be an alternative indicator for future diagnosis and treatment in knee OA

Sedimentary Response to Climate Change in the Central Bay of Bengal since the Last Glacial Maximum

AbstractAs the largest submarine fan, the Bay of Bengal (BoB) captures the abundant environment and climate fingerprints on different time scales. To investigate the sedimentary response to climate change since the Last Glacial Maximum (LGM), an integrated survey was performed to study grain size, major, and trace elements (Al2O3, CaO, K2O, Na2O, TiO2, Sr, and Rb) of core BoB-24 sediments from the central BoB. The (K/Al)-TiO2 (%) relationship of the sediments was taken for the discrimination of provenance, which indicated that sediments from core BoB-24 in 24~6.5 cal ka BP were primarily from terrigenous material input from the Himalayas. In contrast, the material contribution from the Indian subcontinent increased distinctly since 6.5 cal ka BP. The rising sea level severed direct material supply, thus causing the evolution of sediment provenance of the central BoB. Meanwhile, the strengthened Indian summer monsoon (ISM) in the Holocene affected detrital material transport from offshore to the central BoB. After understanding the sediment provenance in the study, we choose the sensitive grain-size fraction to show the evolution of hydrodynamic conditions. The chemical index of alteration (CIA) and Ti/Ca and Rb/Sr ratios are calculated to indicate the change in terrigenous input and weathering intensity. The contents of sediment fraction from 11.05 to 15.63 μm, CIA, and ratios of Ti/Ca and Rb/Sr in core BoB-24 showed the same trends, which were low during the last deglaciation and late Holocene but high in the Early Holocene. The trends were strongly correlated with the variation of the Indian summer monsoon, indicating the possible impact of Indian monsoon on sediment transport in the Bay of Bengal. Alternative indicators such as the contents of ratios of Ti/Ca and Rb/Sr, CIA, and sensitive grain-size content in sediments of core BoB-24 jointly record the evolution history of ISM since 24 ka BP in the Bay of Bengal. Although the sensitivity and response of each indicator to the paleoenvironment and paleoclimate change are slightly different, on the whole, the change trend is the same. Specifically, four warm-cold alternating periods (Heinrich Event 1, Bølling/Allerød, Younger Dryas, and Early Holocene Climatic Optimum) had a strong signal in these proxies that indicated that the millennial-scale climate controls the terrigenous input to the Bay of Bengal, where a high value occurs in warm events and low value in cold events. The sedimentary pattern of the northeastern Indian Ocean provides scientific evidence for an insight into the regional response to global climate change and the long-term climate change trend of the human environment across the monsoon region

Effect of cervical suspensory traction in the treatment of severe cervical kyphotic deformity

ObjectiveThis study aimed to investigate a new noninvasive traction method on the treatment of severe cervical kyphotic deformity.MethodsThe clinical data of patients with severe cervical kyphosis (Cobb &gt; 40°) treated in Peking University Third Hospital from March 2004 to March 2020 were retrospectively summarized. 46 cases were enrolled, comprising 27 males and 19 females. Fifteen patients underwent skull traction, and 31 patients underwent suspensory traction. Among them, seven used combined traction after one week of suspensory traction. Bedside lateral radiographs were taken every two or three days during traction. The cervical kyphosis angle was measured on lateral radiographs in and extended position at each point in time. The correction rate and evaluated Japanese Orthopedic Association (JOA) scoring for the function of the spinal cord were also measured. The data before and after the operation were compared with paired sample t-test or Wilcoxon signed-rank test.ResultsNo neurological deterioration occurred during the skull traction and the cervical suspensory traction. There were 12 patients with normal neurological function, and the JOA score of the other 34 patients improved from 11.5 ± 2.8 to 15.4 ± 1.8 at the end of follow up (P &lt; 0.05). The average kyphotic Cobb angle was 66.1° ± 25.2, 28.7° ± 20.1 and 17.4° ± 25.7 pre-traction, pre-operative, and at the final follow-up, respectively (P &lt; 0.05). The average correction rate of skull traction and suspensory traction was 34.2% and 60.6% respectively. Among these, the correction rate of patients with simple suspensory traction was 69.3%. For patients with a correction rate of less than 40% by suspensory traction, combined traction was continued, and the correction rates after suspensory traction and combined traction were 30.7% and 67.1% respectively.ConclusionsPre-correction by cervical suspensory traction can achieve good results for severe cervical kyphotic deformity, with no wound and an easy process. Combined traction is effective for supplemental traction after suspensory traction

Evaluation and Comparation of a Novel Surgical Technique and Hemivertebra Resection to the Correction of Congenital Cervical Scoliosis in Lower Cervical and Cervicothoracic Spine

Objective To report concave-side distraction technique to treat congenital cervical scoliosis in lower cervical and cervicothoracic spine. To evaluate and compare clinical and radiographic results of this procedure with classic hemivertebra resection procedure. Methods This study reviewed 29 patients in last 13 years. These patients were divided into convex-side resection group (group R) and concave-side distraction group (group D). Radiographic assessment was based on parameter changes preoperatively, postoperatively and at last follow-up. Demographic data, surgical data and complications were also evaluated and compared between the 2 groups. Results In group R, mean age was 8.9 ± 3.3 years and follow-up was 46 ± 18 months. Operation time and blood loss averaged 500 ± 100 minutes, 703 ± 367 mL. In group D, mean age was 9.9 ± 2.8 years and follow-up was 34 ± 14 months. Operation time and blood loss averaged 501 ± 112 minutes, 374 ± 181 mL. Structural Cobb angle was corrected from 29.4° ± 12.5° to 5.3° (2.1°–18.1°) (p = 0.001) and 33.7° ± 14.1° to 12.8° ± 11.4° (p < 0.001) in groups R and D. Compensatory Cobb angle had a spontaneous correction rate of 59.6% (40.0%–80.8%) and 59.7% ± 23.0% in groups R and D. Mandibular incline, clavicle angle and spine coronal balance were significantly improved at last follow-up in both groups. All correction rates were not statistically different between groups. However, group D had significant less blood loss (p < 0.001) and operation time (p = 0.004) per vertebra than group R. Seven patients developed C5 nerve root palsy and recovered by 6 months of follow-up. Conclusion Both surgical procedures are safe and effective in correcting congenital cervical scoliosis. But concave-side distraction technique has less blood loss and time-consuming during surgery, which provides a better option for the treatment of congenital cervical scoliosis