Intelligently Quantifying the Entire Irregular Dental Structure

Quantitative analysis of irregular anatomical structures is crucial in oral medicine, but clinicians often typically measure only several representative indicators within the structure as references. Deep learning semantic segmentation offers the potential for entire quantitative analysis. However, challenges persist, including segmentation difficulties due to unclear boundaries and acquiring measurement landmarks for clinical needs in entire quantitative analysis. Taking the palatal alveolar bone as an example, we proposed an artificial intelligence measurement tool for the entire quantitative analysis of irregular dental structures. To expand the applicability, we have included lightweight networks with fewer parameters and lower computational demands. Our approach finally used the lightweight model LU-Net, addressing segmentation challenges caused by unclear boundaries through a compensation module. Additional enamel segmentation was conducted to establish a measurement coordinate system. Ultimately, we presented the entire quantitative information within the structure in a manner that meets clinical needs. The tool achieved excellent segmentation results, manifested by high Dice coefficients (0.934 and 0.949), intersection over union (0.888 and 0.907), and area under the curve (0.943 and 0.949) for palatal alveolar bone and enamel in the test set. In subsequent measurements, the tool visualizes the quantitative information within the target structure by scatter plots. When comparing the measurements against representative indicators, the tool's measurement results show no statistically significant difference from the ground truth, with small mean absolute error, root mean squared error, and errors interval. Bland-Altman plots and intraclass correlation coefficients indicate the satisfactory agreement compared with manual measurements. We proposed a novel intelligent approach to address the entire quantitative analysis of irregular image structures in the clinical setting. This contributes to enabling clinicians to swiftly and comprehensively grasp structural features, facilitating the design of more personalized treatment plans for different patients, enhancing clinical efficiency and treatment success rates in turn.

Application of deep learning in radiation therapy for cancer

In recent years, with the development of artificial intelligence, deep learning has been gradually applied to clinical treatment and research. It has also found its way into the applications in radiotherapy, a crucial method for cancer treatment. This study summarizes the commonly used and latest deep learning algorithms (including transformer, and diffusion models), introduces the workflow of different radiotherapy, and illustrates the application of different algorithms in different radiotherapy modules, as well as the defects and challenges of deep learning in the field of radiotherapy, so as to provide some help for the development of automatic radiotherapy for cancer.

Aluminum ion chemistry of Na4Fe3(PO4)2(P2O7) for all-climate full Na-ion battery

Na4Fe3(PO4)2(P2O7) (NFPP) is currently drawing increased attention as a sodium-ion batteries (SIBs) cathode due to the cost-effective and NASICON-type structure features. Owing to the sluggish electron and Na+ conductivities, however, its real implementation is impeded by the grievous capacity decay and inferior rate capability. Herein, multivalent cation substituted microporous Na3.9Fe2.9Al0.1(PO4)2(P2O7) (NFAPP) with wide operation-temperature is elaborately designed through regulating structure/interface coupled electron/ion transport. Greatly, the derived Na vacancy and charge rearrangement induced by trivalent Al3+ substitution lower the ions diffusion barriers, thereby endowing faster electron transport and Na+ mobility. More importantly, the existing Al-O-P bonds strengthen the local environment and alleviate the volume vibration during (de)sodiation, enabling highly reversible valence variation and structural evolution. As a result, remarkable cyclability (over 10,000 loops), ultrafast rate capability (200 C), and exceptional all-climate stability (-40-60 °C) in half/full cells are demonstrated. Given this, the rational work might provide an actionable strategy to promote the electrochemical property of NFPP, thus unveiling the great application prospect of sodium iron mixed phosphate materials.

A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence

Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences' repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan's performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.

[Seroprevalence of the specific antibody against Toxoplasma gondii among patients with hematological diseases]

OBJECTIVE

To investigate the seroprevalence of Toxoplasma gondii infections among patients with hematological diseases, so as to provide insights into improving the prognosis and quality of life among patients with hematological diseases.

METHODS

A total of 240 patients with hematological diseases (including 170 patients with hematological tumors and 70 patients with non-tumor hematological diseases) admitted to The Affiliated Hospital of Putian University during the period from January 1, 2021 through October 10, 2023 and 500 healthy volunteers in the hospital during the same period were enrolled. Subjects' demographics and serum samples were collected, and serum specific IgG and IgM antibodies against T. gondii were detected using the chemiluminescence assay, with any of a positive IgG or IgM antibody defined as a positive T. gondii infection. The seroprevalence of specific IgG and IgM antibodies against T. gondii was compared between patients with hematological diseases and healthy volunteers.

RESULTS

The mean age (F = 2.034, P > 0.05) and gender distribution (χ2 = 0.462, P > 0.05) were comparable among patients with hematological tumors, patients with non-tumor hematological diseases and healthy volunteers, and there was no significant difference in the proportion of history of cat or dog contacts between patients with hematological diseases and healthy volunteers (χ2 = 0, P > 0.05). The seroprevalence of anti-T. gondii antibody was significantly higher among patients with hematological diseases than among healthy volunteers (15.8% vs. 0.6%; χ2 = 71.902, P < 0.01), and there was a significant difference in the seroprevalence of anti-T. gondii antibody among patients with hematological tumors (18.2%), patients with non-tumor hematological diseases (10.0%) and healthy volunteers (χ2 = 78.327, P < 0.01). The seroprevalence of anti-T. gondii antibody was significantly higher among patients with hematological tumors and non-tumor hematological diseases than among healthy volunteers (both P values < 0.05), while no significant difference was seen in the seroprevalence of anti-T. gondii antibody between patients with hematological tumors and non-tumor hematological diseases (P > 0.05). In addition, the proportion of history of cat or dog contacts was significantly higher among patients with hematological diseases that were positive for serum anti-T. gondii anti-body than among those negative for serum anti-T. gondii antibody (21.1% vs. 5.4%; χ2 = 8.653, P < 0.05).

CONCLUSIONS

There is a high seroprevalene rate of T. gondii infections among hematological diseases, which is significantly greater than that among healthy volunteers.

Effects of lysolecithins on performance, egg quality, blood profiles and liver histopathology in late-phase laying hens

1. This study investigated the effects of lysolecithins (LL) on performance, egg quality, blood profiles, relative organ weight and liver histopathology in laying hens.2. A total of 480 healthy 65-week-old Lohmann laying hens were randomly allocated into four treatments in a 2 × 2 factorial arrangement design with two levels of energy (AMEn, 11.08 MJ/kg and 12.94 MJ/kg) and two levels of LL (0 and 0.05%).3. Birds fed high energy diets had lower (P < 0.05) average daily intake and feed conversion rate during weeks 0-4, 5-8 and 0-8, but higher (P < 0.05) average egg weight (AEW) during trial weeks 0-4. There was an interaction in (P < 0.05) AEW during trial weeks 0-14 and 0-8 for energy and LL. The high energy diets increased yolk colour at the end of weeks 2 and 4, while addition of LL increased albumen height at the end of week 2. There was an interaction (P < 0.05) in yolk colour between energy and LL at the end of week 2. There was an interaction (P < 0.05) in serum superoxide dismutase and LDL-C throughout the experiment.4. The high energy diets increased (P < 0.05) the relative weight of abdominal fat compared with low energy diets. The high energy diets increased (P < 0.05) liver ether extract content and liver pathological injury score compared with low energy diets at the end of week 8, while the addition of LL decreased (P < 0.05) liver pathological injury score.5. The supplementation of LL in high energy diets could alleviate some negative effects on liver injury in late laying hens.

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

The productivity of smallholder dairy farms is very low in developing countries. Important genetic gains could be realized using genomic selection, but genetic evaluations need to be tailored for lack of pedigree information and very small farm sizes. To accommodate this situation, we propose a flexible Bayesian model for the genetic evaluation of milk yield, which allows us to simultaneously account for nongenetic random effects for farms and varying SNP variance (BayesR model). First, we used simulations based on real genotype data from Indian crossbred dairy cattle to demonstrate that the proposed model can separate the true genetic and nongenetic parameters even for small farm sizes (2 cows on average) although with high standard errors in scenarios with low heritability. The accuracy of genomic genetic evaluation increased until farm size was approximately 5. We then applied the model to real data from 4,655 crossbred cows with 106,109 monthly test day milk records and 689,750 autosomal SNPs. We estimated a heritability of 0.16 (0.04) for milk yield and using cross-validation, a genomic estimated breeding value (GEBV) accuracy of 0.45 and bias (regression of phenotype on GEBV) of 1.04 (0.26). Estimated genetic parameters were very similar using BayesR, BayesC, and genomic BLUP approaches. Candidate genes near the top variants, IMMP2L and ARHGEF2, have been previously associated with milk protein composition, mastitis resistance, and milk cholesterol content. The estimated heritability and GEBV accuracy for milk yield are much lower than those from intensive or pasture-based systems in many countries. Further increases in the number of phenotyped and genotyped animals in farms with at least 2 cows (preferably 3-5, to allow for dropout of cows) are needed to improve the estimation of genetic effects in these smallholder dairy farms.

Prostate Advanced Radiation Technologies Investigating Quality of Life (PARTIQoL): A Phase III Randomized Clinical Trial of Proton Therapy vs. IMRT for Low or Intermediate Risk Prostate Cancer

PURPOSE/OBJECTIVE(S)

Prostate cancer is the most common non-cutaneous cancer diagnosed among men in the United States, and the majority of patients are diagnosed with localized disease. Men with localized prostate cancer have several treatment options including external beam radiotherapy with either photons or protons. Proton beam therapy (PBT) has certain dosimetric advantages and the potential to reduce treatment-associated morbidity and improve oncologic outcomes, but current PBT is significantly more costly than intensity-modulated radiotherapy (IMRT). The PARTIQoL trial (NCT01617161) is the first multicenter phase 3 randomized trial comparing protons to photons in the treatment of localized prostate cancer.

MATERIALS/METHODS

Patients with low or intermediate risk prostate cancer (Stage T1c-T2c, PSA < 20, Gleason score ≤ 7) are randomized to receive either PBT or IMRT, with targeted recruitment efforts for minority populations. A companion registry study has concurrently enrolled patients who declined randomization or whose insurance denied coverage for PBT. Patients are stratified by clinical site, age, use of rectal spacer, and fractionation schedule (conventional fractionation: 79.2 Gy in 44 fractions vs moderate hypofractionation: 70.0 Gy in 28 fractions). Participants are followed longitudinally to assess patient-reported outcomes (PROs) of bowel, urinary, and erectile function for 60 months after completion of radiotherapy (with an option for additional follow up through 10 years). Participants may also participate in correlative studies, including serial CT imaging during treatment and analyses of biopsy tissue, blood and urine specimens. The primary objective is to compare PROs of bowel function using the EPIC score at 24 months following completion of radiation. Secondary objectives are to assess treatment-related differences in urinary and erectile functions, adverse events, efficacy endpoints (biochemical control, metastasis-free survival, disease-specific survival, and overall survival), health state utilities, perceptions of care, late effects, cost-effectiveness, association between radiotherapy dose distribution and PROs, and to identify biomarkers of radiation response and toxicity.

RESULTS

The randomized trial has completed accrual, with 450 patients enrolled at 27 sites between June 2012 and November 2021. 20.3% of patients enrolled are non-white. Accrual on the companion registry is active, with 354 patients enrolled as of February 2023.

CONCLUSION

Follow-up for the primary endpoint on the randomized trial will be reached in 2024. The PARTIQoL randomized clinical trial will rigorously assess the clinical benefits of PBT relative to IMRT and results will inform decision making by patients, providers, policymakers, and payers.

Proton Radiation Therapy for Stage IIA/IIB Testicular Seminoma

PURPOSE/OBJECTIVE(S)

Testicular seminoma affects young men and is associated with very favorable prognosis. The evolution in treatment paradigm has focused on minimizing acute and especially late toxicities. Following orchiectomy, while surveillance is favored in Stage I patients, radiotherapy (RT) is a standard treatment option for de novo or relapsed stage IIA or select non-bulky stage IIB disease. Despite low doses, standard RT fields to paraaortic and pelvic lymphatics using x-rays exposes a large volume of uninvolved normal tissue/viscera to excess dose. This young patient population is especially vulnerable to risks of late RT toxicities including secondary malignancy. Proton beam therapy (PBT) has dosimetric advantage over x-ray-based RT due to lack of exit dose, and comparative dosimetric/modeling studies show significant sparing of uninvolved abdominal/pelvic organs. However, there is scant reported clinical data at this time for PBT. We review our early institutional outcomes with PBT for testicular seminoma.

MATERIALS/METHODS

Single institution retrospective review from a tertiary care center of patients treated with PBT from 2013-2022 for testicular seminoma. Recurrence free (RFS) and overall survival (OS) were calculated from the completion of PBT. Toxicities were graded (Gr) using CTCAE v5.0.

RESULTS

Four patients underwent PBT, median age 39 (range 36-47). All were Stage I at diagnosis (pT1b n = 3; pT2 n = 1) and were treated for recurrent stage II disease (IIA n = 3; IIB n = 1) at a median of 34 months from orchiectomy (range 3 - 74 months). Nodal extent included 2 with multiple paraaortic nodes, 1 with solitary paraaortic node and 1 with solitary pelvic node. PBT was delivered with pencil-beam scanning, treating paraaortic + ipsilateral pelvic fields (20 Gy in 10 fractions), then sequential boost to involved nodes (10 -16 Gy in 5-8 fractions). Typically, PA or posterior oblique fields were used to minimize dose to out-of-field abdominal/pelvic viscera. Treatment was well tolerated with minimal acute toxicities: fatigue Gr 1 (n = 3), nausea Gr 1 (n = 3). No Gr 2 or higher acute toxicities or significant late toxicities were observed. At median follow up of 30 months (range 3 - 54), no recurrences were observed, and RFS and OS were 100%. Two patients are without evidence of disease > 4 years post-treatment.

CONCLUSION

In this case series, PBT for retroperitoneal and pelvic metastases in Stage IIA/IIB testicular seminoma was associated with oncologic efficacy with minimal toxicity. PBT reduces unnecessary dose to abdominal/pelvic organs compared to x-ray techniques, which is advantageous in young patients who have anticipated long-term survival. This is one of the few series reporting clinical outcomes of PBT in the management of seminoma. Randomized comparisons with x-ray approaches are impractical given the relatively low volume of patients receiving RT in modern seminoma management, so it is essential to report and track longitudinal outcomes across institutions to validate this approach.

Treatment of Thymoma and Thymic Carcinoma with Proton Beam Therapy: Outcomes from the Proton Collaborative Group Prospective Registry

PURPOSE/OBJECTIVE(S)

Given the generally long natural history of thymic malignancies, proton beam therapy (PBT) is advocated to minimize the risk of long-term toxicities to mediastinal organs. Adverse events (AE) and long-term clinical outcomes for this population have not been well-characterized.

MATERIALS/METHODS

The Proton Collaborative Group registry (NCT01255748), a multi-institutional prospective database of academic and community proton centers in the US, was queried for patients with thymomas and thymic carcinomas treated with PBT. Patients with recurrent/metastatic disease, non-thymic histology, received either prior or palliative radiotherapy (dose < 40 Gy RBE) were excluded. Overall survival (OS) and local control (LC) were estimated using Kaplan-Meier methods.

RESULTS

A total of 97 patients were identified in the PCG registry. After applying relevant exclusion criteria, 70 patients from 12 proton centers treated from 2011-2021 were included for analysis. Median follow-up length was 16 months. Median age was 58.5 years (IQR 46-63), and 60% were female. 81.4% had a diagnosis of thymoma, and 18.6% thymic carcinoma. 59 patients underwent surgical resection. 11 were treated with definitive PBT, of which 5 received concurrent chemotherapy. Median dose was 54 Gy RBE (range 41.4 - 70 Gy RBE), median number of fractions was 30 (range 21 - 38). 73.4% received pencil beam scanning and 23% uniform scanning PBT. Treatment was overall well-tolerated: a single patient developed grade 4 pneumonitis. Grade 3 AEs were seen in 3 patients - dyspnea, anorexia, and heart failure. Highest grade toxicity experienced was grade 2 for 47.1% and grade 1 for 42.9% of patients. 3-year overall survival (OS) was 82.6% for the entire cohort. 3-year OS was 94% for resected/adjuvant cohort and 35.6% in the non-surgical/definitive cohort. 3-year local control (LC) was 91.7% for the entire cohort. By surgery/margin status, 3-year LC was 96.8% in patients with close or negative margins (a single failure in a patient with close margins), whereas 3-year LC was 55.1% for patients with positive margins/unresectable disease.

CONCLUSION

Thymic malignancies treated with PBT appear to have favorable outcomes, especially in the adjuvant setting, in this cohort representing the largest series of such patients.

Multi-Institutional Experience of Proton Therapy for Rhabdomyosarcoma and Ewing Sarcoma in the Proton Collaborative Group (PCG) Prospective Registry

PURPOSE/OBJECTIVE(S)

To report on outcomes, acute toxicities, and the use of dose-escalation with proton therapy (PT) in patients with rhabdomyosarcoma and Ewing sarcoma in a prospective multi-institutional registry (PCG).

MATERIALS/METHODS

Data on patients with primary rhabdomyosarcoma and Ewing sarcoma treated with definitive PT (defined as ≥45 Gy) were queried from the PCG registry. A similar query was performed of our institutional database with IRB approval. Overall survival rates were calculated by Kaplan-Meier. Toxicities were scored using CTCAE v4.0.

RESULTS

A total of 354 patients across 10 institutions (203 rhabdomyosarcoma, 151 Ewing sarcoma) met the eligibility criteria. Median age was 9 years (Interquartile Range: 5-15). Median dose was 50.4 GyRBE for rhabdomyosarcoma patients (Range: 45-66 GyRBE) and 55.8 GyRBE for Ewing sarcoma patients (Range: 45-66 GyRBE). Median follow-up was 2.4 years (Range 0.3-12.3 years). Two-year overall survival rates were 81.1% (95% CI: 73.7%-88.5%) for rhabdomyosarcoma and 79.1% (95% CI: 71.7%-86.2%) for Ewing sarcoma. The Table lists the prescription doses delivered by tumor histology; 28.1% of rhabdomyosarcoma and 21.9% of Ewing sarcoma patients, respectively, received dose-escalated radiotherapy (defined as >50.4 Gy for rhabdomyosarcoma and >55.8 Gy for Ewing sarcoma). Excluding alopecia and skin desquamation, 153 patients (43.2%) developed any acute grade 2+ non-hematologic toxicity, while 49 patients (13.8%) developed one or more grade 3 toxicities. The most common grade 3 toxicities were anorexia/weight loss (7.3%), pain (7.3%) mucositis/esophagitis (4.8%), and nausea/vomiting (3.1%). One grade 4 toxicity (esophagitis) and no deaths were reported during treatment.

CONCLUSION

In this multi-institutional prospective registry, 28.1% of rhabdomyosarcoma and 21.9% of Ewing sarcoma patients received dose-escalated PT, with 13.8% of patients developing grade 3 toxicities. Long-term outcomes for disease control and late toxicity and anticipated cooperative group trial results are needed to fully assess the benefits and risks of dose-escalated radiotherapy for these tumors.

Adaptation of a Clinical Proton Pencil Beam Scanning System for FLASH Experiments

PURPOSE/OBJECTIVE(S)

To characterize a proton pencil beam scanning system for ultra-high dose rate (UHDR) irradiations and validate it with FLASH preclinical experiments.

MATERIALS/METHODS

After modifications to the beamline to maximize the beam current at isocenter in our gantry room, we characterized the UHDR beam in terms of: 1) Size and shape of the beam spot in three configurations; pristine beam, 75 mm water-equivalent-thickness (WET) range shifter (RS), and custom-built 135 mm WET RS mounted 310 mm upstream of the aperture in the snout housing. These configurations were analyzed to determine which one achieved the highest dose rate; 2) Beam transport efficiency and beam output. We compared the signal in the monitor chambers of the proton system with a Faraday cup and plane parallel ionization chamber (PPC05, IBA dosimetry) for beam current at the cyclotron from 7.5 nA to 800 nA; 3) Dose homogeneity, beam penumbra, and dose rate for the fields to be used in preclinical irradiations. All measurements were performed at isocenter, in air or at 1 cm depth in solid water, using the highest energy (about 230 MeV), which corresponded to a nominal range of 32.9 cm in water. We modeled the UHDR beam in our treatment planning system (TPS) to optimize the dose homogeneity and lateral penumbra of the irradiation fields. We performed the preclinical experiments in single fractions of 19 Gy (RBE), 21 Gy (RBE) and 23 Gy (RBE) (RBE = 1.1), targeting the pelvis of C57BL/6 mice and using survival as the endpoint. Each arm included 6-10 mice. The proton beam was used in transmission mode, positioning the center of the mouse pelvis at isocenter, and irradiating the pelvis with a 2x6 cm^2 field. Apertures were placed at 9cm from the isocenter to sharpen the lateral penumbra.

RESULTS

The range measurements with a multi-layer ionization chamber were consistent within 1 mm with the nominal range. In UHDR mode, the spot size at the isocenter varied from 4.5 mm for the pristine beam to 9.2 mm for the 135 mm RS. The spot size at isocenter remained constant when the beam intensity varied from 7.5 nA to 800 nA at the cyclotron exit. By employing the configuration with the 135 mm RS and optimizing the fields in the TPS, we achieved a dose rate of 1 Gy (RBE)/s for the conventional regime and 75(RBE) Gy/s for the UHDR regime. The monitor chambers of the proton system were affected by recombination at high dose rates: we observed about 35% higher output for the same number of monitor units delivered at 800 nA vs 7.5 nA. The delivered dose was determined with the PPC05 for each field, as this detector did not show recombination effects. When preclinical irradiations were independently monitored, the delivered dose was typically within 1% of the intended value. In three independent experiments, a dose of 21 Gy (RBE) or higher was associated with an increased survival in the UHDR arm compared to the conventional arm.

CONCLUSION

We adapted a clinical proton system for preclinical irradiations at UHDR. Our results confirm the presence of the FLASH effect.

Multi-Institutional Experience of Proton Therapy for Osteosarcoma in the Proton Collaborative Group (PCG) Prospective Registry

PURPOSE/OBJECTIVE(S)

To report on the utilization of dose-escalated radiotherapy, acute toxicities, and survival following definitive proton therapy (PT) for osteosarcoma patients in a prospective multi-institutional study.

MATERIALS/METHODS

Data on patients with osteosarcoma treated with definitive intent PT were queried from the Proton Collaborative Group (PCG) prospective registry. A similar query was performed on an institutional database with IRB approval. Overall survival rates were calculated by Kaplan-Meier. Toxicities were scored using CTCAE v4.0.

RESULTS

Forty osteosarcoma patients across 9 institutions received definitive intent PT between 2011-2021 and met the eligibility criteria. Median age was 32 years (Range: 6-86 years). Median PT dose was 66.6 GyRBE (Range: 50.4-80.0 GyRBE); 38 patients received proton therapy alone, whereas 2 received combined proton/photon therapy. Seventeen (42.5%) patients received doses ≥70 GyRBE. Median follow-up was 3.1 years (Range: 0.9-10.5 years). One-year and three-year overall survival rates were 83.5% and 59.1%, respectively, with 14 deaths due to disease. Excluding skin desquamation and alopecia, 22 patients (55.0%) developed any acute grade 2+ toxicity, and 5 patients (12.5%) developed any grade 3 toxicities. No acute grade 4-5 toxicities were reported. The most frequent grade 2+ non-skin toxicities were fatigue (37.5%), anorexia/weight loss (17.5%), mucositis/esophagitis (22.5%), pain (20.0%), and nausea/vomiting (10.0%). The most frequent grade 3 toxicities were anorexia/weight loss (5.0%), mucositis/esophagitis (5.0%), and neurologic symptoms (5.0%).

CONCLUSION

In this multi-institutional study, 42.5% of osteosarcoma patients treated with PT received doses between 70-80 Gy, with 12.5% experiencing any grade 3 toxicity. Long-term outcomes for disease control, late toxicity, and quality-of-life are needed to more fully assess the benefits and risks of dose-escalated radiotherapy in this radioresistant tumor. The authors plan to assess the outcomes of osteosarcoma patients treated with dose-escalated radiotherapy for unresectable or gross residual disease in future studies.

CCLHunter: An efficient toolkit for cancer cell line authentication

Cancer cell lines are essential in cancer research, yet accurate authentication of these cell lines can be challenging, particularly for consanguineous cell lines with close genetic similarities. We introduce a new Cancer Cell Line Hunter (CCLHunter) method to tackle this challenge. This approach utilizes the information of single nucleotide polymorphisms, expression profiles, and kindred topology to authenticate 1389 human cancer cell lines accurately. CCLHunter can precisely and efficiently authenticate cell lines from consanguineous lineages and those derived from other tissues of the same individual. Our evaluation results indicate that CCLHunter has a complete accuracy rate of 93.27%, with an accuracy of 89.28% even for consanguineous cell lines, outperforming existing methods. Additionally, we provide convenient access to CCLHunter through standalone software and a web server at https://ngdc.cncb.ac.cn/cclhunter.

Transcriptome-wide association studies: recent advances in methods, applications and available databases

Genome-wide association study has identified fruitful variants impacting heritable traits. Nevertheless, identifying critical genes underlying those significant variants has been a great task. Transcriptome-wide association study (TWAS) is an instrumental post-analysis to detect significant gene-trait associations focusing on modeling transcription-level regulations, which has made numerous progresses in recent years. Leveraging from expression quantitative loci (eQTL) regulation information, TWAS has advantages in detecting functioning genes regulated by disease-associated variants, thus providing insight into mechanisms of diseases and other phenotypes. Considering its vast potential, this review article comprehensively summarizes TWAS, including the methodology, applications and available resources.

Climate-driven variability of the Southern Ocean CO2 sink

The Southern Ocean is a major sink of atmospheric CO2, but the nature and magnitude of its variability remains uncertain and debated. Estimates based on observations suggest substantial variability that is not reproduced by process-based ocean models, with increasingly divergent estimates over the past decade. We examine potential constraints on the nature and magnitude of climate-driven variability of the Southern Ocean CO2 sink from observation-based air-sea O2 fluxes. On interannual time scales, the variability in the air-sea fluxes of CO2 and O2 estimated from observations is consistent across the two species and positively correlated with the variability simulated by ocean models. Our analysis suggests that variations in ocean ventilation related to the Southern Annular Mode are responsible for this interannual variability. On decadal time scales, the existence of significant variability in the air-sea CO2 flux estimated from observations also tends to be supported by observation-based estimates of O2 flux variability. However, the large decadal variability in air-sea CO2 flux is absent from ocean models. Our analysis suggests that issues in representing the balance between the thermal and non-thermal components of the CO2 sink and/or insufficient variability in mode water formation might contribute to the lack of decadal variability in the current generation of ocean models. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.

Elevated ZNF704 expression is associated with poor prognosis of uveal melanoma and promotes cancer cell growth by regulating AKT/mTOR signaling

BACKGROUND

Uveal melanoma (UM) is the most common intraocular malignancy in adults, with a poor survival prognosis. To date, limited understanding of UM's molecular mechanisms constitutes an obstacle to developing effective therapy. In this study, we examined key regulators mediating UM progression and their clinical relevance.

METHODS

Transcriptomics of UM patients and cells were analyzed via RNA sequencing and bioinformatic analysis. Zinc finger protein 704 (ZNF704) was identified as prognosis-related biomarker for UM based on clinical characteristics and RNA-seq data from The Cancer Genome Atlas (TCGA). Gene expression was knocked down by specific shRNAs/siRNAs and overexpressed by transfection with plasmids inserted with investigated gene cDNA. Cell proliferation, viability and invasion abilities were determined by CCK8, colony formation and transwell assays, respectively. For cell cycle and apoptosis, cells were PI or PI/Annexin V-APC stained and analyzed by flow cytometry. Standard immunoblotting and quantitative RT-PCR were employed to assess the mRNA and protein abundance. To determine tumor growth in vivo, 4-week-old BALB/c-nu immune-deficient nude mice were inoculated with tumor cells.

RESULTS

Analysis of differential expressed genes (DEGs) and survival analysis identified ZNF704 as a novel biomarker of UM. Prognostic analysis indicated ZNF704 as an independent predictor of UM overall survival. Expression of ZNF704 is elevated in UM tissues relative to adjacent normal choroid tissues. Knockdown of ZNF704 suppressed the growth and migration of UM cells and vice versa. In addition, expression of ZNF704 arrest UM cells at G0/G1 phase and inhibit cell apoptosis. RNA sequencing analysis indicated that SORBS3 were dysregulated after ZNF704 downregulation. Gene Set Enrichment Analysis (GSEA) revealed that upon ZNF704 knowndown, genes related with PI3K/AKT/mTOR, EMT and metastasis are enriched. Mechanistically, ZNF704 activates AKT/mTOR/glycolysis signaling pathway in UM cells. Moreover, expression of SORBS3 is downregulated by ZNF704 and knockdown of SORBS3 restored tumor cell viability in ZNF704 silenced cells.

CONCLUSIONS

ZNF704 predicts poor prognosis of UM and exhibit pro-oncogenic effect in UM progression in vivo and in vitro, mediated through AKT/mTOR signaling pathway and suppression of SORBS3 expression.

Denosumab salvage therapy in an 11-year-old boy with locally recurrent unresectable giant cell tumor of the lumbar spine after surgery

Giant cell tumors (GCTs) of the bone are locally aggressive primary bone tumors with a benign character. Spinal involvement is rare which accounts for approximately 5% of all primary bone tumors and it is quite rare in the lumbar spine. An 11-year-old boy patient presented with pain of low back and bilateral low extremities. Lumbar CT and MRI revealed a lytic lesion of the L4 vertebra corpus. The patient earned remarkable and timely recovery with 2 surgical interventions and the use of denosumab. Surgical resection for GCTs is still preferable as the initial treatment, denosumab should be utilized after tumor resection whether based on the purpose of prevention or treatment of tumor recurrence.

[Porphyromonas gingivalis infection causes umbilical vein endothelial barrier dysfunction in vitro by down-regulating ZO-1, occludin and VE-cadherin expression]

OBJECTIVE

To explore the molecular mechanisms of Porphyromonas gingivalis infection-induced umbilical vein endothelial barrier dysfunction in vitro.

METHODS

Human umbilical vein endothelial cells (HUVECs) were cultured in vitro, and after the formation of the endothelial barrier, the cells were infected with P. gingivals at a multiplicity of infection (MOI). The transepithelial electrical resistance (TEER) of the cell barrier was measured, and FITC-dextran trans-endothelial permeability assay and bacterial translocation assay were performed to assess the endothelial barrier function. The expression levels of cell junction proteins including ZO-1, occludin and VE-cadherin in the cells were examined by qRT-PCR and Western blotting.

RESULTS

In freshly seeded HUVECs, TEER increased until reaching the maximum on Day 5 (94 Ωcm²), suggesting the formation of the endothelial barrier. P. gingivals infection caused an increase of the permeability of the endothelial barrier as early as 0.5 h after bacterial inoculation, and the barrier function further exacerbated with time, as shown by significantly lowered TEER, increased permeability of FITC-dextran (40 000/70 000), and increased translocation of SYTO9-E. coli cross the barrier. MTT assay suggested that P. gingivals infection did not significantly affect the proliferation of HUVECs (P>0.05), but in P. gingivalsinfected cells, the expressions of ZO-1, occludin and VE-cadherin increased significantly at 24 and 48 h after bacterial inoculation (P < 0.05).

CONCLUSION

P. gingivals may disrupt the endothelial barrier function by down-regulating the expressions of the cell junction proteins (ZO-1, occludin, VE-cadherin) and increasing the permeability of the endothelial barrier.

[Safety and feasibility of robotic-assisted thoracoscopic day surgery for pulmonary nodules: a retrospective analysis based on propensity score matching]

Objective: To evaluate the safety and feasibility of robotic-assisted thoracoscopic day surgery for pulmonary nodules. Methods: Clinical data of 523 patients with pulmonary nodule underwent robotic-assisted thoracoscopic surgery in the Department of Thoracic Surgery, Xiangya Hospital, Central South University from January 2021 to June 2022 were retrospectively analyzed, which including 223 males and 300 females, aged from 19 to 72 (54.0±11.7) years. Those patients were divided into the day surgery group (DSG) and inpatient surgery group (ISG) according to perioperative management methods. Propensity score matching (PSM) (1∶2) was performed according to the general baseline information, T stage of the tumor, surgery approach, and tumor position, and a total of 178 patients were finally included. Clinical outcomes of DSG were observed. The differences in incidence of postoperative complications, treatment-related costs and resource consumption between DSG and ISG were compared. Subgroup analysis was performed according to surgery method to evaluate the difference between DSG and ISG in lobectomy and sublobectomy. Results: In 81 cases DSG, eight patients were transferred to thoracic surgery ward, and the day surgery discharge rate was 90% (73/81). There was no statistically significant difference in incidence of postoperative complications between DSG and ISG (P=0.612). The length of stay after surgery, period of chest draining, average hospital cost, and drug cost of DSG were statistically significant lower than ISG, ((2.19±0.84) vs (4.74±1.81) days, (1.70±0.65) vs (3.45±1.85) days, (6.64±0.74) vs (8.29±0.97)×10⁴ CNY, (0.35±0.07) vs (0.69±0.18)×10⁴ CNY), respectively(all P<0.05). The drainage volume and VAS score at discharge in DSG and ISG group were(220.47±120.02) ml and(242.21±129.96) ml, 1.68±0.79 and 1.64±0.91, respectively, with no statistically significant difference (P>0.05). In subgroup analysis, there was no statistically significant difference in incidence of postoperative complications, drainage volume after surgery and VAS score at discharge between DSG and ISG both for lobectomy and sublobectomy patients. And the results of the length of stay after surgery, period of chest draining, and drug cost in DSG were also significantly lower than ISG (P<0.05). Conclusions: Robotic-assisted thoracoscopic day surgery for pulmonary nodule is safe and feasible, with the advantage of short length of stay after surgery, short period of chest draining, less average hospital cost and drug cost. There is no difference in incidence of postoperative complications between DSG and ISG.

TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies

Transcriptome-wide association studies (TWASs), as a practical and prevalent approach for detecting the associations between genetically regulated genes and traits, are now leading to a better understanding of the complex mechanisms of genetic variants in regulating various diseases and traits. Despite the ever-increasing TWAS outputs, there is still a lack of databases curating massive public TWAS information and knowledge. To fill this gap, here we present TWAS Atlas (https://ngdc.cncb.ac.cn/twas/), an integrated knowledgebase of TWAS findings manually curated from extensive literature. In the current implementation, TWAS Atlas collects 401,266 high-quality human gene-trait associations from 200 publications, covering 22,247 genes and 257 traits across 135 tissue types. In particular, an interactive knowledge graph of the collected gene-trait associations is constructed together with single nucleotide polymorphism (SNP)-gene associations to build up comprehensive regulatory networks at multi-omics levels. In addition, TWAS Atlas, as a user-friendly web interface, efficiently enables users to browse, search and download all association information, relevant research metadata and annotation information of interest. Taken together, TWAS Atlas is of great value for promoting the utility and availability of TWAS results in explaining the complex genetic basis as well as providing new insights for human health and disease research.

TSomVar: a tumor-only somatic and germline variant identification method with random forest

Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.

AB1427 ASSOCIATION BETWEEN HYPERURICEMIA AND OSTEOPOROTIC IN CHINESE ADULTS, A CROSS-SECTIONAL STUDY

Background

Hyperuricemia may have a protective role in diseases characterized by high levels of oxidative stress, such as osteoporosis. Previous studies have shown that hyperuricemia is associated with osteoporotic. However, this association is controversial and even yielded conflicting results.

Objectives

This study investigated the relationship between hyperuricemia and osteoporotic among Chinese adults.

Methods

The data of cross-sectional study was collected at Guangdong Second Provincial General Hospital in Guangzhou City, China between January 2009 and December 2019. Physical examinations and laboratory measurement variables were obtained from the medical check-up system. The multivariate-adjusted logistic regression model was performed to assess the association between hyperuricemia and osteoporotic.

Results

A total of 18917 participants (11334 males and 7579 females) were included in this study, with an average age of 46.23 years (SD: 11.67) at baseline. It included 5881 cases of hyperuricemia and 1587 osteoporotic. After adjusted for the confounding factors in logistic regression analysis, we observed a negative significant association between hyperuricemia and risk of osteoporotic (odds ratio [OR],0.852, 95%CI 0.795–0.967; P <0.05). Further stratified analyses showed a negative significant association with the risk of osteoporotic in women (OR,0.787, 95%CI 0.698–0.853; P <0.05), man (OR,0.897, 95%CI 0.786–0.954; P <0.05) and old adults (OR, 0.808, 95%CI, 0.759-0.894; P <0.05). No significant differences in other groups.

Conclusion

Our study observed participants with hyperuricemia had significantly less osteoporosis. More high-quality research is needed to further support these findings.

References

[1]Zong Q, Hu Y, Zhang Q, Zhang X, Huang J, Wang T. Associations of hyperuricemia, gout, and UA-lowering therapy with the risk of fractures: A meta-analysis of observational studies. Joint Bone Spine. 2019 Jul;86(4):419-427.

[2]Wang Y, Zhou R, Zhong W, Hu C, Lu S, Chai Y. Association of gout with osteoporotic fractures. Int Orthop. 2018 Sep;42(9):2041-2047.

[3]Veronese N, Carraro S, Bano G, Trevisan C, Solmi M, Luchini C, Manzato E,Caccialanza R, Sergi G, Nicetto D, Cereda E. Hyperuricemia protects against low bone mineral density, osteoporosis and fractures: a systematic review and meta-analysis. Eur J Clin Invest. 2016 Nov;46(11):920-930.

[4]Veronese N, Bolzetta F, De Rui M, Maggi S, Noale M, Zambon S, Corti MC, Toffanello ED, Baggio G, Perissinotto E, Crepaldi G, Manzato E, Sergi G. Serum uric acid and incident osteoporotic fractures in old people: The PRO.V.A study. Bone. 2015 Oct;79:183-9.

Figure 1.

Distribution of hyperuricemia and osteoporotic by gender.

Disclosure of Interests

None declared

AB1422 PREVALENCE OF HYPERURICEMIA IN CHINESE ADULTS: DATA FROM A CROSS-SECTIONAL STUDY

Background

Previous studies have observed an increasing trend in the prevalence of hyperuricemia which is linked to the physiological prerequisite for gout in recent years. However, the prevalence of hyperuricemia varies across different populations and different areas.

Objectives

The aim of this study was to explore the prevalence of hyperuricemia and influencing factors in Chinese adults.

Methods

The analysis was a part of a cross-sectional study in Guangdong Second Provincial General Hospital in Guangzhou City, China between January 2009 and December 2019. A total of 205922 participants (21401 with hyperuricemia) were included in this study. Hyperuricemia was defined as serum uric acid ≥416.0 µmol/L (7.0 mg/dl) for men and ≥357.0 µmol/L(6.0 mg/dl) for women. We calculated the prevalence of hyperuricemia and used the multivariate-adjusted logistic regression model to identify the risk factors associated with hyperuricemia.

Results

The overall estimated prevalence of HUA was 10.4% in China. Our study showed the prevalence of hyperuricemia in male (10.7%) was higher than that in female (9.9%) (P<0.05). The prevalence of HUA in the age group(≥75) subjects (13.3%) was higher than others. Multivariate logistic regression analysis revealed that sex (OR=1.75), age (OR=1.68), blood urea nitrogen (BUN) (OR=1.051), creatinine (Cr) (OR=1.045), high-density lipoprotein cholesterol (HDL-C) (OR=1.225), low-density lipoprotein cholesterol (LDL-C) (OR=1.466), systolic blood pressure (SBP) (OR=1.012),triglycerides (TG) (OR=1.460) and Body Mass Index (BMI) (OR=1.080) could increase the risk of hyperuricemia, while diastolic blood pressure (DBP) (OR=0.998), fasting plasma glucose (FPG) (OR=0.902) and total cholesterol (TC) (OR=0.704) were associated with a lower risk of hyperuricemia in all adults.

Conclusion

The latest prevalence of hyperuricemia is high in Chinese adults and is associated with multiple factors, indicating that prevention and control strategies for hyperuricemia are needed urgently.

References

[1]Han B, Wang N, Chen Y, Li Q, Zhu C, Chen Y, Lu Y. Prevalence of hyperuricaemia in an Eastern Chinese population: a cross-sectional study. BMJ Open. 2020 May 20;10(5):e035614.

[2]Liu H, Zhang XM, Wang YL, Liu BC. Prevalence of hyperuricemia among Chinese adults: a national cross-sectional survey using multistage, stratified sampling. J Nephrol. 2014 Dec;27(6):653-8.

[3]Song P, Wang H, Xia W, Chang X, Wang M, An L. Prevalence and correlates of hyperuricemia in the middle-aged and older adults in China. Sci Rep. 2018 Mar 12;8(1):4314.

[4]Dong X, Zhang H, Wang F, Liu X, Yang K, Tu R, Wei M, Wang L, Mao Z, Zhang G,Wang C. Epidemiology and prevalence of hyperuricemia among men and women in Chinese rural population: The Henan Rural Cohort Study. Mod Rheumatol. 2020 Sep;30(5):910-920.

[5]Shan R, Ning Y, Ma Y, Gao X, Zhou Z, Jin C, Wu J, Lv J, Li L. Incidence and Risk Factors of Hyperuricemia among 2.5 Million Chinese Adults during the Years 2017-2018. Int J Environ Res Public Health. 2021 Feb 28;18(5):2360.

Table 1.

The prevalence of hyperuricemia by gender and age groups

VariableNumberHyperuricemianPrevalence (%)GenderMale1242371333010.7Female8168580719.9Age group ＜3048437496510.3 30-4484331898910.7 45-595217549769.5 60-7414710164011.1 ≥75626983113.3Overall2059222140110.4

Disclosure of Interests

None declared

Crizotinib in patients with tumors harboring ALK or ROS1 rearrangements in the NCI-MATCH trial

The NCI-MATCH was designed to characterize the efficacy of targeted therapies in histology-agnostic driver mutation-positive malignancies. Sub-protocols F and G were developed to evaluate the role of crizotinib in rare tumors that harbored either ALK or ROS1 rearrangements. Patients with malignancies that progressed following at least one prior systemic therapy were accrued to the NCI-MATCH for molecular profiling, and those with actionable ALK or ROS1 rearrangements were offered participation in sub-protocols F or G, respectively. There were five patients who enrolled on Arm F (ALK) and four patients on Arm G (ROS1). Few grade 3 or 4 toxicities were noted, including liver test abnormalities, and acute kidney injury. For sub-protocol F (ALK), the response rate was 50% (90% CI 9.8-90.2%) with one complete response among the 4 eligible patients. The median PFS was 3.8 months, and median OS was 4.3 months. For sub-protocol G (ROS1) the response rate was 25% (90% CI 1.3-75.1%). The median PFS was 4.3 months, and median OS 6.2 months. Data from 3 commercial vendors showed that the prevalence of ALK and ROS1 rearrangements in histologies other than non-small cell lung cancer and lymphoma was rare (0.1% and 0.4% respectively). We observed responses to crizotinib which met the primary endpoint for ALK fusions, albeit in a small number of patients. Despite the limited accrual, some of the patients with these oncogenic fusions can respond to crizotinib which may have a therapeutic role in this setting.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

Enhancing Surface Chemical Stability of LiMn2 O4 Cathode by Strontium Enrichment at Grain Boundaries

LiMn₂ O₄ (LMO) cathodes suffer from limited cycle life, resulting from Mn dissolution and side reactions between electrode and electrolyte. In this study, Sr-modified LMO is prepared by using a simple strategy. The nature and position of large-radius Sr ions are investigated, alongside their influence on the structural stability of the bulk. SrMnO₃ (SMO) is found to be enriched at grain boundaries of LMO, with Mn-O-Sr bonds forming at the SMO/LMO interface. Furthermore, stable SMO alleviates the migration of Mn ions in LMO associated with structural integrity and suppresses side reactions between the electrode and electrolyte. The modified LMO cathodes maintain their structural integrity and display improved rate performance and cycling stability under harsh conditions. Remarkably, the discharge capacity of a Sr-modified LMO||Li half-cell maintains 94.8 % at 25 °C and 79.6 % at 55 °C after 500 cycles. Consequently, enrichment of strontium at grain boundaries presents a promising strategy for developing cathodes for long-term use.

Retraction notice: Effect of educational interventions on health in childhood: a meta-analysis of randomized controlled trials [Public Health Volume 164, November 2018, Pages 134-147]

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). The article is a duplicate of a paper that has already been published in Medicine, 97 (2018) e11849 https://doi.org/10.1097/MD.0000000000011849. Redundant publications overweigh the relative importance of published findings and distort the academic record of the authors. One of the conditions of submission of a paper for publication is therefore that authors declare explicitly that the paper has not been previously published and is not under consideration for publication elsewhere. As such this article represents a misuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

CancerSCEM: a database of single-cell expression map across various human cancers

With the proliferating studies of human cancers by single-cell RNA sequencing technique (scRNA-seq), cellular heterogeneity, immune landscape and pathogenesis within diverse cancers have been uncovered successively. The exponential explosion of massive cancer scRNA-seq datasets in the past decade are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment of various cancer types. To fill this gap, we developed a database of Cancer Single-cell Expression Map (CancerSCEM, https://ngdc.cncb.ac.cn/cancerscem), particularly focusing on a variety of human cancers. To date, CancerSCE version 1.0 consists of 208 cancer samples across 28 studies and 20 human cancer types. A series of uniformly and multiscale analyses for each sample were performed, including accurate cell type annotation, functional gene expressions, cell interaction network, survival analysis and etc. Plus, we visualized CancerSCEM as a user-friendly web interface for users to browse, search, online analyze and download all the metadata as well as analytical results. More importantly and unprecedentedly, the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates seven analyze functions, where investigators can interactively perform cancer scRNA-seq analyses. In all, CancerSCEM paves an informative and practical way to facilitate human cancer studies, and also provides insights into clinical therapy assessments.

RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks

Genotype imputation is a statistical method for estimating missing genotypes from a denser haplotype reference panel. Existing methods usually performed well on common variants, but they may not be ideal for low-frequency and rare variants. Previous studies showed that the population similarity between study and reference panels is one of the key factors influencing the imputation accuracy. Here, we developed an imputation reference panel reconstruction method (RefRGim) using convolutional neural networks (CNNs), which can generate a study-specified reference panel for each input data based on the genetic similarity of individuals from current study and references. The CNNs were pretrained with single nucleotide polymorphism data from the 1000 Genomes Project. Our evaluations showed that genotype imputation with RefRGim can achieve higher accuracies than original reference panel, especially for low-frequency and rare variants. RefRGim will serve as an efficient reference panel reconstruction method for genotype imputation. RefRGim is freely available via GitHub: https://github.com/shishuo16/RefRGim

[Incidence of enteral feeding intolerance and its risk factors in patients with oral and maxillofacial malignancies]

OBJECTIVE

To explore the incidence of enteral feeding intolerance and its risk factors in patients with malignant oral and maxillofacial tumors.

METHODS

We conducted a retrospective analysis of 122 patients with malignant oral and maxillofacial tumor admitted in a general hospital for enteral nutrition between March, 2018 and March, 2021. The incidence of intolerance to enteral nutrition was analyzed, and the two groups of patients with and without intolerance were compared for age, gender, height, weight, pathological staging, types of enteral nutrition preparations, clinical treatment (physical hypothermia and nasal delivery), drug usage (sedatives, vasoactive drugs, acid suppressant, potassium preparation, antibiotics and hormones) and biochemical parameters (serum total protein, serum albumin, blood glucose and serum potassium concentration). Logistic regression analysis was used to analyze the influencing factors of enteral nutritional feeding intolerance in patients.

RESULTS

Of the 122 patients, 52 had enteral feeding intolerance with an incidence rate of 42.6%. Logistic regression analysis showed that potassium preparation (OR=4.125, P=0.027, 95%CI: 1.178-14.444), sedatives (OR=4.125, P=0.000, 95%CI: 2.007-11.765) and hypoproteinemia (OR=3.557, P=0.010, 95%CI: 1.351-9.366) were independent risk factors of feeding intolerance in patients with malignant oral and maxillofacial tumors, while adding dietary fiber was a protective factor (OR= 0.108, P=0.015, 95%CI: 0.018-0.643).

CONCLUSION

The incidence of enteral feeding intolerance is high in patients with malignant oral and maxillofacial tumors. Enteral nutrition preparations with dietary fiber are recommended for these patients. The patients with potassium preparations, sedatives and hypoproteinemia should be closely monitored for enteral feeding intolerance, and timely intervention should be administered to reduce its incidence.