bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction
Authors: Hauptmann Tony , Kramer Stefan 
Published: February 2023

AbstractBackgroundRecent years have seen a surge of novel neural network architectures for the integration of multi-omics data for prediction. Most of the architectures include either encoders alone or encoders and decoders, i.e., autoencoders of various sorts, to transform multi-omics data into latent representations. One important parameter is the depth of integration: the point at which the latent representations are computed or merged, which can be either early, intermediate, or late. The literature on integration methods is growing steadily, however, close to nothing is known about the relative performance of these methods under fair experimental conditions and under consideration of different use cases.ResultsWe developed a comparison framework that trains and optimizes multi-omics integration methods under equal conditions. We incorporated early integration, PCA and four recently published deep learning methods: MOLI, Super.FELT, OmiEmbed, and MOMA. Further, we devised a novel method, Omics Stacking, that combines the advantages of intermediate and late integration. Experiments were conducted on a public drug response data set with multiple omics data (somatic point mutations, somatic copy number profiles and gene expression profiles) that was obtained from cell lines, patient-derived xenografts, and patient samples. Our experiments confirmed that early integration has the lowest predictive performance. Overall, architectures that integrate triplet loss achieved the best results. Statistical differences can, overall, rarely be observed, however, in terms of the average ranks of methods, Super.FELT is consistently performing best in a cross-validation setting and Omics Stacking best in an external test set setting.ConclusionsWe recommend researchers to follow fair comparison protocols, as suggested in the paper. When faced with a new data set, Super.FELT is a good option in the cross-validation setting as well as Omics Stacking in the external test set setting. Statistical significances are hardly observable, despite trends in the algorithms’ rankings. Future work on refined methods for transfer learning tailored for this domain may improve the situation for external test sets. The source code of all experiments is available underhttps://github.com/kramerlab/Multi-Omics_analysis
Role of cytoskeleton-related proteins in the acrosome reaction of Eriocheir sinensis spermatozoa
Authors: Tang Yulian , Sun Lishuang , Li Shu , Liu Huiting , Luo Lvjing , Chen Zhengyu , Li Genliang 
Published: February 2023

AbstractCytoskeleton-related proteins are essential for cell shape maintenance and cytoskeleton remodeling. The spermatozoa ofEriocheir sinensis(Chinese mitten crab) have a unique cellular structure, and the mechanism of spermatozoal metamorphosis during the acrosome reaction is not well understood. In this study, theE. sinensisspermatozoa were induced using calcium ionophore A23187 to undergo the acrosome reaction in vitro, and the acrosome-reacting and fresh (non-reacting) spermatozoa were collected separately. The differential expression of cytoskeleton-related protein genes in acrosome-reacting and fresh spermatozoa ofE. sinensiswas analyzed by whole transcriptome sequencing and bioinformatics analysis, and PPI network and miRNA-mRNA regulation network were constructed to analyze their possible function and regulation mechanism. The results showed that numerous differentially expressed cytoskeleton-related protein genes, miRNAs and lncRNAs were found in acrosome-reacting and fresh spermatozoa ofE. sinensis; 27 cytoskeleton-related protein genes were down regulated and 687 miRNAs were up regulated in acrosome-reacting spermatozoa; 147 miRNAs target these 27 cytoskeleton-related protein genes. In the PPI networks, RAC1, BCAR1, RDX, NCKAP1, EPS8, CDC42BPA, LIMK1, ELMO2, GNAI1 and OCRL were identified as hub proteins. These proteins are mainly involved in the regulation of cytoskeleton organization, actin cytoskeleton organization, microtubule skeleton organization and small GTPase-mediated signal transduction and other biological processes, and play roles in pathways such as actin cytoskeletal regulation and axon guidance. miR-9, miR-31 and two novel miRNAs in the miRNA-mRNA regulatory network are the core miRNAs targeting cytoskeleton-related protein genes. miR-9 targets and regulatesOBSCN,CDC42BPA,ELMO2,BCAS3,TPRandOCRL; while miR-31 targets and regulatesCDC42BPAandTPR. This study provides a theoretical basis for revealing the mechanism of acrosome reaction under the special spermatozoa morphology ofE. sinensis.
Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan
Authors: Liang Jiayan , Kong Leilei , Hu Xiaodan , Fu Chongyun , Bai Song 
Published: February 2023

AbstractTheindicarice variety XYXZ carries elite traits including appearance and eating quality. Here, we report the de novo assembly of XYXZ using Illumine paired-end whole-genome shotgun sequencing and Nanopore sequencing. We annotated 39,722 protein-coding genes in the 395.04 Mb assembly. In comparison to other cultivars, XYXZ showed a larger gene size including the transcripts and introns, and more exons per gene. And hundreds of ultra-long genes were also detected. A total of 4362 complete LTRs were annotated, and among them, many were located next to or in protein-coding genes including several genes related to rice quality. We observed the different distributions of LTRs in these genes among XYXZ, Nipponbare, and R498, implying these LTRs might potentially affect expressions of the proximal genes and rice quality. Overall, This chromosome-length genome assembly of XYXZ provides a valuable resource for gene discovery, genetic variation and evolution, and the breeding of high-quality rice.
Results from a systematic programme of evaluating COVID-19 reinfection cases in the early phase of the pandemic, Singapore
Authors: Tan Glorijoy Shi En , Gao Christine Qiuhan , Ow Jievanda Shu Ying , Tan Thuan Thong , Ooi Say Tat , Lin Cui , Lin Raymond Tzer Pin , Lee Vernon Jian Ming , Chan Monica , Leo Yee Sin , Vasoo Shawn 
Published: February 2023

Abstract
Objectives
The objectives of this study were to describe the coronavirus disease caused by SARS-CoV-2 (COVID-19) reinfection evaluation algorithm used in the early phase of the pandemic in Singapore and analyze the clinical and laboratory characteristics of the cases evaluated.

Methods
We performed a retrospective case-control analysis including all COVID-19 cases evaluated for possible reinfection under the local COVID-19 reinfection evaluation programme between 1 June 2020-30 June 2021. Whole genome sequencing (WGS) was used as confirmatory testing. We compared all reinfection (“RI”) cases against those who were evaluated but eventually assessed not to be reinfection (“non-RI”).

Results
There were 74 possible reinfection cases evaluated through the programme, of which 32 were subsequently classified as RI. There was strong statistical evidence that RI cases had a longer interval between 1st and 2nd episode (mean 297 days; 95%-confidence interval (CI) 267–327) compared to non-RI cases (mean 186 days; 95%-CI 144–228). The cycle threshold (Ct) value of initial polymerase chain rection (PCR) at 2nd episode was also found to be significantly lower in RI cases (mean 23; 95%-CI 20–26) compared to non-RI cases (mean 34; 95%-CI 32–36). There was no significant difference in the proportion of individuals who had fever, acute respiratory symptoms or asymptomatic in both groups. Delta and beta variants were most commonly identified from WGS and provide indication of re-infection as these were not ‘wild-type’ and were not circulating during the time period of the index infection.

Conclusions
Using a combination of serologic, microbiologic and genomic criteria to evaluate possible reinfection cases is useful and can provide a framework for evaluation that may be modified for future similar situations.
Association between atmospheric pollutant levels and oxidative stress in pregnant women and newborns in Urumqi
Authors: Zhu Linghui , Lu Ying , Cheng Fang , Zhang Luyi , Yusan Aliya , Alifu Xialidan , Alimasi Ayixiemuguli , Alemujiang Xiahaida 
Published: February 2023

Abstract
Background
Frequent heavy air pollution occurred during the winter heating season of northern China. Particulate air pollution is a serious concern in Urumqi during heating season. Exposure to air pollution is known to increase adverse health outcomes, particularly oxidative damage. This study aimed to evaluate the impact of air pollution on oxidative damage around pregnant women and newborns in Urumqi.

Methods
This prospective observational study enrolled pregnant women in the Fifth Affiliated Hospital of Xinjiang Medical University between January 2019 and October 2019. Pregnant women and newborns were allocated into a heating season group (January - end of April 2019, October 2019) or non-heating season group (June 2019 - end of September) according to the specific delivery time. Venous blood, urine from the women and cord blood from their newborns were collected to measure the levels of PAHs and 8-deoxyguanosine (8-OHdG), a measure of oxidative stress.

Results
A total of 200 pregnant women and newborns were enrolled, with 100 pregnant women and newborns in the heating season group. Compared to the non-heating season group, the total contents of 8-OHdG in maternal urine, PAHs and 8-OHdG in maternal plasma and neonatal cord blood were higher in the heating season group (all P < 0.001). The average values for AQI, PM2.5, PM10, SO2, NO2, and CO were higher in the heating season group (all P < 0.001). Maternal and neonatal PAHs were correlated with 8-OHdG measurements in maternal urine (r = 0.288, P < 0.001 and r = 0.336, P < 0.001) and neonatal umbilical cord blood (r = 0.296, P < 0.001 and r = 0.252, P < 0.001). There was also a positive relationship between PAHs, 8-OHdG levels in pregnant women and their newborns and proximate air pollutant concentrations (all P < 0.05). Based on the results of multiple linear regression analysis, it was found that air pollutants(PM10, 03) had a great influence on the level of 8-OHdG in neonatal cord blood, and the contribution rate was high(R2 = 0.320). Based on the epidemiological questionnaire, a multiple linear regression model was established(R2 = 0.496). We found that 8-OHdG levels in neonatal umbilical cord blood were mainly affected by two aspects: (1) Biological samples collected during heating had higher levels of 8-OHdG in neonatal umbilical cord blood. (2) Study may suggest that in neonates, males are more sensitive to oxidative damage.

Conclusion
Particulate air pollution may increase PAHs exposure and oxidative DNA damage in pregnant women and newborns.
Predictive value of characteristics of resected parathyroid glands for persistent secondary hyperparathyroidism during parathyroidectomy
Authors: Huang Yaoyu , Wang Jing , Zeng Ming , Wan Huiting , Wang Ningning , Yang Guang 
Published: February 2023

Abstract
Background
Parathyroidectomy (PTX), an effective treatment for refractory secondary hyperparathyroidism (SHPT) in chronic kidney disease (CKD) patients, still has a high persistent rate. This study aimed to analyze the predictive value of characteristics of resected parathyroid glands for postoperative persistent SHPT.

Methods
The clinical data of patients with persistent SHPT and successful PTX controls who had or underwent total parathyroidectomy with forearm autotransplantation (TPTX + AT) was retrospectively collected. The characteristics including the number, minimum weight, maximum weight and total weight of resected parathyroid glands from each patient were recorded. Characteristics and cutoff value of resected parathyroid glands for the prediction of persistent SHPT were analyzed.

Results
A total of 227 patients (62 persistent SHPT patients and 165 successful PTX controls) were enrolled in the study. Forty-one (66%) persistent SHPT cases related to supernumerary parathyroid and the remaining 21 (34%) cases related to residual undetected parathyroid. In addition, ectopic parathyroid was found in 8 patients (13%) before PTX. The average number of resected glands in the persistent SHPT group and successful PTX group was 3.53 ± 0.72 and 3.93 ± 0.25 respectively (p < 0.001). There was significance in the number of patients with different resected parathyroid glands between two groups (p < 0.001). When the resected gland number was 4, minimum weight of the parathyroid was noted to be heavier in the persistent SHPT group than that in the successful PTX group (0.52 ± 0.31 g vs. 0.38 ± 0.19 g, p < 0.001). For persistent SHPT prediction, cutoff value of minimum weight was 0.535 g, with sensitivity of 46% and specificity of 82% (AUC = 0.611; p = 0.029).

Conclusions
Major reason for the persistent SHPT is the existence of supernumerary parathyroid glands or resection of less than 4 glands. When 4 glands were resected, a minimum total parathyroid gland weight heavier than 0.535 g implied the potential presence of a missed supernumerary parathyroid gland, which also contributed to the persistent SHPT.
Primary maxillary sinus carcinosarcoma with multidisciplinary management: a case report with 4 years follow-up and literature review
Authors: Li Jiajia , Wang Shaohai , Tang Xiufa , Que Lin , Han Wenzhe , Yu Bo 
Published: February 2023

Abstract
Background
Primary maxillary sinus carcinosarcoma (CS) is an extremely rare malignant tumor characterized by biphasic histologic components, lack of standardized treatment, high recurrence rate, and poor prognosis. This paper presents a case of primary maxillary sinus CS and its treatment.

Case presentation
A 39-year-old female patient complained of right facial pain and maxillary teeth numbness on March 21, 2018. Computed tomography examination revealed a malignant mass with osteolytic destruction. Preoperative biopsy suggested sarcomatoid carcinoma or CS. A total right maxillectomy under general anesthesia was performed on April 12, 2018. The final staging was T3N0M0 (ACJJ 2019). Postoperative radiotherapy and chemotherapy were performed. On May 26, 2018, the patient received the first cycle of doxorubicin plus ifosfamide. Two days before radiotherapy, the patient received an intra-oral prosthesis. From June 20, 2018, to August 22, 2018, the patient received concurrent chemoradiotherapy: radiotherapy (60 Gy in 30 fractions) and the second cycle of doxorubicin. Then, the patient received four cycles of doxorubicin plus ifosfamide. The patient was followed for 39 months with no evidence of disease.

Conclusion
Using multidisciplinary therapy, clinical-stage T3N0M0 (ACJJ 2019) maxillary sinus CS may achieve a good prognosis.
Comparison of three-dimensional maxillary growth across spheno-occipital synchondrosis maturation stages
Authors: Al-Gumaei Waseem S. , Long Hu , Al-Attab Reem , Elayah Sadam A. , Alhammadi Maged S. , Almagrami Ibtehal , Al-Rokhami Remsh K. , Lai Wenli , Zheng Yan 
Published: February 2023

AbstractBackgroundThis study aimed to three-dimensionally compare the maxillary growth among the spheno-occipital synchondrosis (SOS) maturation stages in both genders.MethodsThis is a cross-sectional study of a retrospective type in which cone-beam computed tomography (CBCT) images of 500 patients aged 6 to 25 years (226 males and 274 females) were analyzed. The SOS was evaluated using the four-stage scoring system; completely open, partially fused, semi-fused, or completely fused. The SOS scoring and three-dimensional cephalometric measurements were analyzed by Invivo 6.0.3 software. Descriptive and analytical statistics were performed and aP-value < 0.05 was considered statistically significant.ResultsThere was a statistically significant difference in maxillary measurements among SOS maturation stages in both genders (P < 0.05). The mean differences in the maxillary growth among the SOS maturation stages between SOS stages 2 and 3 were higher than those between stages 1and 2 and stages 3 and 4 for maxillary length and height in both genders. However, the mean difference in the maxillary width was higher between SOS stages 1 and 2 than those stages 2 and 3 and stages 3 and 4. On other hand, there may be lesser maxillary growth between SOS stages 3 and 4 for maxillary width, length (in males), and height. The growth curves showed high active growth of the maxilla as the SOS was still fusing (especially stage 2 and 3) than those of the fused (stage 4). Moreover, the acceleration of growth occurred earlier in females than males regarding chronological age but not for SOS maturation stages.ConclusionsThe SOS maturation stages are valid and reliable maxillary skeletal maturation indicators for three-dimensional maxillary growth in both genders.
Dental caries status and its associated factors among schoolchildren aged 6–8 years in Hangzhou, China: a cross-sectional study
Authors: Chen Zhi , Zhu Junhua , Zhao Jing , Sun Zhe , Zhu Bing , Lu Haiping , Zheng Yuanna 
Published: February 2023

Abstract
Background
Dental caries prevalence reaches the first peak around 6 years old. It is necessary to take effective measures to prevent and treat caries at this stage. This study investigated the prevalence and associated factors of dental caries among schoolchildren aged 6–8 years in Hangzhou City, China.

Methods
A cross-sectional survey was conducted in Hangzhou from October 2017 to May 2018. Oral health status of schoolchildren in 1st and 2nd grades of primary schools aged 6–8 years was examined by well-trained examiners according to the WHO criteria. Questionnaires about potential caries-related factors were distributed to their parents. ANOVA test and logistic regression were conducted for the statistical analyses (α = 0.05).

Results
A total of 7959 pairs of schoolchildren and their parents were invited to participate, and 5595 were included in this study according to the eligible criteria (response rate: 70.3%). The overall prevalence and mean dmft/DMFT of dental caries in the investigated schoolchildren were 52.78% and 2.11. The prevalence and mean dmft/DMFT were 39.05% and 1.63 in the deciduous teeth, while these were 21.45% and 0.48 in the permanent teeth, respectively. For the first permanent molars (FPMs), the rate of fully eruption and pit and fissure sealing (PFS) were 79.09% and 6.60%, respectively. Multiple logistic regression showed that girl (OR = 1.12, 95% CI 1.01–1.25, p < 0.05), seldom or never brush teeth (OR = 2.36, 95% CI 1.08–5.44, p < 0.05), consuming sweet food or drink once or more time a day (OR = 1.14, 95% CI 1.00–1.29, p < 0.05; OR = 1.21, 95% CI 1.07–1.36, p < 0.05), dental visit experiences (OR = 1.58, 95% CI 1.35–1.86, p < 0.001) were positively and no tooth pain in the past 12 months (OR = 0.55, 95% CI 0.38–0.80, p < 0.05) were negatively associated with caries.

Conclusions
Dental caries was prevalent among schoolchildren aged 6–8 years in Hangzhou, and was associated with gender, frequency of toothbrushing, sweet food or drink consuming, tooth pain and dental visit experiences. A large number of fully erupted FPMs did not receive timely PFS.
Evaluation of muco-adhesive tacrolimus patch on caspase-3 induced apoptosis in oral lichen planus: a randomized clinical trial
Authors: Ibrahim Suzan S. , Ragy Nivine I. , Nagy Noha A. , El-kammar Hala , Elbakry Asmaa M. , Ezzatt Ola M. 
Published: February 2023

AbstractBackgroundThe study compared the clinical effectiveness of topical Tacrolimus (TAC) in patches or gel with Triamcinolone acetonide (TRI) gel for erosive/atrophic oral lichen planus (OLP) and investigated the influence of these therapies on Caspase-3 expression as a marker of apoptosis.MethodsThirty patients were randomly assigned into three equal groups to receive either topical TAC 0.1% patch twice daily, topical TAC 0.1% gel, or topical TRI 0.1% gel four times daily for 8 weeks. Each patient's clinical score (CS), visual analogue scale (VAS), and total atrophic area (TAA) of the marker lesion were measured at baseline, 2, 4, and 8 weeks of treatment, as well as after 4 weeks of treatment free period. Caspase-3 expression and lymphocytic counts (LC) were assessed in pre- and post-treatment biopsied stained sections.ResultsTAC patch resulted in a higher reduction in CS [− 14.00 (15.54%)] and VAS [− 70.21 (15.82%)] followed by TAC gel then TRI gel within the first two weeks. The reduction in VAS and TAA were significantly higher in TAC groups compared to TRI gel, although the difference between TAC treatment was not significant and this was observed throughout the treatment and follow-up periods. Caspase-3 expression increased in connective tissue in all groups. It decreased significantly within the epithelium in both TAC groups but increased in TRI gel. (LC) were significantly lowered with the TAC patch compared to other groups. The percentage change in Caspase-3 epithelial expression was significantly correlated to the CS, TAA, and LC.ConclusionBoth TAC patch and gel significantly decreased pain and lesion size than TRI gel, with a significant reduction in Caspase-3 expression within the epithelium in comparison to the increase seen with TRI gel. The study protocol was registered atwww.clinicaltrials.gov(NCT05139667) on 01/12/2021.
In utero and postnatal exposure to Foeniculum vulgare and Linum usitatissimum seed extracts: modifications of key enzymes involved in epigenetic regulation and estrogen receptors expression in the offspring’s ovaries of NMRI mice
Authors: Pourjafari Fahimeh , Ezzatabadipour Massood , Nematollahi-Mahani Seyed Noureddin , Afgar Ali , Haghpanah Tahereh 
Published: February 2023

Abstract
Background
Early-life exposure to exogenous estrogens such as phytoestrogens (plant-derived estrogens) could affect later health through epigenetic modifications. Foeniculum vulgare (fennel) and Linum usitatissimum (flax) are two common medicinal plants with high phytoestrogen content. Considering the developmental epigenetic programming effect of phytoestrogens, the main goal of the present study was to evaluate the perinatal exposure with life-long exposure to hydroalcoholic extracts of both plants on offspring’s ovarian epigenetic changes and estrogen receptors (ESRs) expression level as signaling cascades triggers of phytoestrogens.

Methods
Pregnant mice were randomly divided into control (CTL) that received no treatment and extract-treated groups that received 500 mg/kg/day of fennel (FV) and flaxseed (FX) alone or in combination (FV + FX) during gestation and lactation. At weaning, female offspring exposed to extracts prenatally remained on the maternal-doses diets until puberty. Then, the ovaries were collected for morphometric studies and quantitative real-time PCR analysis.

Results
A reduction in mRNA transcripts of the epigenetic modifying enzymes DNMTs and HDACs as well as estrogen receptors was observed in the FV and FX groups compared to the CTL group. Interestingly, an increase in ESRα/ESRβ ratio along with HDAC2 overexpression was observed in the FV + FX group.

Conclusion
Our findings clearly show a positive relationship between pre and postnatal exposure to fennel and flaxseed extracts, ovarian epigenetic changes, and estrogen receptors expression, which may affect the estrogen signaling pathway. However, due to the high phytoestrogen contents of these extracts, the use of these plants in humans requires more detailed investigations.