bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Resident Outcomes in Cataract Surgery at Different Levels of Experience: A retrospective case series
Authors: Melega Mathias , Lira Rodrigo , Silva Iuri , Ferreira Bruna , Filho Hermano , Martini Alexandre , Reis Roberto , Arieta Carlos , Alves Monica 
Published: August 2020

Abstract
BackgroudTo evaluate outcomes of resident-performed cataract surgeries in different training levels in a retrospective case series.MethodsA total of 730 surgeries performed by residents were evaluated into three groups: surgeries performed during residents’ first semester of training in phacoemulsification (S1), surgeries performed during the second semester (S2), and surgeries performed during the third semester (S3). The primary outcome was the incidence of intraoperative complications in each group. Secondary outcomes were the comparisons between initial and final corrected distance visual acuity (CDVA), intraocular pressure (IOP), endothelial cell density (ECD), and central corneal thickness (CCT) in each group. Descriptive statistical analyses were employed in the presentation of the results using central tendency and variance measurements. The groups’ continuous variables were compared using the t-test or ANOVA (parametric variables) or the Mann-Whitney or Kruskal-Wallis tests (non-parametric variables). Statistical analyses of the categorical variables were performed using Fisher’s exact test or the chi-squared test.ResultsThe rate of complications within six weeks of follow up was 24 out of 102 eyes (23.53%) in the S1 group, 63 out of 301 eyes (20.93%) in the S2 group, and 37 out of 327 (11.31%) in the S3 group (p = 0.001). There was no significant difference in CDVA (p = 0.298), ECD (p = 0.067), IOP (p = 0.217), or CCT (p = 0.807) between the groups.ConclusionsWhen measured by rates of complications and by the aforementioned parameters, surgical competency was found to improve as surgical experience and frequency increased. Therefore, this study identified some patterns of skill development that can be applied to teaching strategies and better assist surgeons in training.
Extrusion of subducted crust explains the emplacement of far-travelled ophiolites
Authors: Porkoláb Kristóf , Duretz Thibault , Yamato Philippe , Auzemery Antoine , Willingshofer Ernst 
Published: August 2020

Abstract
Continental subduction below oceanic plates and associated emplacement of far-travelled ophiolite sheets remain enigmatic chapters in global plate tectonics. Numerous ophiolite belts on Earth exhibit continental rocks that experienced subduction-related high pressure-low temperature (HP-LT) metamorphism and subsequent exhumation coeval with the emplacement of ophiolites. However, the link between continental subduction dynamics and ophiolite emplacement is poorly understood. Here we combine data collected from ophiolite belts worldwide with thermo-mechanical simulations of continental subduction dynamics to show the causal link between the exhumation of subducted continental crust and ophiolite emplacement. Our results reveal that buoyancy-driven extrusion of subducted crust triggers necking and breaking of the overriding oceanic upper plate. This process is fundamental for the formation of a far-travelled ophiolite sheet that is separated from the oceanic domain by the exhumed, HP-LT continental upper crust. Our results indicate that the exhumation of the subducted continental crust and far-travelled ophiolite sheet emplacement are inseparable processes and thus shed light on one of the most mysterious aspect of plate tectonics.
Genomic Profiling of Chinese Urothelial Carcinoma Patients
Authors: Yang Bo , Zhao Xiao , Wan Chong , Ma Xin , Niu Shaoxi , Guo Aitao , Wang Jieli , Wang Jinliang , Sun Decong , Jiao Shunchang 
Published: August 2020

Abstract
Background
Urothelial carcinoma (UC) is the most common genitourinary malignancy in China. In this study, we studied the genomic features in Chinese UC patients, and investigated the concordance of genetic alterations between serum circulating tumor free DNA (ctDNA) and matched tumor tissue.
Methods
A total of 112 UC patients were enrolled, and 31 of which were upper tract UC (UTUC) and 81 were UC of bladder (UCB), respectively. Utilizing target next-generation sequencing, we analyzed genomic alterations of 92 selected genes.
Results
94.64%, 86.61% and 62.50% of patients in our cohort were identified as having valid, oncogenic or actionable somatic alterations, respectively, and the most altered genes were TP53, KMT2D, KDM6A, FAT4, FAT1, CREBBP and ARID1A. HRAS (22.0% vs 3.7%) and KMT2D (59.26% vs 34.57%) were more altered in UTUC than in UCB in our cohort. Comparisons of somatic alterations of UCB and UTUC between our cohort and western cohorts revealed significant differences in gene prevalence. Notably, 28.57%, 17.86% and 47.32% of cases harbored alterations in FGFRs, ERBBs and DNA damage repair genes, respectively. Furthermore, 75% of patients carried non-benign germline variants, but only two (1.79%) were pathogenic. By comparison of ctDNA and matched tumor tissue, the overall concordance for genomic alterations was 42.97% (0-100%). 47.25% of alterations detected in ctDNA were not detected in the matched tissue, and 25.58% of which were oncogenic.
Conclusions
We found a unique genomic feature of Chinese UC patients. A good concordance of genomic features between ctDNA and tissue samples were identified.
Basil interspecific hybridization and transcriptome study indicates altered developmental and metabolic gene expression
Authors: Shah Saumya , Rastogi Shubhra , Vashisth Divya , . Mytrai , Lal R K , Lavania Umesh Chandra , Shasany Ajit 
Published: August 2020

Abstract
Background
In order to understand the developmental modulation of transcriptome and associated gene expression in inter-genomic combinations, a systematic study was planned using two diverse yet closely related species of Ocimum, targeting their hybrid F1 and derived amphidiploid (colchiploid of F1 hybrid). The existing developmental alterations between F1 and amphidiploid through phenotypical and anatomical assessments were analyzed.
Results
Study of several genes and transcription factors putatively involved in the growth and developmental processes of plants clearly amalgamates the transcriptome data linking the phenotypic differences in F1 and amphidiploid. Additionally, differentially expressed genes of stomatal patterning and development revealed their involvement leading to higher density of stomata in F1 while larger size of stomata in the amphidiploid. Absence of 8,330 transcripts of interspecific hybrid F1 in its amphidiploid and exclusive presence of two detected transcripts in amphidiploid provides a set of genes to analyze the suppressed or activated functions between F1 and amphidiploid. Estimation of chlorophyll, lignin, flavonoid and phenylpropenes (eugenol and methyleugenol) content were correlated with the average FPKM and digital gene expression values in F1 and amphidiploid.
Conclusion
This is the first investigation which describes the genes and transcription factors influenced by interspecific hybridization leading to developmental changes and alleviation of intergenomic instability in amphidiploid.
Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes)
Authors: Pinheiro Melquizedec Luiz Silva , Nagamachi Cleusa Yoshiko , Ribas Talita Fernanda Augusto , Diniz Cristovam Guerreiro , O´Brien Patricia Caroline Mary , Ferguson-Smith Malcolm Andrew , Yang Fengtang , Pieczarka Julio Cesar 
Published: August 2020

Abstract
Background: The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results: The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype, suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence In Situ Hybridization using Burhinus oedicnemus whole chromosome probes confirmed these fissions in all pairs of macrochromosomes. Conclusion: Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of ​​how chromosomal evolution occurred in this suborder.
Efficacy-specific Herbal Group Detection from Traditional Chinese Medicine Prescriptions via Hierarchical Attentive Neural Network Model
Authors: Chen Li , Liu Xinglong , Zhang Siyuan , Yi Hong , Lu Yongmei , Yao Pan , Yu Zhonghua 
Published: August 2020

Abstract
Background: Mining massive prescriptions in Traditional Chinese Medicine (TCM) accumulated in the lengthy period of several thousand years to discover essential herbal groups for distinct efficacies is of significance for TCM modernization, thus starting to draw attentions recently. However, most existing methods for the task treat herbs with different surface forms orthogonally and determine efficacy-specific herbal groups based on the raw frequencies an herbal group occur in a collection of prescriptions. Such methods entirely overlook the fact that prescriptions in TCM are formed empirically by different people at different historical stages, and thus full of herbs with different surface forms expressing the same material, or even noisy and redundant herbs.Methods: We propose a two-stage approach for efficacy-specific herbal group detection from prescriptions in TCM. For the first stage we devise a hierarchical attentive neural network model to capture essential herbs in a prescription for its efficacy, where herbs are encoded with dense real-valued vectors learned automatically to identify their differences on the semantical level. For the second stage, frequent patterns are mined to discover essential herbal groups for an efficacy from distilled prescriptions obtained in the first stage.Results: We verify the effectiveness of our proposed approach from two aspects, the first one is the ability of the hierarchical attentive neural network model to distill a prescription, and the second one is the accuracy in discovering efficacy-specific herbal groups.Conclusion: The experimental results demonstrate that the hierarchical attentive neural network model is capable to capture herbs in a prescription essential to its efficacy, and the distilled prescriptions significantly could improve the performance of efficacy-specific herbal group detection.
Identification of SNP markers associated with antler growth rate in sika deer (Cervus nippon)
Authors: Hu Pengfei , Deng Yongyan , Ba Hengxing , li chunyi 
Published: August 2020

Abstract
Sika deer (Cervus nippon) constitutes one of the most valuable animal genetic resources in east Asia. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) from antler growth-related genes of sika deer. The whole genome sequencing data of sika deer were used to identify SNP markers. Among them, 31 SNPs from antler growth-related genes exhibited significant polymorphism using genotyping by mass spectrometry. The observed and expected heterozygosities were ranged from 0.147 to 0.997 and 0.201 to 0.500, respectively. Significant deviation from the Hardy-Weinberg equilibrium was observed in 6 loci. These findings provide effective molecular detection markers for the study of variation in antler growth rate of sika deer.
Genome-Wide Identification and Functional Characterization of the PheE2F/DP Gene Family in Moso Bamboo
Authors: Li Long , Shi Qianqian , Gao Jian 
Published: August 2020

Abstract
Background
E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the E2F/DP family and its functional role in Moso bamboo has been limited.
Results
Here, we identified 24 E2F/DP genes in the Moso bamboo genome, including nine E2F, six DP, and eight DEL genes. Simulation of the divergence time of paralogous gene pairs revealed an important role of whole-genome duplication in the expansion of the E2F/DP family. The regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. Yeast two hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that PheE2F-PheDP complex play important roles in winter moso bamboo shoot growth. Expressional analysis based on qRT-PCR performed diverse expression patterns of PheE2F/DPs in response to both various abiotic stimuli and diurnal cycles.
Conclusion
These findings provide insights into the E2F/DP family members in Moso bamboo and experimental evidence for further functional verification of the E2F/DP family.
2D Crystalline Monolayer Nanosheets Produced from 1D-Amorphous Metal-Organic Framework
Authors: wang jiahui , Yang Pengfei , Liu Lingmei , Zheng Bin , Jiang Jing , Ma Jian-Ping , Yan Yi , Yang Song , Lin Bin , Liu Qi-kui , Han Yu , Chen Yin 
Published: August 2020

Abstract
MOFs are typical 3D crystalline materials, and amorphous MOFs emerges as a new attractive material family very recently. Herein, we report a novel layered MOF, IPM-1, which is synthesized from a cage-like organic linker with extremely weak interlaminar interaction. When subjected to external disturbance, IPM-1 degraded to an intermediate state between the crystalline and amorphous phase (1D-amorphours), in which the layers retain the in-plane two-dimension periodic structure but are misaligned in the third dimension, leading to the loss of apparent porosity and crystallinity. 1D-amorphous IPM-1 is readily exfoliated into crystalline 2D nanosheets with a thickness of 1.15 nm at gram-scale, excellent uniformity and homogeneity, lateral size up to 10 µm, and restored microporosity. They can fabricate wafer-scale thin films and present the first mass-producible 2D monolayer material. This work underlines that MOFs without apparent crystallinity can be idea precursors for the successful preparation of 2D crystalline monolayer nanosheets.
Classification of Sagittal Root Position and Angulation of Premolars for Immediate Implant Placement: A Cone Beam Computed Tomography Study
Authors: Zhan Yalin , Wang Miaozhen , Cheng Xueyuan , Liu Feng 
Published: August 2020

Abstract
Background: Sagittal root position (SRP) and thickness of buccal plate were of clinical guiding significance in implant treatment planning. The study was to classify the SRP and angulations of the maxillary and mandibular premolar to each osseous housing, and to measure the thickness of buccal plate by cone beam computed tomography (CBCT) in order to estimate the distributions and provide clinical decision support. Methods: CBCT images was reviewed on 150 patients who fulfilled the inclusion criteria. The sagittal root position and angulations of the maxillary and mandibular premolars to their respective osseous housing were evaluated and classified using CBCT images. The thickness of buccal plate at 1 mm, 3 mm, 5 mm apical to the alveolar crest was also measured. Results: The frequency distribution of SRP types indicated that, 41.67%, 51.83%, 3.67%, and 2.83% of maxillary premolars; 84.33%, 15%, 0%, and 0.67% of mandibular premolars were classified as type B, M, L, and N. The frequency distribution of angulation classifications indicated that, 20.83%, 46%, 32.17%, and 1% of maxillary premolars; 2%, 5.33%, 36.67%, and 56% of mandibular premolars were classified as class 1, 2, 3, and 4. The buccal bone thickness in most locations of premolar sites was less than 1 mm. Conclusions: The classification of clinical relevance of SRP and angulation of the premolar root to osseous housing would help for treatment planning and improving interdisciplinary communication of immediate implant placement (IIP) in the premolar region.
Nigella A ameliorates experimental colitis via interacting with gut microbiota on dextran sulphate sodium (DSS)-induced C57BL/6 mice
Authors: Hu XingJiang , Xu Nana , Yang Xi , Hu Xi , Zheng Yunliang , Zhang Qiao 
Published: August 2020

Abstract
Nigella A, also named Sieboldianoside A, has been extracted from many kinds of Traditional Chinese Medicine (TCM), such as Nigella glandulifera, Stauntonia chinensis DC., and the leaves of Acanthopanax sieboldianus. Nigella A exhibited potential analgesic, anti-inflammatory, anti-tumor, and antioxidant activities. However, whether Nigella A could treat ulcerative colitis (UC) is still unknown. As saponins always be regarded as the kinds of ingredients that could regulate immunity and intestinal flora. This research aimed to investigate the therapeutic effect of Nigella A on UC and explore its effect on intestinal flora. We noted that Nigella A and SASP could significantly improve the signs and symptoms, alleviate colonic pathological injury in DSS-induced mice. The changing of many specific bacterial genus such as Lactobacillus, Porphyromonadaceae, Bacteroides and Escherichia might closely related to the recovery of intestinal inflammatory response. This study initially confirmed the therapeutic effect of Nigella A and SASP on DSS-induced colitis by improving the diversity of intestinal microbial composition. Nigella A has the potential to be developed for the treatment of UC and other disorders related to the imbalance of intestinal flora.
Isolation and identification of a novel bacterium, Pseudomonas sp. ZyL-01, involved in the biodegradation of CL-20
Authors: Liu Zhiyong , Dang Kai , Li Cunzhi , Gao Junhong , Wang Hong , Gao Yongchao , Zhao Bin , Fan Peng , Qian Airong 
Published: August 2020

Abstract
Hexanitrohexaazaisowurtzitane (CL-20) is a compound with a polycyclic cage and an N-nitro group that has been shown to play an unfavorable role in several aspects, including environmental fate, biosafety, and physical health. The aim of this study was to isolate the microbial community and to identify a single microbial strain that can degrade CL-20 with desirable efficiency. Metagenomic sequencing methods were performed to investigate the dynamic changes in the composition of the community diversity. The most varied genus among the microbial community was Pseudomonas , which increased from 1.46% to 44.63% during the period of incubation (MC0–MC4). Furthermore, the new strain was isolated and identified from the activated sludge by bacterial morphological and 16s rRNA sequencing analyses. The CL-20 concentrations decreased by 75.21 μg/mL and 74.02 μg/mL in 48 h by MC4 and Pseudomonas sp. ZyL-01, respectively. However, the initial speed of CL-20 degradation by MC4 was more rapid than that by ZyL-01. Finally, a draft genome sequence was obtained to predict possible degrading enzymes involved in the biodegradation of CL-20. Specifically, 330 genes that are involved in energy production and conversion were annotated by Gene Ontology functional enrichment analysis, and some of these candidates may encode enzymes that are responsible for CL-20 degradation. In summary, our studies indicate that microbes might be a valuable biological resource for the treatment of environmental contamination caused by CL-20 and that Pseudomonas sp. ZyL-01 might be a promising candidate for eradicating CL-20 to achieve a more biosafe environment and improve public health.
Ovarian Function Preservation in Patients With Cervical Cancer Undergoing Hysterectomy and Ovarian Transposition Before Pelvic Radiotherapy
Authors: Jung Wonguen , Kim Yun Hwan , Kim Kyung Su 
Published: August 2020

Abstract
Background: To examine the factors associated with ovarian failure (OF) and assess the effectiveness of ovarian transposition (OT) before pelvic irradiation for preserving ovarian function in patients with cervical cancer (CC) undergoing hysterectomy.Methods: During 2003-2017, patients who underwent hysterectomy with preservation of one or both ovaries were retrospectively enrolled. Patients were divided into 4 groups, depending on whether radiotherapy (RT) and OT were performed: group 1, RT(+) and OT(+); group 2, RT(+) and OT(-); group 3, RT(-) and OT(+); group 4, RT(-) and OT(-). OF was defined as serum follicle-stimulating hormone levels of ≥30 mIU/mL.Results: Sixty-six patients (59 [89.4%] invasive CC and 7 [10.6%] cervical intraepithelial neoplasia) were included. The 2-year ovarian failure-free survival (OFFS) rate was 61.4% (95% confidence interval (CI) 37.8–86.0), 0%, 91.7% (95% CI 76.0–100), and 75.8% (95% CI 58.2–93.4) for groups 1, 2, 3, and 4, respectively. In groups 1 and 2 receiving RT, OT and combination of external beam radiotherapy and vaginal brachytherapy (VB) were associated with OF on multivariate analysis (MVA) (p-value=0.002 and 0.046, respectively). In groups 3 and 4 without RT, older age (40 years) and OT did not affect OF; however, the number of remaining ovaries was independently associated with OF in MVA (p=0.035).Conclusions: OT could effectively preserve ovarian function in adjuvant RT-treated patients. Lower location of transposed ovary with VB boost was significantly associated with early OF.
Management Practices of Emergency Departments in General Hospitals Based on Blockage of Chain of Infection during an COVID-19 Epidemic
Authors: Hu Xiaojing , Liu Si , Wang Bo , Xiong Hui , Wang Ping 
Published: August 2020

Abstract
In a coronavirus disease 2019 (COVID-19) epidemic, management of the emergency department is a difficult task in terms of prevention and control of the disease in general hospitals. On top of meeting urgent needs of patients for medical treatment, the emergency department also has to devote resources into investigation and prevention of COVID-19. At the beginning of the epidemic, with the strategy to intercept the chain of infection, Peking University First Hospital (PKUFH) focused on three important aspects: controlling the source of infection, cutting off the route of transmission, and protecting vulnerable populations, to expeditiously draft scientific and proper management measures for the emergency department, followed by real-time dynamic adjustments based on the development trend of the epidemic. These measures effectively ensured a smooth, orderly and safe operation of the emergency department. As of the writing of this manuscript, there has been no active COVID-19 infection in patients and medical staff in the emergency department, and no infection in patients admitted to PKUFH through the emergency department. This study describes the prevention and control measures in the emergency department of PKUFH during the outbreak of COVID-19, aiming to provide some reference for domestic and international medical institutions.