Transcriptome sequencing technologies have revolutionized the field of phylogenomics by facilitating the identification of homologous genes for species without whole genome sequences. To infer ...complex evolution relationship among eukaryotes, it is essential to obtain complete sequences of protein‐coding genes to provide informative mutations. However, transcriptomes in eukaryotes often consist of a large number of duplicated genes and alternative isoforms, bringing great challenges for developing effective tools to obtain complete coding gene sequences.
Here, we present a net‐flow based assembler TransMCL, which aims to assemble fragmented transcripts into complete sequences while eliminating redundant isoforms during homologue clustering. By employing Markov clustering strategies and homologous gene guidance, TransMCL can accurately assemble genes for multiple organisms in an affordable time frame, making it well‐suited for phylogenomic studies based on transcriptomic data.
Our results demonstrate that TransMCL can assemble 89.95%–92.95% of the total expressed genes into near‐complete transcripts on benchmark plant/animal datasets. Furthermore, applying TransMCL to multiple transcriptomes in a single run enhances the completeness of genes, even in the absence of guidance homologues from closely related species.
These findings highlight the potential of TransMCL in phylogenomic studies, enabling the comprehensive characterization of gene families at the whole genome scale. By overcoming the challenges of complex gene contents in eukaryotes, TransMCL can significantly enhance our understanding of evolution of gene families across species.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
This study evaluated the welfare and behaviors of Cobb 700 broilers as affected by growth rate (GR) and stocking density (SD). Slower-growth (weight gain < 50 g/d) and medium-growth (weight gain = ...50–60 g/d) broilers were produced by providing 57.1% and 78.6% of the feed intake listed in the Cobb 700 production manual for standard (fed ad libitum) broilers (weight gain > 60 g/d). Broilers at all 3 GRs were reared at 2 SDs of 30 and 40 kg/m2. Broiler welfare indicators, including gait score, tibia strength, feather coverage, and footpad condition were evaluated when birds reached 1, 2, and 3 kg of body weight. The activity index was determined by overhead cameras and image processing, and the time spent at feeders was recorded using the radio-frequency identification (RFID) systems. The results show that it took 45 d for standard, 52 d for medium-growth, and 62 d for slower-growth broilers to reach a 3 kg market body weight. Feed conversion ratios (FCR, kg/kg) were 1.57 for standard, 1.67 for medium-growth, and 1.80 for slower-growth broilers. Growth rate and SD had an interaction effect on feather cleanliness (P = 0.03), and belly feather coverage (P = 0.02). Slower-growth broilers were more active and had better feather coverage and gait scores than medium-growth and standard broilers (all P < 0.01) but may feel hungry and depressed, medium-growth broilers spent the most time at the feeder among the 3 growth groups (P = 0.02), and standard broilers showed the best production performance. Broilers at 30 kg/m2 showed better bone strength (P = 0.04), and footpad condition (P < 0.01) compared to those at 40 kg/m2. In conclusion, reducing GR and SD may slightly improve broiler leg health at the high expense of compromised production performance and prolonged production cycles.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Prussian blue (PB) is an anodic coloring candidate in the wide area of electrochromic (EC) applications. However, the co-influence of weak adhesion and low electrical conductivity leads to the poor ...stability and slow switching speed. To tackle this bottleneck, a novel TiO
2
/Au/PB nanorod array is designed through hydrothermal and electrodeposition approaches on fluorine-doped tin oxide (FTO) glass. Such a designed ternary array structure could not only increase reactive site and conductivity, but also improve ion storage capacity and promote charge transfer, attributed to the synergistic effect of TiO
2
/Au/PB core—shell heterostructure and the localized surface plasmon resonance (LSPR) effect of Au nanoparticles. Besides, density functional theory (DFT) calculation confirms the strong interaction between rutile TiO
2
and FTO substrate, which contributes to the improvement of EC cycle stability. Benefiting from these effects, the TiO
2
/Au/PB film shows a fast coloration/bleaching response of 1.08/2.01 s (2.17/4.48 s, PB film) and ultra-stable EC performance of 86.8% after 20,000 cycles (50% after 600 cycles, PB film). Furthermore, the high-intensity light source can be shot clearly by the designed and assembled EC iris device (ECID) with TiO
2
/Au/PB film as an EC layer, while the photograph without an ECID is blurry, confirming the feasibility of the material in portable digital products.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
This paper discusses the optimization of emergency resource scheduling for major railway emergencies under multiple uncertainties while considering the uncertainties in demand, reserve, and ...transportation costs of resources. We introduce a novel approach that integrates stochastic mathematical programming, interval parameter programming, and fuzzy mathematical programming to study uncertain parameter interactions and coupling. A two-stage interval fuzzy credibility-constrained model is established and solved using an interval interactive algorithm. Finally, through a case study on China Railway Nanchang Group Co., Ltd., the novelty and effectiveness of the proposed method for optimizing emergency resource scheduling strategies under multiple uncertainties are demonstrated.
This study aimed to propose a new user-friendly, cost effective and robust risk model to facilitate risk stratification for diffuse large B-cell lymphoma (DLBCL) treated with frontline R-CHOP ...regimens.
Data on 998 patients with de novo DLBCL diagnosed between Jan 1st, 2005 and Dec 31st, 2018 at our center, who received frontline R-CHOP or R-CHOP-like regimens, were retrospectively collected. Patients were randomly divided into the training cohort (n = 701) and the validation cohort (n = 297). A new prognostic model for overall survival (OS) was built based on the training cohort. The performance of the new model was compared with International prognostic index (IPI), revised IPI (R-IPI) and National Comprehensive Cancer Network (NCCN)-IPI (NCCN-IPI). The new model was validated in the validation cohort.
The multivariate analysis of the training cohort showed that the IPI, β2-microglobulin, platelet count and red blood cell distribution width were independent factors for OS, which were incorporated into the new prognostic model. Patients were stratified into low risk, low-intermediate risk, high-intermediate risk, high risk and very high risk groups, with distinct survival outcomes. The new model achieved good C-indexes for 5-year OS prediction of 0.750 (95%CI 0.719-0.781) and 0.733 (95%CI 0.682-0.784) in the training and validation cohorts, respectively, and displayed well-fitted calibration curves. The C-index and the time-dependent ROC analysis demonstrated better performance of the new model than the IPI, R-IPI and NCCN-IPI in both training and validation cohorts. The integrated Brier score for predicting 5-year OS of the new model was lower than that of the IPI, R-IPI and NCCN-IPI in both cohorts, and decision curve analysis also showed a higher net benefit, indicating the superiority of the new model over the conventional models.
The new prognostic model might be a useful predictive tool for DLBCL treated with R-CHOP regimens. Further external validation is warranted.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Little is known about the association between frailty level and medical financial hardship among older adults with cancer. This study aims to describe the prevalence of frailty and to identify its ...association with medical financial hardship among older cancer survivors in the United States.
The National Health Interview Survey (NHIS; 2019-2020) was used to identify older cancer survivors (n = 3,919). Both the five-item (Fatigue, Resistance, Ambulation, Illnesses, and Low weight-for-height) FRAIL and the three-domain (Material, Psychological, and Behavioral) medical financial hardship questions were constructed based on the NHIS questionnaire. Multivariable logistic models were used to identify the frailty level associated with financial hardship and its intensity.
A total of 1,583 (40.3%) older individuals with cancer were robust, 1,421 (35.9%) were pre-frail, and 915 (23.8%) were frail. Compared with robust cancer survivors in adjusted analyses, frail cancer survivors were more likely to report issues with material domain (odds ratio (OR) = 3.19, 95%CI: 2.16-4.69; p < 0.001), psychological domain (OR = 1.47, 95%CI: 1.15-1.88; p < 0.001), or behavioral domain (ORs ranged from 2.19 to 2.90, all with p < 0.050), and greater intensities of financial hardship.
Both pre-frail and frailty statuses are common in the elderly cancer survivor population, and frail cancer survivors are vulnerable to three-domain financial hardships as compared with robust cancer survivors. Ongoing attention to frailty highlights the healthy aging of older survivors, and efforts to targeted interventions should address geriatric vulnerabilities during cancer survivorship.
ROS proto‐oncogene 1, receptor tyrosine kinase (
ROS1
) rearrangements are a crucial therapeutic target in non‐small cell lung cancer (NSCLC). However, there is limited comprehensive analysis of the ...molecular patterns of
ROS1
fusions. This study aimed to address this gap by analysing 135
ROS1
fusions from 134 Chinese NSCLC patients using next‐generation sequencing (NGS). The fusions were categorized into common and uncommon based on their incidence. Our study revealed, for the first time, a unique distribution preference of breakpoints within
ROS1
, with common fusions occurring in introns 31–33 and uncommon fusions occurring in introns 34 and 35. Additionally, we identified previously unknown breakpoints within intron 28 of
ROS1
. Furthermore, we identified a close association between the distribution patterns of fusion partners and breakpoints on
ROS1
, providing important insights into the molecular landscape of
ROS1
fusions. We also confirmed the presence of inconsistent breakpoints in
ROS1
fusions between DNA‐based NGS and RNA‐based NGS through rigorous validation methods. These inconsistencies were attributed to alternative splicing resulting in out‐of‐frame or exonic
ROS1
fusions. These findings significantly contribute to our understanding of the molecular characteristics of
ROS1
fusions, which have implications for panel design and the treatment of NSCLC patients with
ROS1
rearrangements.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
To explore the clinicobiologic features and outcomes of diffuse large B-cell lymphoma (DLBCL) patients in China according to the primary site.
A total of 1,085 patients diagnosed with DLBCL in ...National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College during a 6-year period were enrolled. Their clinical characteristics and outcomes were analyzed according to the primary site.
In the 1,085 patients, 679 (62.6%) cases were nodal DLBCL (N-DLBCL) and 406 cases (37.4%) were extranodal DLBCL (EN-DLBCL). The most common sites of N-DLBCL were lymphonodus (64.8%), Waldeyer's ring (19.7%), mediastinum (12.8%) and spleen (2.7%), while in EN-DLBCL, stomach (22.4%), intestine (16.0%), nose and sinuses (8.9%), testis (8.4%), skin (7.9%), thyroid (6.9%), central nervous system (CNS) (6.4%), breast (5.7%), bone (3.4%), and salivary gland (2.7%) were most common. N-DLBCL patients tend to present B symptoms, bulky disease, and elevated LDH more often, while age >60 years, extranodal sites >1, Ann Arbor stage I or II, bone marrow involvement, and Ki-67 index >90% were usually seen in EN-DLBCL. The 5-year overall survival (OS) rate and progression-free survival (PFS) rate for all patients were 62.5% and 54.2%. The 5-year OS rate for patients with N-DLBCL and EN-DLBCL were 65.5% and 56.9% (P=0.008), and the 5-year PFS were 57.0% and 49.0% (P=0.020). Waldeyer's ring originated DLBCL possessed the highest 5-year OS rate (83.6%) and PFS rate (76.9%) in N-DLBCL. The top five EN-DLBCL subtypes with favorable prognosis were stomach, breast, nose and sinuses, lung, salivary gland, with 5-year OS rate: 70.3%, 69.6%, 69.4%, 66.7% and 63.6%, respectively. While CNS, testis, oral cavity and kidney originated EN-DLBCL faced miserable prognosis, with 5-year OS rate of 26.9%, 38.2%, and 42.9%.
In our study, primary sites were associated with clinical characteristics and outcomes. Compared with EN-DLBCL, N-DLBCL had better prognosis.
The number of migrant older adults with children (MOAC) in China has been increasing in recent years, and most of them are women. This study aimed to explore the mediating effect of social support ...between social integration and loneliness among the female MOAC in Jinan, China.
In this study, 418 female MOAC were selected using multi-stage cluster random sampling in Jinan, Shandong Province, China. Loneliness was measured by the eight-item version of the University of California Los Angeles Loneliness Scale (ULS-8), and social support was measured by The Social Support Rating Scale (SSRS). Descriptive analyses, t-tests, ANOVA, and structural equation modeling (SEM) were used to illustrate the relationship between social integration, social support, and loneliness.
The average scores of ULS-8 and SSRS were 12.9 ± 4.0 and 39.4 ± 5.9 among female MOAC in this study. Social integration and social support were found to be negatively related to loneliness, and the standardized direct effect was -0.20 95% CI: -0.343 to -0.068 and -0.39 95% CI: -0.230 to -0.033, respectively. Social support mediated the relationship between social integration and loneliness, and the indirect effect was -0.16 95% CI: -0.252 to -0.100.
The female MOAC's loneliness was at a relatively lower level in this study. It was found that social integration was negatively associated with loneliness, and social support mediated the relationship between them. Helping female MOAC integrate into the inflow city and improving their social support could be beneficial for alleviating their loneliness.
Inflammatory bowel disease (IBD) is a complex group of chronic intestinal diseases, the cause of which has not yet been clarified, but it is widely believed that the disorder of the intestinal ...microenvironment and its related functional changes are key factors in the development of the disease. Houttuynia cordata thunb. is a traditional plant with abundant resources and long history of utilization in China, which has attracted widespread attention in recent years due to its potential in the treatment of IBD. However, its development and utilization are limited owing to the aristolochic acid alkaloids contained in it. Therefore, based on the relationship between the intestinal microenvironment and IBD, this article summarizes the potential mechanisms by which the main active ingredients of Houttuynia cordata thunb., such as volatile oils, polysaccharides, and flavonoids, and related traditional Chinese medicine preparations, such as Xiezhuo Jiedu Formula, alleviate IBD by regulating the intestinal microenvironment. At the same time, combined with current reports, the medicinal and edible safety of Houttuynia cordata thunb. is explained for providing ideas for further research and development of Houttuynia chordate thunb. in IBD disease, more treatment options for IBD patients, and more insights into the therapeutic potential of plants with homology of medicine and food in intestinal diseases, and even more diseases.
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