Health locus of control and symptom distress: The mediating role of illness acceptance and symptom severity in acute leukemia patients.

OBJECTIVE: This study aims to explore the multiple mediating roles of illness acceptance and symptom severity between health locus of control and symptom distress in acute leukemia patients. METHODS: From June 2022 to March 2023, a convenience sampling method was used to recruit 208 acute leukemia patients in the inpatient center of a hospital in Hebei. The Chinese versions of Multidimensional Health Locus of Control Scale, Illness Acceptance Scale, and Anderson Symptom Assessment Scale was used in the cross-sectional study. RESULTS: All participants reported the presence of symptom distress. Symptom distress was significantly correlated with chance health locus of control, illness acceptance, and symptom severity (P＜0.05). Illness acceptance alone played a mediating role in the relationship between chance health locus of control and symptom distress in acute leukemia patients (ß=0.087, 95%CI 0.030-0.167). The indirect role of chance health locus of control on symptom distress through symptom severity alone was also statistically significant (ß=0.131, 95%CI 0.008-0.252). Furthermore, the multiple mediating role of chance health locus of control and symptom distress through illness acceptance and symptom severity combined was verified (ß=0.027, 95%CI 0.001-0.089). The alternative model is also valid, indicating bidirectional relationships between symptom severity, illness acceptance, and chance health locus of control, collectively influencing symptom distress. CONCLUSION: There is a positive relationship between chance health locus of control and symptom distress; additionally, increasing social psychological interventions for illness acceptance and strengthening the management of core symptoms will help alleviate the impact of health chance locus of control on symptom distress in acute leukemia patients. Longitudinal studies are needed to confirm the causal relationships among the variables explored within the model. IMPACT ON NURSING PRACTICE: It is recommended that healthcare professionals pay attention to the assessment of health locus of control in patients, identify patients with health chance locus of control in a timely manner, take measures to enhance their disease acceptance, and strengthen the management of core symptoms, thereby reducing their level of symptom distress.

Integrating single-cell and bulk expression data to identify and analyze cancer prognosis-related genes.

Compared with traditional evaluation methods of cancer prognosis based on tissue samples, single-cell sequencing technology can provide information on cell type heterogeneity for predicting biomarkers related to cancer prognosis. Therefore, the bulk and single-cell expression profiles of breast cancer and normal cells were comprehensively analyzed to identify malignant and non-malignant markers and construct a reliable prognosis model. We first screened highly reliable differentially expressed genes from bulk expression profiles of multiple breast cancer tissues and normal tissues, and inferred genes related to cell malignancy from single-cell data. Then we identified eight critical genes related to breast cancer to conduct Cox regression analysis, calculate polygenic risk score (PRS), and verify the predictive ability of PRS in two data groups. The results show that PRS can divide breast cancer patients into high-risk group and low-risk group. PRS is related to the overall survival time and relapse-free interval and is a prognosis factor independent of conventional clinicopathological characteristics. Breast cancer is usually regarded as a cancer with a relatively good prognosis. In order to further explore whether this workflow can be applied to cancer with poor prognosis, we selected lung cancer for a comparative study. The results show that this workflow can also build a reasonable prognosis model for lung cancer. This study provides new insight and practical source code for further research on cancer biomarkers and drug targets. It also provides basis for survival prediction, treatment response prediction, and personalized treatment.

Lean nonalcoholic fatty liver disease and risk of incident type 2 diabetes mellitus: A literature review and meta-analysis.

OBJECTIVE: There is limited data regarding the risk of incident type 2 diabetes mellitus (T2DM) among lean nonalcoholic fatty liver disease (NAFLD) individuals. We performed a meta-analysis of relevant studies. RESEARCH DESIGN AND METHODS: We collected data using PubMed, Scopus, Cochrane and Web of Science from the databases' inception until December 2022. We included cohort studies in which lean NAFLD was diagnosed through imaging methods or biopsy. Eligible studies were selected according to predefined keywords and clinical outcomes. RESULTS: A total of 16 observational studies with 304,975 adult individuals (7.7% with lean NAFLD) and nearly 1300 cases of incident diabetes followed up over a median period of 5.05 years were included in the final analysis. Patients with lean NAFLD had a greater risk of incident diabetes than those without NAFLD (random-effects hazard ratio [HR] 2.72, 95% CI 1.56-4.74; I2 = 93.8%). Compared with the lean without NAFLD group, the adjusted HRs (95% CIs) of incident diabetes for participants in the overweight/obese without NAFLD and overweight/obese with NAFLD groups were 1.32 (0.99- 1.77) and 2.98(1.66-5.32). It appeared to be even greater among NAFLD patients with advanced high NAFLD fibrosis score (random-effects HR 3.48, 95% CI 1.92-6.31). Sensitivity analyses and publication bias did not alter these findings. CONCLUSIONS: Lean NAFLD is significantly associated with at least twofold increased risk of incident diabetes in non-overweight subjects. This risk parallels the underlying severity of NAFLD. The presence of NAFLD in non-overweight individuals had a more significant impact on the development of diabetes than being overweight itself.

Multiple rib and vertebral fractures associated with Bordetella pertussis infection: a case report.

BACKGROUND: Pertussis is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis, characterized by paroxysms of severe coughing, and predominantly affects children. We report the first case of multiple fractures in the ribs, lumbar spine, and sacrum associated with severe coughing caused by Bordetella pertussis infection in an adult. CASE PRESENTATION: A 49-year-old female presented with acute-onset chest wall pain for 3 weeks. Imaging results revealed multiple fractures in the ribs and vertebrae, as well as bilateral pleural effusion, pericardial effusion, right pneumothorax, and enlargement of the left parapharyngeal and subclavian lymph nodes. The patient's bone density scan, autoimmune antibodies, bone marrow biopsy, and sacral bone biopsy all came back normal. Imaging test results found no evidence of solid tumors or active TB infection. The patient later recalled having violent coughing prior to the onset of chest pain and several family members having similar symptoms. Her blood sample was sent to the CDC, revealing Bordetella pertussis toxin (PT) IgG titer of 110.68 IU/mL. The patient was diagnosed with pertussis and multiple stress fractures from violent coughing. Symptomatic treatments were administered, and the patient's symptoms improved. The patient was followed up 8 weeks later, she reported no more coughing or chest pain. CONCLUSIONS: Pertussis is not just a pediatric disease, but diagnosis in adults is challenging as patients may present with a myriad of confusing symptoms, such as multiple stress fractures due to violent coughing. Medical and epidemiological histories are key to reaching the correct diagnosis, which is essential for appropriate treatments to avoid further complications. Adult immunization should be suggested both for the protection of the adult population and to prevent transmission to children.

Double [4]Helicene-like Naphthobisbenzothiophene Diimides and Their Thienyl-S,S-dioxidized Derivatives with Attractive Solid-State Fluorescence and High Electron Affinity.

A series of double [4]helicene-like naphthobisbenzothiophene diimides and their thienyl-S,S-dioxidized derivatives are synthesized via MoCl5-catalyzed cyclization and m-CPBA-mediated oxidation reactions. The functional five-membered ring diimides show a helicene-like geometry, strong solid-state fluorescence, and deep LUMO of -4.37 eV.

Effect of sodium-glucose cotransporter 2 inhibitors on the rate of decline in kidney function: A systematic review and meta-analysis.

AIM: To investigate the influence of sodium/glucose cotransporter-2 inhibitors (SGLT-2i) on renal function during the course of its administration, particularly in the initial weeks. MATERIALS AND METHODS: Randomized controlled trials (RCTs) related to SGLT-2i were searched in databases (MEDLINE, EMBASE, and Cochrane Central Register) from the database's inception to August 31, 2021. All RCTs reported the kidney outcomes of SGLT2i versus active or placebo control were included, regardless of the presence of diabetes in the patients and the baseline estimated glomerular filtration rate (eGFR). The Cochrane Collaboration risk of bias tool was used to assess the quality of the included studies. All outcome comparisons were performed using the RevMan 5.4 software. RESULTS: Eleven RCTs with 58 534 participants reporting prespecified renal outcomes were identified. There was no heterogeneity in the baseline eGFR and urine albumin-to-creatinine ratio in the included studies. In the initial 2-4 weeks, there was an acute decline of eGFR in the SGLT-2i group compared with placebo group (weighted mean difference [WMD] -3.35 ml/min/1.73 m2 ; 95% CI, -3.81 to -2.90; I2  = 35%, p = .15); When compared to baseline eGFR in the SGLT-2i group, the WMD was -4.02 ml/min/1.73 m2 (95% confidence interval [CI], -3.61 to -4.44; I2  = 0%, p = .45). The renoprotective effect gradually appeared, and the decline rate of eGFR in the SGLT-2i group was sustained slower than placebo. However, the statistically significant benefit of SGLT-2i did not appear until the 104th week (the second year) (WMD 0.35 ml/min/1.73 m2 , 95% CI, 0.04 to 0.66; I2  = 45%, p = .08). Subgroup analysis showed SGLT-2i had a similar benefit on renal function regardless of baseline eGFR values. CONCLUSION: SGLT-2i consistently slowed the deterioration of eGFR since the early stage of administration, even in patients with chronic kidney disease. However, there was an acute decline in eGFR in the initial 2-4 weeks; afterwards the renoprotective effect of SGLT-2i gradually appeared and remained stable in the next few years.

Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice.

Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs. Many studies have revealed translational regulation in plants in response to various environmental stimuli. However, there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues, especially those of rice, a main staple crop that feeds nearly half of the world's population. Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice, Shanyou 63 (SY63), and its parental varieties Zhenshan 97 and Minghui 63. The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels. We identified 3392 upstream open reading frames (uORFs), and the uORF-containing genes were enriched in transcription factors. Only 668 of 13 492 long non-coding RNAs could be translated into peptides. Finally, we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency. Overall, these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.

Medium- and Long-Term Effects of Dapagliflozin on Serum Uric Acid Level in Patients with Type 2 Diabetes: A Real-World Study.

We aimed to explore the medium- and long-term (≥12 weeks) effects of dapagliflozin on serum uric acid (SUA) level in patients with type 2 diabetes mellitus (T2DM) in the real world study and to explore the influencing factors of dapagliflozin on reducing SUA level. This observational, prospective cohort study was based on the real world. There were 77 patients included in this study. They were divided into two groups. Patients in treatment group (n = 38) were treated as dapagliflozin 10 mg/d combined with therapy of routine glucose-lowering drugs (GLDs), and patients in the control group (n = 39) were treated with their routine GLDs. All measurements of physical examinations, blood, and urine samples, including age, sex, weight, height, systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting blood glucose (FBG), glycosylated hemoglobin (HbA1c), and SUA, were collected at baseline for all patients in these two groups and repeated after 12, 24, and 48 weeks of therapy. We compared the changes of metabolic indicators including SUA in these two groups to evaluate the effects of dapagliflozin and analyzed its influencing factors. In the dapagliflozin group, mean SUA levels significantly decreased from 334.2 ± 99.1 µmol/L at baseline to 301.9 ± 73.2 µmol/L after 12 weeks therapy (t = 2.378, p = 0.023). There was no significant statistical difference of SUA levels after 24 weeks treatment of dapagliflozin compared with 12-week and 48-week treatment with dapagliflozin (p > 0.05). We found that baseline SUA had a significant impact on the effect of dapagliflozin on reducing SUA (OR 1.014, 95%CI 1.003−1.025, p = 0.014) by logistic regression analysis. Receiver operating characteristic (ROC) curve showed that T2DM patients with SUA level ≥ 314.5 µmol/L had relative accuracy in recognizing the good effects of dapagliflozin on reducing SUA (sensitivity 76.9%, specificity 76.2%). Combination therapy of dapagliflozin with routine blood-glucose-lowering drugs in T2DM patients showed the significant and sustained stable effect of lowering SUA level in this real-world study.

Patterns of Insulin Secretion During First-Phase Insulin Secretion in Normal Chinese Adults.

Background: The increase in diabetes worldwide is alarming. Decreased acute insulin response to intravenous glucose tolerance test (IVGTT) during first-phase insulin secretion (FPIS) is a characteristic of diabetes. However, knowledge of the insulin secretion characteristics identified by different time to glucose peak in subjects with different metabolic state is sparse. Aims: This study aimed to find different patterns of FPIS in subjects with normal glucose tolerance (NGT) and analyzed the relationship between insulin secretion patterns and the risk for development of type 2 diabetes mellitus (T2DM). Methods: A total of 126 subjects were divided into three groups during a 10-min IVGTT, including NGT with time to glucose peak after 3 min (G1, n = 21), NGT with time to glucose peak at 3 min (G2, n = 95), and prediabetes or diabetes with time to glucose peak at 3 min (G3, n = 10). Glucose, insulin, and C-peptide concentrations at 0, 3, 5, 7, and 10 min during the IVGTT were tested. IVGTT-based indices were calculated to evaluate the insulin secretion and insulin sensitivity. Results: Age, body mass index (BMI), waist-to-hip ratio, triglyceride (TG), and hemoglobin A1c (HbA1c) of subjects were gradually higher, while high-density lipoprotein cholesterol (HDL-C) was gradually lower from G1 to G3 (p for linear trend <0.05), and the differences between G1 and G2 were also statistically significant (p < 0.05). Glucose peak of most participants in G1 converged at 5 min, and the curves shape of insulin and C-peptide in G2 were the sharpest among three groups. There was no significant difference in all IVGTT-based indices between G1 and G2, but AUCIns, AUCIns/AUCGlu, and △Ins3/△Glu3 in G2 were the highest, and the p-value for linear trend of those indices among three groups were statistically significant (p < 0.05). Conclusions: Two patterns of FPIS were in subjects with NGT, while subjects with later time to glucose peak during FPIS might be less likely to develop T2DM in the future.

Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance.

The calmodulin binding transcription activator (CAMTA) is a transcription factor that is widely present in eukaryotes with conserved structure. It contributes to the response to biotic and abiotic stresses and promotes the growth and development of plants. Although previous studies have investigated the number and function of CAMTAs in some species, there is still a lack of comprehensive understanding of the evolutionary process, phylogenetic relationship, expression patterns, and functions of CAMTAs in plants. Here we identified 465 CMATA genes from 112 plants and systematically studied the origin of CAMTA family, gene expansion, functional differentiation, gene structure, and conservative motif distribution. Based on these analyses, we presented the evidence that CAMTA family was originated from chlorophyta, and we speculated that CAMTA might experience obvious structure variation during its early evolution, and that the number of CAMTA genes might gradually increase in higher plants. To reveal potential functions of CAMTA genes, we analyzed the expression patterns of 12 representative species and found significant species specificity, tissue specificity, and developmental stage specificity of CAMTAs. The results also indicated that the CAMTA genes might promote the maturation and senescence. The expression levels and regulatory networks of CAMTAs revealed that CAMTAs could enhance cold tolerance of rice by regulating carbohydrate metabolism-related genes to accumulate carbohydrates or by modulating target genes together with other transcription factors. Our study provides an insight into the molecular evolution of CAMTA family and lays a foundation for further study of related biological functions.

CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes.

Chromatin accessibility is a highly informative structural feature for understanding gene transcription regulation, because it indicates the degree to which nuclear macromolecules such as proteins and RNAs can access chromosomal DNA. Studies have shown that chromatin accessibility is highly dynamic during stress response, stimulus response, and developmental transition. Moreover, physical access to chromosomal DNA in eukaryotes is highly cell-specific. Therefore, current technologies such as DNase-seq, ATAC-seq, and FAIRE-seq reveal only a portion of the open chromatin regions (OCRs) present in a given species. Thus, the genome-wide distribution of OCRs remains unknown. In this study, we developed a bioinformatics tool called CharPlant for the de novo prediction of OCRs in plant genomes. To develop this tool, we constructed a three-layer convolutional neural network (CNN) and subsequently trained the CNN using DNase-seq and ATAC-seq datasets of four plant species. The model simultaneously learns the sequence motifs and regulatory logics, which are jointly used to determine DNA accessibility. All of these steps are integrated into CharPlant, which can be run using a simple command line. The results of data analysis using CharPlant in this study demonstrate its prediction power and computational efficiency. To our knowledge, CharPlant is the first de novo prediction tool that can identify potential OCRs in the whole genome. The source code of CharPlant and supporting files are freely available from https://github.com/Yin-Shen/CharPlant.

Auricular acupuncture for breast cancer-related depression: A protocol for systematic review and meta-analysis.

BACKGROUND: Breast cancer is a common disease in galactophore department. Patients with breast cancer are prone to depression, with the incidence of depression ranging from 13% to 23% and as high as 70% in patients with advanced stage. On the one hand, it is related to the physiological characteristics, personality characteristics, and social factors of women themselves. On the other hand, it is related to the common tumors of women, such as breast cancer, examination, and antitumor treatment. Due to the serious side effects of chemotherapy drugs, patients can always feel the presence of cancer. In addition, the mark of radiotherapy and fatigue make the psychological burden continue to have excessive economic burden, and lack of understanding from both social and family, discrimination and patients' own psychological endurance are all causes of breast cancer factors contributing to depressive symptoms in patients. Auricular acupuncture as a form of acupuncture therapy which is proved to be effective in RCTs and very suitable for patients, has been used in patients who suffer from breast cancer-related depression for a long time, therefore, a systematic review is necessary to provide available evidence for further study. METHODS: The following databases will be searched from their inception to August 2020: Electronic database includes PubMed, Embase, Cochrane Library, Web of Science, Nature, Science online, VIP medicine information, and China National Knowledge Infrastructure. Primary outcomes: Score of depression symptoms. Additional outcomes: The overall effective rate. Data will be extracted by 2 researchers independently, risk of bias of the meta-analysis will be evaluated based on the Cochrane Handbook for Systematic Reviews of Interventions. All data analysis will be conducted by data statistics software Review Manager V.5.3. and Stata V.12.0. RESULTS: The results of this study will systematically evaluate the effectiveness and safety of auricular acupuncture intervention for people with breast cancer-related depression. CONCLUSION: The systematic review of this study will summarize the current published evidence of auricular acupuncture for the treatment of breast cancer-related depression, which can further guide the promotion and application of it. OPEN SCIENCE FRA NETWORK (OSF) REGISTRATION NUMBER: September 11, 2020 osf.io/5b7yw. (https://osf.io/5b7yw).

The effect of scalp electroacupuncture combined with Memantine in patients with vascular dementia: A retrospective study.

Currently there is no effective treatment for vascular dementia (VaD). Pharmacological treatment often lead to severe complications and require drug dosage adjustment. This study investigated the effect of scalp electroacupuncture combined with Memantine in VaD. The safety and antioxidative effect of scalp electroacupuncture were also explored.A retrospective study was conducted and data of inpatients of Linyi Central Hospital with VaD between June 2017 and May 2018 were collected and sorted. The patients were divided into scalp electroacupuncture-medication (A), scalp electroacupuncture (B) and medication (control) (C) groups, in which Memantine was prescribed as medication. Cognitive function, activities of daily living and quality of life assessed by Montreal Cognitive Assessment (MoCA), Barthel index and dementia quality of life questionnaire; the contents of superoxide dismutase, lipid peroxide and nitric oxide in blood samples; and adverse reaction were compared.Data from a total of 150 patients were collected (Group A, n = 55; Group B, n = 50; Group C, n = 45). The post-treatment/follow-up Montreal Cognitive Assessment, Barthel index and dementia quality of life questionnaire scores were significantly improved in all groups compared to pre-treatment (groups A and B, P<.01; group C, P<.05). The improvements were significant for groups A vs C, B vs C (P<0.01, both), and group A vs B (P<.05). The post-treatment/follow-up levels of lipid peroxide and nitric oxide decreased significantly while superoxide dismutase increased significantly in groups A and B compared to pre-treatment (P<.01, both). The differences were significant for groups A vs C, and B vs C (P < .01, both), but not significant between groups A and B (P > .05). There were no significant adverse events occurred during the study and follow-up.In combined treatment, scalp electroacupuncture works in parallel with Memantine and significantly increase the therapeutic effect in VaD with no significant adverse events. Scalp electroacupuncture may have the potential to serve as an option or alternative treatment for VaD. Scalp electroacupuncture may alleviate VaD symptoms through its antioxidative mechanism.

A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations.

Prioritization of cancer-related genes from gene expression profiles and proteomic data is vital to improve the targeted therapies research. Although computational approaches have been complementing high-throughput biological experiments on the understanding of human diseases, it still remains a big challenge to accurately discover cancer-related proteins/genes via automatic learning from large-scale protein/gene expression data and protein-protein interaction data. Most of the existing methods are based on network construction combined with gene expression profiles, which ignore the diversity between normal samples and disease cell lines. In this study, we introduced a deep learning model based on a sparse auto-encoder to learn the specific characteristics of protein interactions in cancer cell lines integrated with protein expression data. The model showed learning ability to identify cancer-related proteins/genes from the input of different protein expression profiles by extracting the characteristics of protein interaction information, which could also predict cancer-related protein combinations. Comparing with other reported methods including differential expression and network-based methods, our model got the highest area under the curve value (>0.8) in predicting cancer-related genes. Our study prioritized ~500 high-confidence cancer-related genes; among these genes, 211 already known cancer drug targets were found, which supported the accuracy of our method. The above results indicated that the proposed auto-encoder model could computationally prioritize candidate proteins/genes involved in cancer and improve the targeted therapies research.

Lane Marking Detection via Deep Convolutional Neural Network.

Research on Faster R-CNN has recently witnessed the progress in both accuracy and execution efficiency in detecting objects such as faces, hands or pedestrians in photograph or video. However, constrained by the size of its convolution feature map output, it is unable to clearly detect small or tiny objects. Therefore, we presented a fast, deep convolutional neural network based on a modified Faster R-CNN. Multiple strategies, such as fast multi-level combination, context cues, and a new anchor generating method were employed for small object detection in this paper. We demonstrated performance of our algorithm both on the KITTI-ROAD dataset and our own traffic scene lane markings dataset. Experiments demonstrated that our algorithm obtained better accuracy than Faster R-CNN in small object detection.

Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2.

As an industrial bacterium, Bacillus licheniformis DW2 produces bacitracin which is an important antibiotic for many pathogenic microorganisms. Our previous study showed AbrB-knockout could significantly increase the production of bacitracin. Accordingly, it was meaningful to understand its genome features, expression differences between wild and AbrB-knockout (ΔAbrB) strains, and the regulation of bacitracin biosynthesis. Here, we sequenced, de novo assembled and annotated its genome, and also sequenced the transcriptomes in three growth phases. The genome of DW2 contained a DNA molecule of 4,468,952 bp with 45.93% GC content and 4,717 protein coding genes. The transcriptome reads were mapped to the assembled genome, and obtained 4,102∼4,536 expressed genes from different samples. We investigated transcription changes in B. licheniformis DW2 and showed that ΔAbrB caused hundreds of genes up-regulation and down-regulation in different growth phases. We identified a complete bacitracin synthetase gene cluster, including the location and length of bacABC, bcrABC, and bacT, as well as their arrangement. The gene cluster bcrABC were significantly up-regulated in ΔAbrB strain, which supported the hypothesis in previous study of bcrABC transporting bacitracin out of the cell to avoid self-intoxication, and was consistent with the previous experimental result that ΔAbrB could yield more bacitracin. This study provided a high quality reference genome for B. licheniformis DW2, and the transcriptome data depicted global alterations across two strains and three phases offered an understanding of AbrB regulation and bacitracin biosynthesis through gene expression.

Note: Optimal choice of the reflector by phase analysis for heterodyne interferometric roll angle measurement.

The choice of an actual reflector instead of an ideal or perfect reflector has to be dealt with for heterodyne-interferometric roll angle measurement methods. The candidates of regular reflectors such as corner cube prism and right angle prism are analyzed by the homogeneous coordinate transformation method, which provides a theoretical basis for the determination of the actual reflector. Furthermore, the influences of the phase loss of the determined reflector are strictly argued due to non-perfect or natural characteristics itself. Several tactics are considered to solve this problem by phase analysis. By contrast, it is an optimal choice that mirrors-based right angle prism can improve evidently the phase loss by experiment.

Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A.

Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A (Xoo PXO99A), which is the causal agent of bacterial blight on rice. Based on the parameters of 28 nucleotide frequencies and support vector machine algorithm, 41 originally annotated hypothetical genes were recognized as noncoding sequences, which were further supported by principal component analysis and other evidence. Ten of them were tested with reverse transcription-polymerase chain reaction experiments (RT-PCR), and all of them were confirmed to be noncoding sequences. Furthermore, 197 potential new genes not annotated in RefSeq were both recognized by two ab initio gene finding programs. Most of them only have sequence similarities with part of the known genes in other species, so they are unlikely to be protein-coding genes. Twelve potential new genes have high full-length sequence similarities with function-known genes, which are very likely to be true protein-coding genes. All the 12 potential genes were tested with RT-PCR, and 11 of them (92%) were successfully amplified in cDNA template. The RT-PCR experiments confirm that our theoretical prediction has high accuracy. The improvement of Xoo PXO99A annotation is helpful for the research of lifestyle, metabolism, and pathogenicity of this important plant pathogen. The improved annotation can be obtained from http://211.69.128.148/Xoo .