Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization

INTRODUCTION

The clinical presentations of dry eye disease (DED) and depression (DEP) often comanifest. However, the robustness and the mechanisms underlying this association were undetermined.

OBJECTIVES

To this end, we set up a three-segment study that employed multimodality results (meta-analysis, genome-wide association study [GWAS] and Mendelian randomization [MR]) to elucidate the association, common pathways and causality between DED and DEP.

METHODS

A meta-analysis comprising 26 case-control studies was first conducted to confirm the DED-DEP association. Next, we performed a linkage disequilibrium (LD)-adjusted GWAS and targeted phenotype association study (PheWAS) in East Asian TW Biobank (TWB) and European UK Biobank (UKB) populations. Single-nucleotide polymorphisms (SNPs) were further screened for molecular interactions and common pathways at the functional gene level. To further elucidate the activated pathways in DED and DEP, a systemic transcriptome review was conducted on RNA sequencing samples from the Gene Expression Omnibus. Finally, 48 MR experiments were implemented to examine the bidirectional causation between DED and DEP.

RESULTS

Our meta-analysis showed that DED patients are associated with an increased DEP prevalence (OR = 1.83), while DEP patients have a concurrent higher risk of DED (OR = 2.34). Notably, cross-disease GWAS analysis revealed that similar genetic architecture (rG = 0.19) and pleiotropic functional genes contributed to phenotypes in both diseases. Through protein-protein interaction and ontology convergence, we summarized the pleiotropic functional genes under the ontology of immune activation, which was further validated by a transcriptome systemic review. Importantly, the inverse variance-weighted (IVW)-MR experiments in both TWB and UKB populations (p value <0.001) supported the bidirectional exposure-outcome causation for DED-to-DEP and DEP-to-DED. Despite stringent LD-corrected instrumental variable re-selection, the bidirectional causation between DED and DEP remained.

CONCLUSION

With the multi-modal evidence combined, we consolidated the association and causation between DED and DEP.

[Effect of sirolimus combined with anti-CD20 monoclonal antibody desensitization on the prognosis of patients underwent haploidentical stem cell transplantation]

Objective: To investigate the effects of sirolimus combined with anti-CD20 monoclonal antibody desensitization on the prognosis of patients with haploidentical stem cell transplantation (haplo-SCT). Methods: Fifteen consecutive patients who received haplo-SCT and pre-transplant donor specific anti-human leukocyte antigen (HLA) antibody (DSA) positive [mean fluorescence intensity (MFI)≥2 000] in the Institute of Hematological Diseases from November 2021 to March 2023 were retrospectively recruited into the desensitized group. There were 4 males and 11 females, with a median age [M(Q1, Q3)] of 48 (37, 59) years. All patients were desensitized with sirolimus combined with anti-CD20 monoclonal antibody. The non-desensitized group included 29 patients with haplo-SCT who had not received desensitization treatment from August 2012 to June 2016. There were 12 males and 17 females with a median age of 42 (26, 50) years. Up to October 1, 2023, the median follow-up time was 13 (9, 18) months in the study group and 23 (14, 29) months in the control group. The changes of MFI before and after desensitization treatment and the prognosis of patients in the desensitized group were compared, including the incidence of primary implantation failure (pGF), neutrophil implantation time, platelet implantation time, grade Ⅱ-Ⅳ acute graft-versus-host disease (GVHD) and chronic GVHD incidence, non-recurrence related mortality, event-free survival rate, disease-free survival rate and overall survival rate. The survival curve was drawn by Kaplan-Meier method, and the survival rate between groups was compared with Log-rank test. Results: After desensitization treatment, the level of DSA MFI in the desensitized group decreased from 8 879 (7 544, 11 495) to 3 781 (1 638, 4 165) after desensitization treatment (P<0.01). All of the patients achieved hematopoietic recovery, and the median time for neutrophil and platelet engraftment were 14 (11, 15) and 20 (18, 25) days, respectively. The incidence of pGF in the desensitized group was 0, which was lower than that in the non-desensitized group (34.5%, 10/29) (P=0.011). The expected 1-year disease-free survival rate and overall survival rate in the desensitized group were 100% (15/15) and 100% (15/15) respectively, while those in the non-desensitized group were 75.9% (22/29) and 75.9% (22/29) respectively, the difference was not statistically significant (both P>0.05). The one-year event-free survival rate in the desensitized group was expected to be 100% (15/15), which was higher than that in the non-desensitized group (51.3%, 15/29) (P=0.002). Conclusion: Sirolimus combined with anti-CD20 monoclonal antibody desensitization therapy can reduce the DSA level of haplo-SCT recipients, promote hematopoietic engraftment after transplantation, and avoid the occurrence of pGF after transplantation.

[Clinical significance of monitoring NUP98::NSD1 fusion genes before and after allogeneic hematopoietic stem cell transplantation]

Objective: This study aimed to observe the dynamic changes of NUP98::NSD1 expression before and after allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Moreover, the clinical value of measurable residual disease (MRD) was analyzed. Methods: Sixteen AML patients who were diagnosed with the NUP98::NSD1 fusion gene and received allo-HSCT at Peking University People's Hospital were included. The NUP98::NSD1 fusion gene and leukemia-associated immunophenotype (LAIP) were monitored before and after transplantation to evaluate their MRD status. Results: The median follow-up time for all patients was 526 days (139-1136 days) , with four patients (25.0%) experiencing hematological recurrence at a median of 474 days (283-607 days) after transplantation. Three patients (18.8%) died, two of whom (12.5%) died of leukemia recurrence. The median expression level of NUP98::NSD1 in newly diagnosed patients with complete data was 78.5% (18.9%-184.4%) at the time of initial diagnosis. The recurrence rate was higher in NUP98::NSD1-positive patients after transplantation, with 44.4% of patients experiencing recurrence, whereas no recurrence occurred in NUP98::NSD1-negative patients after transplantation. The area under the receiver operating characteristic curve predicted by the NUP98::NSD1 level after transplantation was 1.000 (95% confidence interval: 1.000-1.000, P=0.003) . Among the four patients with recurrence, NUP98::NSD1 was more sensitive than flow cytometry residual (FCM) and Wilms' tumor gene 1 (WT1) . Conclusions: The NUP98::NSD1 fusion gene can be used to evaluate the MRD status of allo-HSCT. NUP98::NSD1-positive patients after transplantation have a high relapse rate and poor prognosis. NUP98::NSD1 was more sensitive than FCM and WT1 in predicting posttransplant relapse.

A brain circuit and neuronal mechanism for decoding and adapting to change in daylength

Changes in daylight amount (photoperiod) drive pronounced alterations in physiology and behaviour1,2. Adaptive responses to seasonal photoperiods are vital to all organisms - dysregulation is associated with disease, from affective disorders3 to metabolic syndromes4. Circadian rhythm circuitry has been implicated5,6 yet little is known about the precise neural and cellular substrates that underlie phase synchronization to photoperiod change. Here we present a previously unknown brain circuit and novel system of axon branch-specific and reversible neurotransmitter deployment that together prove critical for behavioural and sleep adaptation to photoperiod change. We found that the recently defined neuron type called mrEn1-Pet17 located in the mouse brainstem Median Raphe Nucleus (MRN) segregates serotonin versus VGLUT3 (here proxy for the neurotransmitter glutamate) to different axonal branches innervating specific brain regions involved in circadian rhythm and sleep/wake timing8,9. We found that whether measured during the light or dark phase of the day this branch-specific neurotransmitter deployment in mrEn1-Pet1 neurons was indistinguishable; however, it strikingly reorganizes on photoperiod change. Specifically, axonal boutons but not cell soma show a shift in neurochemical phenotype upon change away from equinox light/dark conditions that reverses upon return to equinox. When we genetically disabled the deployment of VGLUT3 in mrEn1-Pet1 neurons, we found that sleep/wake periods and voluntary activity failed to synchronize to the new photoperiod or was significantly delayed. Combining intersectional rabies virus tracing and projection-specific neuronal silencing in vivo, we delineated a Preoptic Area-to-mrEn1Pet1 connection responsible for decoding the photoperiodic inputs, driving the neurochemical shift and promoting behavioural synchronization. Our results reveal a previously unrecognized brain circuit along with a novel form of periodic, branch-specific neurotransmitter deployment that together regulate organismal adaptation to photoperiod changes.

Efficacy of HEPA Air Cleaner on Improving Indoor Particulate Matter 2.5 Concentration

High-efficiency particulate air (HEPA) filters is a potential tool used to remove fine particles and improve indoor air quality. This study aims to analyze the real-world efficacy of portable HEPA air cleaners in a household environment. Laser light dispersion PM_2.5 sensors are used to continuously monitor the indoor and outdoor PM_2.5 level before and after HEPA air cleaner filtration. Overall, HEPA air cleaners significantly reduce the indoor PM_2.5 level (33.5 ± 10.3 vs. 17.2 ± 10.7 µg/m³, mean difference (MD) = -16.3 µg/m³, p < 0.001) and indoor/outdoor PM_2.5% (76.3 ± 16.8 vs. 38.6 ± 19.8%, MD = -37.7%, p < 0.001). The efficacy to reduce PM_2.5 is strongest in three machines with medium-flow setting group (indoor PM_2.5 MD: -26.5 µg/m³, indoor/outdoor PM_2.5 percentage MD: -56.4%). Multiple linear regression demonstrates that outdoor PM_2.5, machine number, airflow speed, and window ventilation are significant factors associated with indoor PM_2.5 concentrations (R = 0.879) and percentage of the indoor/outdoor PM_2.5 ratio (R = 0.808). HEPA air cleaners can effectively improve indoor PM_2.5 air pollution. Adequate air cleaner machine numbers, appropriate airflow, and window ventilation limitations are important to achieve the best efficacy of the HEPA air cleaner.

Ketamine promotes breast tumor growth in a mouse breast tumor model involving with high expression of miR-27b-3p and EGFR

Non-medical use of ketamine as an adulterant to ecstasy is more prevalent than amphetamine in Taiwan. Ketamine's effect on immunosuppression might play some functional role in tumor growth, while it is still controversial whether ketamine abuse could increase tumor growth or not. This study aimed to investigate the influence of ketamine addiction in breast tumors and related gene expressions. The effect of ketamine treatment on proliferation, colony formation, migration, and invasion of triple-negative breast cancer cell line EO771 was examined. In addition, a ketamine addiction mice model was established by intraperitoneal injection (IP) of ketamine in mice and used to investigate the effects of ketamine addiction on tumor growth and the possible mechanisms. In the in vitro studies, ketamine treatment at different concentrations did not affect EO771 cell proliferation and colony formation. But ketamine did enhance migration and invasion of EO771 cells. The in vivo experiments showed significantly increased breast tumor volume and weight in ketamine-addicted mice than in normal saline groups. miR-27b-3p level, human epidermal growth factor receptor 2 (HER2), and epidermal growth factor receptor (EGFR) significantly increased in tumors of ketamine addiction mice compared to control mice. In vivo evidence showed that Ketamine might increase tumor growth on the tumor microenvironment, and miR-27b-3p, HER2, and EGFR might play a role in the process.

Preterm oral feeding scale to assist in deciding initial oral feeding of preterm infants in neonatal intensive care units

BACKGROUND

The inconsistency in decisions to commence oral feeding indicates that health professionals require clearer guidelines to determine when to initiate oral feeding in preterm infants. This study applied the Taiwan version of Preterm Oral Feeding Readiness Assessment Scale (TW-POFRAS) to clinical decision-making, especially for preterm infants with a birth weight less than 1,500 g or gestational age (GA) less than 32 weeks.

METHODS

This was a single-center observational cross-sectional study and 81 preterm infants were recruited. Lengths of stay from admission to initial one-meal oral feeding, to one-day all-meal oral feeding, and to discharge were analyzed. Scale scores, physician orders, and smooth oral intake of 5 mL of milk were analyzed. Kappa coefficients were examined to determine concordances within the results.

RESULTS

At least moderate concordance was evident (k = 0.492). Most preterm infants can begin to consume one meal of the least 5 mL of milk smoothly and proceed to consume a full day of meals with a week; they are typically discharged from the hospital within a month, except for those with a birth weight less than 1,500 g or a GA less than 32 weeks. For 17 of 81 participants, assessment results for physician orders, 5-mL milk consumption, and scale scores were inconsistent. Participants with a birth weight less than 1,500 g or GA less than 32 weeks were able to meet the 5-mL standard by the postmenstrual age of 35 weeks, at latest.

CONCLUSION

We recommend that TW-POFRAS should be used in conjunction with physicians' clinical decision-making for oral feeding readiness for preterm infants in the NICU.

Improve the clinical effective decision of the oral feeding readiness in preterm infants: Revise and validate the TC-POFRAS

BACKGROUND

Currently there is limited information to guide health professionals regarding the optimal time frame to initiate safe and effective oral feedings to preterm infants. The study aims to revise and validate a streamlined version of the Traditional Chinese-Preterm Oral Feeding Readiness Assessment Scale, the TC-POFRAS®, and evaluate its construct validity in the clinical decisions regarding feeding readiness of preterm infants.

METHODS

Eighty-one clinically stable preterm infants were assessed using the TC-POFRAS for oral feeding readiness. Item-total correlation analysis was used to check if any item was inconsistent with the averaged TC-POFRAS scores. Cronbach's α coefficient was used to evaluate the inter-item consistency. Exploratory factor analysis was used to determine the coherence of variables to reorganize assessment domains. The revised version of TC-POFRAS (TC-POFRAS®) was developed and a new cut-off score based on discriminant accuracy was established.

RESULTS

Based on the results from statistical analysis, five items ("lips posture," "tongue posture," "biting reflex," "gag reflex," and "tongue cupping") were deleted from the original TC-POFRAS to form the TC-POFRAS®. The TC-POFRAS®'s global accuracy was 92.1%. The cut-off value of 19 was the one that presented the most optimization of sensitivity based on specificity. The TC-POFRAS® was reconstructed into corrected gestational age and five behavioral domains.

CONCLUSIONS

The TC-POFRAS® is considered a valid, safe, and accurate objective instrument to assist health professionals to initiate oral feeding of preterm infants.

[Prognostic significance of DEK-NUP214 fusion gene in patients with acute myeloid leukemia after allogeneic hematopoietic stem cell transplantation]

Objective: To investigate the dynamic change and clinical impact of DEK-NUP214 fusion gene in patients with acute myeloid leukemia (AML) receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: Real-time quantitative polymerase chain reaction (RQ-PCR) and multicolor flow cytometry (FCM) were used to detect DEK-NUP214 gene expression and leukemia-associated immunophenotype (LAIP) in 15 newly diagnosed patients with positive DEK-NUP214 and receiving allo-HSCT from September 2012 to September 2017 at Peking University People's Hospital. The clinical outcome was analyzed using Kaplan-Meier survival curves. The impact of DEK-NUP214 expression was analyzed by log-rank test. Results: The subjects were followed-up with a median period of 657 (62-2 212) days. The median DEK-NUP214 expression level at diagnosis was 488% (274%-1 692%). Thirteen patients achieved complete remission before allo-HSCT. Thirteen patients had a residual DEK-NUP214 expression of 0.38% (0.029%-738.9%) before allo-HSCT. After allo-HSCT, DEK-NUP214 expression in 9/13 patients remained positive, which dropped by around 500 folds (5.7-5 663.0 folds) within a month post-transplant. Five patients died and 2 patients relapsed. The 3-year cumulative incidence of relapse in patients with positive DEK-NUP214 before transplant was 17.5%±11.3% and the 3-year overall survival was 60.5%±13.8%. After allo-HSCT, DEK-NUP214-negative patients had a better outcome. Conclusion: Quantitative monitor of DEK-NUP214 fusion gene could be a sensitive indicator of MRD status after allo-HSCT.

[Negative effects of donor specific anti-HLA antibody on poor hematopoietic recovery in patients with hematological diseases receiving haploidentical stem cell transplantation and rituximab for desensitization]

Objective: To investigate the incidences and risk factors of poor hematopoietic reconstitution (PHR) in patients with hematological diseases who underwent haploidentical allograft and were treated with rituximab for desensitization. Methods: Eight-three donor specific anti-HLA antibody (DSA, 2000 ≤MFI<10 000) positive patients who underwent haploidentical allograft were prospectively enrolled. Rituximab (375 mg/m²) was used for desensitization day-3 of conditioning regimen. Incidence and factors associated with PHR, including primary poor graft function and prolonged thrombocytopenia, were investigated. Results: There were 22 males and 61 females with a median age of 39(range: 1-65) years. Kaplan-Meier analysis showed that the 100 day cumulative incidences of neutrophil and platelet engraftment were 93.0% and 90.7%, respectively. The incidences of PHR were 14.7%. The 3-year relapse rate, non-relapse mortality (NRM) rate, event-free survival (EFS), leukemia-free survival (DFS) and overall survival (OS) were 6.5%, 15.1%, 70.8%, 79.4% and 79.4%, respectively. Patients with DSA MFI<5 000 (group A, n=46) experienced lower PHR (4.4% vs. 27.5%, P=0.003), and higher 3-year EFS (79.5% vs. 59.8%, P=0.020) compared to those with DSA MFI≥5 000 (group B, n=37). Multivariate analysis showed that DSA MFI≥5 000 was correlated with PHR (HR=6.101, P=0.021). PHR was associated with higher NRM (HR=4.110, P=0.026), lower DFS (HR=3.656, P=0.019) and OS (HR=3.656, P=0.019). Conclusion: Our data suggest that high pre-transplant DSA level is a risk factor for PHR in patients with hematological diseases receiving haploidentical allograft and rituximab for desensitization.

Clinical Validation of the Preterm Oral Feeding Readiness Assessment Scale in Taiwan

PURPOSE

A successful transition from gavage to full oral feeding is a decisive indicator for discharging premature infants from the neonatal intensive care unit. A clinically useful measure of oral feeding readiness would help nurses initiate implementation of the cue-based feeding model in Taiwan. The study aimed to assess the validity and reliability of the Traditional Chinese Preterm Oral Feeding Readiness Assessment Scale (TC-POFRAS).

DESIGN AND METHODS

81 preterm infants were enrolled and assessed by TC-POFRAS regarding their oral feeding readiness. This study included two phases. Phase 1 conducted a cross language validation procedure and item-level content validity indices (I-CVIs) for content validity were estimated. In phase 2, Cronbach's alpha for internal consistency at each category and total scale levels were estimated. A receiver operating characteristic (ROC) curve was estimated to explore the scale's performance. The optimal cut-off value of TC-POFRAS was identified by the best Youden's Index [maximum (sensitivity + specificity - 1)].

RESULTS

All of the I-CVIs were 1.00. The whole Cronbach's alpha for internal consistency was 0.804 (95% CI = 0.736-0.862), and Cronbach's alpha values were between 0.538 (95% = 0.332-0.689) and 0.687 (95%CI = 0.572-0.781) for categories. The area under ROC was 92.2%, and an optimal cut-off value of TC-POFRAS was 29 (sensitivity: 0.938, specificity: 0.941).

CONCLUSIONS

The TC-POFRAS has been verified to be an effective and accurate instrument to determine the initiation of oral feeding in preterm infants.

PRACTICE IMPLICATIONS

The TC-POFRAS is an appropriate and complementary assessment instrument for professionals to conveniently use in clinical practice.

[Comparison of prognostic significance between multiparameter flow cytometry and real-time quantitative polymerase chain reaction in the detection of minimal residual disease of Philadelphia chromosome-positive acute B lymphocytic leukemia before allogeneic hematopoietic stem cell transplantation]

目的

探讨多参数流式细胞术（MFC）与实时定量聚合酶链反应技术（RQ-PCR）两种方法检测费城染色体阳性（Ph⁺）急性B淋巴细胞白血病（B-ALL）患者异基因造血干细胞移植（allo-HSCT）前微小残留病（MRD）的预后意义。

方法

回顾性分析2014年7月至2018年2月在北京大学血液病研究所接受allo-HSCT的280例Ph⁺ B-ALL患者，同时用MFC和RQ-PCR法（检测BCR-ABL融合基因表达）检测移植前MRD。

结果

RQ-PCR与MFC检测MRD具有相关性（rs＝0.435，P<0.001）。MFC、RQ-PCR法检测移植前MRD的阳性率分别为25.7％（72/280）、60.7％（170/280）。移植前MFC-MRD阳性组患者移植后白血病3年累积复发率（CIR）明显高于MFC-MRD阴性组（23.6％对8.6％，P<0.001）。RQ-PCR检测BCR/ABL融合基因阳性组（RQ-PCR MRD阳性组）的3年CIR、非复发死亡（NRM）、无白血病生存（LFS）、总生存（OS）与BCR/ABL融合基因阴性组（RQ-PCR MRD阴性组）相比差异均无统计学意义（P>0.05）。移植前RQ-PCR MRD≥1％组比<1％组具有更高的3年CIR（23.1％对11.4％，P＝0.032）、更低的LFS率（53.8％对74.4％，P＝0.015）与OS率（57.7％对79.1％，P＝0.009）。多因素分析显示，移植前MFC-MRD阳性是影响移植后CIR的危险因素（HR＝2.488，95％CI1.216～5.088，P＝0.013），移植前RQ-PCR MRD≥1％是影响LFS（HR＝2.272，95％CI 1.225～4.215，P<0.001）、OS（HR＝2.472，95％ CI 1.289～4.739，P＝0.006）的危险因素。MFC检测MRD预测复发的敏感性、特异性、阳性预测值（PPV）、阴性预测值（NPV）分别为48.50％、77.56％、23.62％、87.16％。以RQ-PCR MRD≥1％预测复发的敏感性、特异性、PPV、NPV分别为23.00％、88.59％、17.15％、91.84％。移植前MFC-MRD阳性或RQ-PCR MRD≥1％二者任一成立为指标预测移植后复发的敏感性、特异性、PPV、NPV分别为54.29％、73.88％、45.70％、91.87％。

结论

MFC和RQ-PCR法检测移植前MRD水平均可预测Ph⁺ B-ALL患者移植预后。移植前MFC-MRD阳性是移植后复发的危险因素。联合使用两种方法（移植前MFC-MRD阳性状态或RQ-PCR MRD≥1％成立）可提高预测移植后复发的敏感性、阳性预测值与阴性预测值，有助于更好筛选出高危患者。

Mitochondrial ROS1 Increases Mitochondrial Fission and Respiration in Oral Squamous Cancer Carcinoma

Simple Summary

The clinical efficacy of anti-epidermal growth factor receptor (EGFR) antibody cetuximab for oral squamous cell carcinomas (OSCCs) is low. We previously reported that an increased oncogenic ROS proto-oncogene 1 (ROS1) is responsible for the invasiveness and metastasis of OSCC. This study demonstrates for the first time that ROS1, a receptor tyrosine kinase, can localize to mitochondria. Mitochondrial ROS1 in the highly invasive OSCC promotes mitochondrial fission, enhances mitochondrial oxidative phosphorylation and ATP production but reduces mitochondrial biogenesis. These findings highlight the novel function of ROS1 in mitochondrial morphogenesis and metabolic adaptation to promote OSCC invasiveness.

Abstract

Increased ROS proto-oncogene 1 (ROS1) expression has been implicated in the invasiveness of human oral squamous cell carcinoma (OSCC). The cellular distribution of ROS1 has long-been assumed at the plasma membrane. However, a previous work reported a differential cellular distribution of mutant ROS1 derived from chromosomal translocation, resulting in increased carcinogenesis. We thus hypothesized that cellular distribution of upregulated ROS1 in OSCC may correlate with invasiveness. We found that ROS1 can localize to mitochondria in the highly invasive OSCC and identified a mitochondria-targeting signal sequence in ROS1. We also demonstrated that ROS1 targeting to mitochondria is required for mitochondrial fission phenotype in the highly invasive OSCC cells. OSCC cells expressing high levels of ROS1 consumed more oxygen and had increased levels of cellular ATP levels. Our results also revealed that ROS1 regulates mitochondrial biogenesis and cellular metabolic plasticity. Together, these findings demonstrate that ROS1 targeting to mitochondria enhances OSCC invasion through regulating mitochondrial morphogenesis and cellular respiratory.

Discovery of Isoplumbagin as a Novel NQO1 Substrate and Anti-Cancer Quinone

Isoplumbagin (5-hydroxy-3-methyl-1,4-naphthoquinone), a naturally occurring quinone from Lawsonia inermis and Plumbago europaea, has been reported to have anti-inflammatory and antimicrobial activity. Inflammation has long been implicated in cancer progression. In this study, we examined the anticancer effect of chemically synthesized isoplumbagin. Our results revealed that isoplumbagin treatment suppressed cell viability and invasion of highly invasive oral squamous cell carcinoma (OSCC) OC3-IV2 cells, glioblastoma U87 cells, non-small cell lung carcinoma H1299 cells, prostate cancer PC3 cells, and cervical cancer HeLa cells by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Boyden chamber assays. In vivo studies demonstrate the inhibitory effect of 2 mg/kg isoplumbagin on the growth of orthotopic xenograft tumors derived from OSCC cells. Mechanistically, isoplumbagin exerts its cytotoxic effect through acting as a substrate of reduced nicotinamide adenine dinucleotide phosphate [NAD(P)H] dehydrogenase quinone 1 (NQO1) to generate hydroquinone, which reverses mitochondrial fission phenotype, reduces mitochondrial complex IV activity, and thus compromises mitochondrial function. Collectively, this work reveals an anticancer activity of isoplumbagin mainly through modulating mitochondrial dynamics and function.

[Observation on the efficacy of consolidation chemotherapy combined with allogeneic natural killer cell infusion in the treatment of low and moderate risk acute myeloid leukemia]

Objective: To evaluate the efficacy of consolidation chemotherapy combined with allogeneic natural killer (NK) cell infusion in the treatment of low or intermediate-risk (LIR) acute myeloid leukemia (AML) . Methods: A cohort of 23 LIR AML patients at hematologic complete remission (CR) received NK cell transfusion combined with consolidation chemotherapy after 3 consolidation courses from January 2014 to June 2019 were reviewed. Control group cases were concurrent patients from Department of Hematology, and their gender, age, diagnosis, risk stratification of prognosis, CR and the number of courses of consolidate chemotherapy before NK cell transfusion were matched with LIR AML patients. Results: A total of 45 times of NK cells were injected into 23 LIR AML patients during 4 to 7 courses of chemotherapy. The median NK cell infusion quantity was 7.5 (6.6-8.6) ×10(9)/L, and the median survival rate of NK cells was 95.4% (93.9%-96.9%) . Among them, the median CD3(-)CD56(+) cell number was 5.0 (1.4-6.4) ×10(9)/L, accounting for 76.8% (30.8%-82.9%) ; The number of CD3(+) CD56(+) cells was 0.55 (0.24-1.74) ×10(9)/L, accounting for 8.8% (4.9%-20.9%) . Before NK cell infusion, the number of patients with positive MRD in the treatment and control groups were 9/23 (39.1%) and 19/46 (41.3%) (χ(2)=0.030, P=0.862) respectively. After NK infusion, There was no significant difference in terms of MRD that went from negative to positive between the treatment and the control groups (14.3% vs 22.2%, χ(2)=0.037, P=0.847) . In the treatment group, 66.7% (6/9) of the MRD were converted from positive to negative, which was significantly higher than that in the control group (10.5%, 2/19) (χ(2)=6.811, P=0.009) . Morphological recurrence occurred in 1 case of MRD negative in the treatment group and 2 cases of MRD positive in the control group. By the end of follow-up, the median follow-up was 35 (10-59) months, the number of patients with morphological recurrence in the treatment group was 30.4% (7/23) , which was significantly lower than that in the control group (50.2%, 24/46) (χ(2)=2.929, P=0.087) , although there was no statistically significant difference between the two groups. There was no significant difference on MRD-negative between the treatment and the control groups (43.5% vs 43.5%, χ(2)=1.045, P=0.307) . The 3-year leukemia-free survival was better in the treatment group [ (65.1±11.1) %] than that in the control group [ (50.0±7.4) %] (P=0.047) . The 3-year overall survival in the treatment and control groups were (78.1±10.2) % and (65.8±8.0) % (P=0.212) , respectively. Conclusion: The consolidation of chemotherapy combined with allogeneic NK cell infusion contributed to the further remission of patients with LMR AML and the reduction of long-term recurrence.

SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies

Background

With the rapid increase in genome sequencing projects for non-model organisms, numerous genome assemblies are currently in progress or available as drafts, but not made available as satisfactory, usable genomes. Data quality assessment of genome assemblies is gaining importance not only for people who perform the assembly/re-assembly processes, but also for those who attempt to use assemblies as maps in downstream analyses. Recent studies of the quality control, quality evaluation/ assessment of genome assemblies have focused on either quality control of reads before assemblies or evaluation of the assemblies with respect to their contiguity and correctness. However, correctness assessment depends on a reference and is not applicable for de novo assembly projects. Hence, development of methods providing both post-assembly and pre-assembly quality assessment reports for examining the quality/correctness of de novo assemblies and the input reads is worth studying.

Results

We present SQUAT, an efficient tool for both pre-assembly and post-assembly quality assessment of de novo genome assemblies. The pre-assembly module of SQUAT computes quality statistics of reads and presents the analysis in a well-designed interface to visualize the distribution of high- and poor-quality reads in a portable HTML report. The post-assembly module of SQUAT provides read mapping analytics in an HTML format. We categorized reads into several groups including uniquely mapped reads, multiply mapped, unmapped reads; for uniquely mapped reads, we further categorized them into perfectly matched, with substitutions, containing clips, and the others. We carefully defined the poorly mapped (PM) reads into several groups to prevent the underestimation of unmapped reads; indeed, a high PM% would be a sign of a poor assembly that requires researchers’ attention for further examination or improvements before using the assembly. Finally, we evaluate SQUAT with six datasets, including the genome assemblies for eel, worm, mushroom, and three bacteria. The results show that SQUAT reports provide useful information with details for assessing the quality of assemblies and reads.

Availability

The SQUAT software with links to both its docker image and the on-line manual is freely available at https://github.com/luke831215/SQUAT.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5445-3) contains supplementary material, which is available to authorized users.

[The comparison of predicting clinical outcomes between immunolophenotype and hematological complete remission before human leukocyte antigen-matched sibling donor transplantation in acute myeloid leukemia]

目的

比较移植前免疫表型缓解（ICR）和血液形态学缓解对急性髓系白血病（AML）患者同胞HLA相合造血干细胞移植（MSDT）疗效的预测价值。

方法

回顾性分析182例接受MSDT的AML患者（除外急性早幼粒细胞白血病），将移植前血液形态学缓解分为血细胞恢复的完全缓解（CR）、血小板未恢复的CR（CRp）、血小板和中性粒细胞均未恢复的CR（CRi），将多参数流式细胞术检测微小残留病阴性定义为ICR。

结果

①全部182例AML患者中，男97例，女85例，中位年龄41（4~62）岁。②移植前CR、CRp+CRi率分别为80.8%（147/182）、19.2%（35/182）；移植前CRp+CRi组、CR组的预期4年累积复发率（CIR）[（11.0±4.3）%对（16.0±7.1）%，χ²=0.274，P=0.600]、非复发死亡率（NRM）[（14.0±4.3）%对（9.0±6.3）%，χ²=0.913，P=0.339]、无白血病生存（LFS）率[（75.0±5.1）%对（75.0±8.3）%，χ²=0.256，P=0.613]、总生存（OS）率[（77.0±5.2）%对（80.0±8.1）%，χ²=0.140，P=0.708]差异均无统计学意义。③移植前ICR组（147例）与非ICR组（35例）比较，4年CIR较低[（11.3±3.4）%对（55.2±8.8）%，χ²=32.687，P<0.001]，LFS率[（76.2±4.7）%对（32.8±8.7）%，χ²=26.234，P<0.001]和OS率[（79.0±4.7）%对（39.0±9.1）%，χ²=25.253，P<0.001]较高，NRM差异无统计学意义[（12.5±4.1）%对（12.0±7.1）%，χ²=1.002，P=0.656]。④多因素分析显示，移植前非ICR是影响AML患者MSDT后复发[HR=11.026（95% CI 4.685~25.949），P<0.001]、LFS[HR=5.785（95% CI 2.974~11.254），P< 0.001]和OS[HR=5.578（95%CI 2.575~27.565），P<0.001]的独立危险因素。

结论

移植前ICR对AML患者MSDT的疗效预测价值优于HCR。

Anti-cancer effects of 3,5-dimethylaminophenol in A549 lung cancer cells

Exposure to 3,5-dimethylaminophenol (3,5-DMAP), the metabolite of the 3-5-dimethylaniline, was shown to cause high levels of oxidative stress in different cells. The aim of the present work was to observe whether this metabolite can lead to cytotoxicity, oxidative stress, DNA damage and cell cycle changes in non-small cell lung cancer A549 cells. 3,5-DMAP caused a dose-dependent increase in cytotoxicity, generation of superoxide (O₂^-.), inductions in the enzyme activities orchestrating cellular antioxidant balance, increases in lipid peroxidation as well as DNA damage. However, 3,5-DMAP showed significantly lower cytotoxicity towards human lung fibroblast (HLF) cells. 3,5-DMAP also led to molecular events, like inducing apoptotic markers (ie. p53, Bad, Bax and cytochrome c); decreasing anti-apoptotic proteins (Bcl-2) and alterations in cell cycle. Our findings indicate that the cytotoxicity caused by this particular alkylaniline metabolite led to initiation of caspase 3-mediated apoptosis. Furthermore, 3,5-DMAP attenuated carcinogenic properties like migration capacity of A549 cells and eventually inhibited growth of A549 cells in an in vivo mouse model. Tumor sections showed that 3,5-DMAP down-regulated c-Myc expression but up-regulated p53 and cytochrome c, all of which might result in tumor growth arrest. Co-treatment with N-acetylcysteine provided reductions in cytotoxicity and positively modulated genetic events induced by 3,5-DMAP in A549 cells. In conclusion, our findings demonstrate 3,5-DMAP may be a potential anti-cancer drug in cancer, due to its self redox cycling properties.

Acute exposure to DEHP metabolite, MEHP cause genotoxicity, mutagenesis and carcinogenicity in mammalian Chinese hamster ovary cells

Di-(2-ethylhexyl) phthalate (DEHP), the common plasticizer used in the production of polyvinyl chloride, can be converted to the more potent metabolite mono-ethylhexyl phthalate (MEHP). Epidemiological studies have shown an association with elevated induction of rat hepatic cancer and reproductive toxicity in response to MEHP exposure. However, the mechanism of genotoxicity and carcinogenicity induced by MEHP treatment remains unclear. As a means to elucidate the mechanisms of action, lethality and mutagenicity in the adenine phosphoribosyltransferase (aprt+/-) gene induced in several CHO cell types by MEHP were assessed. Dose-response relationships were determined in the parental AA8 cell line, its nucleotide repair-deficient UV5 and base repair-deficient EM9 subclones, and also in AS52 cells harboring the bacterial guanine-hypoxanthine phosphoribosyltransferase (gpt) gene and its derived AS52-XPD-knockdown and AS52-PARP-1-knockdown cells. Treatment of AS52 with MEHP led to intracellular production of reactive oxygen species (ROS) and DNA strand breaks in a dose-dependent manner. Separately, mutations in the gpt gene of AS52 cells were characterized and found to be dominated by G:C to A:T and A:T to G:C transitions. Independent AS52-mutant cell (ASMC) clones were collected for the sequential in vivo xenograft tumorigenic studies, 4 of total 20 clones had aggressive tumor growth. Moreover, microarray analysis indicated miR-let-7a and miR-125b downregulated in ASMC, which might raise oncogenic MYC and RAS level and activate ErbB pathway. Comparative evaluation of the results indicates that the principal mechanism of this mutagenic action is probably to be through generation of ROS, causing base excision damage resulting in carcinogenicity.

SH2B1 modulates chromatin state and MyoD occupancy to enhance expressions of myogenic genes

As mesoderm-derived cell lineage commits to myogenesis, a spectrum of signaling molecules, including insulin growth factor (IGF), activate signaling pathways and ultimately instruct chromatin remodeling and the transcription of myogenic genes. MyoD is a key transcription factor during myogenesis. In this study, we have identified and characterized a novel myogenic regulator, SH2B1. Knocking down SH2B1 delays global chromatin condensation and decreases the formation of myotubes. SH2B1 interacts with histone H1 and is required for the removal of histone H1 from active transcription sites, allowing for the expressions of myogenic genes, IGF2 and MYOG. Chromatin immunoprecipitation assays suggest the requirement of SH2B1 for the induction of histone H3 lysine 4 trimethylation as well as the reduction of histone H3 lysine 9 trimethylation at the promoters and/or enhancers of IGF2 and MYOG genes during myogenesis. Furthermore, SH2B1 is required for the transcriptional activity of MyoD and MyoD occupancy at the enhancer/promoter regions of IGF2 and MYOG during myogenesis. Together, this study demonstrates that SH2B1 fine-tunes global-local chromatin states, expressions of myogenic genes and ultimately promotes myogenesis.

Long-term survival of patients undergoing liver resection for very large hepatocellular carcinomas

BACKGROUND

This study aimed to assess long-term survival after liver resection for huge hepatocellular carcinoma (HCC).

METHODS

Patients with stage I-III HCC who underwent hepatectomy from 2002 to 2010 were identified retrospectively from prospective national databases and followed until December 2012. Patients were assigned into four groups according to tumour size: less than 3·0 cm (small), 3·0-4·9 cm (medium), 5·0-10·0 cm (large) and over 10·0 cm (huge). The primary endpoint was overall survival. The Kaplan-Meier method and Cox proportional hazards model were used for survival analysis.

RESULTS

A total of 11 079 patients with HCC (mean(s.d.) age 59·7 (12·0) years) were eligible for this study. Median follow-up was 72·5 months. Patients with huge HCC had the worst prognosis; overall survival rates for patients with small, medium, large and huge HCC were 72·0, 62·1, 50·8 and 35·0 per cent respectively at 5 years, and 52·6, 41·8, 35·8 and less than 20·0 per cent at 10 years (P < 0·001). Multivariable analysis showed that tumour size affected long-term survival (hazard ratio (HR) 1·31, 1·55 and 2·38 for medium, large and huge HCC respectively versus small HCC). Prognostic factors for huge HCC were surgical margin larger than 0·2 cm (HR 0·70; P = 0·025), poor differentiation (HR 1·34; P = 0·004), multiple tumours (HR 1·64; P < 0·001), vascular invasion (HR 1·52; P = 0·008), cirrhosis (HR 1·37; P = 0·013) and the use of nucleoside analogues (HR 0·69; P = 0·004).

CONCLUSION

Huge HCCs have a worse prognosis than smaller HCCs after liver resection. A wide resection margin and antiviral therapy with nucleoside analogues may be associated with favourable long-term survival.

Exposure to High-Dose Diesel Exhaust Particles Induces Intracellular Oxidative Stress and Causes Endothelial Apoptosis in Cultured In Vitro Capillary Tube Cells

Previous studies suggest a direct correlation between exposure to diesel exhaust particles (DEP) and the onset of vascular permeability, presumably through the disruption of the adherens junctions. This would lead to deleterious effects on vasculature, such as acute myocardial infarction and atherosclerosis. Although the mechanism remains unclear, we demonstrate DEP-induced mitochondrial reactive oxygen species generation, which may be a central cause of the above vascular disorders. In vitro capillary-like HUVEC tube cells are used in this study and show that acute DEP exposure stimulates ATP depletion, followed by depolarization of their actin cytoskeleton, which sequentially inhibits PI3K/Akt activity and induces endothelial apoptosis. These events are accompanied by induction of p53/Mdm2 feedback regulation at 10 µg/mL DEP and produce 20 % cell apoptosis. Nevertheless, 100 µg/mL DEP augments tube cell apoptosis up to 70 % but disrupts the p53 negative regulator Mdm2. Addition of N-acetylcysteine provides substantial protection against the cytotoxic effects of DEP. In summary, exposure to a low dose of DEP actin triggers cytoskeleton depolarization, reduces PI3K/Akt activity, and induces a p53/Mdm2 feedback loop, and a high dose causes apoptosis by depleting Mdm2.

PotentIn VitroProtection Against PM2.5-Caused ROS Generation and Vascular Permeability by Long-Term Pretreatment withGanoderma tsugae

Epidemiological studies show increased particulate matter (PM[Formula: see text]) particles in ambient air are correlated with increased myocardial infarctions. Given the close association of capillaries and alveoli, the dysfunction is caused when inhaled PM[Formula: see text] particles come in close proximity to capillary endothelial cells. We previously suggested that the inhalation of PM[Formula: see text] diesel exhaust particles (DEP) induces oxidative stress and upregulates the Nrf2/HO-1 pathway, inducing vascular permeability factor VEGFA secretion, which results in cell-cell adherens junction disruption and PM[Formula: see text] transmigratation into circulation. Here, we minimized the level that PM[Formula: see text] traveled in the bloodstream by pre-supplementing with a traditional Chinese medicine (TCM) Ganoderma tsugae DMSO extract (GTDE) prior to PM[Formula: see text] exposure. Our results show that PM[Formula: see text] caused alterations in enzyme activities and cellular anti-oxidant balance. We found decreased glutathione levels, a reduced cellular redox ratio, increased ROS generation and cytotoxicity in the cellular fractions. The oxidative stress caused DNA damage and apoptosis, likely causing downstream molecular events that trigger vasculature permeabilization and, eventually, cardiovascular disorders. Our results show long-term GTDE treatment increased endogenous glutathione level, while PM[Formula: see text]-reduced glutathione levels and the cellular redox ratio. GTDE was protective against the genotoxic and apoptotic effects initiated by PM[Formula: see text] oxidative stress. Vascular permeability revealed that PM[Formula: see text] only accumulated on the surface of cells after GTDE treatment; no penetration was detected. After two weeks of GTDE treatment, VEGFA secretion was significantly reduced in human umbilical vein endothelial cells (HUVEC) and endothelial cell migration was blocked. Our results suggest GTDE prevents PM[Formula: see text] transmigration into the bloodstream, and the resultant dysfunction, by inhibiting oxidative stress production and endothelial permeability.

Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework

BACKGROUND

Recent progress in next-generation sequencing technology has afforded several improvements such as ultra-high throughput at low cost, very high read quality, and substantially increased sequencing depth. State-of-the-art high-throughput sequencers, such as the Illumina MiSeq system, can generate ~15 Gbp sequencing data per run, with >80% bases above Q30 and a sequencing depth of up to several 1000x for small genomes. Illumina HiSeq 2500 is capable of generating up to 1 Tbp per run, with >80% bases above Q30 and often >100x sequencing depth for large genomes. To speed up otherwise time-consuming genome assembly and/or to obtain a skeleton of the assembly quickly for scaffolding or progressive assembly, methods for noise removal and reduction of redundancy in the original data, with almost equal or better assembly results, are worth studying.

RESULTS

We developed two subset selection methods for single-end reads and a method for paired-end reads based on base quality scores and other read analytic tools using the MapReduce framework. We proposed two strategies to select reads: MinimalQ and ProductQ. MinimalQ selects reads with minimal base-quality above a threshold. ProductQ selects reads with probability of no incorrect base above a threshold. In the single-end experiments, we used Escherichia coli and Bacillus cereus datasets of MiSeq, Velvet assembler for genome assembly, and GAGE benchmark tools for result evaluation. In the paired-end experiments, we used the giant grouper (Epinephelus lanceolatus) dataset of HiSeq, ALLPATHS-LG genome assembler, and QUAST quality assessment tool for comparing genome assemblies of the original set and the subset. The results show that subset selection not only can speed up the genome assembly but also can produce substantially longer scaffolds.

AVAILABILITY

The software is freely available at https://github.com/moneycat/QReadSelector.

Tissue-specific control of midbody microtubule stability by Citron kinase through modulation of TUBB3 phosphorylation

Cytokinesis, the physical separation of daughter cells at the end of cell cycle, is commonly considered a highly stereotyped phenomenon. However, in some specialized cells this process may involve specific molecular events that are still largely unknown. In mammals, loss of Citron-kinase (CIT-K) leads to massive cytokinesis failure and apoptosis only in neuronal progenitors and in male germ cells, resulting in severe microcephaly and testicular hypoplasia, but the reasons for this specificity are unknown. In this report we show that CIT-K modulates the stability of midbody microtubules and that the expression of tubulin β-III (TUBB3) is crucial for this phenotype. We observed that TUBB3 is expressed in proliferating CNS progenitors, with a pattern correlating with the susceptibility to CIT-K loss. More importantly, depletion of TUBB3 in CIT-K-dependent cells makes them resistant to CIT-K loss, whereas TUBB3 overexpression increases their sensitivity to CIT-K knockdown. The loss of CIT-K leads to a strong decrease in the phosphorylation of S444 on TUBB3, a post-translational modification associated with microtubule stabilization. CIT-K may promote this event by interacting with TUBB3 and by recruiting at the midbody casein kinase-2α (CK2α) that has previously been reported to phosphorylate the S444 residue. Indeed, CK2α is lost from the midbody in CIT-K-depleted cells. Moreover, expression of the nonphosphorylatable TUBB3 mutant S444A induces cytokinesis failure, whereas expression of the phospho-mimetic mutant S444D rescues the cytokinesis failure induced by both CIT-K and CK2α loss. Altogether, our findings reveal that expression of relatively low levels of TUBB3 in mitotic cells can be detrimental for their cytokinesis and underscore the importance of CIT-K in counteracting this event.

SH2B1 orchestrates signaling events to filopodium formation during neurite outgrowth

Morphogenesis during development is fundamental to the differentiation of several cell types. As neurite outgrowth marks neuritogenesis, formation of filopodia precede the formation of dendrites and axons. While the structure of filopodia is well-known, the initiation of filopodia during neurite outgrowth is not clear. SH2B1 is known to promote neurite outgrowth of PC12 cells, hippocampal and cortical neurons. As a signaling adaptor protein, SH2B1 interacts with several neurotrophin receptors, and regulates signaling as well as gene expression. Our recent findings suggest that SH2B1 can be recruited to the plasma membrane and F-actin fractions by IRSp53. IRSp53 bends plasma membrane and facilitates actin bundling to set the stage for filopodium formation. We further demonstrate that SH2B1-IRSp53 complexes enhance the formation of filopodia, dendrites and dendritic branches of hippocampal and cortical neurons. While the molecular mechanism underlying filopodium initiation is not clear, we propose that SH2B1-neurotrophin interacting sites may mark the putative sites of filopodium initiation.

Protective Effects of N-Acetyl Cysteine against Diesel Exhaust Particles-Induced Intracellular ROS Generates Pro-Inflammatory Cytokines to Mediate the Vascular Permeability of Capillary-Like Endothelial Tubes

Exposure to diesel exhaust particles (DEP) is associated with pulmonary and cardiovascular diseases. Previous studies using in vitro endothelial tubes as a simplified model of capillaries have found that DEP-induced ROS increase vascular permeability with rearrangement or internalization of adherens junctional VE-cadherin away from the plasma membrane. This allows DEPs to penetrate into the cell and capillary lumen. In addition, pro-inflammatory cytokines are up-regulated and mediate vascular permeability in response to DEP. However, the mechanisms through which these DEP-induced pro-inflammatory cytokines increase vascular permeability remain unknown. Hence, we examined the ability of DEP to induce permeability of human umbilical vein endothelial cell tube cells to investigate these mechanisms. Furthermore, supplementation with NAC reduces ROS production following exposure to DEP. HUVEC tube cells contributed to a pro-inflammatory response to DEP-induced intracellular ROS generation. Endothelial oxidative stress induced the release of TNF-α and IL-6 from tube cells, subsequently stimulating the secretion of VEGF-A independent of HO-1. Our data suggests that DEP-induced intracellular ROS and release of the pro-inflammatory cytokines TNF- α and IL-6, which would contribute to VEGF-A secretion and disrupt cell-cell borders and increase vasculature permeability. Addition of NAC suppresses DEP-induced ROS efficiently and reduces subsequent damages by increasing endogenous glutathione.

Delayed Presentation of Catheter-related Subclavian Artery Pseudoaneurysm

Central venous catheterization is a common diagnostic and therapeutic procedure in modern clinical practice. Pseudoaneurysms of the subclavian artery are rare and usually occur immediately after the causative event, whether the cause was trauma or a medical procedure. Here, we report a case of a 71-year-old woman with delayed presentation of catheter-related subclavian pseudoaneurysm. The patient’s symptoms began two weeks after the initial catheterization, probably because of slow leakage of blood from the injured subclavian artery caused by incomplete compression of the puncture site and uremic coagulopathy. She was successfully treated with ultrasound-guided thrombin and angiography-guided histoacryl injection without stent insertion or surgery. Keywords: butyl 2-cyanacrylate; pseudoaneurysm; subclavian; thrombin.

Association between information provision and decisional conflict in cancer patients

BACKGROUND

In this study, we aimed to identify demographic and clinical variables that correlate with perceived information provision among cancer patients and determine the association of information provision with decisional conflict (DC).

PATIENTS AND METHODS

We enrolled a total of 625 patients with cancer from two Korean hospitals in 2012. We used the European Organization for Research and Treatment of Cancer (EORTC) quality-of-life questionnaire (QLQ-INFO26) to assess patients' perception of the information received from their doctors and the Decisional Conflict Scale (DCS) to assess DC. To identify predictive sociodemographic and clinical variables for adequate information provision, backward selective logistic regression analyses were conducted. In addition, adjusted multivariate logistic regression analyses were carried out to identify clinically meaningful differences of perceived level of information subscales associated with high DC.

RESULTS

More than half of patients with cancer showed insufficient satisfaction with medical information about disease (56%), treatment (73%), other services (83%), and global score (80%). In multiple logistic regression analyses, lower income and education, female, unmarried status, type of cancer with good prognosis, and early stage of treatment process were associated with patients' perception of inadequate information provision. In addition, Information about the medical tests with high DCS values clarity [adjusted odds ratio (aOR), 0.54; 95% confidence interval (CI) 0.30-0.97] and support (aOR, 0.53; 95% CI 0.33-0.85) showed negative significance. For inadequate information perception about treatments and other services, all 5 DCS scales (uncertainty, informed, values clarity, support, and effective decision) were negatively related. Global score of inadequate information provision also showed negative association with high DCS effective decision (aOR, 0.43; 95% CI 0.26-0.71) and DCS uncertainty (aOR, 0.46; 95% CI 0.27-0.77).

CONCLUSION

This study found that inadequate levels of perceived information correlated with several demographic and clinical characteristics. In addition, sufficient perceived information levels may be related to low levels of DC.

SH2B1 and IRSp53 proteins promote the formation of dendrites and dendritic branches

SH2B1 is an adaptor protein known to enhance neurite outgrowth. In this study, we provide evidence suggesting that the SH2B1 level is increased during in vitro culture of hippocampal neurons, and the β isoform (SH2B1β) is the predominant isoform. The fact that formation of filopodia is prerequisite for neurite initiation suggests that SH2B1 may regulate filopodium formation and thus neurite initiation. To investigate whether SH2B1 may regulate filopodium formation, the effect of SH2B1 and a membrane and actin regulator, IRSp53 (insulin receptor tyrosine kinase substrate p53), is investigated. Overexpressing both SH2B1β and IRSp53 significantly enhances filopodium formation, neurite outgrowth, and branching. Both in vivo and in vitro data show that SH2B1 interacts with IRSp53 in hippocampal neurons. This interaction depends on the N-terminal proline-rich domains of SH2B1. In addition, SH2B1 and IRSp53 co-localize at the plasma membrane, and their levels increase in the Triton X-100-insoluble fraction of developing neurons. These findings suggest that SH2B1-IRSp53 complexes promote the formation of filopodia, neurite initiation, and neuronal branching.

Angle-resolved photoemission spectroscopy of tetragonal CuO: evidence for intralayer coupling between cupratelike sublattices

We investigate by angle-resolved photoemission the electronic structure of in situ grown tetragonal CuO, a synthetic quasi-two-dimensional edge-sharing cuprate. We show that, in spite of the very different nature of the copper oxide layers, with twice as many Cu in the CuO layers of tetragonal CuO as compared to the CuO(2) layers of the high-T(c) cuprates, the low-energy electronic excitations are surprisingly similar, with a Zhang-Rice singlet dispersing on weakly coupled cupratelike sublattices. This system should thus be considered as a member of the high-T(c) cuprate family, with, however, interesting differences due to the intralayer coupling between the cupratelike sublattices.

Size tunable Ge quantum dots for near-ultraviolet to near-infrared photosensing with high figures of merit

We report a unique approach for the inclusion of size-tunable (7-50 nm), spherical Ge quantum dots (QDs) into gate stacks of metal-oxide-semiconductor (MOS) diodes, through selective oxidation of SiGe layers over the buffer layer of Si3N4 deposited over the Si substrate. In this complementary MOS (CMOS)-compatible approach, we successfully realized high performance nm scale Ge-QD MOS photodetectors with high figures of merit of low dark current density (1.5 × 10(-3) mA cm(-2)), superior photo-current-to-dark current ratio (13 500), high photoresponsivity (2.2 A W(-1)), and fast response time (5 ns), which are ready for direct integration with Si CMOS electronic circuits. Most importantly, the detection wavelength of the Ge QDs is tunable from near infrared to near ultraviolet by reducing the QD size from 50 to 7 nm as well as the optimal photoresponsivity is tailored by the Ge QD size and the effective thickness of gate dielectrics.

Reproductive biology of female bigeye tuna Thunnus obesus in the western Pacific Ocean

The reproductive biology of female bigeye tuna Thunnus obesus was assessed by examining 888 fish (ranging from 84·9 to 174·4 cm fork length, LF ) caught by Taiwanese offshore longliners in the western Pacific Ocean from November 1997 to November 1998 and November to December 1999 and 258 gonad samples from these fish. The overall sex ratio of the catch during the sampling differed significantly from 0·5, but males were predominant in sizes >140 cm LF . Reproductive activity (assessed by histology), a gonado-somatic index, and the size-frequency distributions of whole oocytes indicated that spawning occurred throughout the year and the major spawning season appeared to be from February to September. The estimated sizes at 50% maturity (LF50 ) of females was 102·85 cm (95% c.i.: 90·79-110·21 cm) and the smallest mature female was 99·7 cm LF . They are multiple spawners and oocytes develop asynchronously. The proportion of mature (0·63) and reproductively active (0·70) females with ovaries containing postovulatory follicles indicated that they spawn almost daily. Batch fecundity for 15 females with the most advanced oocytes (>730 µm) ranged from 0·84 to 8·56 million eggs (mean ± s.d. = 3·06 ± 2·09). The relationships between batch fecundity (FB , in millions of eggs) and LF (cm) and round mass (MR , kg) were FB=9·91×10-14LF6·38 (r(2)  = 0·84) and FB=8·89×10-4MR2·05 (r(2)  = 0·80), respectively. The parameters estimated in this study are key information for stock assessments of T. obesus in the western Pacific Ocean and will contribute to the conservation and sustainable yield of this species.

Tunable polaronic conduction in anatase TiO2

Oxygen vacancies created in anatase TiO(2) by UV photons (80-130 eV) provide an effective electron-doping mechanism and induce a hitherto unobserved dispersive metallic state. Angle resolved photoemission reveals that the quasiparticles are large polarons. These results indicate that anatase can be tuned from an insulator to a polaron gas to a weakly correlated metal as a function of doping and clarify the nature of conductivity in this material.

Needs regarding care and factors associated with unmet needs in disease-free survivors of surgically treated lung cancer

BACKGROUND

To evaluate the long-term needs of lung cancer survivors and to explore factors associated with unmet need.

PATIENTS AND METHODS

We recruited lung patients treated with curative surgery from 2001 through 2006 at two centers in Korea. Needs in the domains of information, supportive care, education and counseling, and socioeconomic support were measured. We selected the four most frequently reported items of unmet need among 19 items in four domains.

RESULTS

The most frequently reported unmet needs were Complementary and alternative medicine (CAM) and folk remedies (59.8%) in the Information domain, Counseling and treatment of depression and anxiety (63.5%) in the Supportive care domain, diet, exercise and weight control (55.1%) in the Education and counseling domain and Financial support (90.4%) in the socioeconomic support domain. Unmet needs for psychological treatment was significantly greater in participants who were employed (adjusted odds ratio [aOR], 2.25; 95% confidential interval [CI], 1.12 to 4.53). Unmet needs for diet, exercise and weight control were significantly greater in participants who had not received chemotherapy (aOR, 1.76; 95% CI, 1.09 to 2.85). Unmet need for financial support was greater in participants who were married (aOR, 4.14, 95%CI, 1.12 to 15.22) and those who had not received chemotherapy (aOR, 5.91, 95%CI, 1.91 to 18.31).

CONCLUSION

There were substantial unmet needs for information regarding psychological support, education for diet and exercise, and financial support among lung cancer survivors.

Characteristic dermoscopic features of primary cutaneous amyloidosis: a study of 35 cases

BACKGROUND

Primary cutaneous amyloidosis (PCA) is a relatively common skin disorder among Asians and South Americans. It is usually diagnosed clinically. However, for cases with atypical presentations, the diagnosis can be a challenge and skin biopsy may be necessary. Dermoscopy has been proved to be a valuable, noninvasive tool in the diagnosis of cutaneous pigmented diseases. Most lesions of PCA show hyperpigmentation and the major histopathological abnormalities of PCA occur in the epidermis and dermal papillae. Dermoscopy might be a powerful tool to provide valuable information for the diagnosis of PCA.

OBJECTIVES

We aimed to find characteristic dermoscopic features of PCA.

MATERIALS AND METHODS

Cases with typical clinical presentations of PCA, either macular or lichen subtypes, were included in this study. All were evaluated using a hand-held, polarized and nonpolarized dermoscope.

RESULTS

A total of 35 patients with clinically diagnosed PCA were enrolled. Eighteen patients had lesions consistent with macular amyloidosis and 17 with lichen amyloidosus. We found two major dermoscopic patterns characteristic of PCA. The most common dermoscopic finding of PCA was a central hub, which could be either white or brown, surrounded by various configurations of pigmentation. For cases of lichen amyloidosus with prominent hyperkeratosis, the central hub was replaced by a scar-like morphology.

CONCLUSIONS

This is the first study to report the characteristic dermoscopic features of PCA. We demonstrate that the use of a dermoscope may assist in achieving an accurate diagnosis of PCA.

A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework

Background

State-of-the-art high-throughput sequencers, e.g., the Illumina HiSeq series, generate sequencing reads that are longer than 150 bp up to a total of 600 Gbp of data per run. The high-throughput sequencers generate lengthier reads with greater sequencing depth than those generated by previous technologies. Two major challenges exist in using the high-throughput technology for de novo assembly of genomes. First, the amount of physical memory may be insufficient to store the data structure of the assembly algorithm, even for high-end multicore processors. Moreover, the graph-theoretical model used to capture intersection relationships of the reads may contain structural defects that are not well managed by existing assembly algorithms.

Results

We developed a distributed genome assembler based on string graphs and MapReduce framework, known as the CloudBrush. The assembler includes a novel edge-adjustment algorithm to detect structural defects by examining the neighboring reads of a specific read for sequencing errors and adjusting the edges of the string graph, if necessary. CloudBrush is evaluated against GAGE benchmarks to compare its assembly quality with the other assemblers. The results show that our assemblies have a moderate N50, a low misassembly rate of misjoins, and indels of > 5 bp. In addition, we have introduced two measures, known as precision and recall, to address the issues of faithfully aligned contigs to target genomes. Compared with the assembly tools used in the GAGE benchmarks, CloudBrush is shown to produce contigs with high precision and recall. We also verified the effectiveness of the edge-adjustment algorithm using simulated datasets and ran CloudBrush on a nematode dataset using a commercial cloud. CloudBrush assembler is available at https://github.com/ice91/CloudBrush.

The effects of fatigue on the torque-frequency curve of the human paralysed soleus muscle

An advanced understanding of the torque-generating properties of the chronically paralysed soleus muscle may be instrumental in developing improved methods to activate human paralysed muscle. We established the shape of the torque-frequency curve before and after fatigue of the human paralysed soleus muscle. After fatigue, the normalized torque-frequency curve was shifted to the right, suggesting a higher frequency was required to generate the same relative torque. Low frequency fatigue (LFF) consisting of reduced torques at low frequencies and normal torques at higher frequencies was demonstrated. Conversely, the acutely paralysed soleus muscle was found to be fatigue-resistant and showed no shift in the torque-frequency curve. The muscle activation history (potentiation), LFF, and changing contractile speeds may affect the torque-frequency curve after fatigue. These factors may also play an important role in the development of optimal methods to activate paralysed muscle to attenuate fatigue.

Giant ambipolar Rashba effect in the semiconductor BiTeI

We observe a giant spin-orbit splitting in the bulk and surface states of the noncentrosymmetric semiconductor BiTeI. We show that the Fermi level can be placed in the valence or in the conduction band by controlling the surface termination. In both cases, it intersects spin-polarized bands, in the corresponding surface depletion and accumulation layers. The momentum splitting of these bands is not affected by adsorbate-induced changes in the surface potential. These findings demonstrate that two properties crucial for enabling semiconductor-based spin electronics-a large, robust spin splitting and ambipolar conduction-are present in this material.

Complete genome sequence of Thauera aminoaromatica strain MZ1T

Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Sequencing Program CSP_776774.

Comparative proteomic analysis for the insoluble fractions of colorectal cancer patients

We used label-free quantitative proteomics with the insoluble fractions from colorectal cancer (CRC) patients to gain further insight into the utility of profiling altered protein expression as a potential biomarker for cancer. The insoluble fractions were prepared from paired tumor/normal biopsies from 13 patients diagnosed with CRC (stages I to IV). Fifty-six proteins identified in data pooled from the 13 cases were differentially expressed between the tumor and adjacent normal tissue. The connections between these proteins are involved in reciprocal networks related to tumorigenesis, cancer incidence based on genetic disorder, and skeletal and muscular disorders. To assess their potential utility as biomarkers, the relative expression levels of the proteins were validated using personal proteomics and a heat map to compare five individual CRC samples with five normal tissue samples. Further validation of a panel of proteins (KRT5, JUP, TUBB, and COL6A1) using western blotting confirmed the differential expression. These proteins gave specific network information for CRC, and yielded a panel of novel markers and potential targets for treatment. It is anticipated that the experimental approach described here will increase our understanding of the membrane environment in CRC, which may provide direction for making diagnoses and prognoses through molecular biomarker targeting.

Enhancing de novo transcriptome assembly by incorporating multiple overlap sizes

Background. The emergence of next-generation sequencing platform gives rise to a new generation of assembly algorithms. Compared with the Sanger sequencing data, the next-generation sequence data present shorter reads, higher coverage depth, and different error profiles. These features bring new challenging issues for de novo transcriptome assembly. Methodology. To explore the influence of these features on assembly algorithms, we studied the relationship between read overlap size, coverage depth, and error rate using simulated data. According to the relationship, we propose a de novo transcriptome assembly procedure, called Euler-mix, and demonstrate its performance on a real transcriptome dataset of mice. The simulation tool and evaluation tool are freely available as open source. Significance. Euler-mix is a straightforward pipeline; it focuses on dealing with the variation of coverage depth of short reads dataset. The experiment result showed that Euler-mix improves the performance of de novo transcriptome assembly.

Interplay between cell migration and neurite outgrowth determines SH2B1β-enhanced neurite regeneration of differentiated PC12 cells

The regulation of neurite outgrowth is crucial in developing strategies to promote neurite regeneration after nerve injury and in degenerative diseases. In this study, we demonstrate that overexpression of an adaptor/scaffolding protein SH2B1β promotes neurite re-growth of differentiated PC12 cells, an established neuronal model, using wound healing (scraping) assays. Cell migration and the subsequent remodeling are crucial determinants during neurite regeneration. We provide evidence suggesting that overexpressing SH2B1β enhances protein kinase C (PKC)-dependent cell migration and phosphatidylinositol 3-kinase (PI3K)-AKT-, mitogen activated protein kinase (MAPK)/extracellular signal-regulated protein kinase (ERK) kinase (MEK)-ERK-dependent neurite re-growth. Our results further reveal a cross-talk between pathways involving PKC and ERK1/2 in regulating neurite re-growth and cell migration. We conclude that temporal regulation of cell migration and neurite outgrowth by SH2B1β contributes to the enhanced regeneration of differentiated PC12 cells.