PeakNet: Bragg peak finding in X-ray crystallography experiments with U-Net

Serial crystallography at X-ray free electron laser (XFEL) sources has experienced tremendous progress in achieving high data rate in recent times. While this development offers potential to enable novel scientific investigations, such as imaging molecular events at logarithmic timescales, it also poses challenges in regards to real-time data analysis, which involves some degree of data reduction to only save those features or images pertaining to the science on disks. If data reduction is not effective, it could directly result in a substantial increase in facility budgetary requirements, or even hinder the utilization of ultra-high repetition imaging techniques making data analysis unwieldy. Furthermore, an additional challenge involves providing real-time feedback to users derived from real-time data analysis. In the context of serial crystallography, the initial and critical step in real-time data analysis is finding X-ray Bragg peaks from diffraction images. To tackle this challenge, we present PeakNet, a Bragg peak finder that utilizes neural networks and runs about four times faster than Psocake peak finder, while delivering significantly better indexing rates and comparable number of indexed events. We formulated the task of peak finding into a semantic segmentation problem, which is implemented as a classical U-Net architecture. A key advantage of PeakNet is its ability to scale linearly with respect to data volume, making it well-suited for real-time serial crystallography data analysis at high data rates

The Antiinfective Effects of Velvet Antler of Formosan Sambar Deer (Cervus unicolor swinhoei) on Staphylococcus aureus-Infected Mice

We assayed the effects of velvet antler (VA) of Formosan sambar deer (Cervus unicolor swinhoei) and its extracts on the anti-infective activity against pathogenic Staphylococcus aureus in vitro and in vivo in this study. In vitro data indicated that the VA extracts stimulated the proliferation of resting splenocytes and macrophages in a dose-dependent manner up to the highest concentration used (150 μg mL−1). The production of proinflammatory cytokines (TNF-α, IL-6, IL-12) by lipoteichoic acid was significantly suppressed after being cocultured with the VA extracts in a dose-dependent manner. Animal test in S. aureus-infected mice demonstrated that the numbers of bacteria determined in the kidneys and peritoneal lavage fluid of S. aureus-infected mice were significantly higher than those found in the same organs of mice pretreated with the VA samples. Moreover, the highly enhanced phagocytic activity of macrophages was further verified after in vitro treatment with the VA samples. The protective mechanisms of the VA samples might include an immune enhancer and an inflammatory cytokine suppressor

Comparison of visual outcomes after epiretinal membrane surgery

AbstractPurposeTo elucidate the anatomical and visual outcomes of patients with idiopathic epiretinal membranes (ERM) who underwent vitrectomy, membrane removal only, or with internal limiting membrane (ILM) peeling under the assistance of different dyes.MethodsA retrospective chart review of patients with idiopathic ERM who received surgical treatment between January 2004 and December 2009. The patients were grouped according to the usage of staining materials assisting ILM peeling. Group 1 consisted of 61 eyes that underwent conventional vitrectomy and ERM peeling without staining-assisted ILM peeling. Group 2 consisted of 20 eyes with triamcinolone acetonide-assisted ILM peeling following conventional vitrectomy. Group 3 consisted of 23 eyes with indocyanine green-assisted ILM peeling following conventional vitrectomy.ResultsThis study included 104 eyes from 104 patients. There was no significant difference in age, sex, preoperative visual acuity, retinal thickness or follow-up duration among the three groups. Overall, the mean best-corrected visual acuity improved significantly from baseline 0.15 to postoperative 0.41 (p<0.0001). Among the three groups, the mean logarithm minimum angle of resolution acuity markedly improved. There was no significant difference in postoperative visual acuity among groups. As measured by ocular coherent tomography, the mean central foveal thickness decreased from 465.21±86.18 to 299.16±70.14μm. Although there was no difference between groups, postoperative retinal thickness was thicker than that observed in the normal population. The incidence of recurrent ERM was 13.1% in Group 1 and 0% in Groups 2 and 3; this incidence was significantly higher than in the conventional surgery group. Visual outcome was statistically more deteriorated in recurrent cases than in non-recurrent cases (p=0.011).ConclusionsERM surgeries with or without dye-assisted ILM peeling showed similar results. Moreover, the incidence of recurrence is lower in the ILM peeling groups and plays a primary role in determining the final postoperative vision outcome

Phase 2 Study of Anti-Human Cytomegalovirus Monoclonal Antibodies for Prophylaxis in Hematopoietic Cell Transplantation.

Human cytomegalovirus (HCMV) can cause significant disease in immunocompromised patients, and treatment options are limited by toxicities. CSJ148 is a combination of two anti-HCMV human monoclonal antibodies (LJP538 and LJP539) that bind to and inhibit the functions of viral HCMV glycoprotein B (gB) and the pentameric complex, consisting of glycoproteins gH, gL, UL128, UL130, and UL131. In this phase 2, randomized, placebo-controlled trial, we evaluated the safety and efficacy of CSJ148 for prophylaxis of HCMV in patients undergoing allogeneic hematopoietic stem cell transplantation. As would be expected in the study population, all the patients (100%) reported at least one treatment-emergent adverse event. There were 22 deaths during this study, and over 80% of the patients receiving placebo or CSJ148 developed at least one adverse event of grade 3 or higher severity. No subject who received antibody developed a hypersensitivity- or infusion-related reaction. CSJ148-treated patients showed trends toward decreased viral load, shorter median duration of preemptive therapy, and fewer courses of preemptive therapy. However, the estimated probability that CSJ148 decreases the need for preemptive therapy compared to placebo was 69%, with a risk ratio of 0.89 and a 90% credible interval of 0.61 to 1.31. The primary efficacy endpoint was therefore not met, indicating that CSJ148 did not prevent clinically significant HCMV reactivation in recipients of allogeneic hematopoietic cell transplants. (This study has been registered at ClinicalTrials.gov under identifier NCT02268526 and at EudraCT under number 2017-002047-15.)

Current and state of the art on the electrophysiologic characteristics and catheter ablation of arrhythmogenic right ventricular dysplasia/cardiomyopathy

AbstractArrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is an inherited genetic disease caused by defective desmosomal proteins, and it has typical histopathological features characterized by predominantly progressive fibro-fatty infiltration of the right ventricle. Clinical presentations of ARVD/C vary from syncope, progressive heart failure (HF), ventricular tachyarrhythmias, and sudden cardiac death (SCD). The 2010 modified Task Force criteria were established to facilitate the recognition and diagnosis of ARVD/C. An implantable cardiac defibrillator (ICD) remains to be the cornerstone in prevention of SCD in patients fulfilling the diagnosis of definite ARVD/C, especially among ARVD/C patients with syncope, hemodynamically unstable ventricular tachycardia (VT), ventricular fibrillation, and aborted SCD. Further risk stratification is clinically valuable in the management of patients with borderline or possible ARVD/C and mutation carriers of family members. However, given the entity of heterogeneous penetrance and non-uniform phenotypes, the standardization of clinical practice guidelines for at-risk individuals will be the next frontier to breakthrough.Antiarrhythmic drugs are prescribed frequently to patients experiencing frequent ventricular tachyarrhythmias and/or appropriate ICD shocks. Amiodarone is the recommended drug of choice. Radiofrequency catheter ablation (RFCA) has been demonstrated to effectively eliminate the drug-refractory VT in patients with ARVD/C. However, the efficacy and clinical prognosis of RFCA via endocardial approach alone was disappointing prior to the era of epicardial approach. In recent years, it has been proven that the integration of endocardial and epicardial ablation by targeting the critical isthmus or eliminating abnormal electrograms within the diseased substrates could yield higher acute success and lower recurrence of ventricular tachyarrhythmias during long-term follow-up. Heart transplantation is the final option for patients with extensive disease, biventricular HF with uncontrollable hemodynamic compromise, and refractory ventricular tachyarrhythmias despite aggressive medical and ablation therapies

Invasive fungal infection among hematopoietic stem cell transplantation patients with mechanical ventilation in the intensive care unit

<p>Abstract</p> <p>Background</p> <p>Invasive fungal infection (IFI) is associated with high morbidity and high mortality in hematopoietic stem cell transplantation (HSCT) patientsThe purpose of this study was to assess the characteristics and outcomes of HSCT patients with IFIs who are undergoing MV at a single institution in Taiwan.</p> <p>Methods</p> <p>We performed an observational retrospective analysis of IFIs in HSCT patients undergoing mechanical ventilation (MV) in an intensive care unit (ICU) from the year 2000 to 2009. The characteristics of these HSCT patients and risk factors related to IFIs were evaluated. The status of discharge, length of ICU stay, date of death and cause of death were also recorded.</p> <p>Results</p> <p>There were 326 HSCT patients at the Linkou Chang-Gung Memorial Hospital (Taipei, Taiwan) during the study period. Sixty of these patients (18%) were transferred to the ICU and placed on mechanical ventilators. A total of 20 of these 60 patients (33%) had IFIs. Multivariate analysis indicated that independent risk factors for IFI were admission to an ICU more than 40 days after HSCT, graft versus host disease (GVHD), and high dose corticosteroid (<it>p </it>< 0.01 for all). The overall ICU mortality rate was 88% (53 of 60 patients), and was not significantly different for patients with IFIs (85%) and those without IFIs (90%, <it>p </it>= 0.676).</p> <p>Conclusion</p> <p>There was a high incidence of IFIs in HSCT patients requiring MV in the ICU in our study cohort. The independent risk factors for IFI are ICU admission more than 40 days after HSCT, GVHD, and use of high-dose corticosteroid.</p

Transforming Growth Factor-β1 Suppresses Hepatitis B Virus Replication by the Reduction of Hepatocyte Nuclear Factor-4α Expression

Several studies have demonstrated that cytokine-mediated noncytopathic suppression of hepatitis B virus (HBV) replication may provide an alternative therapeutic strategy for the treatment of chronic hepatitis B infection. In our previous study, we showed that transforming growth factor-beta1 (TGF-β1) could effectively suppress HBV replication at physiological concentrations. Here, we provide more evidence that TGF-β1 specifically diminishes HBV core promoter activity, which subsequently results in a reduction in the level of viral pregenomic RNA (pgRNA), core protein (HBc), nucleocapsid, and consequently suppresses HBV replication. The hepatocyte nuclear factor 4alpha (HNF-4α) binding element(s) within the HBV core promoter region was characterized to be responsive for the inhibitory effect of TGF-β1 on HBV regulation. Furthermore, we found that TGF-β1 treatment significantly repressed HNF-4α expression at both mRNA and protein levels. We demonstrated that RNAi-mediated depletion of HNF-4α was sufficient to reduce HBc synthesis as TGF-β1 did. Prevention of HNF-4α degradation by treating with proteasome inhibitor MG132 also prevented the inhibitory effect of TGF-β1. Finally, we confirmed that HBV replication could be rescued by ectopic expression of HNF-4α in TGF-β1-treated cells. Our data clarify the mechanism by which TGF-β1 suppresses HBV replication, primarily through modulating the expression of HNF-4α gene

Women with endometriosis have higher comorbidities: Analysis of domestic data in Taiwan

AbstractEndometriosis, defined by the presence of viable extrauterine endometrial glands and stroma, can grow or bleed cyclically, and possesses characteristics including a destructive, invasive, and metastatic nature. Since endometriosis may result in pelvic inflammation, adhesion, chronic pain, and infertility, and can progress to biologically malignant tumors, it is a long-term major health issue in women of reproductive age. In this review, we analyze the Taiwan domestic research addressing associations between endometriosis and other diseases. Concerning malignant tumors, we identified four studies on the links between endometriosis and ovarian cancer, one on breast cancer, two on endometrial cancer, one on colorectal cancer, and one on other malignancies, as well as one on associations between endometriosis and irritable bowel syndrome, one on links with migraine headache, three on links with pelvic inflammatory diseases, four on links with infertility, four on links with obesity, four on links with chronic liver disease, four on links with rheumatoid arthritis, four on links with chronic renal disease, five on links with diabetes mellitus, and five on links with cardiovascular diseases (hypertension, hyperlipidemia, etc.). The data available to date support that women with endometriosis might be at risk of some chronic illnesses and certain malignancies, although we consider the evidence for some comorbidities to be of low quality, for example, the association between colon cancer and adenomyosis/endometriosis. We still believe that the risk of comorbidity might be higher in women with endometriosis than that we supposed before. More research is needed to determine whether women with endometriosis are really at risk of these comorbidities