Polarization-diversified photonic comb filter with independently tunable free spectrum range

A polarization-diversified photonic comb filter with tunable free spectrum range (FSR) is proposed using two variable differential group delay (DGD) elements in a loop configuration. Two different cosine transfer functions could be simultaneously realized on orthogonal polarization states. Experimental demonstrations also verify feasibilities in various reconfigurable transfer functions.

Synthesis and antifungal activity of novel triazole compounds containing piperazine moiety

Design and synthesis of triazole library antifungal agents having piperazine side chains, analogues to fluconazole were documented. The synthesis highlighted utilization of the click chemistry on the basis of the active site of the cytochrome P450 14α-demethylase (CYP51). Their structures were characterized by ¹H-NMR, ¹³C-NMR, MS and IR. The influences of piperazine moiety on in vitro antifungal activities of all the target compounds were evaluated against eight human pathogenic fungi.

Cryptococcal meningitis in patients with autoimmune hemolytic anemia

To summarize the epidemiology, clinical features, treatment, and outcome of cryptococcal meningitis (CM) in autoimmune hemolytic anemia (AIHA) patients and to provide a reference for the prevention and control of AIHA complicated with CM, we evaluated five cases of CM in patients with AIHA treated in our hospital from 2003 to 2013 and eight related foreign cases. All of the clinical isolates were Cryptococcus neoformans var. grubii and grouped into the VNI genotype and serotype A. The clinical features exhibit significant features. Headache, nausea, and fever are common symptoms of AIHA complicated with CM. The early clinical manifestations lack specificity, which may lead to delayed diagnosis and treatment. Long-term use of prednisone (≥15 mg day(-1)), poor control of anemia, and splenectomy are risk factors for AIHA complicated with cryptococcal infection. The combination of intravenous amphotericin B and oral 5-fluorocytosine remains the preferred treatment for AIHA complicated with CM.

WinHAP2: an extremely fast haplotype phasing program for long genotype sequences

Background

The haplotype phasing problem tries to screen for phenotype associated genomic variations from millions of candidate data. Most of the current computer programs handle this problem with high requirements of computing power and memory. By replacing the computation-intensive step of constructing the maximum spanning tree with a heuristics of estimated initial haplotype, we released the WinHAP algorithm version 1.0, which outperforms the other algorithms in terms of both running speed and overall accuracy.

Results

This work further speeds up the WinHAP algorithm to version 2.0 (WinHAP2) by utilizing the divide-and-conquer strategy and the OpenMP parallel computing mode. WinHAP2 can phase 500 genotypes with 1,000,000 SNPs using just 12.8 MB in memory and 2.5 hours on a personal computer, whereas the other programs require unacceptable memory or running times. The parallel running mode further improves WinHAP2's running speed with several orders of magnitudes, compared with the other programs, including Beagle, SHAPEIT2 and 2SNP.

Conclusions

WinHAP2 is an extremely fast haplotype phasing program which can handle a large-scale genotyping study with any number of SNPs in the current literature and at least in the near future.

Detection and phylogenetic characterization of a case of Histoplasma capsulatum infection in mainland China

Histoplasmosis usually occurs in specific endemic areas. Sporadic cases have also been reported in mainland China. Here, we described an indigenous case of disseminated histoplasmosis. Phylogenetic analysis revealed that the Histoplasma capsulatum isolated in our case belongs to the Australian clade. Combined with previous studies, it revealed high genetic diversity among Chinese H. capsulatum isolates.

Gliotoxin promotes Aspergillus fumigatus internalization into type II human pneumocyte A549 cells by inducing host phospholipase D activation

The internalization of Aspergillus fumigatus into lung epithelial cells is critical for the infection process in the host. Gliotoxin is the most potent toxin produced by A. fumigatus. However, its role in A. fumigatus internalization into the lung epithelial cells is still largely unknown. In the present study, the deletion of the gliP gene regulating the production of gliotoxin in A. fumigatus suppressed the internalization of conidia into the A549 lung epithelial cells, and this suppression could be rescued by the exogenous addition of gliotoxin. At lower concentrations, gliotoxin enhanced the internalization of the conidia of A. fumigatus into A549 cells; in contrast, it inhibited the phagocytosis of J774 macrophages in a dose-dependent manner. Under a concentration of 100 ng/ml, gliotoxin had no effect on A549 cell viability but attenuated ROS production in a dose-dependent manner. Gliotoxin significantly stimulated the phospholipase D activity in the A549 cells at a concentration of 50 ng/ml. This stimulation was blocked by the pretreatment of host cells with PLD1- but not PLD2-specific inhibitor. Morphological cell changes induced by gliotoxin were observed in the A549 cells accompanying with obvious actin cytoskeleton rearrangement and a moderate alteration of phospholipase D distribution. Our data indicated that gliotoxin might be responsible for modulating the A. fumigatus internalization into epithelial cells through phospholipase D1 activation and actin cytoskeleton rearrangement.

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization

The metagenomic method directly sequences and analyses genome information from microbial communities. The main computational tasks for metagenomic analyses include taxonomical and functional structure analysis for all genomes in a microbial community (also referred to as a metagenomic sample). With the advancement of Next Generation Sequencing (NGS) techniques, the number of metagenomic samples and the data size for each sample are increasing rapidly. Current metagenomic analysis is both data- and computation- intensive, especially when there are many species in a metagenomic sample, and each has a large number of sequences. As such, metagenomic analyses require extensive computational power. The increasing analytical requirements further augment the challenges for computation analysis. In this work, we have proposed Parallel-META 2.0, a metagenomic analysis software package, to cope with such needs for efficient and fast analyses of taxonomical and functional structures for microbial communities. Parallel-META 2.0 is an extended and improved version of Parallel-META 1.0, which enhances the taxonomical analysis using multiple databases, improves computation efficiency by optimized parallel computing, and supports interactive visualization of results in multiple views. Furthermore, it enables functional analysis for metagenomic samples including short-reads assembly, gene prediction and functional annotation. Therefore, it could provide accurate taxonomical and functional analyses of the metagenomic samples in high-throughput manner and on large scale.

Up-regulation of miR-200b in biliary atresia patients accelerates proliferation and migration of hepatic stallate cells by activating PI3K/Akt signaling

An increasing body of evidence suggests that miRNAs are involved in fibrotic process of several organs including heart, lung and kidney. It has been observed recently that aberrant expression of miR-200s are associated with hepatic fibrosis. However, the role and underlying mechanism of miR-200s in hepatic fibrogenesis remains unknown. Here, we investigate the role of miR-200b in the activation of immortalized human hepatic stallate cells (HSCs), LX-2 cells. We firstly found that miR-200b significantly enhanced proliferation and migration of LX-2 cells. Secondly, our findings showed that miR-200b enhanced the phosphorylation of Akt, a downstream effector of phosphatidyl-inositol 3-Kinase (PI3K). FOG2, as the targets of fly miR-8 and human miR-200s, directly binds to p85α and inhibits the activation of the PI3K/Akt pathway. Here, we showed that FOG2 protein levels in LX-2 cells were suppressed significantly by miR-200b mimics. FOG2 knockdown by siRNAs activated the PI3K/Akt signaling, which increased cell growth and migration that mimicked the effect of miR-200b. Conversely, LY294002, a highly selective inhibitor of PI3K, could block phosphorylation of Akt and effect of miR-200b. In addition, we showed that miR-200b enhanced the expression of matrix metalloproteinase-2 (MMP-2), which may increase the migration of LX-2 cells. Finally, our results indicated that the expression of miR-200b was unregulated in the biliary atresia (BA) and associated with liver fibrotic progression. These data suggest a potential mechanism for Akt activation through FOG2 down-regulation by miR-200b that can lead to HSC growth and migration. In view of the putative pathogenic role of miR-200b in HSCs, miR-200b may constitute a potential marker for HSC activation and liver fibrosis progression.

Associations of clinical features and prognosis with age at disease onset in patients with systemic lupus erythematosus

The objective of this study is to evaluate the association of clinical features and prognosis with age at disease onset in patients with systemic lupus erythematosus (SLE) in a large, multicenter Chinese cohort. Medical records of 1898 SLE inpatients from 15 hospitals were reviewed and classified into three groups according to their ages at disease presentation. Categorical data were analyzed by chi-square test and potentially associated factors were tested by multinomial logistic regression. Among the patients studied, 259 (13.6%) were juvenile onset (≤18 years), 1444 (76.1%) were early onset (>18 and ≤45 years) and 195 (10.3%) were late onset (>45 years). Whenever manifestations occurred, most patients (>80%) were diagnosed within two years. Juvenile-onset patients were more likely to be untreated before admission ( p < 0.001) and have mucocutaneous manifestations ( p < 0.001), but musculoskeletal symptoms ( p < 0.05) and leukopenia ( p < 0.05) were less frequent, while comorbidities were much higher in patients with late-onset SLE ( p < 0.001). Neuropsychiatric, cardiopulmonary, renal and gastrointestinal involvement, disease activity index and damage scores were similar among three groups. Anti-Sm antibodies were less prevalent in late-onset patients ( p < 0.05) and antimalarial drugs were more often applied to juvenile-onset patients ( p < 0.001). As expected, mortality was elevated in the late-onset SLE group ( p < 0.05), in which nearly half died of infections, which was much higher than those in the other two groups ( p < 0.001). Logistic regression confirmed that patients with juvenile- and early-onset disease were associated with high incidence of being untreated prior to admission, and with low incidence of comorbidities as well as deaths caused by infection compared to patients with late-onset lupus. Interestingly, our data showed that more patients with late-onset disease had a SLEDAI score change of >7 at discharge. In conclusion, age at onset has an impact on SLE disease status, and infection is the main cause of death in those with late-onset lupus. Considering that the late-onset patients had simultaneously easily controllable diseases and high incidence of comorbidities, a different treatment strategy from younger patients should be considered.

Structure and function of mycobacterium glycopeptidolipids from comparative genomics perspective

Glycopeptidolipids (GPLs) attached to the outer surface of the greasy cell envelope, are a class of important glycolipids synthesized by several non-tuberculosis mycobacteria. The deletion or structure change of GPLs confers several phenotypical changes including colony morphology, hydrophobicity, aggregation, sliding motility, and biofilm formation. In addition, GPLs, particular serovar specific GPLs, are important immunomodulators. This review aims to summarize the advance on the structure, function and biosynthesis of mycobacterium GPLs.

Pulmonary fungus ball caused by Penicillium capsulatum in a patient with type 2 diabetes: a case report

Background

Following the recent transfer of all accepted species of Penicillium subgenus Biverticillium to Talaromyces (including Talaromyces marneffei, formerly Penicillium marneffei), Penicillium species are becoming increasingly rare causal agents of invasive infections. Herein, we present a report of a type 2 diabetes patient with a fungus ball in the respiratory tract caused by Penicillium capsulatum.

Case presentation

A 56-year-old Chinese female gardener with a 5-year history of type 2 diabetes presented at the Shanghai Changzheng Hospital with fever, a cough producing yellow-white sputum, and fatigue. The therapeutic effect of cefoxitin was poor. An HIV test was negative, but the β-D-glucan test was positive (459.3 pg/ml). Chest radiography revealed a cavitary lesion in the left upper lobe, and a CT scan showed globate cavities with a radiopaque, gravity-dependent ball. The histopathologic features of the tissue after haematoxylin-eosin staining showed septate hyphae. The fungus was isolated from the gravity-dependent ball and identified as Penicillium capsulatum based on the morphological analysis of microscopic and macroscopic features and on ribosomal internal transcribed spacer sequencing. After surgery, the patient was cured with a sequential treatment of fluconazole 400 mg per day for 90 days and caspofungin 70 mg per day for 14 days.

Conclusions

Although the prognosis is often satisfactory, clinicians, mycologists and epidemiologists should be aware of the possibility of infection by this uncommon fungal pathogen in diabetes patients, since it may cause severe invasive infections in immunocompromised hosts such as diabetes and AIDS patients.

Geographically structured populations of Cryptococcus neoformans Variety grubii in Asia correlate with HIV status and show a clonal population structure

Cryptococcosis is an important fungal disease in Asia with an estimated 140,000 new infections annually the majority of which occurs in patients suffering from HIV/AIDS. Cryptococcus neoformans variety grubii (serotype A) is the major causative agent of this disease. In the present study, multilocus sequence typing (MLST) using the ISHAM MLST consensus scheme for the C. neoformans/C. gattii species complex was used to analyse nucleotide polymorphisms among 476 isolates of this pathogen obtained from 8 Asian countries. Population genetic analysis showed that the Asian C. neoformans var. grubii population shows limited genetic diversity and demonstrates a largely clonal mode of reproduction when compared with the global MLST dataset. HIV-status, sequence types and geography were found to be confounded. However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates. Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

Intriguing arms race between phages and hosts and implications for better anti-infectives

Phages are viruses of bacteria. The interaction between phages and bacteria shall boost both parties' evolution. During the lengthy coevolution, the host has evolved multiple mechanisms against the phages. The phages also have evolved unique strategies to facilitate their own survival accordingly. This article summarizes the measures and countermeasures employed by the both parties and their implications for better biomedicines.

Magnetoplasmons in quasineutral epitaxial graphene nanoribbons

We present an infrared transmission spectroscopy study of the inter-Landau-level excitations in quasineutral epitaxial graphene nanoribbon arrays. We observed a substantial deviation in energy of the L(0(-1)) → L(1(0)) transition from the characteristic square root magnetic-field dependence of two-dimensional graphene. This deviation arises from the formation of an upper-hybrid mode between the Landau-level transition and the plasmon resonance. In the quantum regime, the hybrid mode exhibits a distinct dispersion relation, markedly different from that expected for conventional two-dimensional systems and highly doped graphene.

Feeding Artemisia annua alters digesta pH and muscle lipid oxidation products in broiler chickens

Because of growing consumer concern about the use of antimicrobials and the ban on most antibiotic feed additives in the European Union, there is increased interest in using alternatives to antimicrobials in poultry diets. Dried leaves of Artemisia annua have been used in Oriental medicine due to their antimicrobial activities. In the current study, the effect of including A. annua in broiler diets on hindgut and ceca pH, lipid oxidation products, and phenolic content of dark and white meat, and bird performance were investigated. A total of 96 broiler chicks were kept in 48 cages. Two cages with 2 birds per each cage are considered as 1 replicate, and there were 8 replications per treatment. The birds were fed corn-soy diets containing 0% (control), 2% (ART2), or 4% (ART4) dried A. annua leaves from d 14 through d 42. Cecal digesta pH was the lowest in birds fed the ART4 diet (P < 0.02), whereas the pH of ileal digesta was the lowest in ART2 (P < 0.01). Lipid oxidation products measured as TBA reactive substances (TBARS) were lower in the breast and thigh muscle of birds fed ART2 and ART4 diets compared with the control (P < 0.0001). No difference was found in total fat content of the liver, abdominal fat pads, or breast or thigh muscle content (P > 0.05). Artemisia annua addition did not affect final BW, weight gain, feed consumption, carcass weight, or feed:gain. No difference was observed in the relative weight of liver, abdominal fat, spleen, or heart tissue. Gastric acidity is protective against intestinal colonization and translocation of pathogenic bacteria. Therefore, gut pH and muscle tissue TBARS reduction in birds fed ART2 and ART4 suggest that A. annua may prove useful as a natural phytogenic feed additive with antioxidant potential that could be incorporated into poultry diets.

Photonic generation of phase-coded microwave signals with tunable carrier frequency

A photonic scheme to generate a phase-coded microwave signal with tunable carrier frequency based on a simple single-trip and two-pass structure is proposed. Facilitated by the fiber Bragg grating and phase modulator along the trip, both frequency doubling and signal phase coding could be achieved simultaneously. Phase-coded microwave signals at 20 and 22 GHz are experimentally generated.

Photonic arbitrary waveform generation based on crossed frequency to time mapping

Microwave photonic arbitrary waveform generation based on incoherent frequency-to-time-mapping (FTTM) accompanied by intersymbol interference, so called crossed FTTM (CFTTM). The pulse shape can be defined and tuned by properly adjusting the spectrum shaper (symbol shape) and the degree of intersymbol interference. UWB-, triangular-, rectangle-, comb- and user-defined pulse shapes are experimentally obtained.

Peripheral blood CD40-CD40L expression in human breast cancer

BACKGROUND

Breast cancer is the most common cancer in women. T cell-based immunotherapy for cancer has attracted much attention recently. CD40 and CD40L occupy an important position of specific immune response. In this paper, we want to study the role of co-stimulatory molecules CD40/CD40L and their clinical significance in peripheral blood of patients with breast cancer.

METHODS

Thirty breast cancer patients served as observation group, who were diagnosed as having infiltrating ductal breast cancer histopathologically, and 30 healthy as control group. Flow cytometric analysis was conducted to detect the expression of CD40 and CD40L on B and T lymphocytes in peripheral blood. The relationship between the CD40/CD40L expression levels and pathological grades was analyzed.

RESULTS

The expression levels of CD40/CD40L on B cells and T cells in breast cancer patients were significantly higher than those in the controls (all P < 0.001), and CD40/CD40L levels had a significant positive relationship with pathological grades (all P < 0.001).

CONCLUSIONS

The upregulated levels of co-stimulators CD40/CD40L on B cells and T cells may play an important role in the immune pathogenesis of breast cancer.

Successful sleeve lobectomy of inflammatory myofibroblastic tumor in a 4-year-old child

Primary pulmonary tumors in small children have remained a challenge for pediatric surgeons. Pneumonectomy and radical lobectomy are limitedly indicated due to surgical difficulties and sequelae. Here, we present our experience with a 4-year-old patient who suffered from an inflammatory myofibroblastic tumor. A left lower sleeve lobectomy was performed, and the patient recovered significantly after surgery. At the last follow-up, the child was growing well without any sequel, which supports our hypothesis that in small children, sleeve resection is the preferred treatment for tumors on the main stem bronchus and presents an alternative to an otherwise unavoidable pneumonectomy.

Autophagy during Mycobacterium tuberculosis infection and implications for future tuberculosis medications

Autophagy is a cellular homeostasis mechanism to eliminate unwanted or excessive organelles, or for the turnover of long-life cytosolic macromolecules. During Mycobacterium tuberculosis infection, autophagy represents not only an antimicrobial mechanism for the clearance of the intracellular pathogen, but also prevents excessive inflammation, avoiding the adverse effects on host. Here we focus on the anti-tuberculosis autophagy and signal pathways involved, and attempt to depict an integrative map of the interaction between autophagy and cytokine, ROS production, vitamin D, and inflammatory response. Novel autophagy-based therapy is also summarized. This integrative insight might add some novel thoughts for better tuberculosis medications.