CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

BACKGROUND

The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.

RESULTS

Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.

CONCLUSIONS

Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Traffic-related air pollution, chronic stress, and changes in exhaled nitric oxide and lung function among a panel of children with asthma living in an underresourced community

We examined associations between short-term exposure to traffic-related air pollutants (TRAP) and airway inflammation and lung function in children with asthma, and whether these associations are modified by chronic psychological stress. Residents of underresourced port-adjacent communities in New Jersey were concerned about the cumulative impacts of exposure to TRAP, particularly diesel-engine truck emissions, and stress on exacerbation of asthma among children. Children with asthma aged 9-14 (n = 35) were recruited from non-smoking households. We measured each participant's (1) continuous personal exposure to black carbon (BC, a surrogate of TRAP) at 1-min intervals, (2) 24-h integrated personal exposure to nitrogen dioxide (NO2), (3) daily fractional exhaled nitric oxide (FeNO), and (4) lung function for up to 30 consecutive days. Personal BC was recorded by micro-aethalometers. We measured daily FeNO using the NIOX MINO, forced expiratory volume in one second (FEV1), and forced vital capacity (FVC) using Easy One Frontline spirometers. Chronic stress was measured with the UCLA Life Stress Interview for Children. The association was examined using linear mixed-effect models. In the fully adjusted model, an interquartile range (IQR) increase in BC at lag 0-6 h before the FeNO measurement was associated with 8 % (95 % CI: 3 % - 12 %) increase in FeNO, whereas an IQR increase in BC at lag 7-12 h and lag 0-24 h were associated with 6 % (95 % CI: 2 % - 11 %) and 7 % (2 % - 12 %) FeNO increases, respectively. There were no significant lung function changes per IQR increase in BC. No interactions were observed between chronic stress and BC on FeNO. Chronic stress was negatively associated with individual average FeNO levels. Our findings suggest that higher levels of BC exposure within the prior 24 h increased airway inflammation levels in children with asthma, with the strongest effect observed within the first 6 h.

[MDT management of nonalcoholic fatty liver disease]

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the clinic and is closely associated with obesity and related metabolic diseases such as type 2 diabetes, cardiovascular and cerebrovascular diseases, and chronic renal disease. The clinical harm is becoming increasingly severe. Multidisciplinary diagnosis and treatment (MDT) management is an effective way to improve the efficiency of NAFLD prevention and treatment, but the specific implementation path remains to be explored. This article reviews the theoretical basis, implementation path, dilemmas, and challenges of MDT management for NAFLD patients in order to provide a reference for better NAFLD prevention and treatment.

[Comparison of the efficacy of thulium fiber laser and holmium laser lithotripsy in the treatment of upper urinary tract stones]

Objective: To compare the efficacy of thulium fiber laser (TFL) and holmium laser (HL) in the treatment of upper urinary tract stones. Methods: A total of 76 patients diagnosed with upper urinary tract stones by radiographic examination and who required ureteroscopy lithotripsy or retrograde intrarenal stone surgery were prospectively enrolled from the Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine between January 2022 and June 2022. Patients were divided into TFL group (n=38) and HL group (n=38) in a 1∶1 ratio according to the randomization schedule. The perioperative outcomes and stone-free rate of two groups were recorded and compared. Results: Finally, the clinical data of 71 patients were completely collected, including 55 males and 16 females, with a mean age of (45.7±14.1) years old. There were 36 patients in TFL group and 35 patients in HL group, and there was no significant difference in age, body mass index, gender, Charlson comorbidity index, stone site, stone location, stone size and stone density between two groups (all P>0.05). All the surgeries were successfully performed with no intraoperative complications. There were no significant differences between the two groups in terms of operation time, stone displacement during lithotripsy, visual field clarity, changes in hemoglobin, leukocyte, and C-reactive protein, and length of postoperative hospital stay (all P>0.05), but the laser action time[M (Q1,Q3)] in the TFL group was 30.0 (20.0, 48.8)s, which was significantly shorter than that in the HL group [90.0 (50.0, 120.0)s, P<0.001]. The stone-free rates of TFL group and HL group were 97.2% (35/36) and 88.6% (31/35), and there was no significant difference (P=0.337). The postoperative complication incidences of TFL group and HL group were 36.1% (13/36)and 22.9% (8/35), respectively, and the difference was not significant either (P=0.221). For ureter stones, the laser action time in TFL group was 22.5 (20.0, 43.8)s, which was significantly shorter than that in HL group [80.0 (50.0, 120.0)s, P<0.001]. For stones with maximum diameter≤10 mm, the laser action time in TFL group was 20.0 (10.0, 25.0)s, which was significantly shorter than that in HL group [50.0 (40.0, 80.0)s, P<0.001]. For stones with maximum diameter>10 mm, the laser action time in TFL group was 60.0(42.5, 180.0)s, which was significantly shorter than that in HL group [180.0(120.0, 210.0)s, P=0.035]. For stones with density≤1 000 CT, the laser action time in TFL group was 30.0 (20.0, 45.0)s, which was significantly shorter than that in HL group [95.0 (47.5, 120.0), P=0.001]. For stones with density>1 000 CT, the laser action time in TFL group was 30.0 (20.0, 90.0)s, which was significantly shorter than that in HL group [80.0 (55.0, 180.0)s, P=0.033]. Conclusion: TFL lithotripsy is an effective and safe surgical procedure for the treatment of upper urinary tract stones, with similar clinical efficacy but shorter laser action time compared to HL lithotripsy.

[Progress in the pharmacological treatment of tobacco dependence in special populations]

Schizophrenic and pregnant smokers with tobacco dependence had always been excluded from most large treatment trials for nicotine dependence. As weight gain was found to be common after smoking cessation, obese people were more likely to have a reduced willingness to quit smoking and an increased risk of relapse. This article reviewed the latest research progress in pharmacological treatment of tobacco dependence in schizophrenia, pregnant women, and obese people.

[Effects of tensile force on the vascular lumen formation in three-dimensional printed tissue]

Objective: To explore the effects of tensile force on vascular lumen formation in three-dimensional printed tissue. Methods: The experimental research method was used. Human umbilical vein endothelial cells (HUVECs) were extracted from discarded umbilical cord tissue of 3 healthy women (aged 22 to 35 years) who gave birth in the Department of Gynaecology and Obstetrics of Suzhou Ruihua Orthopaedic Hospital from September 2020 to May 2021. Human skin fibroblasts (HSFs) were extracted from discarded normal skin tissue of 10 male patients (aged 20 to 45 years) who underwent wound repair in the Department of Hand Surgery of Suzhou Ruihua Orthopaedic Hospital from September 2020 to September 2022. After identification of the two kinds of cells, the 4th to 6th passage of cells were taken for the follow-up experiments. HUVECs and HSFs were used as seed cells, and polycaprolactone, gelatin, hyaluronic acid, and fibrin were used as scaffold materials, and the three-dimensional printed vascularized tissue was created by three-dimensional bioprinting technology. The printed tissue with polycaprolactone scaffold of 6 and 10 mm spacing, and without polycaprolactone scaffold were set as 6 mm spacing polycaprolactone group, 10 mm spacing polycaprolactone group, and non-polycaprolactone group, respectively. After 4 days of culture, the printed tissue in 10 mm spacing polycaprolactone group was selected to detect the cell survival by cell viability detection kit, and the cell survival rate was calculated. After 14 days of culture, the printed tissue in three groups were taken, and the shape change of tissue was observed by naked eyes; immunofluorescence staining was performed to observe the arrangement of filamentous actin, and lumen diameter, total length, and number of branches of vessel in the tissue. The tissue with micro-spring structure in the above-mentioned three groups was designed, printed, and cultured for 9 days, and the tensile force applied in the printed tissue was measured according to the force-displacement curve. The number of samples was all 3 in the above experiments. Data were statistically analyzed with one-way analysis of variance and Tukey test. Results: After 4 days of culture, the cell survival rate in printed tissue in 10 mm spacing polycaprolactone group was (91.3±2.2)%. After 14 days of culture, the shape change of printed tissue in non-polycaprolactone group was not obvious, while the shape changes of printed tissue in 6 mm spacing polycaprolactone group and 10 mm spacing polycaprolactone group were obvious. After 14 days of culture, the arrangement of filamentous actin in the printed tissue in non-polycaprolactone group had no specific direction, while the arrangement of filamentous actin in the printed tissue in 6 mm spacing polycaprolactone group and 10 mm spacing polycaprolactone group had a specific direction. After 14 days of culture, The vascular lumen diameters of the printed tissue in 6 mm spacing polycaprolactone group and 10 mm spacing polycaprolactone group were (6.0±1.3) and (10.8±1.3) μm, respectively, which were significantly larger than 0 μm in non-polycaprolactone group (P<0.05), and the vascular lumen diameter of printed tissue in 10 mm spacing polycaprolactone group was significantly larger than that in 6 mm spacing polycaprolactone group (P<0.05); the total length and number of branches of blood vessel in the printed tissue in 6 mm spacing polycaprolactone group and 10 mm spacing polycaprolactone group were significantly shorter or less than those in non-polycaprolactone group (P<0.05), and the total length and number of branches of blood vessel in the printed tissue in 10 mm spacing polycaprolactone group were significantly shorter or less than those in 6 mm spacing polycaprolactone group. After 9 days of culture, the tensile forces applied in the printed tissue in 6 mm spacing polycaprolactone group and 10 mm spacing polycaprolactone group were (2 340±59) and (4 284±538) μN, respectively, which were significantly higher than 0 μN in non-polycaprolactone group (P<0.05), and the tensile force applied in the printed tissue in 10 mm spacing polycaprolactone group was significantly higher than that in 6 mm spacing polycaprolactone group (P<0.05). Conclusions: The three-dimensional printed scaffold structure can exert different tensile force in the printed tissue, and the vascular lumen diameter of the printed tissue can be regulated by adjusting the tensile force.

[A case of chronic refractory wound in the abdomen caused by residual foreign body]

A 59-year-old male patient with local sinus tract formation due to residual foreign body was admitted to the Second Affiliated Hospital of Zhejiang University College of Medicine on December 17, 2018. The examination showed that the residual foreign body was the component of a sticky cloth implanted when the patient underwent appendectomy 27 years ago. Hypertrophic scar developed at the right-lower abdominal incision for appendectomy 23 years ago and the secondary infection after cicatrectomy resulted in non-healing of the wound. The chronic refractory wound healed completely after surgical treatment in our hospital after this admission. The postoperative pathological examination revealed local inflammatory granuloma. This case suggests that chronic refractory wound is likely to form when secondary infection occurs following the surgical procedure near the implant, and aggressive surgery is an effective way to solve this problem.

Dual-energy CT perfusion imaging for differentiating invasive thymomas, thymic carcinomas, and lymphomas in adults

AIM

To evaluate the role of dual-energy computed tomography perfusion (DECTP) imaging in differentiating invasive thymomas (ITs), thymic cancers (TCs), and lymphomas in adults.

MATERIALS AND METHODS

Ninety-five patients with solid masses in the prevascular mediastinum who underwent DECTP examinations were enrolled in this study. The perfusion parameters (blood flow, BF; blood volume, BV; mean transit time, MTT; permeability surface, PS) and spectral parameters (water concentration, WC; iodine concentration, IC; normalised iodine concentration, NIC; the slope of spectral radiodensity [Hounsfield units] curve, λ_HU) of the lesions were analysed.

RESULTS

There were no differences in the MTT or WC values among ITs, TCs, and lymphomas (all p>0.05). The IC, NIC, and λ_HU values in the optimal arterial and venous phases and PS values of TCs were higher than those of ITs and lymphomas (all p<0.05), and there were no differences between ITs and lymphomas (all p>0.05). The BF and BV values of lymphomas were lower than those of ITs and TCs (all p<0.05), and there were no differences between ITs and TCs (all p>0.05). The cut-off values for BF and BV used to differentiate lymphomas from ITs and TCs were 42.83 ml/min/100 g and 4.66 ml/100 g, respectively (area under the receiver operating characteristic curve: 0.847 and 0.839; sensitivity, 80.6% and 82.1%; specificity, 75% and 71.4%; accuracy, 78.9% and 81.1%).

CONCLUSIONS

The perfusion and spectral parameters of DECTP imaging help to identify ITs, TCs, and lymphomas, and BF and BV values help to differentiate lymphomas from ITs and TCs.

The trend of environmental and clinical methicillin-resistant Staphylococcus aureus in a hospital in Taiwan: Impact of USA300

BACKGROUND

The environment may facilitate transmission of health care-associated methicillin-resistant Staphylococcus aureus (MRSA) and the pathogen is frequently shed by patients. However, the molecular characteristics and genetic relatedness between clinical and environmental MRSA isolates remain largely unclear in the clinical setting.

METHODS

A total of 100 hospitalized patients with MRSA infection and 25 hospitalized patients without MRSA infection were enrolled in a medical center, Taiwan in 2019. Environmental and clinical MRSA isolates were characterized by antibiotic susceptibility testing and molecular methods.

RESULTS

In the study, we detected 17 MRSA isolates in the environment that surrounded 15 MRSA-infected patients and one environmental MRSA isolate from one patient without MRSA infection. The molecular analysis revealed a high genetic diversity within either environmental or clinical MRSA isolates, while the USA300 clone (pulsotype AI, SCCmec IV, ST8, PVL-positive) accounts for 39% (7/18) of environmental and 33% (7/21) of clinical MRSA isolates. Moreover, 13 of the 15 MRSA-infected patients had identical paired clinical-environmental MRSA isolates, which exhibited indistinguishable genetic relatedness and highly similar antibiotic susceptibility phenotype, suggesting a possible transmission cycle of MRSA in the hospital.

CONCLUSIONS

The environmental MRSA was closely linked to MRSA isolated from patients, suggesting that the environment may act as a reservoir of MRSA. Besides, the USA300 MRSA has become a major clone in the hospital setting. An effective and rigorous approach to environmental cleaning and decontamination is suggested to eradicate MRSA in the hospital.

Near-GeV Electron Beams at a Few Per-Mille Level from a Laser Wakefield Accelerator via Density-Tailored Plasma

A simple, efficient scheme was developed to obtain near-gigaelectronvolt electron beams with energy spreads of few per-mille level in a single-stage laser wakefield accelerator. Longitudinal plasma density was tailored to control relativistic laser-beam evolution, resulting in injection, dechirping, and a quasi-phase-stable acceleration. With this scheme, electron beams with peak energies of 780-840 MeV, rms energy spreads of 2.4‰-4.1‰, charges of 8.5-23.6 pC, and rms divergences of 0.1-0.4 mrad were experimentally obtained. Quasi-three-dimensional particle-in-cell simulations agreed well with the experimental results. The dechirping strength was estimated to reach up to 11  TeV/mm/m, which is higher than previously obtained results. Such high-quality electron beams will boost the development of compact intense coherent radiation sources and x-ray free-electron lasers.

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses

Cryptococcus neoformans is an opportunistic fungal pathogen that at its peak epidemic levels caused an estimated million cases of cryptococcal meningitis per year worldwide. This species can grow in diverse environmental (trees, soil and bird excreta) and host niches (intracellular microenvironments of phagocytes and free-living in host tissues). The genetic basic for adaptation to these different conditions is not well characterized, as most experimental work has relied on a single reference strain of C. neoformans. To identify genes important for yeast infection and disease progression, we profiled the gene expression of seven C. neoformans isolates grown in five representative in vitro environmental and in vivo conditions. We characterized gene expression differences using RNA-Seq (RNA sequencing), comparing clinical and environmental isolates from two of the major lineages of this species, VNI and VNBI. These comparisons highlighted genes showing lineage-specific expression that are enriched in subtelomeric regions and in lineage-specific gene clusters. By contrast, we find few expression differences between clinical and environmental isolates from the same lineage. Gene expression specific to in vivo stages reflects available nutrients and stresses, with an increase in fungal metabolism within macrophages, and an induction of ribosomal and heat-shock gene expression within the subarachnoid space. This study provides the widest view to date of the transcriptome variation of C. neoformans across natural isolates, and provides insights into genes important for in vitro and in vivo growth stages.

[Teicoplanin-induced hypersensitivity syndrome in a diabetic foot patient with malignant ulcer]

A 58-year-old male patient with diabetic foot ulcer was admitted to the Second Affiliated Hospital of Zhejiang University School of Medicine on December 11, 2018. The patient was treated with local debridement, vacuum sealing drainage treatment, and dressing change and discharged after basic wound healing. On January 15, 2019, the patient was hospitalized again due to local infection and rupture of wound surface. He underwent a surgical debridement on the third day after second admission and was given intravenous infusion of 0.4 g teicoplanin twice daily. Histopathological examination after surgery showed keratinizing squamous-cell carcinoma. An extended squamous-cell carcinoma resection plus autologous split-thickness skin grafting and vacuum sealing drainage treatment was carried out on the 10th day after second admission. The patient's whole body turned red after surgery with rash, recurrent fever over 39 ℃, leucopenia, and thrombocytopenia. A multi-disciplinary consultation of physicians attributed these symptoms to teicoplanin-induced hypersensitivity syndrome. After withdrawal of teicoplanin and administration of hormone, the patient's temperature returned to normal, and the leucocyte count and platelet count recovered gradually. The patient was cured and discharged on the 49th day after second admission. The case presented reminds us of need to strictly follow the indications of teicoplanin prior to medication, be resolute to the administration and withdrawal, and be alert to adverse drug reactions when above-mentioned abnormalities occur, meanwhile, infection and rheumatic diseases are excluded.

Correction: Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype

[This corrects the article DOI: 10.1371/journal.ppat.1007945.].

[Research progress in saliva collection, analysis and its relationship with oral diseases]

As one of the major body fluid, saliva has various components that can shift according to the systemic health state. With the atraumatic way of collection, saliva can be a promising media to help the detection of oral diseases. With the development of salivaomics and the application of unbiased, highly sensitive, and high throughout separation techniques for salivary components, there's now more possibilities for effective identification of biomarkers correlated with oral diseases. This review aimed to introduce the current state of saliva collection and detection techniques as well as their correlation with oral diseases, hoping to provide evidence for further research.

[One case of severe subcutaneous soft tissue infection caused by nonstandard insulin injection]

On January 1st 2018, a male 44 years old diabetic patient with subcutaneous soft tissue infection in right thigh was admitted to our hospital. The patient repeatedly used the same needle to inject insulin subcutaneously in the unsterilized right thigh, and his blood glucose was badly controlled in the long term. Severe subcutaneous soft tissue infection of the right thigh occurred after his fatigue, accompanied with ketoacidosis. Then he received conservative treatment in the local hospital for one month, but the infection persisted. After being transferred to our hospital, we highly suspected the diagnosis of necrotizing fasciitis according to previous test indicators and local B-ultrasound results, but suggestion of aggressive surgery was refused. So we treated him with conservative therapies using sensitive antibiotics and supportive remedies. The patient was basically healed after treatment of 1 month and he was recovered well during the follow-up 2 months after discharged from our hospital. This case emphasizes the importance of standard injection of insulin and early diagnosis of severe subcutaneous soft tissue infection.

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype

Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce Cryptococcus neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy in C. neoformans. We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial mass increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC. Altogether, these data show that we were able to generate for the first time VBNC phenotype in C. neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.

Level Attraction Due to Dissipative Magnon-Photon Coupling

We report dissipative magnon-photon coupling caused by the cavity Lenz effect, where the magnons in a magnet induce a rf current in the cavity, leading to a cavity backaction that impedes the magnetization dynamics. This effect is revealed in our experiment as level attraction with a coalescence of hybridized magnon-photon modes, which is distinctly different from level repulsion with mode anticrossing caused by coherent magnon-photon coupling. We develop a method to control the interpolation of coherent and dissipative magnon-photon coupling, and observe a matching condition where the two effects cancel. Our work sheds light on the so-far hidden side of magnon-photon coupling, opening a new avenue for controlling and utilizing light-matter interactions.

Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans

The ability of the human fungal pathogen Cryptococcus neoformans to adapt to variable copper (Cu) environments within the host is key for successful dissemination and colonization. During pulmonary infection, host alveolar macrophages compartmentalize Cu into the phagosome and C. neoformans Cu-detoxifying metallothioneins, MT1 and MT2, are required for survival of the pathogen. In contrast, during brain colonization the C. neoformans Cu⁺ importers Ctr1 and Ctr4 are required for virulence. Central for the regulation and expression of both the Cu detoxifying MT1/2 and the Cu acquisition Ctr1/4 proteins is the Cu-metalloregulatory transcription factor Cuf1, an established C. neoformans virulence factor. Due to the importance of the distinct C. neoformans Cu homeostasis mechanisms during host colonization and virulence, and to the central role of Cuf1 in regulating Cu homeostasis, we performed a combination of RNA-Seq and ChIP-Seq experiments to identify differentially transcribed genes between conditions of high and low Cu. We demonstrate that the transcriptional regulation exerted by Cuf1 is intrinsically complex and that Cuf1 also functions as a transcriptional repressor. The Cu- and Cuf1-dependent regulon in C. neoformans reveals new adaptive mechanisms for Cu homeostasis in this pathogenic fungus and identifies potential new pathogen-specific targets for therapeutic intervention in fungal infections.

A rare oesophageal inflammatory myofibroblastic tumour treated by endoscopy

An inflammatory myofibroblastic tumour is a mesenchymal neoplasm that mostly involves the lung and rarely involves the oesophagus. Surgery has been most commonly used for the treatment of oesophageal inflammatory myofibroblastic tumours but there are no definite guidelines for their diagnosis and treatment. We describe the case of a 60-year-old woman presenting with dysphagia and poor appetite who was diagnosed with a submucosal oesophageal tumour by contrast enhanced computed tomography and ultrasonography endoscopy. She was treated successfully by endoscopic submucosal dissection with no complications. The final diagnosis was confirmed by pathological examination.

Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic fungal pathogen that causes approximately 625,000 deaths per year from nervous system infections. Here, we leveraged a unique, genetically diverse population of C. neoformans from sub-Saharan Africa, commonly isolated from mopane trees, to determine how selective pressures in the environment coincidentally adapted C. neoformans for human virulence. Genome sequencing and phylogenetic analysis of 387 isolates, representing the global VNI and African VNB lineages, highlighted a deep, nonrecombining split in VNB (herein, VNBI and VNBII). VNBII was enriched for clinical samples relative to VNBI, while phenotypic profiling of 183 isolates demonstrated that VNBI isolates were significantly more resistant to oxidative stress and more heavily melanized than VNBII isolates. Lack of melanization in both lineages was associated with loss-of-function mutations in the BZP4 transcription factor. A genome-wide association study across all VNB isolates revealed sequence differences between clinical and environmental isolates in virulence factors and stress response genes. Inositol transporters and catabolism genes, which process sugars present in plants and the human nervous system, were identified as targets of selection in all three lineages. Further phylogenetic and population genomic analyses revealed extensive loss of genetic diversity in VNBI, suggestive of a history of population bottlenecks, along with unique evolutionary trajectories for mating type loci. These data highlight the complex evolutionary interplay between adaptation to natural environments and opportunistic infections, and that selection on specific pathways may predispose isolates to human virulence.

Consensus Genome-Wide Expression Quantitative Trait Loci and Their Relationship with Human Complex Trait Disease

Most of the risk loci identified from genome-wide association (GWA) studies do not provide direct information on the biological basis of a disease or on the underlying mechanisms. Recent expression quantitative trait locus (eQTL) association studies have provided information on genetic factors associated with gene expression variation. These eQTLs might contribute to phenotype diversity and disease susceptibility, but interpretation is handicapped by low reproducibility of the expression results. To address this issue, we have generated a set of consensus eQTLs by integrating publicly available data for specific human populations and cell types. Overall, we find over 4000 genes that are involved in high-confidence eQTL relationships. To elucidate the role that eQTLs play in human common diseases, we matched the high-confidence eQTLs to a set of 335 disease risk loci identified from the Wellcome Trust Case Control Consortium GWA study and follow-up studies for 7 human complex trait diseases-bipolar disorder (BD), coronary artery disease (CAD), Crohn's disease (CD), hypertension (HT), rheumatoid arthritis (RA), type 1 diabetes (T1D), and type 2 diabetes (T2D). The results show that the data are consistent with ∼50% of these disease loci arising from an underlying expression change mechanism.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.

[Impact of daily mean temperature, cold spells, and heat waves on stroke mortality a multivariable Meta-analysis from 12 counties of Hubei province, China]

Objective: To assess the acute effects of daily mean temperature, cold spells, and heat waves on stroke mortality in 12 counties across Hubei province, China. Methods: Data related to daily mortality from stroke and meteorology in 12 counties across Hubei province during 2009-2012, were gathered. Distributed lag nonlinear model (DLNM) was first used, to estimate the county-specific associations between daily mean temperature, cold spells, heat waves and stroke mortality. Multivariate Meta-analysis was then applied to pool the community-specific relationships between temperature and stroke mortality (exposure-response relationship) as well as both cold- and- heat-associated risks on mortality at different lag days (lag-response relationship). Results: During 2009-2012, a total population of 6.7 million was included in this study with 42 739 persons died of stroke. An average of 2.7 (from 0.5 to 6.0) stroke deaths occurred daily in each county, with annual average mean temperature as 16.6 ℃ (from 14.7 ℃ to 17.4 ℃) during the study period. An inverse J-shaped association between temperature and stroke mortality was observed at the provincial level. Pooled mortality effect of cold spells showed a 2-3-day delay and lasted about 10 days, while effect of heat waves appeared acute but attenuated within a few days. The mortality risks on cold-spell days ranged from 0.968 to 1.523 in 12 counties at lag 3-14, with pooled effect as 1.180 (95%CI:1.043-1.336). The pooled mortality risk (ranged from 0.675 to 2.066) on heat-wave days at lag 0-2 was 1.114 (95%CI: 1.012-1.227). Conclusions: An inverse J-shaped association between temperature and stroke mortality was observed in Hubei province, China. Both cold spells and heat waves were associated with increased stroke mortality, while different lag patterns were observed in the mortality effects of heat waves and cold spells.

[Research advances in diagnosis of non-alcoholic fatty liver disease]

Non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in clinical practice, and the spectrum of NAFLD includes nonalcoholic simple fatty liver, nonalcoholic steatohepatitis, and liver cirrhosis. Some patients may even progress to hepatocellular carcinoma. At present, the gold standard for the diagnosis of NAFLD is liver biopsy, but since this is an invasive examination and has high costs, its application is limited in clinical practice. More and more studies have focused on noninvasive diagnostic methods for NAFLD, including serological markers, fatty liver predictive model, and imaging examinations. Emerging diagnostic techniques, including genomics, proteomics, glycomics, and metabolomics, also play an important role in the diagnosis of NAFLD.

[Acute effect of daily mean temperature on ischemic heart disease mortality: a multivariable meta-analysis from 12 counties across Hubei Province, China]

Objective: To evaluate the acute effects of daily mean temperature on ischemic heart disease (IHD) mortality in 12 counties across Hubei Province, China. Methods: We obtained the daily IHD mortality data and meteorological data of the 12 counties for 2009-2012. The distributed lag nonlinear model (DLNM) was used to estimate the community-specific association between mean temperature and IHD mortality. A multivariate meta-analysis was then applied to pool the community-specific relationship between temperature and IHD mortality, and the effects of cold and heat on mortality risk. Results: In 2009-2012, of the 6 702 012 people included in this study, 19 688 died of IHD. A daily average of 1.2 IHD deaths occurred in each community. The annual average mean temperature was 16.6 ℃ during the study period. A nonlinear temperature-IHD mortality relationship was observed for different cumulative lag days at the provincial level. The pooled heat effect was acute but attenuated within 2 days. In contrast, the cold effect was delayed and persisted for more than 2 weeks. Compared with a reference temperature (25^th percentile of mean temperature during the study period, P₂₅), the cold effect for P₁₀ of mean temperature was associated with IHD mortality, the RR(95% CI) was 1.084 (1.008-1.167) at lag 0-14, and 1.149 (1.053-1.253) at lag 0-21. For the P₁ cold temperature, the mortality RR (95% CI) values were 1.116 (0.975-1.276) and 1.220 (1.04-1.428), respectively. We found no significant association between high temperatures and IHD mortality in the present study at different lag days. Conclusion: In Hubei Province, low temperature was associated with increased IHD mortality risk, and cold effects lasted for several days; no significant effect of high temperature was observed.

LECT2 association with macrophage-mediated killing of Helicobacter pylori by activating NF-κB and nitric oxide production

Helicobacter pylori employs unique methods to colonize the stomach, which induces chronic inflammation. It is also able to avoid eradication by macrophages and other immune cells. Leukocyte cell-derived chemotaxin 2 (LECT2), a multi-functional cytokine involved in many pathological conditions, has recently been shown to activate macrophages via the CD209a receptor. Therefore, we aimed to investigate the effects of LECT2 on H. pylori-infected macrophages. Macrophages were treated with recombinant LECT2, and both their ability to kill H. pylori and produce nitric oxide were analyzed. Western blot was performed to determine nuclear translocation and protein phosphorylation of p65, a subunit of nuclear factor (NF)-κB. Transfection experiments were performed to analyze the signaling pathway of LECT2 in macrophages. We found that treatment with LECT2 enhanced H. pylori killing and nitric oxide production in macrophages. In addition, DNA-binding activity and nuclear translocation of p65 were up-regulated by LECT2 treatment. Furthermore, we found that NF-κB activation by LECT2 was mediated by Raf-1 in macrophages, and Raf-1 phosphorylation was specifically altered in response to LECT2. Moreover, LECT2 induced Ser28 phosphorylation in the intracellular domain of CD209a. CD209a Ser28 phosphorylation was required for LECT2-induced Raf-1 and NF-κB activation in RAW264.7 macrophages. Our study showed that the effects of LECT2 on H. pylori killing and nitric oxide production were dependent on CD209a phosphorylation, Raf-1, and NF-κB activation. Together, these results demonstrate for the first time that exposure to LECT2 can modulate specific intracellular mechanisms downstream of CD209a to enhance H. pylori killing and nitric oxide production in macrophages.

High-Brightness High-Energy Electron Beams from a Laser Wakefield Accelerator via Energy Chirp Control

By designing a structured gas density profile between the dual-stage gas jets to manipulate electron seeding and energy chirp reversal for compressing the energy spread, we have experimentally produced high-brightness high-energy electron beams from a cascaded laser wakefield accelerator with peak energies in the range of 200-600 MeV, 0.4%-1.2% rms energy spread, 10-80 pC charge, and ∼0.2  mrad rms divergence. The maximum six-dimensional brightness B_{6D,n} is estimated as ∼6.5×10^{15}  A/m^{2}/0.1%, which is very close to the typical brightness of e beams from state-of-the-art linac drivers. These high-brightness high-energy e beams may lead to the realization of compact monoenergetic gamma-ray and intense coherent x-ray radiation sources.

Long-term exposure of K562 cells to benzene metabolites inhibited erythroid differentiation and elevated methylation in erythroid specific genes

Benzene is a common occupational hazard and a widespread environmental pollutant. Previous studies have revealed that 72 h exposure to benzene metabolites inhibited hemin-induced erythroid differentiation of K562 cells accompanied with elevated methylation in erythroid specific genes. However, little is known about the effects of long-term and low-dose benzene metabolite exposure. In this study, to elucidate the effects of long-term benzene metabolite exposure on erythroid differentiation, K562 cells were treated with low-concentration phenol, hydroquinone and 1,2,4-benzenetriol for at least 3 weeks. After exposure of K562 cells to benzene metabolites, hemin-induced hemoglobin synthesis declined in a concentration- and time-dependent manner, and the hemin-induced expressions of α-, β- and γ-globin genes and heme synthesis enzyme porphobilinogen deaminase were significantly suppressed. Furthermore, when K562 cells were continuously cultured without benzene metabolites for another 20 days after exposure to benzene metabolites for 4 weeks, the decreased erythroid differentiation capabilities still remained stable in hydroquinone- and 1,2,4-benzenetriol-exposed cells, but showed a slow increase in phenol-exposed K562 cells. In addition, methyltransferase inhibitor 5-aza-2'-deoxycytidine significantly blocked benzene metabolites inhibiting hemoglobin synthesis and expression of erythroid genes. Quantitative MassARRAY methylation analysis also confirmed that the exposure to benzene metabolites increased DNA methylation levels at several CpG sites in several erythroid-specific genes and their far-upstream regulatory elements. These results demonstrated that long-term and low-dose exposure to benzene metabolites inhibited the hemin-induced erythroid differentiation of K562 cells, in which DNA methylation played a role through the suppression of erythroid specific genes.

[Investigation and analysis for impact factors of distress in patients with first diagnosed lung cancer]

OBJECTIVE

To study the impact factors of psychological distress in patients with first diagnosed lung cancer.

METHODS

The cross-sectional study was applied to newly diagnosed lung cancer patients who received treatments in Cancer Center of West China Hospital of Sichuan University in Chengdu from June 2013 to March 2015 by distributed questionnaires. The general information of the patients, the hospital anxiety and depression scale (HADS) and distress management screening measure (DMSM) were included in the questionnaire to evaluate the states of distress, pain and the factors related to the distress of the patients.

RESULTS

The survey investigated a total of 390 patients with first diagnosed lung cancer, including 291 male patients and 99 female patients. The proportion of the patients with positive anxiety symptom was 26.7% (104/390), with positive depression symptom was 27.7% (108/390), and with positive distress symptom was 30.0% (117/390). On the top five problem list of DMSM were worry, disease treatment, breathing, pain and sleep. The Spearman correlation analysis showed that anxiety score, depression score, and the pain intensity were positively correlated with the distress. Multiple linear regression analysis showed that gender (β=-0.209, P=0.003), age (β=-0.098, P=0.042), chronic disease (β=0.378, P<0.001), and pain score (β=0.100, P=0.029) could affect the distress of the patients. Smoking (β=0.111, P=0.041) could affect the anxiety of newly diagnosed lung cancer patients.

CONCLUSION

The gender, age, chronic disease and pain score of the patients are the independent factors of the psychological distress of first diagnosed lung cancer patients. Smoking is the predictive factors of the patients with anxiety. Controlling the pain intensity and the clinical process of chronic disease of the patients actively, solving the sleep and breathing problem and helping the patients to quit smoking progressively could alleviate the psychological distress of the patients.

Meta-Prediction of MTHFR Gene Polymorphism Mutations and Associated Risk for Colorectal Cancer

The methylenetetrahydrofolate reductase (MTHFR) gene is one of the most investigated of the genes associated with chronic human diseases because of its associations with hyperhomocysteinemia and toxicity. It has been proposed as a prototype gene for the prevention of colorectal cancer (CRC). The major objectives of this meta-analysis were to examine the polymorphism-mutation patterns of MTHFR and their associations with risk for CRC as well as potential contributing factors for mutations and disease risks. This analysis included 33,626 CRC cases and 48,688 controls across 92 studies for MTHFR 677 and 16,367 cases and 24,874 controls across 54 studies for MTHFR 1298, comprising data for various racial and ethnic groups, both genders, and multiple cancer sites. MTHFR 677 homozygous TT genotype was protective (p < .05) for CRC for all included populations; however, with heterogeneity across various racial–ethnic groups and opposing findings, it was a risk genotype for the subgroup of Hispanics (p < .01). Additional countries for which subgroup analyses resulted in 677 TT as a risk genotype included Turkey, Romania, Croatia, Hungary, Portugal, Mexico, Brazil, U.S. Hawai’i, Taiwan, India, and Egypt. Countries with the highest mutation rates and risks for both MTHFR 677 and 1298 genotypes are presented using global maps to visualize the grouping patterns. Meta-predictive analyses revealed that air pollution levels were associated with gene polymorphisms for both genotypes. Future nursing research should be conducted to develop proactive measures to protect populations in cities where air pollution causes more deaths.

Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease

BACKGROUND

There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, there must be some molecular level mechanism relevant to the disease. What are these mechanisms and how do they contribute to disease?

RESULTS

Here we consider the roles of three primary mechanism classes: changes that directly alter protein function (missense SNPs), changes that alter transcript abundance as a consequence of variants close-by in sequence, and changes that affect splicing. Missense SNPs are divided into those predicted to have a high impact on in vivo protein function, and those with a low impact. Splicing is divided into SNPs with a direct impact on splice sites, and those with a predicted effect on auxiliary splicing signals. The analysis was based on associations found for seven complex trait diseases in the classic Wellcome Trust Case Control Consortium (WTCCC1) GWA study and subsequent studies and meta-analyses, collected from the GWAS catalog. Linkage disequilibrium information was used to identify possible candidate SNPs for involvement in disease mechanism in each of the 356 loci associated with these seven diseases. With the parameters used, we find that 76% of loci have at least of these mechanisms. Overall, except for the low incidence of direct impact on splice sites, the mechanisms are found at similar frequencies, with changes in transcript abundance the most common. But the distribution of mechanisms over diseases varies markedly, as does the fraction of loci with assigned mechanisms. Many of the implicated proteins have previously been suggested as relevant, but the specific mechanism assignments are new. In addition, a number of new disease relevant proteins are proposed.

CONCLUSIONS

The high fraction of GWAS loci with proposed mechanisms suggests that these classes of mechanism play a major role. Other mechanism types, such as variants affecting expression of genes remote in the DNA sequence, will contribute in other loci. Each of the identified putative mechanisms provides a hypothesis for further investigation.

Suitable calcineurin inhibitor concentrations for liver transplant recipients in the Chinese population

AIM

The aim was to deduce suitable calcineurin inhibitor concentrations for the Chinese liver transplantation population.

METHODS

We retrospectively studied 97 liver transplant recipients who displayed stable liver and renal function. No grafts were obtained from prisoners, procurements were performed with donor consent conforming to international ethics regulations. At 3, 6, and 12 months, we increased the concentrations and doses of calcineurin inhibitors as well as the values of alanine transaminase and serum creatinine.

RESULTS

Twenty-eight recipients received cyclosporine and 69 tacrolimus. The mean cyclosporine daily dosages were 203 ± 62 mg at 3, 188 ± 55 mg at 6, and 173 ± 52 mg at 12 months, the tacrolimus daily dosages were 3.08 ± 0.98, 2.82 ± 0.98, and 2.58 ± 0.93 mg, respectively. The corresponding mean cyclosporine peak concentrations (C(2)) were 806 ± 322 ng/mL, 681 ± 206 ng/mL, and 644 ± 190 ng/mL and the mean tacrolimus trought concentrations (C(0)) 6.61 ± 3.02 ng/mL, 5.85 ± 2.44 ng/mL, and 5.22 ± 2.33 ng/mL, respectively. In both groups, transaminases and serum creatinine were stable over time.

CONCLUSIONS

An individualized immunosuppressive regimen for the local population is necessary. We delayed calcineurin inhibitors with subsequent low-dose mycophenolate mofetil plus minimized calcineurin inhibitors, which seemed to be nephroprotective and safe for Chinese liver transplantation patients.

First Report of Root and Basal Rot of Angelica acutiloba Caused by Fusarium solani in Taiwan

Angelica (Angelica acutiloba (Siebold. & Zucc.) Kitag.) is one of the most important traditional Chinese medicines in Taiwan. The medicinal herb has been mainly imported from China, but cultivation at a commercial scale has also been established in recent years in Hualien County, Taiwan. In September 2008, angelica plants in a field at Liou-shih-dan Mountain displayed symptoms of yellowing, stunting, rotting of roots and basal stem, and wilting. A severe brown discoloration of vascular tissue along the stems of infected plants was observed. One or more Fusarium spp. was consistently isolated from the roots and stems of diseased plants. Isolates R3, R4, and R5 were incubated for 14 days on celery tissues to produce chlamydospores, and 33 g of celery tissue with chlamydospores were mixed with 500 ml of soil per pot as inoculum. One 4-month-old angelica seedling was planted per pot. Three angelica plants were inoculated with each isolate in the first test and nine plants were inoculated with each isolate in the second test. Other seedlings were inoculated with water as checks. Pathogenicity tests were conducted twice. Incidence of diseased plants was 66, 100, and 33% in the first test, and 66, 100, and 44% in the second test for the R3, R4, and R5 isolates, respectively. Symptoms similar to those on the diseased plants in the field were produced, with leaves turning yellow starting 7 days after inoculation and wilt and discoloration of roots 14 days after inoculation. Fusarium spp. also were reisolated from the diseased plants. Genomic DNA was extracted from mycelium with a fungal genomic DNA purification kit, and the internal transcribed spacer (ITS) rDNA region was amplified and sequenced with primers ITS-4 and ITS-5. The sequence of the resulting ~550-bp amplicon was compared with those in GenBank. The ITS sequences of the R3, R4, and R5 isolates shared 98.7, 98.7, and 97.9% similarity with F. solani isolate AF129104 (3), respectively. Phylogenetic analysis also showed that the three isolates were closer to F. solani than to other Fusarium species. Both macroconidia and microconidia of the R4 isolate were produced on potato dextrose agar. Macroconidia were three to five septate and 27.2 to 37.8 × 4.4 to 6.2 μm; microconidia were zero to one septate and 9.3 to 14.7 × 2.9 to 4.8 μm. Chlamydospores produced on celery juice agar were terminal or intercalary, solitary, in pairs or in chains, and 9.3 to 12.1 μm. Morphological characteristics identified the three isolates as F. solani (Martius) Snyder & Hansen according to Fu and Chang (2) and Chung et al. (1), which agrees with the ITS comparison. To our knowledge, this is the first report of root and basal rot caused by F. solani on angelica in Taiwan. References: (1) W. C. Chung et al. Plant Prot. Bull. 40:177, 1998. (2) C. H. Fu and T. T. Chang. Taiwan J. For. Sci. 14:223, 1999. (3) H. Suga et al. Mycol. Res. 104:1175, 2000.

Magnetic field control of the quantum chaotic dynamics of hydrogen analogs in an anisotropic crystal field

We report magnetic field control of the quantum chaotic dynamics of hydrogen analogues in an anisotropic solid state environment. The chaoticity of the system dynamics was quantified by means of energy level statistics. We analyzed the magnetic field dependence of the statistical distribution of the impurity energy levels and found a smooth transition between the Poisson limit and the Wigner limit, i.e., transition between regular Poisson and fully chaotic Wigner dynamics. The effect of the crystal field anisotropy on the quantum chaotic dynamics, which manifests itself in characteristic transitions between regularity and chaos for different field orientations, was demonstrated.

Surgical management of primary non-small-cell carcinoma of lung with synchronous solitary brain metastasis: local experience

OBJECTIVE

To report the surgical experience in the management of patients with synchronous primary lung cancer and solitary brain metastasis.

DESIGN

Retrospective cohort study.

SETTING

Regional hospital, Hong Kong.

PATIENTS

Seventeen patients with synchronous primary lung cancer and solitary brain metastasis were treated by pulmonary resection and neurosurgical intervention between 1994 and 2007.

RESULTS

Median patient survival was 52 months (95% confidence interval, 9-95 months) and the 5-year survival was 27%. The univariate analysis yielded no significant prognostic factor. Four out of six patients who had lymph node metastases developed tumour recurrence.

CONCLUSION

In view of encouraging survival results, aggressive therapy including pulmonary resection and neurosurgical intervention should be recommended for patients with synchronous presentation with primary lung cancer and solitary brain metastasis.

Design and implementation of robust controllers for a gait trainer

This paper applies robust algorithms to control an active gait trainer for children with walking disabilities. Compared with traditional rehabilitation procedures, in which two or three trainers are required to assist the patient, a motor-driven mechanism was constructed to improve the efficiency of the procedures. First, a six-bar mechanism was designed and constructed to mimic the trajectory of children's ankles in walking. Second, system identification techniques were applied to obtain system transfer functions at different operating points by experiments. Third, robust control algorithms were used to design Hinfinity robust controllers for the system. Finally, the designed controllers were implemented to verify experimentally the system performance. From the results, the proposed robust control strategies are shown to be effective.

Realization of anisotropic diamagnetic kepler problem in a solid state environment

The anisotropic diamagnetic Kepler problem (ADKP) is realized experimentally by the orbital electrons of a P donor in Si under magnetic fields. The interference of electron wave packets which leads to quasi-Landau resonances (QLR) were observed. Applying the closed-orbit theory to an anisotropic solid state environment, we have identified orbits responsible for the QLR manifesting the quantum chaotic behavior in Rydberg atoms. The excellent consistency between the measured spectra and theoretical calculation provides unambiguous evidence of quantum chaotic dynamics of electrons in the ADKP.

Real-time RT-PCR of Hantaan virus RNA used for the detection of virus response to antiviral drugs

Hantaan virus (HTN) is an important cause of hemorrhagic fever with renal syndrome (HFRS) in Korea. HTN RNA can be detected with the RT-PCR and the quantity of HTN RNA in infected cells can be measured by competitive RT-PCR. The current study used the real-time RT-PCR for the detection of viral RNA S gene in a more detailed fashion than in the previous study (Nam et al., Virus Genes 26, 31-38, 2003). A standard curve was generated with serial 10-fold dilutions of the HTN RNA. The sensitivity of RNA detection was approximately 10 PFU of HTN. The cells infected with HTN were treated with the antiviral drugs ribavirin, zidovudine, and amantadine. 24 hrs after infection, real-time RT-PCR was used to detect the HTN RNA synthesized in the infected cells. No viral RNA was detected in the HTN-infected cells treated with antiviral drugs, but HTN RNA was detected in untreated HTN-infected cells. This finding suggested that real-time RTPCR should be used for the detection of antiviral activity against HTN.

Visualization of the release behaviour of microcapsules

This paper describes an experimental technique that visualizes the release behaviour that microcapsules loaded initially with a halide salt experience when immersed in aqueous media. The technique, based on the principle of silver halide photography, involves observing the effect that contact with a dilute aqueous silver nitrate solution has on individual microcapsules. Rapid precipitation of an insoluble silver halide salt on a capsule surface provides a permanent record of the location(s) on a capsule surface at which halide ion release occurs. Results obtained by examining the behaviour of individual capsules selected from one KCl and three NaCl capsule samples produced by fluidized bed coating illustrate the wide variety of halide ion release behaviour exhibited by capsules from different capsule samples as well as capsules from the same sample. Scanning electron microscopy showed that halide ion release from all capsules studied does not occur uniformly over the capsule surface, but is limited to specific points on the capsule surface. Whereas most capsules from two NaCl samples broke open spontaneously after a short immersion time, thereby producing a large plume of AgCl precipitate, capsules from one NaCl and the KCl sample remained intact even after prolonged immersion. In these latter cases, a AgCl bolus typically grows on the surface of a capsule as immersion time increased.

New magnetic nano-absorbent for the determination of n-octanol/water partition coefficients

A novel and generic miniaturization methodology for the determination of partition coefficient values of organic compounds in n-octanol/water by using magnetic nanoparticles is, for the first time, described. We have successfully designed, synthesised and characterised new colloidal stable porous silica-encapsulated magnetic nanoparticles of controlled dimensions. These nanoparticles absorbing a tiny amount of n-octanol in their porous silica over-layer are homogeneously dispersed into a bulk aqueous phase (pH 7.40) containing an organic compound prior to magnetic separation. The small size of the particles and the efficient mixing allow a rapid establishment of the partition equilibrium of the organic compound between the solid supported n-octanol nano-droplets and the bulk aqueous phase. UV-vis spectrophotometry is then applied as a quantitative method to determine the concentration of the organic compound in the aqueous phase both before and after partitioning (after magnetic separation). logD values of organic compounds of pharmaceutical interest (0.65-3.50), determined by this novel methodology, were found to be in excellent agreement with the values measured by the shake-flask method in two independent laboratories, which are also consistent with the literature data. It was also found that this new technique gives a number of advantages such as providing an accurate measurement of logD value, a much shorter experimental time and a smaller sample size required. With this approach, the formation of a problematic emulsion, commonly encountered in shake-flask experiments, is eliminated. It is envisaged that this method could be applicable to the high throughput logD screening of drug candidates.

Degradation of nonylphenol by anaerobic microorganisms from river sediment

We investigated the degradation of nonylphenol monoethoxylate (NP1EO) and nonylphenol (NP) by anaerobic microbes in sediment samples collected at four sites along the Erren River in southern Taiwan. Anaerobic degradation rate constants (k1) and half-lives (t1/2) for NP (2 microg/g) ranged from 0.010 to 0.015 1/day and 46.2 to 69.3 days respectively. For NP1EO (2 microg/g), the ranges were 0.009-0.014 1/day and 49.5-77.0 days respectively. Degradation rates for NP and NP1EO were enhanced by increasing temperature and inhibited by the addition of acetate, pyruvate, lactate, manganese dioxide, ferric chloride, sodium chloride, heavy metals, and phthalic acid esters. Degradation was also measured under three anaerobic conditions. Results show the high-to-low order of degradation rates to be sulfate-reducing conditions > methanogenic conditions > nitrate-reducing conditions. The results show that sulfate-reducing bacteria, methanogen, and eubacteria are involved in the degradation of NP and NP1EO, with sulfate-reducing bacteria being a major component of the river sediment.

Biodegradation of nonylphenol in river sediment

We investigated the biodegradation of nonylphenol monoethoxylate (NP1EO) and nonylphenol (NP) by aerobic microbes in sediment samples collected at four sites along the Erren River in southern Taiwan. Aerobic degradation rate constants (k1) and half-lives (t1/2) for NP (2 microg g(-1)) ranged from 0.007 to 0.051 day(-1) and 13.6 to 99.0 days, respectively; for NP1EO (2 microg g(-1)) the ranges were 0.006 to 0.010 day(-1) and 69.3 to 115.5 days. Aerobic degradation rates for NP and NP1EO were enhanced by shaking and increased temperature, and delayed by the addition of Pb, Cd, Cu, Zn, phthalic acid esters (PAEs), and NaCl, as well as by reduced levels of ammonium, phosphate, and sulfate. Of the microorganism strains isolated from the sediment samples, we found that strain JC1 (identified as Pseudomonas sp.) expressed the best biodegrading ability. Also noted was the presence of 4'-amino-acetophenone, an intermediate product resulting from the aerobic degradation of NP by Pseudomonas sp.

Application of cDNA microarray technique to detection of gene expression in host cells infected with viruses

cDNA microarray technique was used to monitor changes in mRNA levels in cells after Hantaan virus (HTNV) infection. The values of the ratio of medians for HTNV and Japanese encephalitis virus (JEV) at the early stage of infection were compared and found similar, suggesting that the same or similar genes are associated with the early events of infection with either virus. The reproducibility of values of the "ratio of medians" for HTNV was examined. We found that applying cluster analysis to the gene expression data groups efficiently together genes with the same function. Therefore, in analyzing the effects of viral infection on host cells by the cDNA microarray technique, clustering data appear to be necessary for gaining biological meaning from a dump of gene expression profiles obtained from virus-infected cells.

Fine structure in proton emission from 145Tm discovered with digital signal processing

Fine structure in proton emission from the 3.1(3) mus activity of 145Tm was discovered by using a novel technique of digital processing of overlapping recoil implantation and decay signals. Proton transitions to the ground state of 144Er and to its first excited 2(+) state at 0.33(1) MeV with a branching ratio I(p)(2(+))=9.6+/-1.5% were observed. The structure of the 145Tm wave function and the emission process were analyzed by using particle-core vibration coupling models.

HIV-risk behaviours of American spring break vacationers: a case of situational disinhibition?

Young adults are at high risk for acquiring STDs/HIV due primarily to multiple sex partners, unprotected sex, and substance use combined with sexual activity. Contranormative settings--such as the annual spring break vacation--provide ideal conditions for the potentially lethal interaction between alcohol, drugs, and sexual risk-taking. As a steadily growing form of youth travel and characterized by binge drinking, illicit drug use, and unsafe sexual practices, spring break has become a North American institution involving large numbers of travellers. In this study, the theory of interpersonal behaviour was used to explain college students' health-risk behaviours in the context of spring break and pre- and post-spring break surveys were used to examine casual sex and condom use behaviours. Multivariate analyses revealed peer influences, prior experiences with casual sex, alcohol consumption prior to sex, and impulsivity to be significant predictors of casual sex, while impulsivity and condom availability were significant predictors of students' use of condoms during casual sex.