GenEpi: gene-based epistasis discovery using machine learning.

BackgroundGenome-wide association studies (GWAS) provide a powerful means to identify associations between genetic variants and phenotypes. However, GWAS techniques for detecting epistasis, the interactions between genetic variants associated with phenotypes, are still limited. We believe that developing an efficient and effective GWAS method to detect epistasis will be a key for discovering sophisticated pathogenesis, which is especially important for complex diseases such as Alzheimer's disease (AD).ResultsIn this regard, this study presents GenEpi, a computational package to uncover epistasis associated with phenotypes by the proposed machine learning approach. GenEpi identifies both within-gene and cross-gene epistasis through a two-stage modeling workflow. In both stages, GenEpi adopts two-element combinatorial encoding when producing features and constructs the prediction models by L1-regularized regression with stability selection. The simulated data showed that GenEpi outperforms other widely-used methods on detecting the ground-truth epistasis. As real data is concerned, this study uses AD as an example to reveal the capability of GenEpi in finding disease-related variants and variant interactions that show both biological meanings and predictive power.ConclusionsThe results on simulation data and AD demonstrated that GenEpi has the ability to detect the epistasis associated with phenotypes effectively and efficiently. The released package can be generalized to largely facilitate the studies of many complex diseases in the near future

Effective Radiotherapy Cured Cauda Equina Syndrome Caused by Remitted Intracranial Germinoma Depositing

Cauda equina syndrome (CES) in children is very rare and can permanently disable. A remitted intracranial germinoma depositing on the spinal cord, leading to CES, has never been reported. We discuss the case of a 10-year-old girl who presented with sudden ataxia, low back pain, sensory deficits of the left lower extremity, and difficulty urinating and defecating 7 months after totally remitted intracranial germinoma postintracranial surgery and cranial irradiation. Magnetic resonance imaging (MRI) of the brain and spine showed multiple intradural extramedullary homogeneous masses from the cervical to lumbar levels, compressing the conus medullaris and cauda equina. After emergent craniospinal irradiation, the patient's neurologic symptoms dramatically subsided. A remitted intracranial germinoma depositing on her spinal cord could be the cause of CES. Early identification and a proper craniospinal irradiation may halt the progression of symptoms

Pleural Epithelioid Hemangioendothelioma

Epithelioid hemangioendothelioma (EHE) is a rare tumor of vascular origin. While it can be found in any tissue, it is most often found in lung and liver and usually has an intermediate behavior. EHEs originating from pleural tissue have been less frequently described than those from other sites. Furthermore, to date, all of the cited pleural EHEs were described as highly aggressive. In the present report, we describe a rare case of pleural EHE extending to lung and bone in a 31-year-old woman. The histological diagnosis was confirmed by both conventional examination and immunohistochemistry. Her disease stabilized during the 4th course of adriamycin (45 mg/m2, day 1-3), dacarbazine (300 mg/m2, day 1-3) and ifosfamide (2,500 mg/m2, day 1-3) with mesna, and she survived for 10 months after the diagnosis

Rare gallbladder adenomyomatosis presenting as atypical cholecystitis: case report

<p>Abstract</p> <p>Background</p> <p>Gallbladder adenomyomatosis is a benign condition characterized by hyperplastic change in the gallbladder wall and overgrowth of the mucosa because of an unknown cause. Patients with gallbladder adenomyomatosis usually present with abdominal pain. However, we herein describe a case of a patient with gallbladder adenomyomatosis who did not present with abdominal pain, but with only fever.</p> <p>Case presentation</p> <p>A 34-year-old man presented to our hospital with a fever. No abdominal discomfort was declared. His physical examination showed no abnormalities. Ultrasound of the abdomen revealed thickness of the gallbladder. Acute cholecystitis was diagnosed. The fever persisted even after 1 week of antibiotic therapy. Magnetic resonance imaging of the abdomen showed gallbladder adenomyomatosis with intramural Rokitansky-Aschoff sinuses. Exploratory laparotomy with cholecystectomy was performed. The fever recovered and no residual symptoms were reported at the 3-year follow-up.</p> <p>Conclusions</p> <p>Gallbladder adenomyomatosis can present with fever as the only symptom. Although the association between gallbladder adenomyomatosis and malignancy has yet to be elucidated, previous reports have shown a strong association between gallbladder carcinoma and a subtype of gallbladder adenomyomatosis. Surgical intervention remains the first-choice treatment for patients with gallbladder adenomyomatosis.</p

Unprecedented Ambient Sulfur Trioxide (SO3) Detection : Possible Formation Mechanism and Atmospheric Implications

Sulfur trioxide (SO3) is a crucial compound for atmospheric sulfuric acid (H2SO4) formation, acid rain formation, and other atmospheric physicochemical processes. During the daytime, SO3 is mainly produced from the photo-oxidation of SO2 by OH radicals. However, the sources of SO3 during the early morning and night, when OH radicals are scarce, are not fully understood. We report results from two field measurements in urban Beijing during winter and summer 2019, using a nitrate-CI-APi-LTOF (chemical ionization-atmospheric pressure interface-long-time-offlight) mass spectrometer to detect atmospheric SO3 and H2SO4. Our results show the level of SO3 was higher during the winter than during the summer, with high SO3 levels observed especially during the early morning (similar to 05:00 to similar to 08:30) and night (similar to 18:00 to similar to 05:00 the next day). On the basis of analysis of SO2, NOx, black carbon, traffic flow, and atmospheric ions, we suggest SO3 could be formed from the catalytic oxidation of SO2 on the surface of traffic-related black carbon. This previously unidentified SO3 source results in significant H2SO4 formation in the early morning and thus promotes sub-2.5 nm particle formation. These findings will help in understanding urban SO3 and formulating policies to mitigate secondary particle formation in Chinese megacities.Peer reviewe

Linear B-cell epitopes in the spike and nucleocapsid proteins as markers of SARS-CoV-2 exposure and disease severity

BACKGROUND Given the unceasing worldwide surge in COVID-19 cases, there is an imperative need to develop highly specific and sensitive serology assays to define exposure to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). METHODS Pooled plasma samples from PCR positive COVID-19 patients were used to identify linear B-cell epitopes from a SARS-CoV-2 peptide library of spike (S), envelope (E), membrane (M), and nucleocapsid (N) structural proteins by peptide-based ELISA. Hit epitopes were further validated with 79 COVID-19 patients with different disease severity status, 13 seasonal human CoV, 20 recovered SARS patients and 22 healthy donors. FINDINGS Four immunodominant epitopes, S14P5, S20P2, S21P2 and N4P5, were identified on the S and N viral proteins. IgG responses to all identified epitopes displayed a strong detection profile, with N4P5 achieving the highest level of specificity (100%) and sensitivity (&gt;96%) against SARS-CoV-2. Furthermore, the magnitude of IgG responses to S14P5, S21P2 and N4P5 were strongly associated with disease severity. INTERPRETATION IgG responses to the peptide epitopes can serve as useful indicators for the degree of immunopathology in COVID-19 patients, and function as higly specific and sensitive sero-immunosurveillance tools for recent or past SARS-CoV-2 infections. The flexibility of these epitopes to be used alone or in combination will allow for the development of improved point-of-care-tests (POCTs)

New way of healing : experienced counsellors’ perceptions of the influence of ch’i-related exercises on counselling practice in Taiwan

This study examines how Taiwanese senior counsellors with substantial experience of ch’i-related exercise (CRE) perceived the influence of their regular CRE on their counselling practice. I am interested in the perceived influence of CRE on both self-care and professional practice. In this studyn this studyn this study n this study n this study n this study, CRE, CRE, CRE, CRE, CRE refers to any refers to any refers to any refers to any ch'i enhancing exercise that coordinates movement with breathing and inner concentration wherein ch'i is a first order concept used by practitioners and regarded by them as an embodiment of ideas related to human life and human existence and able to be experienced and refined through any ch'i related exercise. CRE is a set of practices and an intrinsic part of local culture in Taiwan which in recent years, has become popular practice in Taiwanese society. There are growing numbers of counselling professionals involved in regular CRE in recent years. Studies examining the effects of CRE indicate the benefits of CRE on practitioners' global health and personal growth. However, no previous study has investigated the influence of the long-term regular use of CRE on counsellors‟ self-care and counselling practice. The narrative research design for this study was developed from a post-structural theoretical perspective located in the domain of social constructivism. The data were co-constructed between the researcher and 12 senior Taiwanese counsellors with substantial CRE experience using a semi-structured in-depth interview approach. Interview data were analysed using the structure-based approach developed by William Labov in the field of socio-linguistics. The study reveals an overall benefit of regular involvement in CRE for practitioners' global wellbeing and personal growth counsellor' self-care. The research findings also reveals the potential of ch’i to be used as a way of expressing health and illness and a way of understanding in therapy and CRE to be lived out in therapy as an embodiment. I argue that collectively the narratives, as a whole, give evidence of an increasing integratin of the ideas and practices of ch’i into counselling practice in contemporary Taiwan. This might even make up a new form of integrated and culturally appropriate practice, what I term "a new way of healing." These are therapeutic practices which value the potential of CRE for counsellor's self-care and personal growth; recognize the integral whole of the human person; promote conscious use of the knowledge and experience of ch’i and CRE in therapy as an important aspect of the therapeutic use of self. Implications for practice such as the potential of CRE to be introduced into counsellor training programmes for counsellors' preparation or ongoing education are provided. Recommendations for future research such as the development of a new healing modality based on the research findings are offered

Macrophage Migration Inhibitory Factor Induces Autophagy via Reactive Oxygen Species Generation

Autophagy is an evolutionarily conserved catabolic process that maintains cellular homeostasis under stress conditions such as starvation and pathogen infection. Macrophage migration inhibitory factor (MIF) is a multifunctional cytokine that plays important roles in inflammation and tumorigenesis. Cytokines such as IL-1β and TNF-α that are induced by MIF have been shown to be involved in the induction of autophagy. However, the actual role of MIF in autophagy remains unclear. Here, we have demonstrated that incubation of human hepatoma cell line HuH-7 cells with recombinant MIF (rMIF) induced reactive oxygen species (ROS) production and autophagy formation, including LC3-II expression, LC3 punctae formation, autophagic flux, and mitochondria membrane potential loss. The autophagy induced by rMIF was inhibited in the presence of MIF inhibitor, ISO-1 as well as ROS scavenger N-acetyl-L-cysteine (NAC). In addition, serum starvation-induced MIF release and autophagy of HuH-7 cells were partly blocked in the presence of NAC. Moreover, diminished MIF expression by shRNA transfection or inhibition of MIF by ISO-1 decreased serum starvation-induced autophagy of HuH-7 cells. Taken together, these data suggest that cell autophagy was induced by MIF under stress conditions such as inflammation and starvation through ROS generation

A Prediction Rule to Identify Severe Cases among Adult Patients Hospitalized with Pandemic Influenza A (H1N1) 2009

The purpose of this study was to establish a prediction rule for severe illness in adult patients hospitalized with pandemic influenza A (H1N1) 2009. At the time of initial presentation, the baseline characteristics of those with severe illness (i.e., admission to intensive care unit, mechanical ventilation, or death) were compared to those of patients with non-severe illnesses. A total of 709 adults hospitalized with pandemic influenza A (H1N1) 2009 were included: 75 severe and 634 non-severe cases. The multivariate analysis demonstrated that altered mental status, hypoxia (PaO2/FiO2 ≤ 250), bilateral lung infiltration, and old age (≥ 65 yr) were independent risk factors for severe cases (all P < 0.001). The area under the ROC curve (0.834 [95% CI, 0.778-0.890]) of the number of risk factors were not significantly different with that of APACHE II score (0.840 [95% CI, 0.790-0.891]) (P = 0.496). The presence of ≥ 2 risk factors had a higher sensitivity, specificity, positive predictive value and negative predictive value than an APACHE II score of ≥ 13. As a prediction rule, the presence of ≥ 2 these risk factors is a powerful and easy-to-use predictor of the severity in adult patients hospitalized with pandemic influenza A (H1N1) 2009

Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast

Background: Genome mining facilitated by heterologous systems is an emerging approach to access the chemical diversity encoded in basidiomycete genomes. In this study, three sesquiterpene synthase genes, GME3634, GME3638, and GME9210, which were highly expressed in the sclerotium of the medicinal mushroom Lignosus rhinocerotis, were cloned and heterologously expressed in a yeast system. Results: Metabolite profile analysis of the yeast culture extracts by GC-MS showed the production of several sesquiterpene alcohols (C 15 H 26 O), including cadinols and germacrene D-4-ol as major products. Other detected sesquiterpenes include selina-6-en-4-ol, ß-elemene, ß-cubebene, and cedrene. Two purified major compounds namely (+)-torreyol and a-cadinol synthesised by GME3638 and GME3634 respectively, are stereoisomers and their chemical structures were confirmed by 1 H and 13 C NMR. Phylogenetic analysis revealed that GME3638 and GME3634 are a pair of orthologues, and are grouped together with terpene synthases that synthesise cadinenes and related sesquiterpenes. (+)-Torreyol and a-cadinol were tested against a panel of human cancer cell lines and the latter was found to exhibit selective potent cytotoxicity in breast adenocarcinoma cells (MCF7) with IC 50 value of 3.5 ± 0.58 µg/ml while a-cadinol is less active (IC 50 = 18.0 ± 3.27 µg/ml). Conclusions: This demonstrates that yeast-based genome mining, guided by transcriptomics, is a promising approach for uncovering bioactive compounds from medicinal mushrooms