Distribution of biological databases over lowbandwidth networks

Databases are integral part of bioinformatics and need to be accessed most frequently, thus downloading and updating them on a regular basis is very critical. The establishment of bioinformatics research facility is a challenge for developing countries as they suffer from inherent low-bandwidth and unreliable internet connections. Therefore, the identification of techniques supporting download and automatic synchronization of large biological database at low bandwidth is of utmost importance. In current study, two protocols (FTP and Bit Torrent) were evaluated and the utility of a BitTorren based peer-to-peer (btP2P) file distribution model for automatic synchronization and distribution of large dataset at our facility in Pakistan have been discussed

Moxifloxacin (Avelox) Induced Thrombotic Thrombocytopenic Purpura

We report a case of a 66-year-old African-American female who presented with complaints of progressively worsening weakness, shortness of breath on minimal exertion, lethargy for the last few days, and short episodes of aphasia lasting 20–30 seconds. Prior to presentation, she was treated with two courses of moxifloxacin for sinusitis. Laboratory examination was remarkable for anemia and thrombocytopenia with elevated lactate dehydrogenase and no evidence of renal failure. Peripheral smear showed numerous schistocytes and she was diagnosed with thrombotic thrombocytopenic purpura. Moxifloxacin was identified as the offending agent. The patient was treated with prednisone and plasmapheresis. To the best of our knowledge, this is the first reported case of thrombotic thrombocytopenic purpura associated with the use of moxifloxacin. Although rare, physicians should be aware of this serious complication associated with its use

Role of Nutraceuticals in COVID-19 Mediated Liver Dysfunction.

COVID-19 is known as one of the deadliest pandemics of the century. The rapid spread of this deadly virus at incredible speed has stunned the planet and poses a challenge to global scientific and medical communities. Patients with COVID-19 are at an increased risk of co-morbidities associated with liver dysfunction and injury. Moreover, hepatotoxicity induced by antiviral therapy is gaining importance and is an area of great concern. Currently, alternatives therapies are being sought to mitigate hepatic damage, and there has been growing interest in the research on bioactive phytochemical agents (nutraceuticals) due to their versatility in health benefits reported in various epidemiological studies. Therefore, this review provides information and summarizes the juncture of antiviral, immunomodulatory, and hepatoprotective nutraceuticals that can be useful during the management of COVID-19

Spectrum of fireworks related ocular injuries on the day of Deepavali

Fireworks are often associated with severe ocular injury. In India, fireworks are an important cause of ocular injury during Deepavali festival. We present the spectrum of fire-cracker related ocular injuries on the day of Deepavali and their associated risk factors. All patients with cracker related ocular injuries on Deepavali day, seen at a tertiary care eye hospital, are included in this case series. This case series evaluates the type of ocular injury, type of firecracker involved and the associated risk factors leading to the casualtie

Chemical and microbial leaching of valuable metals from PCBs and tantalum capacitors of spent mobile phones

We compared chemical and microbial leaching for multi-metal extraction from printed circuit boards (PCBs) and tantalum capacitor scrap. A mixed consortium of acidophiles and heterotrophic fungal strains were used in the experiments and compared to chemical leaching using specific acids (sulfuric, citric and oxalic acids). Under optimum conditions, 100% extraction efficiency of Cu, and nearly 85% of Zn, Fe, Al and Ni were achieved from PCB and tantalum capacitor scrap samples using sulfuric acid. The mixed consortium of acidophiles successfully mobilized, Ni and Cu (99% and 96%, respectively) while Fe, Zn, Al and Mn reached an extraction yield of 89, 77, 70 and 43%, respectively, from the PCB samples. For the tantalum capacitor samples, acidophiles mobilized 92% Cu, 88% Ni, 78% Fe, 77% Al, 70% Zn and 57% Mn. Metal mobilization from PCBs and tantalum capacitor scrap by A. niger filtrate showed efficient solubilization of Cu, Fe, Al, Mn, Ni, Pb and Zn at an efficiency of 52, 29, 75, 5, 61, 21 and 35% from PCB samples and 61, 25, 69, 23, 68, 15 and 45% from tantalum capacitor samples, respectively. Microbial leaching proved viable as a method to extract base metals but was less specific for tantalum and precious metals in electronic waste. The implications of these results for further processing of waste electronic and electrical equipment (WEEE) are considered in potential hybrid treatment strategies

PconsFold: improved contact predictions improve protein models

Motivation: Recently it has been shown that the quality of protein contact prediction from evolutionary information can be improved significantly if direct and indirect information is separated. Given sufficiently large protein families, the contact predictions contain sufficient information to predict the structure of many protein families. However, since the first studies contact prediction methods have improved. Here, we ask how much the final models are improved if improved contact predictions are used. Results: In a small benchmark of 15 proteins, we show that the TM-scores of top-ranked models are improved by on average 33% using PconsFold compared with the original version of EVfold. In a larger benchmark, we find that the quality is improved with 15–30% when using PconsC in comparison with earlier contact prediction methods. Further, using Rosetta instead of CNS does not significantly improve global model accuracy, but the chemistry of models generated with Rosetta is improved. Availability: PconsFold is a fully automated pipeline for ab initio protein structure prediction based on evolutionary information. PconsFold is based on PconsC contact prediction and uses the Rosetta folding protocol. Due to its modularity, the contact prediction tool can be easily exchanged. The source code of PconsFold is available on GitHub at https://www.github.com/ElofssonLab/pcons-fold under the MIT license. PconsC is available from http://c.pcons.net/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Mucin 13 expression correlates with tumor development in hepatocellular carcinoma

Background: Hepatocellular carcinoma (HCC) has a poor prognosis due to ineffective therapeutic modality and lack of early diagnostic marker. Accumulating studies have shown that elevated expression of mucin 13 as potential oncogene and predictive biomarker for various cancer. However, very little is known about its expression and function for development and progression of HCC Objective: To investigate mucin 13 expression in chemically induced hepatocellular carcinoma model. Methodology: Diethyl nitrosamine (DEN) and 2-Acetylaminofluorene (2-AAF) induced method was employed for the development of hepatocellular carcinoma in Male Wistar rats. Serum and tissues were collected at regular interval of time and routinely validated for liver cancer stages. Immunohistochemistry and in situ hybridization were performed on formalin-fixed, paraffin-embedded tissues. Molecular docking studies were performed to study the interaction of mucin 13 and DEN. Results: Our results demonstrate hepatocellular adenoma as observed by histopathological analysis. Biochemical analysis showed a progressive increase in the levels of serum ALT, AST and ALP, suggesting the development and progression of hepatocellular damage. Notably, mucin 13 expression gradually elevated during consecutive stages of hepatocellular carcinoma. Interestingly, an increase in nuclear localization of mucin 13 was observed in treated group as compared to control group. In situ hybridization analysis showed that a decrease in miR-132 and miR-145, which are inversely related with mucin 13 expression. Moreover, DEN efficiently binds mucin 13 with high affinity and thus stabilize it as demonstrated by molecular docking analysis. Conclusion: These results suggest that mucin 13 expression is closely associated with hepatocarcinogenesis and could serve as a predictive candidate biomarker for HCC

Mucin 13 expression is an early indicator of hepatocellular carcinoma development

Background: Hepatocellular carcinoma (HCC) has a poor prognosis due to ineffective therapeutic modality and lack of an early marker for diagnosis. Studies show that increased mucin 13 (MUC13) expression as a possible oncogene and predictive biomarker for various cancers has been shown. But its expression and role in the development of HCC is very little known. Objective: The aim of this study is to investigate the MUC13 expression in chemically induced hepatocellular carcinoma model. Methodology: Male Wistar rats were subjected to a DEN and 2-Acetylaminofluorene (2-AAF) induced method for the development of hepatocellular carcinoma. Serum and tissues were collected at regular intervals and routinely validated for various stages of liver cancer. On formalin-fixed, paraffin-embedded tissues, immunohistochemistry and in situ hybridization were performed. The molecular interaction of mucin 13 and DEN were also performed using in silico analysis. Results: Histopathological analysis of liver tissues revealed the development of hepatocellular carcinoma with successive stages in chemically induced model HCC. Moreover, biochemical analysis showed a progressive increase in serum ALT, AST, and ALP levels, indicating the development and progression of hepatocellular damage. Notably, mucin 13 expression gradually increased during the progression of hepatocellular carcinoma. The treated group showed an increase in nuclear localization of mucin 13 as compared to the control group. In situ hybridization analysis revealed a reduction in miR-132 and miR145, both of which are inversely related to mucin 13 expression. Furthermore, molecular docking analysis showed that DEN efficiently binds mucin 13 with high affinity and thus stabilizes it. Conclusion: These findings suggest that mucin 13 expression is linked to hepatocarcinogenesis and could be used as a candidate biomarker for HCC

Hepatoprotective role of Cucurbitacin D on benzo[a]pyrene induced liver injury

Background: Epidemiological findings show the strong correlation of co-morbidity factors including smoking with the development and progression of liver cancer. Moreover, benzo[a]pyrene, a main component of tobacco smoke, is extremely carcinogenic and contributes to liver injury as well. Cucurbitacin, chemically classified as triterpenes, have shown diverse biological activities including potent antioxidant, anti-inflammatory and anti-cancer activities. However, their hepatoprotective activities are not completely understood. Objective: In the present study, we investigated the cytoprotective activity of novel analog of cucurbitacin, cucurbitacin D, against benzo[a]pyrene-induced liver injury in human HepG2 cells. Method: Proliferation, clonogenicity, migration, invasion, Western blotting and qPCR analysis were conducted to investigate the cytoprotective effect of cucurbitacin D against benzo[a]pyrene induced liver damage. DCFDA assay was performed to analyze intracellular reactive oxygen species (ROS) level in liver cells. Results: Functional assays showed that cucurbitacin D exhibited cytoprotective effects against dose-dependent growth inhibition by benzo[a]pyrene in human HepG2 cells. This protective effect was likely associated with antioxidant potential of cucurbitacin D, as evidenced by the attenuation of ROS observed by fluorimeter and fluorescence microscopy. Further study is ongoing to examine the effect of cucurbitacin D on oxidative stress markers by employing western blotting and qPCR techniques. Collectively, these results exhibited that cucurbitacin D alleviate benzo[a]pyreneinduced liver injury through its antioxidant effects. Conclusion: These results have demonstrated hepatoprotective effects of cucurbitacin D against benzo[a]pyrene-induced liver damage, rendering it as an effective potential ingredient in food supplements

Contribution of suicide and injuries to pregnancy-related mortality in low-income and middle-income countries: a systematic review and meta-analysis.

BACKGROUND: Although suicide is one of the leading causes of deaths in young women in low-income and middle-income countries, the contribution of suicide and injuries to pregnancy-related mortality remains unknown. METHODS: We did a systematic review to identify studies reporting the proportion of pregnancy-related deaths attributable to suicide or injuries, or both, in low-income and middle-income countries. We used a random-effects meta-analysis to calculate the pooled prevalence of pregnancy-related deaths attributable to suicide, stratified by WHO region. To account for the possible misclassification of suicide deaths as injuries, we calculated the pooled prevalence of deaths attributable to injuries, and undertook a sensitivity analysis reclassifying the leading methods of suicides among women in low-income and middle-income countries (burns, poisoning, falling, or drowning) as suicide. FINDINGS: We identified 36 studies from 21 countries. The pooled total prevalence across the regions was 1·00% for suicide (95% CI 0·54-1·57) and 5·06% for injuries (3·72-6·58). Reclassifying the leading suicide methods from injuries to suicide increased the pooled prevalence of pregnancy-related deaths attributed to suicide to 1·68% (1·09-2·37). Americas (3·03%, 1·20-5·49), the eastern Mediterranean region (3·55%, 0·37-9·37), and the southeast Asia region (2·19%, 1·04-3·68) had the highest prevalence for suicide, with the western Pacific (1·16%, 0·00-4·67) and Africa (0·65%, 0·45-0·88) regions having the lowest. INTERPRETATION: The available data suggest a modest contribution of injuries and suicide to pregnancy-related mortality in low-income and middle-income countries with wide regional variations. However, this study might have underestimated suicide deaths because of the absence of recognition and inclusion of these causes in eligible studies. We recommend that injury-related and other co-incidental causes of death are included in the WHO definition of maternal mortality to promote measurement and effective intervention for reduction of maternal mortality in low-income and middle-income countries. FUNDING: National Institute of Mental Health