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Fulltext IntFOLD: an integrated web resource for high performance protein structure and function prediction

McGuffin LJ, Adiyaman R, Maghrabi AHA, Shuid AN, Brackenridge DA, Nealon JO, et al.

Nucleic Acids Res, 2019 07 02;47(W1):W408-W413.
PMID: 31045208 DOI: 10.1093/nar/gkz322

The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein-ligand interactions. The component methods have been independently evaluated via the successive blind CASP experiments and the continual CAMEO benchmarking project. The IntFOLD server has established its ranking as one of the best performing publicly available servers, based on independent official evaluation metrics. Here, we describe significant updates to the server back end, where we have focused on performance improvements in tertiary structure predictions, in terms of global 3D model quality and accuracy self-estimates (ASE), which we achieve using our newly improved ModFOLD7_rank algorithm. We also report on various upgrades to the front end including: a streamlined submission process, enhanced visualization of models, new confidence scores for ranking, and links for accessing all annotated model data. Furthermore, we now include an option for users to submit selected models for further refinement via convenient push buttons. The IntFOLD server is freely available at: http://www.reading.ac.uk/bioinf/IntFOLD/.

Matched MeSH terms: Benchmarking
Fulltext Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03)

Balakrishnan KN, Abdullah AA, Bala JA, Jesse FFA, Abdullah CAC, Noordin MM, et al.

Virol J, 2020 Oct 27;17(1):164.
PMID: 33109247 DOI: 10.1186/s12985-020-01436-5

BACKGROUND: Cytomegalovirus (CMV) is an opportunistic pathogen that causes severe complications in congenitally infected newborns and non-immunocompetent individuals. Developing an effective vaccine is a major public health priority and current drugs are fronting resistance and side effects on recipients. In the present study, with the aim of exploring new strategies to counteract CMV replication, several anti-CMV siRNAs targeting IE2 and DNA polymerase gene regions were characterized and used as in combinations for antiviral therapy.
METHODS: The rat embryo fibroblast (REF) cells were transfected with multi siRNA before infecting with CMV strain ALL-03. Viral growth inhibition was measured by tissue culture infectious dose (TCID50), cytopathic effect (CPE) and droplet digital PCR (ddPCR) while IE2 and DNA polymerase gene knockdown was determined by real-time PCR. Ganciclovir was deployed as a control to benchmark the efficacy of antiviral activities of respective individual siRNAs.
RESULTS: There was no significant cytotoxicity encountered for all the combinations of siRNAs on REF cells analyzed by MTT colorimetric assay (P > 0.05). Cytopathic effects (CPE) in cells infected by RCMV ALL-03 had developed significantly less and at much slower rate compared to control group. The expression of targeted genes was downregulated successfully resulted in significant reduction (P

Matched MeSH terms: Benchmarking
Fulltext An EEG Database and Its Initial Benchmark Emotion Classification Performance

Seal A, Reddy PPN, Chaithanya P, Meghana A, Jahnavi K, Krejcar O, et al.

Comput Math Methods Med, 2020;2020:8303465.
PMID: 32831902 DOI: 10.1155/2020/8303465

Human emotion recognition has been a major field of research in the last decades owing to its noteworthy academic and industrial applications. However, most of the state-of-the-art methods identified emotions after analyzing facial images. Emotion recognition using electroencephalogram (EEG) signals has got less attention. However, the advantage of using EEG signals is that it can capture real emotion. However, very few EEG signals databases are publicly available for affective computing. In this work, we present a database consisting of EEG signals of 44 volunteers. Twenty-three out of forty-four are females. A 32 channels CLARITY EEG traveler sensor is used to record four emotional states namely, happy, fear, sad, and neutral of subjects by showing 12 videos. So, 3 video files are devoted to each emotion. Participants are mapped with the emotion that they had felt after watching each video. The recorded EEG signals are considered further to classify four types of emotions based on discrete wavelet transform and extreme learning machine (ELM) for reporting the initial benchmark classification performance. The ELM algorithm is used for channel selection followed by subband selection. The proposed method performs the best when features are captured from the gamma subband of the FP1-F7 channel with 94.72% accuracy. The presented database would be available to the researchers for affective recognition applications.

Matched MeSH terms: Benchmarking
Fulltext Defined Daily Dose and Appropriateness of Clinical Application: The Coxibs and Traditional Nonsteroidal Anti-Inflammatory Drugs for Postoperative Orthopaedics Pain Control in a Private Hospital in Malaysia

Bakrin FS, Makmor-Bakry M, Che Hon WH, Faizal SM, Manan MM, Ming LC

Pharmacy (Basel), 2020 Dec 08;8(4).
PMID: 33302438 DOI: 10.3390/pharmacy8040235

INTRODUCTION: Drug utilization of analgesics in a private healthcare setting is useful to examine their prescribing patterns, especially the newer injectable cyclooxygenase (COX)-2 inhibitors (coxibs).
OBJECTIVES: To evaluate the utilization of coxibs and traditional nonsteroidal anti-inflammatory drugs (tNSAIDs) indicated for postoperative orthopaedic pain control using defined daily dose (DDD) and ratio of use density to use rate (UD/UR).
METHOD: A retrospective drug utilization review (DUR) of nonsteroidal anti-inflammatory drugs (NSAIDs) at an inpatient department of a private teaching hospital in Seremban, Malaysia was conducted. Patients' demographic characteristics, medications prescribed, clinical lab results, visual analogue scale (VAS) pain scores and length of hospital stay were documented. Orthopaedic surgeries, namely arthroscopy, reconstructive, and fracture fixation, were included. Stratified random sampling was used to select patients. Data were collected through patients' medical records. The DDD per 100 admissions and the indicator UD/UR were calculated with the World Health Organization's DDD as a benchmark. The inclusion criteria were patients undergoing orthopaedic surgery prescribed with coxibs (celecoxib capsules, etoricoxib tablets, parecoxib injections) and tNSAIDs (dexketoprofen injections, diclofenac sodium tablets). Data were analysed descriptively. This research was approved by the academic institution and the hospital research ethics committee.
RESULT: A total of 195 records of patients who received NSAIDs were randomly selected among 1169 cases. In term of the types of orthopaedic surgery, the ratio of included records for arthroscopy:fracture fixation:reconstructive surgery was 55.4:35.9:8.7. Most of the inpatients had low rates of common comorbidities such as cardiovascular disease as supported by their baseline parameters. The majority were not prescribed with other concomitant prescriptions that could cause drug interaction (74.9%), or gastroprotective agents (77.4%). Overall, DDDs per 100 admissions for all NSAIDs were less than 100, except for parecoxib injections (389.23). The UD/UR for all NSAIDs were less than 100, except for etoricoxib tablets (105.75) and parecoxib injections (108.00).
DISCUSSION: As per guidelines, the majority (96.9%) received other analgesics to ensure a multimodal approach was carried out to control pain. From the UD/UR results, the arthroscopy surgery was probably the most appropriate in terms of NSAID utilization.
CONCLUSION: The prescribing pattern of NSAIDs except parecoxib was appropriate based on adverse effect and concurrent medication profile. The findings of this DUR provide insight for a low-risk patient population at a private specialized teaching hospital on the recommended use of NSAIDs for postoperative orthopaedic pain control.

Matched MeSH terms: Benchmarking
Best practices on immunomodulators and biologic agents for ulcerative colitis and Crohn's disease in Asia

Ooi CJ, Hilmi I, Banerjee R, Chuah SW, Ng SC, Wei SC, et al.

J Gastroenterol Hepatol, 2019 Aug;34(8):1296-1315.
PMID: 30848854 DOI: 10.1111/jgh.14648

The Asia-Pacific Working Group on Inflammatory Bowel Disease was established in Cebu, Philippines, under the auspices of the Asia-Pacific Association of Gastroenterology with the goal of improving inflammatory bowel disease care in Asia. This consensus is carried out in collaboration with Asian Organization for Crohn's and Colitis. With biologic agents and biosimilars becoming more established, it is necessary to conduct a review on existing literature and establish a consensus on when and how to introduce biologic agents and biosimilars in conjunction with conventional treatments for ulcerative colitis and Crohn's disease in Asia. These statements also address how pharmacogenetics influences the treatments of ulcerative colitis and Crohn's disease and provides guidance on response monitoring and strategies to restore loss of response. Finally, the review includes statements on how to manage treatment alongside possible hepatitis B and tuberculosis infections, both common in Asia. These statements have been prepared and voted upon by members of inflammatory bowel disease workgroup employing the modified Delphi process. These statements do not intend to be all-encompassing, and future revisions are likely as new data continue to emerge.

Matched MeSH terms: Benchmarking