A bioinformatics potpourri

© 2018 The Author(s). The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018

Non-contrast coronary artery wall and plaque imaging using inversion-recovery prepared steady-state free precession

13301甲第4377号博士(保健学)金沢大学博士論文本文Full 以下に掲載：BMC Medical Imaging 2015. Bio Medical Central. 共著者：Takeshi Ishimoto, Yasuyo Taniguchi, Tosiaki Miyati, Momoe Kawakami, Masaru Ishihar

Texture analysis in skull magnetic resonance imaging

raumatic brain injury (TBI) represents a serious public health problem worldwide. It is the most common cause of death and disability in the young population (aged 15–45 years), with major family, social and economic implications [1]. In medical terms, the human body can be studied as an object. The reconstruction of bone structures after physical damage generated by such an unfortunate event as disease or trauma can range from the implementation of prostheses to the engineering of artificial bone implants [2]. To make a virtual or physical model of any human anatomy, it must first be captured in three dimensions in a way that can be used by computational processes. Most hospital scanners capture data from the entire body both internally and externally. These machines are typically medical imaging devices capable of scanning the entire human body, among which, the most common is the magnetic resonance imaging (MRI) equipment [3]. The goal of the research is to analyze the texture in magnetic resonance imaging and its relationship to bone mineral content (BMC) using simple linear regression

Systematic review and meta-analysis of the diagnostic accuracy of ultrasonography for deep vein thrombosis

Background Ultrasound (US) has largely replaced contrast venography as the definitive diagnostic test for deep vein thrombosis (DVT). We aimed to derive a definitive estimate of the diagnostic accuracy of US for clinically suspected DVT and identify study-level factors that might predict accuracy. Methods We undertook a systematic review, meta-analysis and meta-regression of diagnostic cohort studies that compared US to contrast venography in patients with suspected DVT. We searched Medline, EMBASE, CINAHL, Web of Science, Cochrane Database of Systematic Reviews, Cochrane Controlled Trials Register, Database of Reviews of Effectiveness, the ACP Journal Club, and citation lists (1966 to April 2004). Random effects meta-analysis was used to derive pooled estimates of sensitivity and specificity. Random effects meta-regression was used to identify study-level covariates that predicted diagnostic performance. Results We identified 100 cohorts comparing US to venography in patients with suspected DVT. Overall sensitivity for proximal DVT (95% confidence interval) was 94.2% (93.2 to 95.0), for distal DVT was 63.5% (59.8 to 67.0), and specificity was 93.8% (93.1 to 94.4). Duplex US had pooled sensitivity of 96.5% (95.1 to 97.6) for proximal DVT, 71.2% (64.6 to 77.2) for distal DVT and specificity of 94.0% (92.8 to 95.1). Triplex US had pooled sensitivity of 96.4% (94.4 to 97.1%) for proximal DVT, 75.2% (67.7 to 81.6) for distal DVT and specificity of 94.3% (92.5 to 95.8). Compression US alone had pooled sensitivity of 93.8 % (92.0 to 95.3%) for proximal DVT, 56.8% (49.0 to 66.4) for distal DVT and specificity of 97.8% (97.0 to 98.4). Sensitivity was higher in more recently published studies and in cohorts with higher prevalence of DVT and more proximal DVT, and was lower in cohorts that reported interpretation by a radiologist. Specificity was higher in cohorts that excluded patients with previous DVT. No studies were identified that compared repeat US to venography in all patients. Repeat US appears to have a positive yield of 1.3%, with 89% of these being confirmed by venography. Conclusion Combined colour-doppler US techniques have optimal sensitivity, while compression US has optimal specificity for DVT. However, all estimates are subject to substantial unexplained heterogeneity. The role of repeat scanning is very uncertain and based upon limited data

Coccidiomycosis infection of the patella mimicking a neoplasm - two case reports.

BackgroundCoccidioidomycosis is an endemic fungal infection in the southwestern of United States. Most infections are asymptomatic or manifest with mild respiratory complaints. Rare cases may cause extrapulmonary or disseminated disease. We report two cases of knee involvement that presented as isolated lytic lesions of the patella mimicking neoplasms.Case presentationThe first case, a 27 year-old immunocompetent male had progressive left anterior knee pain for four months. The second case was a 78 year-old male had left anterior knee pain for three months. Both of them had visited general physicians without conclusive diagnosis. A low attenuation lytic lesion in the patella was demonstrated on their image studies, and the initial radiologist's interpretation was suggestive of a primary bony neoplasm. The patients were referred for orthopaedic oncology consultation. The first case had a past episode of pulmonary coccioidomycosis 2 years prior, while the second case had no previous coccioidal infection history but lived in an endemic area, the central valley of California. Surgical biopsy was performed in both cases due to diagnostic uncertainty. Final pathologic examination revealed large thick walled spherules filled with endospores establishing the final diagnosis of extrapulmonary coccidioidomycosis.ConclusionsThough history and laboratory findings are supportive, definitive diagnosis still depends on growth in culture or endospores identified on histology. We suggest that orthopaedic surgeons and radiologists keep in mind that chronic fungal infections can mimic osseous neoplasm by imaging

Identification of hip fracture patients from radiographs using Fourier analysis of the trabecular structure: a cross-sectional study

Peer reviewedPublisher PD

Altered Achilles Tendon Morphology in Individuals With Chronic Post-Stroke Hemiparesis: A Case Report

Background: Individuals post-stroke walk slowly and with more effort, which puts them at higher risks for falls. The slow walking speed results from insufficient propulsive forces generated by the paretic leg. Current rehabilitative efforts to improve walking function target increasing propulsive forces, but overlook the muscle-tendon unit. Case presentations: Two individuals with chronic post-stroke hemiparesis are presented. In both individuals post-stroke, paretic ankle plantarflexors presented with increased muscle tone. Gait kinetics revealed asymmetric propulsive forces, specifically, insufficient propulsive forces by the paretic legs, consistent with previous literature. Sonography revealed increased thickness of paretic Achilles tendon at the calcaneal insertion, in both stroke cases, in contrast to comparable Achilles tendon thickness between limbs in the non-neurologically impaired controls. Conclusion: Tendon unit integrity should be considered in individuals post-stroke who demonstrate abnormal muscle tone and insufficient propulsion during gait

Dementia assessment and management in primary care settings: a survey of current provider practices in the United States.

BACKGROUND:Primary care providers (PCPs) are typically the first to screen and evaluate patients for neurocognitive disorders (NCDs), including mild cognitive impairment and dementia. However, data on PCP attitudes and evaluation and management practices are sparse. Our objective was to quantify perspectives and behaviors of PCPs and neurologists with respect to NCD evaluation and management. METHODS:A cross-sectional survey with 150 PCPs and 50 neurologists in the United States who evaluated more than 10 patients over age 55 per month. The 51-item survey assessed clinical practice characteristics, and confidence, perceived barriers, and typical practices when diagnosing and managing patients with NCDs. RESULTS:PCPs and neurologists reported similar confidence and approaches to general medical care and laboratory testing. Though over half of PCPs performed cognitive screening or referred patients for cognitive testing in over 50% of their patients, only 20% reported high confidence in interpreting results of cognitive tests. PCPs were more likely to order CT scans than MRIs, and only 14% of PCPs reported high confidence interpreting brain imaging findings, compared to 70% of specialists. Only 21% of PCPs were highly confident that they correctly recognized when a patient had an NCD, and only 13% were highly confident in making a specific NCD diagnosis (compared to 72 and 44% for neurologists, both p < 0.001). A quarter of all providers identified lack of familiarity with diagnostic criteria for NCD syndromes as a barrier to clinical practice. CONCLUSIONS:This study demonstrates how PCPs approach diagnosis and management of patients with NCDs, and identified areas for improvement in regards to cognitive testing and neuroimaging. This study also identified all providers' lack of familiarity with published diagnostic criteria for NCD syndromes. These findings may inform the development of new policies and interventions to help providers improve the efficacy of their decision processes and deliver better quality care to patients with NCDs