Miracle-dz/UniFAR-FTUs huggingface dataset:
Iterative Scaling Fuzzy Additive Spectral Clustering (is-FADDIS) Algorithm for Subtypes Cancer Identification using Gene Expression Data

Cancer is one of main non-communicable disease. Analysis of subtypes cancer identification is important to determine the proper treatment for each patient. However, cancer data analysis is difficult problem since it has multiple risk factors genes and clinical condition of patients. This study aims to identify subtypes cancer using Iterative Scaling-FADDIS (is-FADDIS) algorithm which extends the FADDIS algorithm in sparse data problems. In this research, is-FADDIS technique is applied to microarray data to identify subtypes cancer in two data sets: Colorectal Carcinoma and B-Cell Lymphoma. Then, the clusters structure those to be found will be validated based on Correlation Ratios and Global Silhoutte. For Colorectal Carcinoma cancer, the correlation ratio between cluster and the existence of tumour will be analyzed. The results of experiments show that is-FADDIS works well on both data sets. For Colorectal Carcinoma cancer data, the results show that those clusters to be found by is-FADDIS has successfully correlated with the existence of tumour. For B-Lymphoma dataset, is-FADDIS algorithm has successfully well separated two clusters of cancer subtypes with Global Silhoutte value 0.4035.
Physical Properties of Composites Near Percolation

Dramatic changes in the physical properties of composites occur when filler particles form a percolating network through the composite, particularly when the difference between the properties of the constitutive phases is large. By use of electric conductivity and dielectric properties as examples, recent studies on the physical properties of composites near percolation are reviewed. The effects of geometric factors and intrinsic properties of the fillers and the matrix, and especially of the interface between fillers and matrix, on electric and dielectric properties near percolation are discussed. Contact resistivity at the interface is less desirable for enhancing electrical conductivity. By contrast, an interface with high resistivity suppresses tunneling between adjacent fillers and leads to percolative composites with higher dielectric constant but lower dielectric loss. This review concludes with an outlook on the future possibilities and scientific challenges in the field.
A Negative Group Delay Microwave Circuit Based on Signal Interference Techniques

A novel self-matched negative group delay (NGD) microwave circuit based on the signal interference technique is proposed to eliminate the performance degradation due to the temperature-dependent resistance variation. The proposed circuit consists of unequal power dividing/combining structures and coupled-line phase shifter, which can be directly synthesized with prescribed NGD time and insertion loss (IL). To verify the proposed method, an NGD circuit with a size of <inline-formula> <tex-math notation="LaTeX">$0.41\lambda _{g}\times 0.41\lambda _{g}$ </tex-math></inline-formula> is designed and fabricated. From the measured results, NGD time of −2.09 ns at the center frequency of 1.016 GHz is obtained with NGD bandwidth of 14.2% (0.944–1.088 GHz), in which the IL is less than 18.1 dB and the return loss is greater than 33 dB.
Prevalence of fecal viruses and bacteriophage in Canadian farmed mink (Neovison vison)

Recent viral metagenomic studies have demonstrated the diversity of eukaryotic viruses and bacteriophage shed in the feces of domestic species. Although enteric disease is a major concern in the commercial mink farming industry, few etiologic agents have been well characterized. This study aimed to identify viruses shed in the fecal matter of clinically healthy commercial mink from 40 southern Ontario farms. Viral RNA was extracted from 67 pooled fecal samples (30 adult female mink and 37 kit) and amplified for Illumina sequencing on the NextSeq platform, and the resulting contigs were trimmed and assembled using Trimmomatic 0.36. 0 and Spades 3.8. 0 in iVirus (CyVerse, AZ, USA) and SeqMan NGen 12 (DNAStar, WI, USA). Identification of assembled sequences >100 bp (Geneious 10.1.3) showed an abundance of bacteriophage sequences, mainly from families Siphoviridae (53%), Podoviridae (22%), Myoviridae (20%), Inoviridae (1%), Leviviridae (0.04%), Tectiviridae (0.01%), and Microviridae (0.01%). A diverse range of vertebrate viruses were detected, of which posavirus 3, mink bocavirus, gyroviruses, and avian‐associated viruses were most abundant. Additionally, sequences from nonvertebrate viruses with water and soil‐associated amebal and algal hosts were also highly prevalent. The results of this study show that viruses shed in the fecal matter of healthy commercial mink are highly diverse and could be closely associated with diet, and that more research is necessary to determine how the detected viruses may impact mink health.
Transcriptome Kinetics of Circulating Neutrophils during Human Experimental Endotoxemia

Polymorphonuclear cells (neutrophils) play an important role in the systemic inflammatory response syndrome and the development of sepsis. These cells are essential for the defense against microorganisms, but may also cause tissue damage. Therefore, neutrophil numbers and activity are considered to be tightly regulated. Previous studies have investigated gene transcription during experimental endotoxemia in whole blood and peripheral blood mononuclear cells. However, the gene transcription response of the circulating pool of neutrophils to systemic inflammatory stimulation in vivo is currently unclear. We examined neutrophil gene transcription kinetics in healthy human subjects (n = 4) administered a single dose of endotoxin (LPS, 2 ng/kg iv). In addition, freshly isolated neutrophils were stimulated ex vivo with LPS, TNFα, G-CSF and GM-CSF to identify stimulus-specific gene transcription responses. Whole transcriptome microarray analysis of circulating neutrophils at 2, 4 and 6 hours after LPS infusion revealed activation of inflammatory networks which are involved in signaling of TNFα and IL-1α and IL-1β. The transcriptome profile of inflammatory activated neutrophils in vivo reflects extended survival and regulation of inflammatory responses. These changes in neutrophil transcriptome suggest a combination of early activation of circulating neutrophils by TNFα and G-CSF and a mobilization of young neutrophils from the bone marrow.
Clinical, Diagnostic, and Treatment Disparities between HIV-Infected and Non-HIV-Infected Immunocompromised Patients with Pneumocystis jirovecii Pneumonia

The substantial decline in the Pneumocystis jirovecii pneumonia (PCP) incidence in HIV-infected patients after the introduction of antiretroviral therapy (ART) in resource-rich settings and the growing number of non-HIV-infected immunocompromised patients at risk leads to considerable epidemiologic changes with clinical, diagnostic, and treatment consequences for physicians. HIV-infected patients usually develop a subacute course of disease, while non-HIV-infected immunocompromised patients are characterized by a rapid disease progression with higher risk of respiratory failure and higher mortality. The main symptoms usually include exertional dyspnea, dry cough, and subfebrile temperature or fever. Lactate dehydrogenase may be elevated. Typical findings on computed tomography scans of the chest are bilateral ground-glass opacities with or without cystic lesions, which are usually associated with the presence of AIDS. Empiric treatment should be initiated as soon as PCP is suspected. Bronchoalveolar lavage has a higher diagnostic yield compared to induced sputum. Immunofluorescence is superior to conventional staining. A combination of different diagnostic tests such as microscopy, polymerase chain reaction, and (1,3)-β-D-glucan is recommended. Trimethoprim/sulfamethoxazole for 21 days is the treatment of choice in adults and children. Alternative treatment regimens include dapsone with trimethoprim, clindamycin with primaquine, atovaquone, or pentamidine. Patients with moderate to severe disease should receive adjunctive corticosteroids. In newly diagnosed HIV-infected patients with PCP, ART should be initiated as soon as possible. In non-HIV-infected immunocompromised patients, improvement of the immune status should be discussed (e.g., temporary reduction of immunosuppressive agents). PCP prophylaxis is effective and depends on the immune status of the patient and the underlying immunocompromising disease.
T94. HS-CRP TO EVALUATE CHRONIC INFLAMMATION AND CARDIOVASCULAR DISEASES IN SCHIZOPHRENIA

Abstract Background The metabolic syndrome is a combination of risk factors for cardiovascular disease (RFCV). These complications are responsible for a significant excess mortality found in patients with schizophrenia. C-reactive protein (CRP), the main protein of the acute phase of the inflammatory process, has been chosen as one of the most informative biomarkers for predicting vascular death and major cardiovascular events at 10 years of age. It is the moderate and chronic increase in CRP levels measured by high-sensitivity C – reactive protein (hs-CRP) that represents a risk factor for cardiovascular disease. In the meanwhile, the results of research on autoimmunity and inflammation during psychosis described high levels of inflammatory markers in schizophrenia. In fact, chronic inflammation, measured by high blood C-reactive protein level, has been described in schizophrenia. The aim of this work was to evaluate the association between serum levels of high-sensitivity C – reactive protein, as a marker of chronic inflammation, metabolic syndrome and cardiovascular risk in a cohort of Tunisian patients with schizophrenia during remission. Methods A cross-sectional and retrospective descriptive study was conducted at the “F” psychiatry department at the Razi Hospital, including 80 patients with schizophrenia in period of clinical remission. The evaluation focused on 11 cardiovascular risk factors: age, family history of early heart disease, physical inactivity, alcohol consumption, smoking, type 2 diabetes, android obesity, the elevation of total cholesterol, the decrease of hdl-cholesterol, high blood pressure, elevation of triglycerides. A dosage of high-sensitivity C – reactive protein was performed. Results 25 patients (31%) met the criteria for metabolic syndrome of the International Diabetes Federation (2006). 13 patients (16%) had none of the 5 diagnostic criteria for metabolic syndrome. The average number of cardiovascular risks was 3.66. 22% of patients had significant cardiovascular risk (number of risk factors ≥ 5). The average measured CRP us was 3.43 ± 2.08 mg / l. Taking only the measure of hs-CRP as RFCV, 64% of our patients had a moderate cardiovascular risk and 38% had a significant risk. Hs-CRP levels were not associated with metabolic syndrome (p=0.4). However, a strong association was found between high levels of hs-CRP and high risks for cardiovascular disease (p=0.006). Discussion Chronic inflammation plays a role in the pathophysiology of many chronic diseases, including cardiovascular diseases. It also plays an important role in the pathogenesis of schizophrenia. The role of the immuno-inflammatory system in schizophrenia arouses interest in immuno-psychiatric research. The association between chronic inflammation and cardiovascular diseases in schizophrenia could lead to treatments that would prevent the progression of both diseases overall.
Longitudinal Assessment of Multidrug-Resistant Organisms in Newly Admitted Nursing Facility Patients: Implications for an Evolving Population

Background The spread of multidrug-resistant organisms (MDROs) is a global concern, and much about transmission in healthcare systems remains unknown. To reduce hospital stays, nursing facilities (NFs) have increasingly assumed care of post-acute populations. We estimate the prevalence of MDRO colonization in NF patients on enrollment and discharge to community settings, risk factors for colonization, and rates of acquiring MDROs during the stay. Methods We conducted a prospective, longitudinal cohort study of newly admitted patients in 6 NFs in southeast Michigan using active microbial surveillance of multiple anatomic sites sampled at enrollment, days 14 and 30, and monthly thereafter for up to 6 months. Results We enrolled 651 patients and collected 7526 samples over 1629 visits, with an average of 29 days of follow-up per participant. Nearly all participants were admitted for post-acute care (95%). More than half (56.8%) were colonized with MDROs at enrollment: methicillin-resistant Staphylococcus aureus (MRSA), 16.1%; vancomycin-resistant enterococci (VRE), 33.2%; and resistant gram-negative bacilli (R-GNB), 32.0%. Risk factors for colonization at enrollment included prolonged hospitalization (>14 days), functional disability, antibiotic use, or device use. Rates per 1000 patient-days of acquiring a new MDRO were MRSA, 3.4; VRE, 8.2; and R-GNB, 13.6. MDRO colonization at discharge was similar to that at enrollment (56.4%): MRSA, 18.4%; VRE, 30.3%; and R-GNB, 33.6%. Conclusions Short-stay NF patients exhibit a high prevalence of MDROs near the time of admission, as well as at discharge, and may serve as a reservoir for spread in other healthcare settings. Future interventions to reduce MDROs should specifically target this population.
A radiomics model from joint FDG-PET and MRI texture features for the prediction of lung metastases in soft-tissue sarcomas of the extremities

This study aims at developing a joint FDG-PET and MRI texture-based model for the early evaluation of lung metastasis risk in soft-tissue sarcomas (STSs). We investigate if the creation of new composite textures from the combination of FDG-PET and MR imaging information could better identify aggressive tumours. Towards this goal, a cohort of 51 patients with histologically proven STSs of the extremities was retrospectively evaluated. All patients had pre-treatment FDG-PET and MRI scans comprised of T1-weighted and T2-weighted fat-suppression sequences (T2FS). Nine non-texture features (SUV metrics and shape features) and forty-one texture features were extracted from the tumour region of separate (FDG-PET, T1 and T2FS) and fused (FDG-PET/T1 and FDG-PET/T2FS) scans. Volume fusion of the FDG-PET and MRI scans was implemented using the wavelet transform. The influence of six different extraction parameters on the predictive value of textures was investigated. The incorporation of features into multivariable models was performed using logistic regression. The multivariable modeling strategy involved imbalance-adjusted bootstrap resampling in the following four steps leading to final prediction model construction: (1) feature set reduction; (2) feature selection; (3) prediction performance estimation; and (4) computation of model coefficients. Univariate analysis showed that the isotropic voxel size at which texture features were extracted had the most impact on predictive value. In multivariable analysis, texture features extracted from fused scans significantly outperformed those from separate scans in terms of lung metastases prediction estimates. The best performance was obtained using a combination of four texture features extracted from FDG-PET/T1 and FDG-PET/T2FS scans. This model reached an area under the receiver-operating characteristic curve of 0.984 ± 0.002, a sensitivity of 0.955 ± 0.006, and a specificity of 0.926 ± 0.004 in bootstrapping evaluations. Ultimately, lung metastasis risk assessment at diagnosis of STSs could improve patient outcomes by allowing better treatment adaptation.
Gradation Chart for Asphalt Mixes: Development

The gradation chart approach is based on the two parameters of Fuller's model (i.e., maximum size diameter and shape factor) which are obtained by fitting well-graded structures like those of Superpave or Covenin. ASTM mathematical definitions for gravel and sand, and Fuller's model are used to develop an analytical expression for a gravel-to-sand ratio used here to transform gradation into a numerical that may be correlated to HMA performance parameters. The gradation chart is a Cartesian plot conformed by shape factor and maximum size diameter and thus gradations, specification bands, gravel-to-sand ratios, and response parameters can be represented. Experimental results from recent research works performed by the National Center for Asphalt Technology on the mechanical and hydraulic performance of Superpave mixes are analyzed here. Based on these analyses, the writer resolved the controversy between below the restricted zone and above the restricted zone behavior, and found evidence that gradation specification bands (based on structure and maximum size diameter) would make no sense. Instead, the writer promotes "free design" in which a designer uses available aggregate, supported by a gradation-chart approach, to meet HMA performance parameters required by pavement design.
Demineralized Bone Matrix to Augment Tendon-Bone Healing: A Systematic Review

Background: Following injury to the rotator cuff and anterior cruciate ligament, a direct enthesis is not regenerated, and healing occurs with biomechanically inferior fibrous tissue. Demineralized bone matrix (DBM) is a collagen scaffold that contains growth factors and is a promising biological material for tendon and ligament repair because it can regenerate a direct fibrocartilaginous insertion via endochondral ossification. Purpose: To provide a comprehensive review of the literature investigating the use of DBM to augment tendon-bone healing in tendon repair and anterior cruciate ligament reconstruction (ACLR). Study Design: Systematic review. Methods: Electronic databases (MEDLINE and EMBASE) were searched for preclinical and clinical studies that evaluated the use of DBM in tendon repair and ACLR. Search terms included the following: (“demineralized bone matrix” OR “demineralized cortical bone”) AND (“tissue scaffold” OR “tissue engineering” OR “ligament” OR “tendon” OR “anterior cruciate ligament” OR “rotator cuff”). Peer-reviewed articles written in English were included, and no date restriction was applied (searches performed February 10, 2017). Methodological quality was assessed with peer-reviewed scoring criteria. Results: The search strategy identified 339 articles. After removal of duplicates and screening according to inclusion criteria, 8 studies were included for full review (tendon repair, n = 4; ACLR, n = 4). No human clinical studies were identified. All 8 studies were preclinical animal studies with good methodological quality. Five studies compared DBM augmentation with non-DBM controls, of which 4 (80%) reported positive findings in terms of histological and biomechanical outcomes. Conclusion: Preclinical evidence indicates that DBM can improve tendon-bone healing, although clinical studies are lacking. A range of animal models of tendon repair and ACLR showed that DBM can re-create a direct fibrocartilaginous enthesis, although the animal models are not without limitations. Before clinical trials are justified, research is required that determines the best source of DBM (allogenic vs xenogenic) and the best form of DBM (demineralized cortical bone vs DBM paste) to be used in them.
Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer

Multiplexed small molecule inhibitors covalently bound to Sepharose beads (MIBs) were used to capture functional kinases in luminal, HER2-enriched and triple negative, basal-like and claudin-low breast cancer cell lines and tumors. Kinase MIB-binding profiles at baseline without perturbation proteomically distinguished the four breast cancer subtypes. Kinases lacking defined functions in breast cancer were highly represented in the MIB-binding taxonomies. We show that these understudied kinases, whose disease associations and pharmacology are generally unexplored, are integrated in kinase signaling subnetworks with kinases that have been previously well characterized in breast cancer. Computationally it was possible to define subtypes using profiles of less than 50 of the more than 300 kinases bound to MIBs that included understudied as well as metabolic and lipid kinases. Furthermore, analysis of MIB-binding profiles established potential functional annotations for these understudied kinases. Thus, comprehensive MIBs-based capture of kinases provides a unique proteomics-based method for integration of poorly characterized kinases of the understudied kinome into functional subnetworks in breast cancer cells and tumors that is not possible using genomic strategies. The MIB-binding profiles readily defined subtype-selective differential adaptive kinome reprogramming in response to targeted kinase inhibition, demonstrating how MIB profiles can be used in determining dynamic kinome changes that result in subtype selective phenotypic state changes.
Joint adolescent–adult early phase clinical trials to improve access to new drugs for adolescents with cancer: proposals from the multi-stakeholder platform—ACCELERATE

The impressive progress recently observed in adult cancers through the introduction of new drugs has not yet been translated to adolescents between 12 and 17 years of age. Currently adolescents are grouped with children, so their access to new, effective drugs already available for adults is delayed because paediatric drug development starts late relative to adult programmes. Moreover, specific early phase trials designed exclusively for adolescents in rare diseases recruit poorly, even if conducted internationally. Evidence has shown that adolescents demonstrate similar toxicity profiles, maximum tolerated doses and pharmacokinetic parameters to adults. Although they may have specific vulnerabilities and their interests should be protected, they are, in many countries in Europe, entitled to provide informed consent themselves. There are no insurmountable scientific, medical, or regulatory barriers to their participation in Phase-I to III adult trials. Based on a review of the literature, the multi-stakeholder platform ACCELERATE, with representatives from academia, patient/parent advocacy groups, regulatory agencies and pharmaceutical companies, proposes the inclusion of adolescents in adult Phase-I to III trials of cancer drugs targeting a relevant disease or mechanism of action, without requiring preceding specific paediatric trials. The trials, however, should be delivered in age-appropriate clinical care settings by clinicians with adolescent trial expertise. Joint adolescent-adult trials will not exclude adolescents from participating in paediatric trials, as these approaches are complementary. This strategy is considered to be safe, rational, efficient and would provide more clinical trial options and accelerate drug development for adolescents with cancer.