Dual-intended deep learning model for breast cancer diagnosis in ultrasound imaging

Automated medical data analysis demonstrated a significant role in modern medicine, and cancer diagnosis/prognosis to achieve highly reliable and generalizable systems. In this study, an automated breast cancer screening method in ultrasound imaging is proposed. A convolutional deep autoencoder model is presented for simultaneous segmentation and radiomic extraction. The model segments the breast lesions while concurrently extracting radiomic features. With our deep model, we perform breast lesion segmentation, which is linked to low-dimensional deep-radiomic extraction (four features). Similarly, we used high dimensional conventional imaging throughputs and applied spectral embedding techniques to reduce its size from 354 to 12 radiomics. A total of 780 ultrasound images—437 benign, 210, malignant, and 133 normal—were used to train and validate the models in this study. To diagnose malignant lesions, we have performed training, hyperparameter tuning, crossvalidation, and testing with a random forest model. This resulted in a binary classification accuracy of 78.5% (65.1–84.1%) for the maximal (full multivariate) cross-validated model for a combination of radiomic groups

Data Fusion of Objects Using Techniques Such as Laser Scanning, Structured Light and Photogrammetry for Cultural Heritage Applications

In this paper we present a semi-automatic 2D-3D local registration pipeline capable of coloring 3D models obtained from 3D scanners by using uncalibrated images. The proposed pipeline exploits the Structure from Motion (SfM) technique in order to reconstruct a sparse representation of the 3D object and obtain the camera parameters from image feature matches. We then coarsely register the reconstructed 3D model to the scanned one through the Scale Iterative Closest Point (SICP) algorithm. SICP provides the global scale, rotation and translation parameters, using minimal manual user intervention. In the final processing stage, a local registration refinement algorithm optimizes the color projection of the aligned photos on the 3D object removing the blurring/ghosting artefacts introduced due to small inaccuracies during the registration. The proposed pipeline is capable of handling real world cases with a range of characteristics from objects with low level geometric features to complex ones

Lime Cake as an Alternative Stabiliser for Loose Clayey Loams

Lime Cake (precipitated calcium carbonate PCC), a by-product of sugar production, is proposed as a stabiliser for improvement of loose silty clayey loams. Two inorganic pedogenic and organic precipitated calcium carbonate polymorphs are artificially synthesized into a base loosely compacted loamy soil. Formation, micromorphology, quality of cementing bonds, and physiochemical interactions in the interlayer are modelled at molecular level and verified by a suite of micro-analytical spectrometry techniques. Emphasis is put into determining the impacts of polysaccharides on soil strength and implications on soil pore anatomy. Erodibility, compressibility, volumetric change, and hydro-mechanical behaviour of base, and modified soils at yield and post-yield states are studied. Anomalies in suction-controlled post-yield stress–strain behaviour of modified soils are discussed and explained within the tenets of mechanics of composite soils with double porosity. PCC-reinforcement offers the closest possible packing at optimum water content. Desiccation cracking remains likely, but at relatively higher lower-bound water contents. Under low confinement levels and unsaturated state, strain-hardening prevails. Loss of shear strength on saturation is minimal. When saturated, PCC-reinforced soil develops substantially high levels of shear strength at all strain levels. Higher levels of confinement are needed for organic fibrous and onion-skin coating matters to effectively encrust the soil pore network; such high levels, however, leads to formation of an unwelcomed brittle, strain–softening stress–stress behaviour

Interactions in vivo between the Vif protein of HIV-1 and the precursor (Pr55GAG) of the virion nucleocapsid proteins

The abnormality of viral core structure seen in vif-defective HIV-1 grown in PBMCs has suggested a role for Vif in viral morphogenesis. Using an in vivo mammalian two-hybrid assay, the interaction between Vif and the precursor (Pr55GAG) of the virion nucleocapsid proteins has been analysed. This revealed the amino-terminal (aa 1–22) and central (aa 70–100) regions of Vif to be essential for its interaction with Pr55GAG, but deletion of the carboxy-terminal (aa 158–192) region of the protein had only a minor effect on its interaction. Initial deletion studies carried out on Pr55GAG showed that a 35-amino-acid region of the protein bridging the MA(p17)–CA(p24) junction was essential for its ability to interact with Vif. Site-directed mutagenesis of a conserved tryptophan (Trp21) near the amino terminus of Vif showed it to be important for the interaction with Pr55GAG. By contrast, mutagenesis of the highly conserved YLAL residues forming part of the BC-box motif, shown to be important in Vif promoting degradation of APOBEC3G/3F, had little or no effect on the Vif–Pr55GAG interaction

Optimised plasma sample preparation and LC-MS analysis to support large-scale proteomic analysis of clinical trial specimens : application to the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial

This work was performed by funding from The University of Sydney (CIA Jenkins) and funds provided by the National Health and Medical Research Council (Australia) APP1147897Purpose: Robust, affordable plasma proteomic biomarker workflows are needed for large-scale clinical studies. We evaluated aspects of sample preparation to allow LC-MS analysis of more than 1500 samples from the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial of adults with type 2 diabetes. Methods: Using LC-MS with data-independent acquisition we evaluated four variables: plasma protein depletion, EDTA or citrated anti-coagulant blood collection tubes, plasma lipid depletion strategies and plasma freeze-thaw cycles. Optimised methods were applied in a pilot study of FIELD participants. Results: LC-MS of undepleted plasma conducted over a 45 min gradient yielded 172 proteins after excluding immunoglobulin isoforms. Cibachrome-blue-based depletion yielded additional proteins but with cost and time expenses, while immunodepleting albumin and IgG provided few additional identifications. Only minor variations were associated with blood collection tube type, delipidation methods and freeze-thaw cycles. From 65 batches involving over 1500 injections, the median intra-batch quantitative differences in the top 100 proteins of the plasma external standard was less than 2%. Fenofibrate altered seven plasma proteins. Conclusions and Clinical Relevance: A robust plasma handling and LC-MS proteomics workflow for abundant plasma proteins has been developed for large-scale biomarker studies that balances proteomic depth with time and resource costs.Publisher PDFPeer reviewe

Sacrocolpopexy without concomitant posterior repair improves posterior compartment defects

The aim of this study is to determine posterior compartment topography 1-year after sacrocolpopexy (SC). Women who had SC without concomitant anterior or posterior repairs for symptomatic pelvic organ prolapse (POP) were included. Vaginal topography was assessed at baseline and 1-year postoperatively using POP quantification (POPQ). At baseline, 24% had stage IV POP, 68% stage III, and 8% stage II. One year after surgery, 75% had stage 0/I POP, 24% stage II, and 1% stage III. 112 (75%) were objectively cured (stage 0 or I POP). Anterior compartment was the most common site of POP persistence or recurrence (Ba ≥ stage II in 23 women) followed by posterior compartment (Bp ≥ stage II in 12 women) and apex (C ≥ stage II in 2 women). In 1-year follow-up, SC without concomitant posterior repair restores posterior vaginal topography in the majority of women with undergoing SC

Adipocyte-specific protein tyrosine phosphatase 1B deletion increases lipogenesis, adipocyte cell size and is a minor regulator of glucose homeostasis

Peer reviewedPublisher PD

Renegotiation and Relative Performance Evaluation: Why an Informative Signal may be Useless

Although Holmström's informativeness criterion provides a theoretical foundation for the controllability principle and inter firm relative performance evaluation, empirical and field studies provide only weak evidence on such practices. This paper refines the traditional informativeness criterion by abandoning the conventional full-commitment assumption. With the possibility of renegotiation, a signal's usefulness in incentive contracting depends on its information quality, not simply on whether the signal is informative. This paper derives conditions for determining when a signal is useless and when it is useful. In particular, these conditions will be met when the signal's information quality is either sufficiently poor or sufficiently rich

Platelet-Activating Factor Induces Epigenetic Modifications in Human Mast Cells

UV radiation-induced systemic immune suppression is a major risk factor for skin cancer induction. The migration of dermal mast cells from the skin to the draining lymph nodes has a prominent role in activating systemic immune suppression. UV-induced keratinocyte-derived platelet-activating factor (PAF) activates mast cell migration, in part by upregulating the expression of CXCR4 on the surface of mast cells. Others have indicated that epigenetic mechanisms regulate CXCR4 expression; therefore, we asked whether PAF activates epigenetic mechanisms in mast cells. Human mast cells were treated with PAF, and the effect on DNA methylation and/or acetylation was measured. PAF suppressed the expression of DNA methyltransferase (DNMT) 1 and 3b. On the other hand, PAF increased p300 histone acetyltransferase expression, and the acetylation of histone H3, which coincided with a decreased expression of the histone deacetylase HDAC2. Chromatin immunoprecipitation assays indicated that PAF treatment activated the acetylation of the CXCR4 promoter. Finally, inhibiting histone acetylation blocked p300 upregulation and suppressed PAF-induced surface expression of CXCR4. Our findings suggest a novel molecular mechanism for PAF, activation of epigenetic modifications. We suggest that PAF may serve as an endogenous molecular mediator that links the environment (UV radiation) with the epigenome

Effect of Curcuma longa and Ocimum sanctum on myocardial apoptosis in experimentally induced myocardial ischemic-reperfusion injury

BACKGROUND: In the present investigation, the effect of Curcuma longa (Cl) and Ocimum sanctum (Os) on myocardial apoptosis and cardiac function was studied in an ischemia and reperfusion (I-R) model of myocardial injury. METHODS: Wistar albino rats were divided into four groups and orally fed saline once daily (sham, control IR) or Cl (100 mg/kg; Cl-IR) or Os (75 mg/kg; Os-IR) respectively for 1 month. On the 31(st )day, in the rats of the control IR, Cl-IR and Os-IR groups LAD occlusion was undertaken for 45 min, and reperfusion was allowed for 1 h. The hemodynamic parameters{mean arterial pressure (MAP), heart rate (HR), left ventricular end-diastolic pressure (LVEDP), left ventricular peak positive (+) LVdP/dt (rate of pressure development) and negative (-) LVdP/dt (rate of pressure decline)} were monitored at pre-set points throughout the experimental duration and subsequently, the animals were sacrificed for immunohistopathological (Bax, Bcl-2 protein expression & TUNEL positivity) and histopathological studies. RESULTS: Chronic treatment with Cl significantly reduced TUNEL positivity (p < 0.05), Bax protein (p < 0.001) and upregulated Bcl-2 (p < 0.001) expression in comparison to control IR group. In addition, Cl demonstrated mitigating effects on several myocardial injury induced hemodynamic {(+)LVdP/dt, (-) LVdP/dt & LVEDP} and histopathological perturbations. Chronic Os treatment resulted in modest modulation of the hemodynamic alterations (MAP, LVEDP) but failed to demonstrate any significant antiapoptotic effects and prevent the histopathological alterations as compared to control IR group. CONCLUSION: In the present study, significant cardioprotection and functional recovery demonstrated by Cl may be attributed to its anti-apoptotic property. In contrast to Os, Cl may attenuate cell death due to apoptosis and prevent the impairment of cardiac performance