Miracle-dz/UniFAR-FTUs huggingface dataset:
Decision support system for localizing prostate cancer based on multiparametric magnetic resonance imaging.

PURPOSE There is a growing need to localize prostate cancers on magnetic resonance imaging (MRI) to facilitate the use of image guided biopsy, focal therapy, and active surveillance follow up. Our goal was to develop a decision support system (DSS) for detecting and localizing peripheral zone prostate cancers by using machine learning approach to calculate a cancer probability map from multiparametric MR images (MP-MRI). METHODS This IRB approved Health Insurance Portability and Accountability Act compliant retrospective study consisted of 31 patients (mean age and serum prostate specific antigen of 60.4 and 6.62 ng/ml, respectively) who had MP-MRI at 3 T followed by radical prostatectomy. Seven patients were excluded due to technical issues with their MP-MRI (e.g., motion artifact, failure to perform all sequences). Cancer and normal regions were identified in the peripheral zone by correlating them to whole mount histology slides of the excised prostatectomy specimens. To facilitate the correlation, tissue blocks matching the MR slices were obtained using a MR-based patient-specific mold. Segmented regions on the MP-MRI were correlated to histopathology and used as training sets for the learning system that generated the cancer probability maps. Leave-one-patient-out cross-validation on the cancer and normal regions was performed to determine the learning system's efficacy, an evolutionary strategies approach (also known as a genetic algorithm) was used to find the optimal values for a set of parameters, and finally a cancer probability map was generated. RESULTS For the 24 patients that were used in the study, 225 cancer and 264 noncancerous regions were identified from the region maps. The efficacy of DSS was first determined without optimizing support vector machines (SVM) parameters, where a region having a cancer probability greater than or equal to 50% was considered as a correct classification. The nonoptimized system had an f-measure of 85% and the Kappa coefficient of 71% (Rater's agreement, where raters are DSS and ground truth histology). The efficacy of the DSS after optimizing SVM parameters using a genetic algorithm had an f-measure of 89% and a Kappa coefficient of 80%. Thus, after optimization of the DSS there was a 4% increase in the f-measure and a 9% increase in the Kappa coefficient. CONCLUSIONS This DSS provides a cancer probability map for peripheral zone prostate tumors based on endorectal MP-MRI. These cancer probability maps can potentially aid radiologists in accuratelylocalizing peripheral zone prostate cancers for planning targeted biopsies, focal therapy, and follow up for active surveillance.
Imaging simulated secondary caries lesions with cross polarization OCT

The clinical diagnosis of secondary caries has been found to account for the replacement of the majority of intra-coronal restorations. Current methods to diagnose the presence of these lesions at early stages are considered insufficient due to their low sensitivity. Polarization-sensitive optical coherence tomography (PS-OCT) imaging studies have confirmed its effectiveness for imaging carious subsurface lesions in enamel and dentin. The objective of this study was to determine if PS-OCT can be used to nondestructively image demineralization through resin restorations on extracted teeth with both simulated and natural lesions. Simulated secondary caries lesions were created by exposing cavity preparations made in extracted human teeth to a demineralizing solution for 48 hours and subsequently restoring with resin. Negative control restorations were also prepared on each tooth. Optical changes in demineralized versus control preparations beneath restorations were measured as a function of depth using PS-OCT. PS-OCT images indicated that a significant increase in reflectivity and depth occurred in the simulated lesions compared with the control preparations. This study suggests that PS-OCT is well-suited to nondestructively detect early caries lesions in enamel beneath composite restorations.
Supporting the pillars of life quality in long-term care

ABSTRACT Issues of life quality and what that means for the very old in the population who are ageing and becoming frail in large numbers require new thinking regarding a practical application of quality of-life theory to enhance the experience of living in aged care contexts. Quality of life also has importance for care providers wishing to judge the quality of their services. Assumptions that disease and disability dictate life quality undermine the centrality of individual experiences, and assumptions regarding spirituality and religion can confuse approaches to services offered to a cohort of people whose focus is on spiritual well-being. Information gathered on aged care residents’ experiences of life quality can focus attention on supporting positive experiences during late age. If the potential for quality of life is strengthened, individual pursuit of higher meaning may be fostered. Appropriate support and care within care services can be enhanced through reliable assessment of factors that sustain quality of life. It is argued that quality of life can exist separately from disease or disability, that spirituality and religion are not synonymous, and that concepts of life quality and spirituality are not causally related and are therefore more reliably assessed as separate phenomena.
Early detection of in-the-wild botnet attacks by exploiting network communication uniformity: An empirical study

Distributed attacks originating from botnet-infected machines (bots) such as large-scale malware propagation campaigns orchestrated via spam emails can quickly affect other network infrastructures. As these attacks are made successful only by the fact that hundreds of infected machines engage in them collectively, their damage can be avoided if machines infected with a common botnet can be detected early rather than after an attack is launched. Prior studies have suggested that outgoing bot attacks are often preceded by other “tell-tale” malicious behaviour, such as communication with botnet controllers (C&C servers) that command botnets to carry out attacks. We postulate that observing similar behaviour occuring in a synchronised manner across multiple machines is an early indicator of a widespread infection of a single botnet, leading potentially to a large-scale, distributed attack. Intuitively, if we can detect such synchronised behaviour early enough on a few machines in the network, we can quickly contain the threat before an attack does any serious damage. In this work we present a measurement-driven analysis to validate this intuition. We empirically analyse the various stages of malicious behaviour that are observed in real botnet traffic, and carry out the first systematic study of the network behaviour that typically precedes outgoing bot attacks and is synchronised across multiple infected machines. We then implement as a proof-of-concept a set of analysers that monitor synchronisation in botnet communication to generate early infection and attack alerts. We show that with this approach, we can quickly detect nearly 80% of real-world spamming and port scanning attacks, and even demonstrate a novel capability of preventing these attacks altogether by predicting them before they are launched.
A Low-Power, Highly Scalable, Vertical Double-Gate MOSFET Using Novel Processes

A sub-45-nm body thickness, vertical-channel, double-gate MOSFET (VDFET) is fabricated on a bulk silicon substrate. The process, in principle, is scalable down to sub-5-nm body thicknesses. It is realized that using very coarse lithography (~1 mum resolution) does not require chemical-mechanical polarization (CMP), and is capable of being integrated with a planar CMOS flow. It relies on the following key, novel, unit processes: (1) a spacer process capable of thickness down to 5 nm; (2) an additional self-aligned process for obtaining a thicker bottom/corner oxide, thus, minimizing leakage and parasitic capacitance; (3) a novel drain contact process including etch stop and implant. Each unit process, by itself, exhibits the versatility to be used in other applications too. Various implant conditions, order of implant step, and starting substrate dopings are studied, and best conditions identified through TSUPREM4 simulations, and later, through experiments to ensure process robustness and dopant tunability for the thin-body vertical double-gate MOSFETs (VDFETs). Drain was implanted separately for better channel length control. Excellent electrical properties in terms of Id - Vds,Id - Vgs, and Ig - Vgs are measured. Electrical results show excellent short-channel effect (SCE) immunity and close to an ideal subthreshold slope (64 mV/dec), resulting in a very high ION-IOFF ratio. In addition, the impact of body thickness and the drain contact area on I-V curves and the impact of the Si3N4 etch-stop layer on channel current enhancement are studied.
Cyberterrorism definition patterns and mitigation strategies: A literature review

This paper aim to contribute to the body of knowledge on cyber terrorism, improves awareness of cyber terrorism definition, boundaries, potential targets, crime patterns and effective mitigation strategies through analysis of relevant literature on the issue produced in recent years. It details the definitional origins of the concept and It looks at motivational factors and level of destruction necessary to classify a cyber-attack as cyberterrorism. The second sections is devoted to literature distinguishing cyberterrorism from hacking and cybercrime. Section three details the stages of a cyber attack, Section four lists the types of infrastructure targeted for cyber terrorists and Section five focuses on mitigation strategies.
Stimulation of nitric oxide, cytokine and prostaglandin production by low-molecular weight fractions of probiotic Lactobacillus casei lysate.

OBJECTIVES Major medical indications of probiotic bacteria are conditions associated with the gastrointestinal tract. They exhibit not only the local but also systemic effects, the molecular mechanisms of which are poorly understood. We hypothesized that the action at remote sites of the body could be at least partially attributed to substances of the low molecular mass released from digested bacteria and able to cross the intestinal barrier. The aim of the study was the analysis of immunobiological properties of bacterial lysates and characterization of chemical constituents participating on this mode of action. METHODS Lactobacillus casei probiotic strain DN-114001 was employed. Lysates were prepared by passing bacteria through a French press (1500 psi) followed by lyophilisation. The fractions were prepared by the microfiltration of the crude lysate using the 3-, 10-, 30-, 50-, and 100-kDa cutoff filters (Amicon® Ultra 0.5 ml, Millipore Corp.). This procedure completely removes biologically active bacterial macromolecules such as peptidoglycan (PGN), lipoteichoic acid (LTA) and lipopolysaccharide (LPS). Effects of microfiltrates on the in vitro production of nitric oxide (NO), cytokines, and prostaglandin E2 (PGE2) were investigated in rat peritoneal cells. RESULTS The original crude lysate (≤10 µg/ml) activated the biosynthesis of NO, PGE2, and secretion of cytokines. The amount of the lysate needed for the preparation of microfiltered fractions exhibiting immunostimulatory effects was 10-fold higher (100 µg/ml). The molecules with the molecular mass ≤3 kDa were responsible for approximately 45% and 83% of the NO- and PGE2-enhancing activities of the crude lysate, respectively. The microfiltered fractions of the lysate also enhanced secretion of interleukin-6 and tumor necrosis factor-α but not that of interleukin-10 and interferon-γ. CONCLUSION The Lactobacillus casei probiotic strain DN-114001 contains low molecular mass (≤3 kDa) molecules possessing immunostimulatory properties. Their chemical nature remains to be identified.
Stitching proteins into membranes, not sew simple

Abstract Most integral membrane proteins located within the endomembrane system of eukaryotic cells are first assembled co-translationally into the endoplasmic reticulum (ER) before being sorted and trafficked to other organelles. The assembly of membrane proteins is mediated by the ER translocon, which allows passage of lumenal domains through and lateral integration of transmembrane (TM) domains into the ER membrane. It may be convenient to imagine multi-TM domain containing membrane proteins being assembled by inserting their first TM domain in the correct orientation, with subsequent TM domains inserting with alternating orientations. However a simple threading model of assembly, with sequential insertion of one TM domain into the membrane after another, does not universally stand up to scrutiny. In this article we review some of the literature illustrating the complexities of membrane protein assembly. We also present our own thoughts on aspects that we feel are poorly understood. In short we hope to convince the readers that threading of membrane proteins into membranes is ‘not sew simple’ and a topic that requires further investigation.
Descending necrotizing mediastinitis after a trigger point injection

Descending necrotizing mediastinitis (DNM) is a rare form of mediastinal infection. Most cases are associated with esophageal rupture. DNM after a trigger point injection in the upper trapezius has not been described previously. We present a case of DNM after a trigger point injection in the upper trapezius. A 70-year-old man visited the emergency department with chest discomfort and fever after a trigger point injection in the left upper trapezius. Chest computed tomography showed evidence of DNM, and antibiotic therapy was immediately administered intravenously. Because of the risk of sudden death, poor prognosis due to underlying disease, and his age, he declined surgical treatment and died of septic shock. Although trigger point injections are generally considered safe, caution should be used in patients with an underlying disease or in the elderly. Early diagnosis, broad-spectrum antibiotics, and aggressive surgical management are essential to improve the prognosis.
Application of UWB and GPS technologies for vehicle localization in combined indoor-outdoor environments

Ultra-wide band (UWB) sensors are innovative devices constructed for efficient wireless communications that have recently being used for vehicle localization in indoor environments. In contrast, GPS sensors are well-known satellite-based positioning devices widely extended for outdoor applications. We evaluate in this paper the combination of both technologies for efficient positioning of vehicles in a mixed scenario (both indoor and outdoor situations), which is typical in applications such as automatic guided vehicles transporting and storing goods among warehouses. The framework we propose for combining sensor information is Monte Carlo localization (also known as particle filters), which is a versatile solution to the fusion of different sensory data and exhibits a number of advantages with respect to other localization techniques. In the paper we describe our approach and evaluate it with several simulated experiments that have yielded promising results. This work, supported by the European project CRAFT-COOP-CT-2005-017668, becomes a first step toward a robust and reliable localization system for automated industrial vehicles.
Expression of cadherin 23 isoforms is not conserved: implications for a mouse model of Usher syndrome type 1D

Purpose We compared cadherin 23 (Cdh23) mRNA and protein variants in the inner ear and retina of wild-type and mutant mice and primates to better understand the pleiotropic effects of Cdh23 mutations, and specifically to understand the absence of retinal degeneration in Cdh23 mutant mice. Methods Semiquantitative real-time PCR was used to compare the level of expression of Cdh23 alternative transcripts in the inner ear and retina of wild-type and homozygous Cdh23v-6J (waltzer) mice. Antibodies generated against CDH23 isoforms were used in immunohistochemistry, immunohistology, electron microscopy, and western blot analyses of mouse and primate inner ear and retina to study the distribution of these isoforms in various cellular compartments. Results Cdh23 mRNA alternative splice variants were temporally and spatially regulated in the inner ear and retina. In the mature mouse retina, CDH23 isoforms were broadly expressed in various cellular compartments of the photoreceptor layer. The wild-type CDH23_V3 protein isoform, which has PDZ binding motifs but neither extracellular domains nor a transmembrane domain, localized exclusively to the outer plexiform layer of the retina containing photoreceptor cell synapses and to the synaptic region of auditory and vestibular hair cells. The longest CDH23 protein isoform, CDH23_V1, appeared by western blotting to be the only one affected by the Cdh23v-6J mutation; it was expressed in the wild-type mouse inner ear, but not in the mouse retina. However, CDH23_V1 was detected in western blot analyses of monkey and human retinas. Conclusions The time- and tissue-dependent expression patterns that we have shown for Cdh23 alternative transcripts suggest developmental roles and tissue-specific functions for the various transcripts. Many of these isoforms continue to be expressed in waltzer mice. The longest CDH23 isoform (CDH23_V1), however, is not expressed in mutant mice and is necessary for normal inner ear function. The longest isoform is expressed in the retinas of primates, but not detected in the mouse retina. This species difference suggests that the mouse may not be a suitable model for studying the retinitis pigmentosa phenotype of human Usher syndrome type 1D.
Investigating into the Prevalence of Complex Event Processing and Predictive Analytics in the Transportation and Logistics Sector: Initial Findings From Scientific Literature

As ever new sensor solutions are invading people’s everyday lives and business processes, the use of the signals and events provided by the devices poses a challenge. Innovative ways of handling the large amount of data promise an effective and efficient means to overcome that challenge. With the help of complex event processing and predictive techniques, added value can be created. While complex event processing is able to process the multitude of signals coming from the sensors in a continuous manner, predictive analytics addresses the likelihood of a certain future state or behavior by detecting patterns from the signal database and predicting the future according to the detections. As to the transportation and logistics domain, processing the signal stream and predicting the future promises a big impact on the operations because the transportation and logistics sector is known as a very complex one. The complexity of the sector is linked with the many stakeholders taking part in a variety of operations and the partly high level of automation often being accompanied by manual processes. Hence, predictions help to prepare better for upcoming situations and challenges and, thus, to save resources and cost. The present paper is to investigate the prevalence of complex event processing and predictive analytics in logistics and transportation cases in the research literature in order to motivate a subsequent systematic literature view as the next step in the research endeavor.
Biological Significance of the Importin‐β Family‐Dependent Nucleocytoplasmic Transport Pathways

Importin‐β family proteins (Imp‐βs) are nucleocytoplasmic transport receptors (NTRs) that import and export proteins and RNAs through the nuclear pores. The family consists of 14–20 members depending on the biological species, and each member transports a specific group of cargoes. Thus, the Imp‐βs mediate multiple, parallel transport pathways that can be regulated separately. In fact, the spatiotemporally differential expressions and the functional regulations of Imp‐βs have been reported. Additionally, the biological significance of each pathway has been characterized by linking the function of a member of Imp‐βs to a cellular consequence. Connecting these concepts, the regulation of the transport pathways conceivably induces alterations in the cellular physiological states. However, few studies have linked the regulation of an importin‐β family NTR to an induced cellular response and the corresponding cargoes, despite the significance of this linkage in comprehending the biological relevance of the transport pathways. This review of recent reports on the regulation and biological functions of the Imp‐βs highlights the significance of the transport pathways in physiological contexts and points out the possibility that the identification of yet unknown specific cargoes will reinforce the importance of transport regulation.
Speech modelling using cepstral-time feature matrices and hidden Markov models

Conventional HMMs assume that speech spectral vectors are uncorrelated. The use of information on the temporal evolution of spectral features, within each state, can improve recognition accuracy and produce a more robust recognition system. The authors present experimental results on improvements in speech recognition using cepstral-time matrix units. Experimental evaluation using a spoken digit data base and a spoken alphabet data base, indicates that the use of cepstral-time matrix features in noisy conditions can provide an improvement in recognition of as much as 20% in comparison to a conventional spectral vector comprising of cepstral, delta cepstral and delta-delta cepstral features. <<ETX>>
Blogging: Digital media and society series (second edition) [Book Review]

Review(s) of: Blogging: Digital media and society series (second edition), by Walker Rettberg, Jill, Polity, Cambridge, 2013, ISBN 9 7807 4566 3654, viii+196 pp., AU$31.95, Distributor Wiley.
Breast cancer patients' personality style, age, and treatment decision making

Previous studies have shown that whereas nearly all cancer patients want information, far fewer wish to make treatment decisions. Although breast cancer patients who were given a choice of lumpectomy versus mastectomy and were encouraged to make the decision were believed to do better psychologically, a 1994 study refuted this. Some authors suggest that patient personality style is an important consideration in decisional preference.
Modest nonadherence to antiretroviral therapy promotes residual HIV-1 replication in the absence of virological rebound in plasma.

BACKGROUND Modern antiretroviral therapy (ART) regimens are widely assumed to forgive modest nonadherence, because virological suppression in plasma is common at adherence levels of >70%. Yet, it is unknown whether human immunodeficiency virus type 1 (HIV-1) replication is completely suppressed at these levels of adherence. METHODS We longitudinally quantified levels of cell-associated HIV-1 RNA and DNA in 40 patients (median duration of successful ART before study initiation, 46 months), whose 1-week adherence to therapy prior to the sampling moments was measured electronically. RESULTS Patients were constantly 100% adherent (the optimal-adherence group), demonstrated improving adherence over time (the improving-adherence group), or neither of the above (the poor-adherence group). Adherence never decreased to <70% in any patient, and no rebound in plasma virological levels was observed. Nevertheless, poor adherence but not optimal or improving adherence caused a significant longitudinal increase in cell-associated HIV RNA levels (P = .006). Time-weighted changes and regression slopes of viral RNA load for the poor-adherence group were significantly higher than those for the optimal-adherence group (P < .01). CONCLUSIONS Because ART only blocks infection of new cells but not viral RNA transcription in cells infected before therapy initiation, the observed effects strongly suggest that modest nonadherence can cause new cycles of HIV-1 replication that are undetectable by commercial plasma viral load assays.