Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design.

The relaxed complex scheme, a virtual-screening methodology that accounts for protein receptor flexibility, was used to identify a low-micromolar, non-bisphosphonate inhibitor of farnesyl diphosphate synthase. Serendipitously, we also found that several predicted farnesyl diphosphate synthase inhibitors were low-micromolar inhibitors of undecaprenyl diphosphate synthase. These results are of interest because farnesyl diphosphate synthase inhibitors are being pursued as both anti-infective and anticancer agents, and undecaprenyl diphosphate synthase inhibitors are antibacterial drug leads

Biobehavioral effects of Tai Chi Qigong in men with prostate cancer: Study design of a three-arm randomized clinical trial.

Fatigue is often one of the most commonly reported symptoms in prostate cancer survivors, but it is also one of the least understood cancer-related symptoms. Fatigue is associated with psychological distress, disruptions in sleep quality, and impairments in health-related quality of life. Moreover, inflammatory processes and changes related to the hypothalamic-pituitary-adrenal (HPA) axis and/or autonomic nervous system may also play a role in cancer-related fatigue. Thus, effective treatments for fatigue in prostate cancer survivors represent a current unmet need. Prior research has shown that Tai Chi Qigong, a mind-body exercise intervention, can improve physical and emotional health. Herein, we describe the protocol of the ongoing 3-arm randomized controlled Health Empowerment & Recovery Outcomes (HERO) clincal trial. One hundred sixty-six prostate cancer survivors with fatigue are randomized to a modified Tai Chi Qigong intervention (TCQ), intensity-matched body training intervention (BT), or usual care (UC) condition. Guided by biopsychosocial and psychoneuroimmunology models, we propose that TCQ, as compared to BT or UC will: i) reduce fatigue (primary outcome) in prostate cancer survivors; ii) reduce inflammation; and iii) regulate the expression of genes from two major functional clusters: a) inflammation, vasodilation and metabolite sensing and b) energy and adrenergic activation. Assessments are conducted at baseline, the 6-week midpoint of the intervention, and 1 week, 3 months, and 12 months post-intervention. If our findings show that TCQ promotes recovery from prostate cancer and its treatment, this type of intervention can be integrated into survivorship care plans as the standard of care. The study's findings will also provide novel information about underlying biobehavioral mechanisms of cancer-related fatigue. Trial registration number:NCT03326713; clinicaltrials.gov

Lysine 53 Acetylation of Cytochrome c in Prostate Cancer: Warburg Metabolism and Evasion of Apoptosis

Prostate cancer is the second leading cause of cancer-related death in men. Two classic cancer hallmarks are a metabolic switch from oxidative phosphorylation (OxPhos) to glycolysis, known as the Warburg effect, and resistance to cell death. Cytochrome c (Cytc) is at the intersection of both pathways, as it is essential for electron transport in mitochondrial respiration and a trigger of intrinsic apoptosis when released from the mitochondria. However, its functional role in cancer has never been studied. Our data show that Cytc is acetylated on lysine 53 in both androgen hormone-resistant and -sensitive human prostate cancer xenografts. To characterize the functional effects of K53 modification in vitro, K53 was mutated to acetylmimetic glutamine (K53Q), and to arginine (K53R) and isoleucine (K53I) as controls. Cytochrome c oxidase (COX) activity analyzed with purified Cytc variants showed reduced oxygen consumption with acetylmimetic Cytc compared to the non-acetylated Cytc (WT), supporting the Warburg effect. In contrast to WT, K53Q Cytc had significantly lower caspase-3 activity, suggesting that modification of Cytc K53 helps cancer cells evade apoptosis. Cardiolipin peroxidase activity, which is another proapoptotic function of the protein, was lower in acetylmimetic Cytc. Acetylmimetic Cytc also had a higher capacity to scavenge reactive oxygen species (ROS), another pro-survival feature. We discuss our experimental results in light of structural features of K53Q Cytc, which we crystallized at a resolution of 1.31 Å, together with molecular dynamics simulations. In conclusion, we propose that K53 acetylation of Cytc affects two hallmarks of cancer by regulating respiration and apoptosis in prostate cancer xenografts

Integrated Attack Tree in Residual Risk Management Framework

Safety-critical cyber-physical systems (CPSs), such as high-tech cars having cyber capabilities, are highly interconnected. Automotive manufacturers are concerned about cyber attacks on vehicles that can lead to catastrophic consequences. There is a need for a new risk management approach to address and investigate cybersecurity risks. Risk management in the automotive domain is challenging due to technological improvements and advances every year. The current standard for automotive security is ISO/SAE 21434, which discusses a framework that includes threats, associated risks, and risk treatment options such as risk reduction by applying appropriate defences. This paper presents a residual cybersecurity risk management framework aligned with the framework presented in ISO/SAE 21434. A methodology is proposed to develop an integrated attack tree that considers multiple sub-systems within the CPS. Integrating attack trees in this way will help the analyst to take a broad perspective of system security. Our previous approach utilises a flow graph to calculate the residual risk to a system before and after applying defences. This paper is an extension of our initial work. It defines the steps for applying the proposed framework and using adaptive cruise control (ACC) and adaptive light control (ALC) to illustrate the applicability of our work. This work is evaluated by comparing it with the requirements of the risk management framework discussed in the literature. Currently, our methodology satisfies more than 75% of their requirements

Communication reduction techniques in numerical methods and deep neural networks

Inter-node communication has turned out to be one of the determining factors of the performance on modern HPC systems. Furthermore, the situation only gets worse with the ever-incresing size of the cores involved. Hence, this thesis explore the various possible techniques to reduce the communication during the execution of a parallel program. It turned out that there is no one-size-fit-all approach to the challenge. Despite this, the problems in each field, due to their unique characteristics, dispose of distinct opportunities for the communication reduction. The thesis, first devles into numerical linear algebra, develops an evolution of the Pipelined CG called IFCG. It eliminates the synchronizations normally take place towards the end of each iteration to increase the parallelism. Secondly, the thesis draws its attention on reducing the necessity to transfer the parameters between the CPU host and GPUs during a neural network training. It develops two routines: ADT and AWP in order to compress and decompress the weights with a reduced data representation format prior and right after the data transfer takes place. The compress rate is adjusted vis-à-vis the L2-norm of the weights of every layer. In the third contribution, the thesis diminish the communication in model parallelizing a deep neural network. Instead of splitting and distributing the neurons of each layer to the available processes on the system, now it is done every other layers. This results in a 50% percent reduction of the communication whereas it introduces 50% of extra local FP computation.La comunicació entre els nodes de computació multi-core sorgeix com un dels factors principals que impacta el rendiment d’un sistema HPC d’avui en dia. I més, mentre més core es pusa, pitjor la situació. Per tant aquesta tesi explora les possibles tècniques per a reduir la comunicació en l’execució d’un programa paral·lel. Tot i això, resulta que no existeix una sola tècnica que pugui resoldre aquest obstacle. Tot i que els problemes en cada àmbit, com que té els seus propis caracristics, disposa variosos oportunitats per la reducció de comunicació. La tesi, en primer lloc, dins de l’àmbit de l’àlgebra lineal numèriques desenvolupa un algoritme IFCG que és una evolució de Pipelined CG. IFCG elimina les sincronitzacions normalment posa cap al final de cada iteració per augmentar el paral·lelisme. En la segona contribució, la tesi dirigeix l’atenció a reduir la necessitat de transferir els paràmetres entre el CPU i els GPUs durant l’entrenament d’una xarxa neuronal. Desenvolupa rutines ADT i AWP per comprimir i descomprimir els pesos amb una representació de dades reduïda abans i just desprès de la transferència. La representació es decideix dinàmicament segons el L2-norm dels pesos a cada capa. Al final la tesi disminueix la comunicació en paral·lelitzar el model duna xarxa neurona. En lloc de distribuir les neurones de cada capa als processos disponibles en el sistema, es fa cada dues capes. Així que corta com mitja de la comunicació. En canvi, com que distribueix només cada dues capes, les capes restes es repliquen, resulta que incorre en una augmenta de 50% de computació local.Postprint (published version

Reversion of Epithelial-Mesenchymal Transition by a Novel Agent DZ-50 via IGF Binding Protein-3 in Prostate Cancer Cells

Dysregulation of transforming growth factor-β1 (TGF-β1) and insulin-like growth factor (IGF) axis has been linked to reactive stroma dynamics in prostate cancer progression. IGF binding protein-3 (IGFBP3) induction is initiated by stroma remodeling and could represent a potential therapeutic target for prostate cancer. In previous studies a lead quinazoline-based Doxazosin® derivative, DZ-50, impaired prostate tumor growth by targeting proteins involved in focal adhesion, anoikis resistance and epithelial-mesenchymal-transition (EMT). This study demonstrates that DZ-50 increased expression of the epithelial marker E-cadherin, and decreased the mesenchymal marker N-cadherin in human prostate cancer cells. In DU-145 cells, the effect of DZ-50 on EMT towards mesenchymal epithelial transition (MET) was inhibited by talin1 overexpression, a focal adhesion regulator promoting anoikis resistance and tumor invasion. DZ-50 treatment of human prostate cancer cells and cancer-associated fibroblasts (CAFs) downregulated IGFBP3 expression at mRNA and protein level. In TGF-β1 responsive LNCaPTβRII, TGF-β1 reversed DZ-50-induced MET by antagonizing the drug-induced decrease of nuclear IGFBP3. Furthermore, co-culture with CAFs promoted prostate cancer epithelial cell invasion, an effect that was significantly inhibited by DZ-50. Our findings demonstrate that the lead compound, DZ-50, inhibited the invasive properties of prostate cancer epithelial cells by targeting IGFBP3 and mediating EMT conversion to MET. This study integrated the mechanisms underlying the effect of DZ-50 and further supported the therapeutic value of this compound in the treatment of advanced metastatic prostate cancer

Communication reduction techniques in numerical methods and deep neural networks

Inter-node communication has turned out to be one of the determining factors of the performance on modern HPC systems. Furthermore, the situation only gets worse with the ever-incresing size of the cores involved. Hence, this thesis explore the various possible techniques to reduce the communication during the execution of a parallel program. It turned out that there is no one-size-fit-all approach to the challenge. Despite this, the problems in each field, due to their unique characteristics, dispose of distinct opportunities for the communication reduction. The thesis, first devles into numerical linear algebra, develops an evolution of the Pipelined CG called IFCG. It eliminates the synchronizations normally take place towards the end of each iteration to increase the parallelism. Secondly, the thesis draws its attention on reducing the necessity to transfer the parameters between the CPU host and GPUs during a neural network training. It develops two routines: ADT and AWP in order to compress and decompress the weights with a reduced data representation format prior and right after the data transfer takes place. The compress rate is adjusted vis-à-vis the L2-norm of the weights of every layer. In the third contribution, the thesis diminish the communication in model parallelizing a deep neural network. Instead of splitting and distributing the neurons of each layer to the available processes on the system, now it is done every other layers. This results in a 50% percent reduction of the communication whereas it introduces 50% of extra local FP computation.La comunicació entre els nodes de computació multi-core sorgeix com un dels factors principals que impacta el rendiment d’un sistema HPC d’avui en dia. I més, mentre més core es pusa, pitjor la situació. Per tant aquesta tesi explora les possibles tècniques per a reduir la comunicació en l’execució d’un programa paral·lel. Tot i això, resulta que no existeix una sola tècnica que pugui resoldre aquest obstacle. Tot i que els problemes en cada àmbit, com que té els seus propis caracristics, disposa variosos oportunitats per la reducció de comunicació. La tesi, en primer lloc, dins de l’àmbit de l’àlgebra lineal numèriques desenvolupa un algoritme IFCG que és una evolució de Pipelined CG. IFCG elimina les sincronitzacions normalment posa cap al final de cada iteració per augmentar el paral·lelisme. En la segona contribució, la tesi dirigeix l’atenció a reduir la necessitat de transferir els paràmetres entre el CPU i els GPUs durant l’entrenament d’una xarxa neuronal. Desenvolupa rutines ADT i AWP per comprimir i descomprimir els pesos amb una representació de dades reduïda abans i just desprès de la transferència. La representació es decideix dinàmicament segons el L2-norm dels pesos a cada capa. Al final la tesi disminueix la comunicació en paral·lelitzar el model duna xarxa neurona. En lloc de distribuir les neurones de cada capa als processos disponibles en el sistema, es fa cada dues capes. Així que corta com mitja de la comunicació. En canvi, com que distribueix només cada dues capes, les capes restes es repliquen, resulta que incorre en una augmenta de 50% de computació local