We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired ...by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5 ×.
Members of the Bromodomain and Extra-Terminal (BET) family of bromodomain-containing proteins (BRD2, BRD3, BRD4, and BRDT) bind to acetylated lysine residues on histone tails and act as epigenetic ...readers to regulate chromatin structure and gene expression. In particular, BET family member BRD4 has been shown to positively regulate the expression of MYC and other critical cancer-associated genes through the localization of BRD4 to super-enhancer regulatory elements. Results from preclinical studies conducted using the small molecule tool BET inhibitor (+)-JQ1, and emerging data from clinical trials of BET inhibitors in leukemia and lymphoma patients, have provided support for the therapeutic potential of BET inhibitors in hematologic malignancies.
A protein structure-guided drug design approach was employed to explore small molecule acetyl lysine mimetics and led to the identification of the BET inhibitor FT-1101, which is structurally unrelated to reported clinical-stage BET inhibitors in the (+)-JQ1 class. In biochemical binding assays, FT-1101 displayed equipotent inhibition of binding of both bromodomains in all four BET family members to a known bromodomain ligand (Kd ≤ 20 nM). In vitro, FT-1101 displayed potent anti-proliferative activity across a broad panel of human leukemia, lymphoma, and multiple myeloma cell lines, with 66 out of 123 cell lines having IC50 values < 500 nM. For the MV-4-11 acute myeloid leukemia cell line, the anti-proliferative activity of FT-1101 (IC50 = 40 nM) correlated with down-regulation of MYC gene and protein expression, suggesting that its anti-proliferative activity was at least in part due to suppression of MYC. Additionally, genome-wide mapping of BRD4 super-enhancer binding sites in MV-4-11 cells by ChIP-sequencing identified several potential pharmacodynamic biomarkers outside of the MYC signaling network.
In vivo, in the MV-4-11 xenograft model, oral treatment with FT-1101 at its maximum tolerated dose resulted in significant tumor growth inhibition, including tumor regressions, on schedules ranging from once daily to once weekly, and similar activity was also observed in the THP-1 AML xenograft model. Superior in vivo efficacy in the MV-4-11 model was observed for FT-1101 relative to BET inhibitors of the (+)-JQ1 class. In vivo efficacy was associated with prolonged drug exposure and a >75% decrease in MYC gene expression in tumors that was sustained for at least 12 hours. FT-1101 also crossed the blood-brain barrier in mice, achieving a pharmacologically relevant free drug concentration in the brain.
The promising preclinical profile of FT-1101 warranted its rapid progression into human clinical trials, and a Phase 1 study in patients with relapsed refractory acute leukemia or high-risk myelodysplastic syndrome is currently underway.
No relevant conflicts of interest to declare.
ObjectivesDescribe the use and findings of cardiopulmonary imaging-chest X-ray (cX-ray), echocardiography (cEcho), chest CT (cCT), lung ultrasound (LUS), and/or cardiac magnetic resonance imaging ...(cMRI)-in COVID-19 hospitalizations in Latin America (LATAM). BackgroundThere is a lack of information on the images used and their findings during the SARS-CoV-2 pandemic in LATAM. MethodsMulticenter, prospective, observational study of COVID-19 inpatients, conducted from March to December 2020, from 12 high-complexity centers, in nine LATAM countries. Adults (>18 years) with at least one imaging modality performed, followed from admission until discharge and/or in-hospital death, were included. ResultsWe studied 1,435 hospitalized patients (64% males) with a median age of 58 years classified into three regions: Mexico (Mx), 262; Central America and Caribbean (CAC), 428; and South America (SAm), 745. More frequent comorbidities were overweight/obesity, hypertension, and diabetes. During hospitalization, 58% were admitted to the ICU. The in-hospital mortality was 28%, and it was highest in Mx (37%).The most frequent images performed were cCT (61%), mostly in Mx and SAm, and cX-ray (46%), significant in CAC. The cEcho was carried out in 18%, similarly among regions, and LUS was carried out in 7%, with a higher frequently in Mx. Abnormal findings on the cX-ray were peripheral or basal infiltrates, and in cCT abnormal findings were the ground glass infiltrates, more commonly in Mx. In LUS, interstitial syndrome was the most abnormal finding, predominantly in Mx and CAC.Renal failure was the most prevalent complication (20%), predominant in Mx and SAm. Heart failure developed in 13%, predominant in Mx and CAC. Lung thromboembolism was higher in Mx while myocardial infarction was in CAC.Logistic regression showed associations of abnormal imaging findings and their severity, with comorbidities, complications, and evolution. ConclusionsThe use and findings of cardiopulmonary imaging in LATAM varied between regions and had a great impact on diagnosis and prognosis.
The melting transition of two-dimensional (2D) systems is a fundamental problem in condensed matter and statistical physics that has advanced significantly through the application of computational ...resources and algorithms. 2D systems present the opportunity for novel phases and phase transition scenarios not observed in 3D systems, but these phases depend sensitively on the system and thus predicting how any given 2D system will behave remains a challenge. Here we report a comprehensive simulation study of the phase behavior near the melting transition of all hard regular polygons with \(3\leq n\leq 14\) vertices using massively parallel Monte Carlo simulations of up to one million particles. By investigating this family of shapes, we show that the melting transition depends upon both particle shape and symmetry considerations, which together can predict which of three different melting scenarios will occur for a given \(n\). We show that systems of polygons with as few as seven edges behave like hard disks; they melt continuously from a solid to a hexatic fluid and then undergo a first-order transition from the hexatic phase to the fluid phase. We show that this behavior, which holds for all \(7\leq n\leq 14\), arises from weak entropic forces among the particles. Strong directional entropic forces align polygons with fewer than seven edges and impose local order in the fluid. These forces can enhance or suppress the discontinuous character of the transition depending on whether the local order in the fluid is compatible with the local order in the solid. As a result, systems of triangles, squares, and hexagons exhibit a KTHNY-type continuous transition between fluid and hexatic, tetratic, and hexatic phases, respectively, and a continuous transition from the appropriate "x"-atic to the solid. abstract truncated due to arxiv length limitations.
Many studies uphold innovation as a key factor in creating and sustaining a firm's competitive advantage. This research explores this topic by developing the links between a firm's innovation ...outcomes, overall performance, and process of organizational unlearning. This study empirically tests the mediating role of innovation outcomes in the relationship between organizational unlearning and overall performance. Furthermore, this study recognizes the moderating role of firm size in reducing the strong link between organizational unlearning and innovation outcomes.
This study constructs a conditional process model and uses a sample of 145 firms from Spanish automotive components manufacturing sector. This study employs variance-based structural equation modeling and the PROCESS tool to analyze data.
Results show that innovation outcomes partially mediate organizational unlearning influence on overall performance, and that firm size negatively affects this indirect effect.
Findings can guide managers to establish policies that foster unlearning, allow for new knowledge, and enable innovation, which may in turn enhance firm performance.
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