Abstract
A unique experiment was conducted by the STAR Collaboration in 2018 to investigate differences between collisions of nuclear isobars, a potential key to unraveling one of the physics ...mysteries in our field: why the universe is made predominantly of matter. Enhancing the credibility of findings was deemed to hinge on blinding analyzers from knowing which dataset they were examining, necessitating efforts by the data production team to investigate and implement new (in our field) blinding practices. With nearly two decades of established machinery intended to provide open data and metadata access in STAR, the breadth of details to consider for a successful blinding process was substantial.
In this paper, we will review the experience of the first-ever species-blind data production in high energy collider physics. Considerations of what needed blinding, how to blind it, and from whom, will be discussed. Practical impositions on the selection of data to produce and how to produce it will also be highlighted as tell-tales can arise even where there were operational efforts to avoid them. With the appropriate blinding achieved, analyzers and reviewers have been empowered to focus on the physics of interest.
Abstract
For the last 7 years, Accelogic pioneered and perfected a radically new theory of numerical computing codenamed “Compressive Computing”, which has an extremely profound impact on real-world ...computer science 1. At the core of this new theory is the discovery of one of its fundamental theorems which states that, under very general conditions, the vast majority (typically between 70% and 80%) of the bits used in modern large-scale numerical computations are absolutely irrelevant for the accuracy of the end result. This theory of Compressive Computing provides mechanisms able to identify (with high intelligence and surgical accuracy) the number of bits (i.e., the precision) that can be used to represent numbers without affecting the substance of the end results, as they are computed and vary in real time. The bottom-line outcome will be to provide state-of-the-art compression algorithms --and accompanying software libraries-- able to surpass the performance of the compression engines currently available in the ROOT 7 framework. The resulting technology has the capability to enable substantial economic and operational gains (including speedup) for High Energy and Nuclear Physics data storage/analysis. In our initial studies, a factor of nearly x4 (3.9) compression was achieved with RHIC/STAR data where ROOT compression managed only x1.4 6.
As a collaboration of experimental scientists, private industry, and the ROOT Team, our aim is to capitalize on the substantial success delivered by the initial effort and produce a robust technology properly packaged as an open-source tool that could be used by virtually every experiment around the world as means for improving data management and accessibility.
In this contribution, we will present our efforts integrating our concepts of “functionally lossless compression” within the ROOT framework implementation, with the purpose of producing a basic solution readily integrated into HENP applications. We will also present our progress applying this compression through realistic examples of analysis from both the STAR and CMS experiments.
Altered intestinal microbiota has been reported in pancreatic disorders, however, it remains unclear whether these changes alter the course of disease in patients with acute (AP) and chronic ...pancreatitis (CP), or whether these disease states alter the environment to enable pathogenic microbial composition changes to occur. We undertook a systematic review to characterize the gut microbiome in pancreatitis patients.
MEDLINE and EMBASE were searched for studies on microbiota in pancreatitis published from January 1, 2000 to June 5, 2020. Animal studies, reviews, case reports, and non-English articles were excluded. A frequency analysis was performed for outcomes reported in ≥2 studies and studies were analyzed for risk of bias and quality of evidence.
22 papers met inclusion criteria; 15 included AP, 7 included CP. No studies were appropriately designed to assess whether alterations in the gut microbiome exacerbate pancreatitis or develop as a result of pancreatitis. We did identify several patterns of microbiome changes that are associated with pancreatitis. The gut microbiome demonstrated decreased alpha diversity in 3/3 A P studies and 3/3 C P studies. Beta diversity analysis revealed differences in bacterial community composition in the gut microbiome in 2/2 A P studies and 3/3 C P studies. Functionally, gut microbiome changes were associated with infectious pathways in AP and CP. Several studies suffered from high risk of bias and inadequate quality.
Detecting differences in microbial composition associated with AP and CP may represent a diagnostic tool. Appropriately controlled longitudinal studies are needed to determine whether microbiome changes are causative or reactive in pancreatitis.
Background Neuropilin-2 (NRP2) is a high-affinity kinase-deficient receptor for vascular endothelial growth factor (VEGF) and semaphorin 3F. We investigated its function in human colorectal cancers. ...Methods Immunohistochemistry and immunoblotting were used to assess NRP2 expression levels in colorectal tumors and colorectal cancer cell lines, respectively. HCT-116 colorectal cancer cells stably transfected with short hairpin RNA (shRNAs) against NRP2 or control shRNAs were assayed for proliferation by the tetrazolium salt 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and for activation of the VEGFR1 pathway by immunoblotting. Soft agar assays, Annexin V staining, and Boyden chamber assays were used to examine anchorage-independent growth, apoptosis in response to hypoxia, and cell migration/invasion, respectively, in HCT-116 transfectants. Tumor growth and metastasis were analyzed in mice (groups of 10) injected with shRNA-expressing HCT-116 cells. The effect of in vivo targeting of NRP2 by small interfering RNA (siRNA) on the growth of hepatic colorectal tumors derived from luciferase-expressing HCT-116 cells was assessed by measuring changes in bioluminescence and final tumor volumes. All statistical tests were two-sided. Results NRP2 expression was substantially higher in tumors than in adjacent mucosa. HCT-116 transfectants with reduced NRP2 levels had reduced VEGFR1 signaling, but proliferation was unchanged. Anchorage-independent growth, survival under hypoxic conditions, and motility/invasiveness were also reduced. In vivo, HCT-116 transfectants with reduced NRP2 demonstrated decreased tumor growth, fewer metastases, and increased apoptosis compared with control cells. Hepatic colorectal tumors in mice treated with NRP2 siRNAs were statistically significantly smaller than those in mice treated with control siRNAs (at 28 days after implantation, mean control siRNAs = 420 mm3, mean NRP2 siRNAs = 36 mm3, NRP2 vs control: difference = 385 mm3, 95% confidence interval = 174 mm3 to 595 mm3, P = .005). Conclusion NRP2 on colorectal carcinoma cells is important for tumor growth and is a potential therapeutic target in human cancers where it is expressed.
The STAR experiment at the Relativistic Heavy Ion Collider (RHIC) has a rich physics program ranging from studies of the Quark Gluon Plasma to the exploration of the spin structure of the proton. ...Many measurements carried out by the STAR collaboration rely on the efficient reconstruction and precise knowledge of the position of the primary-interaction vertex. Throughout the years two main vertex finders have been predominantly utilized in event reconstruction by the experiment: MinutVF and PPV with their application domains focusing on heavy ion and proton-proton events respectively. In this work we give a brief overview and discuss recent improvements to the vertex finding algorithms implemented in the STAR software library. In our studies we focus on the finding efficiency and the quality of the reconstructed primary vertex. We examine the effect of an additional constraint, imposed by an independent measurement of the beam line position, when it is applied during the fit. We evaluate the significance of the improved primary vertex resolution on identification of the secondary decay vertices occurring inside the beam pipe. Finally, we present a method and its software implementation developed to measure the performance of the primary vertex reconstruction algorithms.
Over the lifetime of the STAR Experiment, a large investment of workforce time has gone into a variety of QA efforts, including continuous processing of a portion of the data for automated ...calibration and iterative convergence and quality assurance purposes. A rotating workforce coupled with ever-increasing volumes of information to examine led to sometimes inconsistent or incomplete reporting of issues, eventually leading to additional work. The traditional approach of manually screening a data sample was no longer adequate and doomed to eventual failure with planned future growth in data extents. To prevent this collapse we have developed a new system employing user-defined reference histograms, permitting automated comparisons and nagging of issues. Based on the ROOT framework at its core, the front end is a web based service allowing shift personnel to visualize the results, and to set test parameters and thresholds defining success or failure. The versatile and flexible approach allows for a slew of histograms to be configured and grouped into categories (results and thresholds may depend on experimental triggers and data types) ensuring framework evolution with the years of running to come. Historical information is also saved to track changes and allow for rapid convergence of future tuning. Database storage and processing of data are handled outside the web server for security and fault tolerance.
During development inhibitor of DNA-bind-2 (Id2) regulates proliferation and differentiation. Id2 expression has been detected in cancer cells, yet its cellular function and validity as a therapeutic ...target remains largely unknown. Immunohistochemical analysis of colorectal cancer (CRC) specimens revealed that Id2 was undetectable in normal colonic mucosa, but occurs in 40% of primary tumors and in most CRC liver metastases (P<0.0001). Additionally, Id2 was expressed in all CRC cell lines assayed. CRC cells with reduced Id2 expression demonstrated reduced proliferation. Analysis of CRC cell cycle regulatory proteins showed that reducing Id2 levels reduces cyclin D1 levels and increased p21 levels. Reduction of Id2 expression also enhanced tumor cell apoptosis, increasing levels of the pro-apoptotic protein Bim/Bod, and cleavage of caspase-7 and poly (ADP-ribose) polymerase. In vivo studies show tumors derived from cells with decreased Id2 levels formed smaller tumors with fewer metastases compared with tumors with normal levels (P<0.05). Furthermore, intraperitoneal administration of Id2 small interfering RNA (siRNA) conjugated with the neutral liposome 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine decreased tumor burden in mice compared with control treatment (P=0.006). We conclude that Id2 is upregulated in CRC, and is important in promoting cell survival. In vivo targeting of Id2 by siRNA establishes that it is a valid therapeutic target where its expression occurs.
Soft physics in STAR Van Buren, G.
Nuclear physics. A,
03/2003, Letnik:
715
Journal Article
Recenzirano
Odprti dostop
The STAR Experiment at RHIC is well-suited to making measurements of particle yields from relativistic nuclear collisions in the low transverse momentum, or “soft”, regime. We present preliminary ...results on measurements of π
0, π
−, π
+,
K
−,
K
+,
K
s
0
, ϱ,
K
*
0
+
K
*
0
¯
, f
0,
p,
p
¯
, φ, λ,
Λ
¯
, Ξ
−,
Ξ
¯
+
, Ω
−, and
Ω
¯
+
from the first two years of physics running at RHIC. An abundance of physics topics can be addressed by these measurements, some of which are discussed here along with the results.
In recent years, the STAR experiment's database demands have grown in accord not only with simple facility growth, but also with a growing physics program. In addition to the accumulated metadata ...from a decade of operations, refinements to detector calibrations force user analysis to access database information post data production. Users may access any year's data at any point in time, causing a near random access of the metadata queried, contrary to time-organized production cycles. Moreover, complex online event selection algorithms created a query scarcity ("sparsity") scenario for offline production further impacting performance. Fundamental changes in our hardware approach were hence necessary to improve query speed. Initial strategic improvements were focused on developing fault-tolerant, load-balanced access to a multi-slave infrastructure. Beyond that, we explored, tested and quantified the benefits of introducing a Tiered storage architecture composed of conventional drives, solid-state disks, and memory-resident databases as well as leveraging the use of smaller database services fitting in memory. The results of our extensive testing in real life usage are presented.
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