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At least 37 records · Page 2

An AT-hook protein DEPRESSED PALEA1 physically interacts with the TCP Family transcription factor RETARDED PALEA1 in rice

Highlights: • The AT-hook protein DP1 physically interacts with the TCP family transcription factor REP1 in rice. • In maize, the AT-hook protein BAD1 physically interacts with the TCP family transcription factor BAF1. • The interaction between AT-hook proteins and TCP proteins may be conserved in rice and maize. The cereal crops (such as rice and maize) which belong to the grass family, are the most important grain crops for human beings, and the development of their flower and inflorescence architecture has attracted extensive attention. Although multiple genes involved in the regulation of floral and inflorescence organogenesis have been identified, the underlying molecular mechanisms are largely unknown. Previously, we identified rice depressed palea1 (dp1) mutants with defects in main structure of palea and its enhancer RETARDED PALEA1 (REP1). DP1 is an AT-hook protein while REP1 is a TCP transcription factor, both of which are important regulators of palea development. However, the relationship of these two proteins has not been elucidated yet. Here, we demonstrated that DP1 interacts physically with REP1 both in yeast and in rice protoplasts. Considering the close phylogenetic relationship between maize and rice, we further hypothesize that their orthologs in maize, BARREN STALK FASTIGIATE (BAF1) and BRANCH ANGLE DEFECTIVE 1 (BAD1), may interact physically. Subsequently, we verified their physical interaction, indicating that the interaction between AT-hook proteins and TCP proteins is conserved in rice and maize. Our findings may reveal a novel molecular mechanism of floral and inflorescence development in grasses.

60 APPLIED LIFE SCIENCES↗

SU-E-J-30: Benchmark Image-Based TCP Calculation for Evaluation of PTV Margins for Lung SBRT Patients

Purpose: Tumor control probability (TCP) calculated with accumulated radiation doses may help design appropriate treatment margins. Image registration errors, however, may compromise the calculated TCP. The purpose of this study is to develop benchmark CT images to quantify registration-induced errors in the accumulated doses and their corresponding TCP. Methods: 4DCT images were registered from end-inhale (EI) to end-exhale (EE) using a “demons” algorithm. The demons DVFs were corrected by an FEM model to get realistic deformation fields. The FEM DVFs were used to warp the EI images to create the FEM-simulated images. The two images combined with the FEM DVF formed a benchmark model. Maximum intensity projection (MIP) images, created from the EI and simulated images, were used to develop IMRT plans. Two plans with 3 and 5 mm margins were developed for each patient. With these plans, radiation doses were recalculated on the simulated images and warped back to the EI images using the FEM DVFs to get the accumulated doses. The Elastix software was used to register the FEM-simulated images to the EI images. TCPs calculated with the Elastix-accumulated doses were compared with those generated by the FEM to get the TCP error of the Elastix registrations. Results: For six lung patients, the mean Elastix registration error ranged from 0.93 to 1.98 mm. Their relative dose errors in PTV were between 0.28% and 6.8% for 3mm margin plans, and between 0.29% and 6.3% for 5mm-margin plans. As the PTV margin reduced from 5 to 3 mm, the mean TCP error of the Elastix-reconstructed doses increased from 2.0% to 2.9%, and the mean NTCP errors decreased from 1.2% to 1.1%. Conclusion: Patient-specific benchmark images can be used to evaluate the impact of registration errors on the computed TCPs, and may help select appropriate PTV margins for lung SBRT patients.

60 APPLIED LIFE SCIENCES↗

TCP Throughput Profiles Using Measurements over Dedicated Connections

Wide-area data transfers in high-performance computing infrastructures are increasingly being carried over dynamically provisioned dedicated network connections that provide high capacities with no competing traffic. We present extensive TCP throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs). Contrary to the general expectation, they show significant statistical and temporal variations, in addition to the overall dependencies on the congestion control mechanism, buffer size, and the number of parallel streams. We analyze several throughput profiles that have highly desirable concave regions wherein the throughput decreases slowly with RTTs, in stark contrast to the convex profiles predicted by various TCP analytical models. We present a generic throughput model that abstracts the ramp-up and sustainment phases of TCP flows, which provides insights into qualitative trends observed in measurements across TCP variants: (i) slow-start followed by well-sustained throughput leads to concave regions; (ii) large buffers and multiple parallel streams expand the concave regions in addition to improving the throughput; and (iii) stable throughput dynamics, indicated by a smoother Poincare map and smaller Lyapunov exponents, lead to wider concave regions. These measurements and analytical results together enable us to select a TCP variant and its parameters for a given connection to achieve high throughput with statistical guarantees.

Rao, Nageswara S.↗

Experimental Study of TCP Throughput Profiles and Dynamics Over Dedicated Connections

A throughput profile expressed as a function of the round-trip times of a data transport infrastructure is a critical indicator of its level of optimization, particularly, over dedicated connections. We study the throughput profiles of eleven TCP versions using measurements collected over dedicated hardware-emulated connections with distances spanning round the earth. Among them, BBR has overall higher temporal variations and lower throughput profiles compared to five loss-based TCP versions, and the comparison with other TCP versions is mixed. Using the Poincare map regions of throughput time traces, we show that the richer dynamics of BBR are correlated with its lower throughput profiles. We present basic analytical results that indicate that higher temporal variations of TCP methods lead to lower throughput profiles, thereby establishing the underlying causality. Under external losses, BBR achieves sustained high throughput compared to others as the loss rate is increased. Overall, our results provide insights into the relationship between time dynamics and throughput profiles of TCP versions, in particular, show that limited time traces can be indicative of global properties of throughput profiles.

Rao, Nageswara↗

Elephants Sharing the Highway: Studying TCP Fairness in Large Transfers over High Throughput Links

Escalating bandwidth demand strains high-performance data networks, posing potential performance risks. TCP congestion control algorithms enhance reliability and optimize bandwidth usage. Network performance is influenced by factors such as AQM algorithms and router buffer size. In the context of constrained network resources, understanding how TCP flows share networks and the resulting performance impact is essential. This paper introduces insights into TCP fairness and performance involving a comparison of TCP CUBIC, Reno, Hamilton, and BBR versions 1 and 2 across real-world networks supporting high bandwidths of up to 25 Gbps. The research explores TCP behaviors with AQM algorithms like FIFO, FQ_CODEL, and RED, alongside diverse buffer sizes. Notably, findings reveal that manipulating buffers and queuing methods yields contrasting outcomes based on bandwidth. BBRv2 emerges as a superior fair algorithm, pivotal for swift transfers, particularly in scientific data scenarios. These results provide crucial guidance for future network design, ensuring equitable performance optimization.

Kiran, Mariam↗

Carbothermic Reduction Kinetics of Phosphorous Vaporization from Tri-calcium Phosphate (TCP) Under Microwave Rapid Heating With/Without the Presence of Fe{sub 3}O{sub 4}

The kinetics of vapor phase dephosphorization from tri-calcium phosphate (TCP) by carbothermic reduction was studied with and without the presence of Fe{sub 3}O{sub 4}. Microwave heating was utilized to obtain large variations in the heating rate (HR). In the reduction of TCP alone, the phosphorous removal fraction (RF; equal to ∆P{sub 2}O{sub 5}/P{sub 2}O{sub 5}{sup 0}, where ∆P{sub 2}O{sub 5} is the weight change and P{sub 2}O{sub 5}{sup 0} is the P{sub 2}O{sub 5} weight before heating) decreased as the HR increased. In other words, a shorter residence time at a high temperature resulted in a smaller reduction fraction of TCP. An apparently third-order reaction was postulated to account for the kinetics using a fitting simulation based on the additive law of the reaction progress. On the other hand, the phosphorous removal (dephosphorization) rate (RR; equal to ∆P{sub 2}O{sub 3}/t{sub MW}, where t{sub MW} is the microwave heating time period) increased as the HR increased above 1200 °C. The reduction ratio of Fe{sub 3}O{sub 4} above 1100 °C is higher than 97 pct regardless of the heating rate. The reduction of TCP in the presence of Fe{sub 3}O{sub 4} showed that RF increased slightly with increasing HR despite a shorter residence time at a high temperature. The RR also increased with the HR even though RF decreased to half of the values observed in the cases without Fe{sub 3}O{sub 4} for temperatures above 1200 °C. The practicality and optimal operation conditions of phosphorus vapor removal were discussed.

36 MATERIALS SCIENCE↗

Enhanced Explicit Congestion Notification (EECN) in TCP with P4 Programming

In current TCP/IP networks, TCP mainly relies on packet drops as an indication of congestion. With the emergence of Explicit Congestion Notification (ECN), TCP can detect the congestion through packets with marked bits instead of dropped packets. ECN thus reduces the unnecessary delay due to packet drops, especially for bandwidth-delay sensitive connections. However, ECN still relies on the receiver for congestion indication, which incurs a round trip time (RTT) before the sender can react to the congestion. In network environments with a high bandwidth-delay product (BDP), this could be problematic. In this paper, we present an enhanced ECN mechanism for the early detection of congestion using P4 programming. In our proposed scheme, the sender does not have to wait for the receiver to indicate congestion because switches in the network can indicate congestion. We evaluate our scheme comparing our proposed solution with standard TCP and TCP with the conventional ECN. Experimental results show that our scheme outperforms ECN as the RTT grows.

ECN↗

Evolutionary Telemetry and Command Processor (TCP) architecture

A low cost, modular, high performance, and compact Telemetry and Command Processor (TCP) is being built as the foundation of command and data handling subsystems for the next generation of satellites. The TCP product line will support command and telemetry requirements for small to large spacecraft and from low to high rate data transmission. It is compatible with the latest TDRSS, STDN and SGLS transponders and provides CCSDS protocol communications in addition to standard TDM formats. Its high performance computer provides computing resources for hosted flight software. Layered and modular software provides common services using standardized interfaces to applications thereby enhancing software re-use, transportability, and interoperability. The TCP architecture is based on existing standards, distributed networking, distributed and open system computing, and packet technology. The first TCP application is planned for the 94 SDIO SPAS 3 mission. The architecture enhances rapid tailoring of functions thereby reducing costs and schedules developed for individual spacecraft missions.

Schneider, John R.↗

On the Generation and Use of TCP Acknowledgments

This paper presents a simulation study of various TCP acknowledgment generation and utilization techniques. We investigate the standard version of TCP and the two standard acknowledgment strategies employed by receivers: those that acknowledge each incoming segment and those that implement delayed acknowledgments. We show the delayed acknowledgment mechanism hurts TCP performance, especially during slow start. Next we examine three alternate mechanisms for generating and using acknowledgments designed to mitigate the negative impact of delayed acknowledgments. The first method is to generate delayed ACKs only when the sender is not using the slow start algorithm. The second mechanism, called byte counting, allows TCP senders to increase the amount of data being injected into the network based on the amount of data acknowledged rather than on the number of acknowledgments received. The last mechanism is a limited form of byte counting. Each of these mechanisms is evaluated in a simulated network with no competing traffic, as well as a dynamic environment with a varying amount of competing traffic. We study the costs and benefits of the alternate mechanisms when compared to the standard algorithm with delayed ACKs.

Allman, Mark↗

High-Speed TCP Testing

Transmission Control Protocol (TCP) is the underlying protocol used within the Internet for reliable information transfer. As such, there is great interest to have all implementations of TCP efficiently interoperate. This is particularly important for links exhibiting long bandwidth-delay products. The tools exist to perform TCP analysis at low rates and low delays. However, for extremely high-rate and lone-delay links such as 622 Mbps over geosynchronous satellites, new tools and testing techniques are required. This paper describes the tools and techniques used to analyze and debug various TCP implementations over high-speed, long-delay links.

Brooks, David E.↗

Radiobiological Impact of Reduced Margins and Treatment Technique for Prostate Cancer in Terms of Tumor Control Probability (TCP) and Normal Tissue Complication Probability (NTCP)

Dose escalation in prostate radiotherapy is limited by normal tissue toxicities. The aim of this study was to assess the impact of margin size on tumor control and side effects for intensity-modulated radiation therapy (IMRT) and 3D conformal radiotherapy (3DCRT) treatment plans with increased dose. Eighteen patients with localized prostate cancer were enrolled. 3DCRT and IMRT plans were compared for a variety of margin sizes. A marker detectable on daily portal images was presupposed for narrow margins. Prescribed dose was 82 Gy within 41 fractions to the prostate clinical target volume (CTV). Tumor control probability (TCP) calculations based on the Poisson model including the linear quadratic approach were performed. Normal tissue complication probability (NTCP) was calculated for bladder, rectum and femoral heads according to the Lyman-Kutcher-Burman method. All plan types presented essentially identical TCP values and very low NTCP for bladder and femoral heads. Mean doses for these critical structures reached a minimum for IMRT with reduced margins. Two endpoints for rectal complications were analyzed. A marked decrease in NTCP for IMRT plans with narrow margins was seen for mild RTOG grade 2/3 as well as for proctitis/necrosis/stenosis/fistula, for which NTCP <7% was obtained. For equivalent TCP values, sparing of normal tissue was demonstrated with the narrow margin approach. The effect was more pronounced for IMRT than 3DCRT, with respect to NTCP for mild, as well as severe, rectal complications.

61 RADIATION PROTECTION AND DOSIMETRY↗

Sci—Fri PM: Topics — 04: What if bystander effects influence cell kill within a target volume? Potential consequences of dose heterogeneity on TCP and EUD on intermediate risk prostate patients

In vitro evidence has suggested that radiation induced bystander effects may enhance non-local cell killing which may influence radiotherapy treatment planning paradigms. This work applies a bystander effect model, which has been derived from published in vitro data, to calculate equivalent uniform dose (EUD) and tumour control probability (TCP) and compare them with predictions from standard linear quadratic (LQ) models that assume a response due only to local absorbed dose. Comparisons between the models were made under increasing dose heterogeneity scenarios. Dose throughout the CTV was modeled with normal distributions, where the degree of heterogeneity was then dictated by changing the standard deviation (SD). The broad assumptions applied in the bystander effect model are intended to place an upper limit on the extent of the results in a clinical context. The bystander model suggests a moderate degree of dose heterogeneity yields as good or better outcome compared to a uniform dose in terms of EUD and TCP. Intermediate risk prostate prescriptions of 78 Gy over 39 fractions had maximum EUD and TCP values at SD of around 5Gy. The plots only dropped below the uniform dose values for SD ∼ 10 Gy, almost 13% of the prescribed dose. The bystander model demonstrates the potential to deviate from the common local LQ model predictions as dose heterogeneity through a prostate CTV is varies. The results suggest the potential for allowing some degree of dose heterogeneity within a CTV, although further investigations of the assumptions of the bystander model are warranted.

60 APPLIED LIFE SCIENCES↗

An Evaluation of TCP with Larger Initial Windows

Transmission Control Protocol (TCP's) slow start algorithm gradually increases the amount of data a sender injects into the network, which prevents the sender from overwhelming the network with an inappropriately large burst of traffic. However, the slow start algorithm can make poor use of the available band-width for transfers which are small compared to the bandwidth-delay product of the link, such as file transfers up to few thousand characters over satellite links or even transfers of several hundred bytes over local area networks. This paper evaluates a proposed performance enhancement that raises the initial window used by TCP from 1 MSS-sized segment to roughly 4 KB. The paper evaluates the impact of using larger initial windows on TCP transfers over both the shared Internet and dialup modem links.

Allman, Mark↗

The Behavior of TCP and Its Extensions in Space

The performance of Transmission Control Protocol (TCP) in space has been examined from the observations of simulation and experimental tests for several years at National Aeronautics and Space Administration (NASA), Department of Defense (DoD) and universities. At New Mexico State University (NMSU), we have been concentrating on studying the performance of two protocol suites: the file transfer protocol (ftp) running over Transmission Control Protocol/Internet Protocol (TCP/IP) stack and the file protocol (fp) running over the Space Communications Protocol Standards (SCPS)-Transport Protocol (TP) developed under the Consultative Committee for Space Data Systems (CCSDS) standards process. SCPS-TP is considered to be TCP's extensions for space communications. This dissertation experimentally studies the behavior of TCP and SCPS-TP by running the protocol suites over both the Space-to-Ground Link Simulator (SGLS) test-bed and realistic satellite link. The study concentrates on comparing protocol behavior by plotting the averaged file transfer times for different experimental configurations and analyzing them using Statistical Analysis System (SAS) based procedures. The effects of different link delays and various Bit-Error-Rates (BERS) on each protocol performance are also studied and linear regression models are built for experiments over SGLS test-bed to reflect the relationships between the file transfer time and various transmission conditions.

Wang, Ruhai↗

TCP Pacing Developed

Transmission control protocol (TCP) was conceived and designed to run over a variety of communication links, including wireless and high-bandwidth links. However, with recent technological advances in satellite and fiber-optic networks, researchers are reevaluating the flexibility of TCP. The TCP pacing and packet pair probing implementation may help overcome two of the major obstacles identified for efficient bandwidth utilization over communication links with large delay-bandwidth products.

Ivancic, William D.↗

Detecting anomalous packets in network transfers: investigations using PCA, autoencoder and isolation forest in TCP

Large-scale scientific workflows rely heavily on high-performance file transfers. These transfers require strict quality parameters such as guaranteed bandwidth, no packet loss or data duplication. To have successful file transfers, methods such as predetermined thresholds and statistical analysis need to be done to determine abnormal patterns. Network administrators routinely monitor and analyze network data for diagnosing and alleviating these, making decisions based on their experience. However, as networks grow and become complex, monitoring large data files and quickly processing them, makes it improbable to identify errors and rectify these. Abnormal file transfers have been classified by simply setting alert thresholds, via tools such as PerfSonar and TCP statistics (Tstat). This paper investigates the feasibility of unsupervised feature extraction methods for identifying network anomaly patterns with three unsupervised classification methods—principal component analysis, autoencoder and isolation forest. Here, we collect file transfer statistics from two experiment sets—synthetic iPerf generated traffic and 1000 Genome workflow runs, with synthetically introduced anomalies. Our results show that while PCA and a simple autoencoder finds it difficult to detect clusters, the tree-variant isolation forest is able to identify anomalous packets by breaking down TCP traces into tree classes early.

97 MATHEMATICS AND COMPUTING↗

A modified hypoxia-based TCP model to investigate the clinical outcome of stereotactic hypofractionated regimes for early stage non-small-cell lung cancer (NSCLC)

Purpose: Stereotactic body radiotherapy (SBRT) has been applied to lung tumors at different stages and sizes with good local tumor control (LC) rates. The linear quadratic model (LQM), in its basic formulation, does not seem to be appropriate to describe the response to radiotherapy for clinical trials, based on a few fractions. Thus, the main aim of this work was to develop a model, which takes into account the hypoxic cells and their reoxygenation. Methods: A parameter named B has been introduced in a modified tumor control probability (TCP) from LQM and linear-quadratic-linear model (LQLM), and represents the fraction of hypoxic cells that survive and become oxygenated after each irradiation. Based on published trials evaluating LC at 3 yr (LC3), values of B were obtained by maximum likelihood minimization between predicted TCP and clinical LC3. Two oxygen enhancement ratio (OER) parameter sets (1 and 2) from literature have been adopted to calculate the B-factors. Initial hypoxic cell fractions ({eta}{sub h}) from 0.05 to 0.50 were assumed. Log-likelihood (L) and Akaike information criterion (AIC) were determined in an independent clinical validation dataset. Results: The B-values of modified TCPs spanned the whole interval from 0 to 1, depending on the fractionation scheme (number of fractions and dose/fraction), showing a maximum (close to 1) at doses/fraction of 8-12 Gy. The B-values calculated using the OER parameter set 1 exhibited a smoother falloff than set 2. An analytical expression was derived to describe the B-value's dependence on the fractionation scheme. The R{sup 2}-adjusted values varied from 0.63 to 0.67 for LQ models and OER set 1 and from 0.75 to 0.78 for LQ model and OER set 2. Lower values of R{sup 2}-adjusted were found for LQLM and both OER sets. L and AIC, calculated using a fraction of {eta}{sub h} = 0.15 and the B-value from the authors analytical expression were higher than for other {eta}{sub h}-values, irrespective of model or OER set. Conclusions: The authors model allows to predict the clinical outcome associated with SBRT treatment, taking into account both direct killing and indirect vasculature or stromal damage.

61 RADIATION PROTECTION AND DOSIMETRY↗

WE-F-304-02: Recurrent HNC Treated with SBRT: TCP-Based Outcome Estimates

Stereotactic Body Radiation Therapy (SBRT) was introduced clinically more than twenty years ago, and many subsequent publications have reported safety and efficacy data. The AAPM Working Group on Biological Effects of Hypofractionated Radiotherapy/SBRT (WGSBRT) extracted published treatment outcomes data from extensive literature searches to summarize and construct tumor control probability (TCP) and normal tissue complication probability (NTCP) models for six anatomical regions: Cranial, Head and Neck, Thoracic, Abdominal, Pelvic, and Spinal. In this session, we present the WGSBRT’s work for cranial sites, and recurrent head and neck cancer. From literature-based data and associated models, guidelines to aid with safe and effective hypofractionated radiotherapy treatment are being determined. Further, the ability of existing and proposed radiobiological models to fit these data is considered as to the ability to distinguish between the linear-quadratic and alternative radiobiological models such as secondary cell death from vascular damage, immunogenic, or bystander effects. Where appropriate, specific model parameters are estimated. As described in “The lessons of QUANTEC,” (1), lack of adequate reporting standards continues to limit the amount of useful quantitative information that can be extracted from peer-reviewed publications. Recommendations regarding reporting standards are considered, to enable such reviews to achieve more complete characterization of clinical outcomes. 1 Jackson A, Marks LB, Bentzen SM, Eisbruch A, Yorke ED, Ten Haken RK, Constine LS, Deasy JO. The lessons of QUANTEC: recommendations for reporting and gathering data on dose-volume dependencies of treatment outcome. Int J Radiat Oncol Biol Phys. 2010 Mar 1;76(3 Suppl):S155–60. Learning Objectives: Describe the techniques, types of cancer and dose schedules used in treating recurrent H&N cancers with SBRT List the radiobiological models that compete with the linear-quadratic model in explaining the results of hypofractionated RT Describe the dose/volume metrics that are considered safe in SBRT treatment of tumors near the optic structures. Discuss the efficacy of hypofractionation and dosing schedules used in treating vestibular schwannomas Identify some difficulties in modeling TCP and NTCP for cranial tumors treated with hypofractionation. One moderator, Dr. Grimm, designed and holds intellectual property rights to the DVH Evaluator software tool which is an FDA-cleared product in commercial use, and can analyze some of this data. No others have relevant conflicts of interest.

60 APPLIED LIFE SCIENCES↗