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3. Trigger and Timing Distributions using the TTC-PON and GBT Bridge Connection in ALICE for the LHC Run 3 Upgrade

Author

Mitra, Jubin, David, Erno, Mendez, Eduardo, Khan, Shuaib Ahmad, Kiss, Tivadar, Baron, Sophie, Kluge, Alex, and Nayak, Tapan

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment, Nuclear Experiment
Abstract

The ALICE experiment at CERN is preparing for a major upgrade for the third phase of data taking run (Run 3), when the high luminosity phase of the Large Hadron Collider (LHC) starts. The increase in the beam luminosity will result in high interaction rate causing the data acquisition rate to exceed 3 TB/sec. In order to acquire data for all the events and to handle the increased data rate, a transition in the readout electronics architecture from the triggered to the trigger-less acquisition mode is required. In this new architecture, a dedicated electronics block called the Common Readout Unit (CRU) is defined to act as a nodal communication point for detector data aggregation and as a distribution point for timing, trigger and control (TTC) information. TTC information in the upgraded triggerless readout architecture uses two asynchronous high-speed serial links connections: the TTC-PON and the GBT. We have carried out a study to evaluate the quality of the embedded timing signals forwarded by the CRU to the connected electronics using the TTC-PON and GBT bridge connection. We have used four performance metrics to characterize the communication bridge: (a)the latency added by the firmware logic, (b)the jitter cleaning effect of the PLL on the timing signal, (c)BER analysis for quantitative measurement of signal quality, and (d)the effect of optical transceivers parameter settings on the signal strength. Reliability study of the bridge connection in maintaining the phase consistency of timing signals is conducted by performing multiple iterations of power on/off cycle, firmware upgrade and reset assertion/de-assertion cycle (PFR cycle). The test results are presented and discussed concerning the performance of the TTC-PON and GBT bridge communication chain using the CRU prototype and its compliance with the ALICE timing requirements.

Published
2018
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5. FOXM1 drives HPV+ HNSCC sensitivity to WEE1 inhibition

Author

Diab, Ahmed, Gem, Hakan, Swanger, Jherek, Kim, Hee Yeon, Smith, Kaleb, Zou, Grace, Raju, Sharat, Kao, Michael, Fitzgibbon, Matthew, Loeb, Keith R., Rodriguez, Cristina P., Méndez, Eduardo, Galloway, Denise A., Sidorova, Julia M., and Clurman, Bruce E.

Published
2020

7. A novel surgeon credentialing and quality assurance process using transoral surgery for oropharyngeal cancer in ECOG-ACRIN Cancer Research Group Trial E3311

Author

Ferris, Robert L., Flamand, Yael, Holsinger, F. Christopher, Weinstein, Gregory S., Quon, Harry, Mehra, Ranee, Garcia, Joaquin J., Hinni, Michael L., Gross, Neil D., Sturgis, Erich M., Duvvuri, Umamaheswar, Méndez, Eduardo, Ridge, John A., Magnuson, J. Scott, Higgins, Kerry A., Patel, Mihir R., Smith, Russel B., Karakla, Daniel W., Kupferman, Michael E., Malone, James P., Judson, Benjamin L., Richmon, Jeremy, Boyle, Jay O., Bayon, Rodrigo, O'Malley, Bert W., Jr, Ozer, Enver, Thomas, Giovana R., Koch, Wayne M., Bell, R. Bryan, Saba, Nabil F., Li, Shuli, Sigurdson, Elin R., and Burtness, Barbara

Published
2020
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11. Water Cycle Algorithm with Fuzzy Logic for Dynamic Adaptation of Parameters

Author

Méndez, Eduardo, Castillo, Oscar, Soria, José, Melin, Patricia, Sadollah, Ali, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Sidorov, Grigori, editor, and Herrera-Alcántara, Oscar, editor

Published
2017
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21. Supplementary Figure from Pharmacologic Targeting of TFIIH Suppresses KRAS-Mutant Pancreatic Ductal Adenocarcinoma and Synergizes with TRAIL

Author

Moser, Russell, primary, Annis, James, primary, Nikolova, Olga, primary, Whatcott, Cliff, primary, Gurley, Kay, primary, Mendez, Eduardo, primary, Moran-Jones, Kim, primary, Dorrell, Craig, primary, Sears, Rosalie C., primary, Kuo, Calvin, primary, Han, Haiyong, primary, Biankin, Andrew, primary, Grandori, Carla, primary, Von Hoff, Daniel D., primary, and Kemp, Christopher J., primary

Published
2023
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22. Supplementary Data from Pharmacologic Targeting of TFIIH Suppresses KRAS-Mutant Pancreatic Ductal Adenocarcinoma and Synergizes with TRAIL

Author

Moser, Russell, primary, Annis, James, primary, Nikolova, Olga, primary, Whatcott, Cliff, primary, Gurley, Kay, primary, Mendez, Eduardo, primary, Moran-Jones, Kim, primary, Dorrell, Craig, primary, Sears, Rosalie C., primary, Kuo, Calvin, primary, Han, Haiyong, primary, Biankin, Andrew, primary, Grandori, Carla, primary, Von Hoff, Daniel D., primary, and Kemp, Christopher J., primary

Published
2023
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25. Pharmacological targeting of TFIIH suppresses KRAS mutant pancreatic ductal adenocarcinoma and synergizes with TRAIL

Author

Moser, Russell, Annis, James, Nikolova, Olga, Whatcott, Clifford J., Gurley, Kay E., Mendez, Eduardo, Moran-Jones, Kim, Dorrell, Craig, Sears, Rosalie C., Kuo, Calvin J., Han, Haiyong, Biankin, Andrew V., Grandori, Carla, Von Hoff, Daniel D., and Kemp, Christopher J.

Abstract

Pancreatic ductal adenocarcinoma (PDAC) typically presents as metastatic disease at diagnosis and remains refractory to treatment. Next generation sequencing efforts have described the genomic landscape, classified molecular subtypes, and confirmed frequent alterations in major driver genes, with coexistent alterations in KRAS and TP53 correlating with the highest metastatic burden and poorest outcomes. However, translating this information to guide therapy remains a challenge. By integrating genomic analysis with an arrayed RNAi druggable genome screen and drug profiling of a KRAS/TP53 mutant PDAC cell line derived from a patient-derived xenograft (PDCL), we identified numerous targetable vulnerabilities that reveal both known and novel functional aspects of pancreatic cancer biology. A dependence on the general transcription and DNA repair factor TFIIH complex, particularly the XPB subunit and the CAK complex (CDK7/CyclinH/MAT1), was identified and further validated utilizing a panel of genomically subtyped KRAS mutant PDCLs. TFIIH function was inhibited with a covalent inhibitor of CDK7/12/13 (THZ1), a CDK7/CDK9 kinase inhibitor (SNS-032), and a covalent inhibitor of XPB (Triptolide), which led to disruption of the protein stability of the RNA polymerase II subunit RPB1. Loss of RPB1 following TFIIH inhibition led to downregulation of key transcriptional effectors of KRAS mutant signaling and negative regulators of apoptosis, including MCL1, XIAP, and CFLAR, initiating caspase-8 dependent apoptosis. All three drugs exhibited synergy in combination with a multivalent TNF-related apoptosis inducing ligand (TRAIL), effectively reinforcing mitochondrial-mediated apoptosis. These findings present a novel combination therapy with direct translational implications for current clinical trials on metastatic pancreatic cancer patients.

Published
2022

28. Biochemical Thermodynamics under near Physiological Conditions

Author

Mendez, Eduardo

Abstract

The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables can be easily employed in the study of the energetics of biochemical equations, regulatory systems, and metabolic pathways under near physiological conditions. (Contains 1 figure and 3 tables.)

Published
2008
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40. Adult survivors of pediatric illness: the impact on pediatric hospitals

Author

Goodman, Denise M., Mendez, Eduardo, Throop, Cheri, and Ogata, Edward S.

Subjects
Children -- Diseases, Diseases -- Prognosis
Abstract

Context. Patients now live well into adulthood surviving diseases with pediatric onset. The size and financial impact of this growing population is unknown. Objective. To describe the demographics of adult inpatients in pediatric facilities and to assess the financial impact of providing care for these patients on freestanding children's hospitals. Design and Data Sources. An observational study using the Pediatric Health Information System, a proprietary database available to Child Health Corporation of America member hospitals, covering years 1994-1999. These data reflect inpatient services and exclude outpatient encounters and adult patients transitioned to adult providers. National estimates of the number of adult survivors of pediatric illness and the financial impact of care were calculated. Hospitals with >100 discharge events for patients [greater than or equal to] age 21 in 1999, and having both clinical and financial data in the dataset, assured an adequate sample size to discern resource utilization. Both 18 and 21 were used as lower limits of adult age to reflect common definitions of legal majority (age 18) and common pediatric practice (age 21). We truncated the data at age 64 to exclude patients eligible for Medicare. Results. Ten hospitals representing all geographic regions of the United States were used for an in-depth analysis of financial impact during 1999. Six of 10 had data for 1994-1999 to describe trends over time. The number of patients admitted over the 6-year period increased, as did average and total adjusted charges. In 1999, 3863 patients 18 to 64 years old incurred 5051 discharge episodes and total charges of $134.5 million. Of these, about half (1785) were [greater than or equal to] 21 with charges of $66 million. Of the hospitals' total discharges and financial charges, on average 2.1% and 3.1%, respectively, were from the inpatient care of patients 21 to 64 years old. Forty percent of patients receive public aid. Extrapolating from census data, up to 15 000 patients [greater than or equal to] 21 years annually may seek inpatient care in part at children's hospitals, with charges exceeding $500 million. The 3 most common diagnostic groups to be admitted were those with cystic fibrosis, mental retardation or cerebral palsy, and congenital heart disease. Conclusions. We describe a subset of adults who have survived diseases of pediatric onset. We focused on the portion of that population that obtains at least some inpatient care at a children's hospital. The data reported here can be used to set a lower boundary for the size of this population, and thereby provide valuable data for health planners as well as clinicians. If one includes estimates of expenses across the continuum of care, the financial impact of this growing population is substantial. Public policy discussions should include the medical, psychological, social, and financial needs of this population. Pediatrics 2002;110:583-589; adult patients, pediatrics, pediatric hospitals, resource utilization, adult survivors, congenital disease, health resources, chronic illness., ABBREVIATIONS. PHIS, Pediatric Health Information System; HCFA, Health Care Financing Administration; ICD-9, International Classification of Diseases, Ninth Revision. Because of therapeutic advances, patients now live well into adulthood surviving diseases [...]

Published
2002

44. Transoral robotic surgical resection followed by randomization to low- or standard-dose IMRT in resectable p16+ locally advanced oropharynx cancer: A trial of the ECOG-ACRIN Cancer Research Group (E3311).

Author

Ferris, Robert L., primary, Flamand, Yael, additional, Weinstein, Gregory S., additional, Li, Shuli, additional, Quon, Harry, additional, Mehra, Ranee, additional, Garcia, Joaquin J., additional, Chung, Christine H., additional, Gillison, Maura L., additional, Duvvuri, Umamaheswar, additional, O'malley, Bert W., additional, Ozer, Enver, additional, Thomas, Giovana R., additional, Koch, Wayne, additional, Kupferman, Michael Elliot, additional, Bell, Richard Bryan, additional, Saba, Nabil F., additional, Lango, Miriam, additional, Mendez, Eduardo, additional, and Burtness, Barbara, additional

Published
2020
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49. History of Infection Before the Onset of Juvenile Dermatomyositis: Results From the National Institute of Arthritis and Musculoskeletal and Skin Diseases Research Registry

Author

PACHMAN, LAUREN M., LIPTON, REBECCA, RAMSEY-GOLDMAN, ROSALIND, SHAMIYEH, ELI, ABBOTT, KATHY, MENDEZ, EDUARDO P., DYER, ALAN, CURDY, DEBORAH MC, VOGLER, LARRY, REED, ANN, CAWKWELL, GAIL, ZEMEL, LAWRENCE, SANDBORG, CHRISTY, RIVAS-CHACON, RAFAEL, HOM, CHRISTINE, ILOWITE, NORMAN, GEDALIA, ABRAHAM, GITLIN, JONATHAN, and BORZY, MICHAEL

Published
2005

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