gebhart/patrepeval huggingface dataset:
Matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry of lipopolysaccharide species separated by slab‐polyacrylamide gel electrophoresis: High‐resolution separation and molecular weight determination of lipooligosaccharides from Vibrio fischeri strain HMK (2004)

We recently demonstrated that the combined use of lipopolysaccharide (LPS) reverse staining and high-efficiency passive elution techniques can be successfully used as a suitable interface between LPS slab-gel separation and electrospray ionization-mass spectrometry (ESI-MS) of LPS-derived oligosaccharides. Here, we extend our micropurification strategy for the analysis of O-deacylated LPS forms from Vibrio fischeri HMK after recovery from single reverse-stained LPS bands using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). The quantities (30-40 microg) obtained from the two gel-resolved LPS bands were sufficient to allow MALDI-TOF-MS detection of O-deacylated LPS glycoforms at m/z 3767.1, 3890.1 for the high-molecular-weight or at m/z 2522.5, 2645.4, 2725.7, and 2848.7 for the low-molecular-weight LPS band. These LPS band heterogeneities resulted not only from variations in the oligosaccharide region of the LPS but also from two phosphorylation states of the lipid A (diphosphoryl and diphosphoryl plus a single phosphoethanolamine substitution). On the other hand, MALDI-TOF mass spectra of the separated LPS bands displayed reduced heterogeneity and increased signal-to-noise ratios as compared to spectra of the unpurified LPS. Furthermore, micropurification of LPS bands prior MALDI-TOF-MS led to a higher sensitivity of detection of less abundant low-molecular-weight LPS glycoforms. Taken together, this and our previous study on gel-micropurified LPS using ESI definitively show how one can unambiguously determine the different molecular species contained within each gel-separated LPS band, their relative abundance and oligosaccharide sequences.
Postoperative Chemoradiotherapy and Cetuximab for High-Risk Squamous Cell Carcinoma of the Head and Neck: Radiation Therapy Oncology Group RTOG-0234 (2014)

The delivery of postoperative chemoradiotherapy and cetuximab to patients with SCCHN is feasible and tolerated with predictable toxicity. The docetaxel regimen shows favorable outcome with improved DFS and OS relative to historical controls and has commenced formal testing in a phase II/III trial.
An underwater wearable computer for two way human-dolphin communication experimentation (2013)

Research in dolphin cognition and communication in the wild is still a challenging task for marine biologists. Most problems arise from the uncontrolled nature of field studies and the challenges of building suitable underwater research equipment. We present a novel underwater wearable computer enabling researchers to engage in an audio-based interaction between humans and dolphins. The design requirements are based on a research protocol developed by a team of marine biologists associated with the Wild Dolphin Project.
65‐1: Invited Paper: Narrow Spectrum Deep Red Emitters for OLED Lighting and Display (2019)

We report narrow lineshape phosphorescent emitters enabling high luminous efficacy deep red emission for automotive lighting applications. As a result of the narrow 43nm FWHM and high efficiency, we achieve 16cd/A LE and 55,000hr LT95 at 1,000nits with a 640nm peak and 625nm dominant wavelength in a bottom emission device.
Flint (2016)

Cloud providers now offer transient servers, which they may revoke at anytime, for significantly lower prices than on-demand servers, which they cannot revoke. The low price of transient servers is particularly attractive for executing an emerging class of workload, which we call Batch-Interactive Data-Intensive (BIDI), that is becoming increasingly important for data analytics. BIDI workloads require large sets of servers to cache massive datasets in memory to enable low latency operation. In this paper, we illustrate the challenges of executing BIDI workloads on transient servers, where revocations (akin to failures) are the common case. To address these challenges, we design Flint, which is based on Spark and includes automated checkpointing and server selection policies that i) support batch and interactive applications and ii) dynamically adapt to application characteristics. We evaluate a prototype of Flint using EC2 spot instances, and show that it yields cost savings of up to 90% compared to using on-demand servers, while increasing running time by < 2%.
Reactive Oxygen Species Mediate Met Receptor Transactivation by G Protein-coupled Receptors and the Epidermal Growth Factor Receptor in Human Carcinoma Cells (2004)

Cross-communication between the Met receptor tyrosine kinase and the epidermal growth factor receptor (EGFR) has been proposed to involve direct association of both receptors and EGFR kinase-dependent phosphorylation. Here, we demonstrate that in human hepatocellular and pancreatic carcinoma cells the Met receptor becomes tyrosine phosphorylated not only upon EGF stimulation but also in response to G protein-coupled receptor (GPCR) agonists. Whereas specific inhibition of the EGFR kinase activity blocked EGF- but not GPCR agonist-induced Met receptor transactivation, it was abrogated in the presence of a reducing agent or treatment of cells with a NADPH oxidase inhibitor. Both GPCR ligands and EGF are further shown to increase the level of reactive oxygen species within the cell. Interestingly, stimulation of the Met receptor by either GPCR agonists, EGF or its cognate ligand HGF, resulted in release of Met-associated beta-catenin and in its Met-dependent translocation into the nucleus, as analyzed by small interfering RNA-mediated knockdown of the Met receptor. Our results provide a new molecular explanation for cell surface receptor cross-talk involving the Met receptor and thereby link the wide diversity of GPCRs and the EGFR to the oncogenic potential of Met signaling in human carcinoma cells.
Myocardial infarction: assessment with an intravascular MR contrast medium. Work in progress. (1991)

The effect of a new intravascular magnetic resonance (MR) contrast medium (gadolinium diethylenetriaminepentaacetic acid [DTPA] polylysine) was evaluated in acute, subacute, and chronic myocardial infarctions in rats. Signal intensity (SI) was measured before and after intravenous administration of Gd-DTPA polylysine. Before administration of contrast material, chronic infarctions had lower SI than normal myocardium. With Gd-DTPA polylysine, three zones were identified in acute and subacute stages of myocardial infarction, but in the chronic stage, images demonstrated two zones. In acute and subacute infarctions, Gd-DTPA polylysine produced greater enhancement (over 60 minutes) in the peri-infarction zone than in the normal or infarcted myocardium. In chronic infarctions, Gd-DTPA polylysine had no discernible effect on the SI of the central infarction zone. Overall, it caused no significant hemodynamic effects. MR imaging with Gd-DTPA polylysine produced differential tissue enhancement in myocardial infarctions, which varied according to the age of the infarction.
EP2 and EP3 receptors as therapeutic targets for underactive bladder/detrusor underactivity due to diabetic cystopathy in a type 1 diabetic rat model (2020)

The present study was unable to demonstrate that stimulation of EP2 and EP3 receptors caused major improvements in UAB/DU due to DC. However, this equivocal result could arise from inherent limitations of the STZ-induced diabetic rat as a UAB/DU model.
Biallelic inactivation of the thyroid hormone receptor beta1 gene in early stage breast cancer. (2002)

Loss of heterozygosity within the short arm of chromosome 3 is a common molecular event in several types of solid tumors. In breast cancer, 3p loss of heterozygosity occurs in invasive tumor cells as well as in morphologically normal terminal ductal lobular units adjacent to carcinoma in some cases [G. Deng et al., Science (Wash. DC), 274: 2057-2059, 1996.]. The most frequent region of allelic loss at 3p24.3 in morphologically normal terminal ductal lobular units encompasses the thyroid hormone receptor beta1 (TRbeta1) gene. Here we have observed a variable degree of TRbeta1 promoter hypermethylation in all 11 cases of primary breast cancer examined. Moreover, hypermethylation occurred at the same CpG sites in nonmalignant tissue peripheral to carcinoma in 4 of 11 cases. The lack of TRbeta1 nuclear staining, a likely result of biallelic gene inactivation, was observed in 25% (22 of 85) of primary tumors. This is a first demonstration of promoter hypermethylation and a concurrent reduction of TRbeta1 transcripts in breast cancer cell lines, although specific CpG sites targeted for gene silencing remain to be determined. Gene expression was restored by treatment with 5-aza-deoxycytidine in such cases. The observation of early, frequent, and multiple mechanisms of TRbeta1 inactivation suggests a potential role for this gene in the suppression of breast tumorigenesis.
Design of Air, Water, Temperature and Hydrogen Controls for a PEM Fuel Cell System (2011)

Polymer electrolyte membrane (PEM) fuel cell is the potential power source for vehicle applications, where supply of fuels and rejection of heat play significant roles in ensuring performance and durability. Operations of the fuel cells require four subsystems, air supply system, water and thermal management and hydrogen delivery system. Air supply system consists of a blower and a gas-to-gas humidifier. The air is supplied to the stack by the blower and humidified by a gas-to-gas humidifier using stack exhaust gas. Controls for the air supply system are designed based on a static feed-forward control and a state feedback control with integrator to maintain the oxygen excess ratio at a desired level regardless of any load applied. Flow rates of air controlled by a voltage of an electric motor driving a blower should be able to supply oxygen to dynamically follow changes of loads, whereby oxygen excess rate should be kept at a level that prevents oxygen starvation. At the same time, water in the stack should be maintained optimally to keep from low proton conductivity and water flooding in porous materials. Therefore, supplying air is humidified with a humidifier that captures moistures exiting the stack. In order to manipulate the amount of humidity, we propose to use an extra bypass valve, which opening is controlled to optimally maintain humidification of the membrane and avoid water flooding. Thermal management system consists of two thermal circuits because of cooling effectiveness, where the inner thermal circuit is made of a bypass valve, a heat exchanger, a water reservoir and a water pump, while the outer thermal circuit is made of a radiator along with a fan, a coolant reservoir and a pump. In order to maintain the stack working temperature at a desired temperature and reduce parasitic powers, a state feedback controller with integrator is employed. Fuel delivery system is a hybridized one that consists of two recirculation lines with an ejector and a blow in order to increase efficiency of fuel usage. The supply line is made of a hydrogen tank, a flow control valve and a low pressure regulator. Controls are designed to track a flow rate where pressure is kept at constant and purging operations are allowed. In this paper, controls for four subsystems of fuel cell system were proposed and examined on a dynamic one dimensional model for a stack that considers non isothermal and two-phase effects. Optimized state feedback controllers with integrator and observers are used to improve control performances and results are presented.
Genetic risk factors for respiratory diseases of preterm infants (2014)

Aims Genetic variants of pulmonary surface glycoproteins like Muc5a and Muc5b are known to affect mucociliary clearance, control of infections and maybe associated with pulmonary fibrosis [1-3]. We tested the hypothesis that Muc5b (rs35705950) is associated with bronchopulmonary dysplasia (BPD) in mechanically ventilated preterm infants. In addition, we aimed to identify common variants associated with the need for surfactant treatment.
Improving Local Tumor Control by Combining Vascular Targeting Drugs, Mild Hyperthermia and Radiation (2001)

Improvement in local control in a foot-implanted (200 mm3) C3H mouse mammary carcinoma by combining vascular targeting drugs, mild hyperthermia and radiation was investigated. The vascular targeting drug was flavone acetic acid (FAA; 150 mg/kg) intraperitoneally injected either 3 h before local tumor water-bath heating or 1 h after local tumor irradiation. For untreated tumors, the average (+/- 1 S.E.) tumor growth time (TGT; time to reach 5 x treatment volume) was 7.1 days (+/- 0.4). This was increased to 9.2 days (+/- 0.7) by using FAA. Heating also increased TGT, the effect being temperature and time dependent, and this heat response was further increased by FAA. The radiation dose (+/- 95% confidence interval) to control 50% of tumors (TCD50) 90 days after irradiation was 52 Gy (50-55) for radiation alone. This was decreased to 42 Gy (39-45) by FAA, 47 Gy (45-50) by heating (41.5 degrees C; 60 min) 4 h after irradiation, and to 28 Gy (22-35) by combining FAA and heat. Thus, vascular targeting drugs can improve the efficacy of mild hyperthermia and radiation.
Approaching the Full Octave: Noncollinear Optical Parametric Chirped Pulse Amplification with Two-Color Pumping (2010)

We amplify ultrabroadband spectra (580-1000 nm) to mJ energies by applying different pump wavelengths in subsequent stages of a NOPCPA chain. As proof-of-principle we compress pulses composed by this new technique close to their Fourier-Limit.
New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention, and Cure (2021)

Previously, we showed that substitution of HIV-1 Env residue 375-Ser by bulky aromatic residues enhances binding to rhesus CD4 and enables primary HIV-1 Envs to support efficient replication as simian-human immunodeficiency virus (SHIV) chimeras in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing SHIVs containing ten primary Envs corresponding to HIV-1 subtypes A, B, C, AE and AG. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4<sup>+</sup> T cells, but only one replicated efficiently in primary rhesus cells. This was a subtype AE SHIV that naturally contained His at Env375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs led to efficient replication in rhesus CD4+ T cells <i>in vitro</i> and <i>in vivo</i> Nine SHIVs containing optimized Env375 alleles were grown large-scale in primary rhesus CD4<sup>+</sup> T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, and transmissible by rectal, vaginal, penile, oral or intravenous routes. To facilitate future SHIV constructions, we engineered a simplified second-generation design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary Envs with bulky aromatic substitutions at Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. Such SHIVs are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used to test vaccine efficacy in preclinical monkey trials.<b>Importance</b>SHIV infection of Indian rhesus macaques is an important animal model for studying HIV-1 transmission, prevention, immunopathogenesis and cure. Such research is timely, given recent progress with active and passive immunization and novel approaches to HIV-1 cure. Given the multifaceted roles of HIV-1 Env in cell tropism and virus entry, and as a target for neutralizing and non-neutralizing antibodies, Envs selected for SHIV construction are of paramount importance. Until recently, it has been impossible to strategically design SHIVs bearing clinically relevant Envs that replicate consistently in monkeys. This changed with the discovery that bulky aromatic substitutions at residue Env375 confer enhanced affinity to rhesus CD4. Here, we show that 10 new SHIVs bearing primary HIV-1 Envs with residue 375 substitutions replicated efficiently in RMs and could be transmitted efficiently across rectal, vaginal, penile and oral mucosa. These findings suggest an expanded role for SHIVs as a model of HIV-1 infection.
Helicobacter pylori induces somatic mutations in TP53 via overexpression of CHAC1 in infected gastric epithelial cells (2018)

Infection with <i>Helicobacter pylori</i> is known to decrease the level of glutathione in gastric epithelial cells and increase the production of reactive oxygen species (ROS), which can lead to DNA damage and the development of gastric cancer. Cation transport regulator 1 (CHAC1) has γ-glutamylcyclotransferase activity that degrades glutathione. We found that <i>cagA</i>-positive <i>H. pylori</i> infection triggered CHAC1 overexpression in human gastric epithelial (AGS) cells leading to glutathione degradation and the accumulation of ROS. Nucleotide alterations in the <i>TP53</i> tumour suppressor gene were induced in AGS cells overexpressing CHAC1, whereas no mutations were detected in cells overexpressing a catalytically inactive mutant of CHAC1. A high frequency of <i>TP53</i> mutations occurred in <i>H. pylori</i>-infected AGS cells, but this was prevented in cells transfected with CHAC1 siRNA. These findings indicate that <i>H. pylori</i>-mediated CHAC1 overexpression degrades intracellular glutathione, allowing the accumulation of ROS which subsequently causes mutations that could contribute to the development of gastric cancer.
Tree-Algorithms with Multi-Packet Reception and Successive Interference Cancellation (2021)

In this paper, we perform a thorough analysis of tree-algorithms with multi-packet reception (MPR) and successive interference cancellation (SIC), showing a number of novel results. We first derive the basic performance parameters, which are the expected length of the collision resolution interval and the normalized throughput, conditioned on the number of contending users. We then study their asymptotic behaviour, identifying an oscillatory component that amplifies with the increase in MPR. In the next step, we derive the throughput for the gated and windowed access, assuming Poisson arrivals. We show that for windowed access, the bound on maximum stable normalized throughput increases with the increase in MPR. his implies that investing in advanced physical capabilities, i.e., MPR and SIC pays off from the perspective of the medium access control algorithm.
Heterotrimeric G-Proteins Are Indispensable for FLT3-ITD autophosphorylation and Oncogenic Function (2016)

Abstract Heterotrimeric G-proteins transmit signals of G-protein coupled receptors and regulate many basic cellular functions. However, their role in normal and malignant hematopoietic stem cells remains obscure. Activating mutations in the heterotrimeric G-protein Gaq were found in various cancers and its expression is enhanced in diffuse large B-cell lymphoma and T-ALL. Our previous data suggested the involvement of heterotrimeric G-proteins in Flt3-ITD-mediated leukemic transformation. FMS-like tyrosine kinase 3 with internal tandem duplication (FLT3-ITD) is a frequent oncoprotein in acute myeloid leukemia causing constitutive active STAT5 signaling. Here, we investigated a novel role of Gaq in Flt3-ITD-induced leukemic transformation. We could show that Gaq is indispensable for aberrant FLT3-ITD activation and oncogenic function as Gaq activity is necessary to maintain the autophosphorylation of FLT3-ITD. Gaq abrogation resulted in diminished cell proliferation and colony formation as well as delayed leukemogenesis in vivo of Flt3-ITD leukemic cells. Importantly, the growth inhibition could be rescued by addition of IL3 and did not occur in the presence of FLT3 ligand-activated FLT3 wildtype receptor, demonstrating the specificity of Gaq requirement for FLT3-ITD oncogenic signaling. Interestingly, co-immunoprecipitations revealed a direct physical interaction between FLT3-ITD and Gaq which did not require phosphorylation of the receptor tyrosine kinase. Hence, FLT3-ITD hyperphosphorylation seems to be rather a consequence of the interaction than a prerequisite. Flt3-ITD-induced transformation of murine hematopoietic stem/progenitor cells (HSPCs) strictly depended on the presence of Gaq, and the ablation of Gaq/11 in transplanted Flt3-ITD-transduced HSPCs from conditional Gaq/11 double knock-out mice delayed leukemic burden. These findings of an unexpected, yet critical, role of Gaq place the molecule as an important target for antileukemic strategies. Disclosures No relevant conflicts of interest to declare.
Kinetic Treatments for Catalyst Activation and Deactivation Processes based on Variable Time Normalization Analysis (2019)

Progress reaction profiles are affected by both catalyst activation and deactivation processes occurring alongside the main reaction. These processes complicate the kinetic analysis of reactions, often directing researchers toward incorrect conclusions. We report the application of two kinetic treatments, based on variable time normalization analysis, to reactions involving catalyst activation and deactivation processes. The first kinetic treatment allows the removal of induction periods or the effect of rate perturbations associated with catalyst deactivation from kinetic profiles when the quantity of active catalyst can be measured. The second treatment allows the estimation of the activation or deactivation profile of the catalyst when the order of the reactants for the main reaction is known. Both treatments facilitate kinetic analysis of reactions suffering catalyst activation or deactivation processes.
Preface (2009)

Hybrid systems have always existed in the computer world. Whether in industrial data centers, national laboratories, or peoples' garages from spare parts, they have generally been the best way to get optimal performance on specialized applications. Now, due to a variety of technical challenges facing the industry, we are poised to see a dramatic growth in the importance of application-driven designs and a corresponding increase in the importance of hybrid systems.