gebhart/patrepeval huggingface dataset:
Tombolo: Performance enhancements for cloud storage gateways (2016)

Object-based cloud storage has been widely adopted for their agility in deploying storage with a very low up-front cost. However, enterprises currently use them to store secondary data and not for expensive primary data. The driving reason is performance; most enterprises conclude that storing primary data in the cloud will not deliver the performance needed to serve typical workloads. Our analysis of real-world traces shows that certain primary data sets can reside in the cloud with its working set cached locally, using a cloud gateway that acts as a caching bridge between local data centers and the cloud. We use a realistic cloud gateway simulator to study the performance and cost of moving such workloads to different cloud backends (like Amazon S3). We find that when equipped with the right techniques, cloud gateways can provide competitive performance and price compared to on-premise storage. We also provide insights on how to build such cloud gateways, especially with respect to caching and prefetching techniques.
Effects of ricin A chain conjugates of monoclonal antibodies to human alpha-fetoprotein and placental alkaline phosphatase on antigen-producing tumor cells in culture. (1985)

Two tumor-associated proteins, alpha-fetoprotein (AFP) and placental alkaline phosphatase (PLAP), were investigated as target proteins for antibody:cytotoxin conjugates. An AFP-producing hepatoma cell line (HepG2) and a PLAP-producing cervical carcinoma cell line (SKGIIIa) were used as target cells. Both cell lines were equally susceptible to the toxic effects of intact ricin. Immunofluorescent studies showed that AFP could be detected at the surface of the HepG2 cells in a speckled distribution, while PLAP was uniformly distributed over the surface of the SKGIIIa cells. The anti-AFP ricin A chain conjugate was not cytotoxic to either cell line at low concentrations and killed both types of cells at high concentrations. The anti-PLAP conjugate at low concentrations was 100-fold more toxic than the anti-AFP conjugate to the PLAP-producing SKGIIIa cells. At high concentrations, it also killed both types of cells. The enhanced toxicity of the anti-PLAP conjugate to the SKGIIIa cells was inhibited by an excess of unconjugated anti-PLAP but not anti-AFP, indicating that the uptake of the conjugate depends on specific cell surface binding to the antigen. The indiscriminate toxicity observed at high concentrations of either conjugate was not inhibited by unconjugated antibody, suggesting that this effect depends on conjugate uptake independent of the identity of the antigen. These results emphasize the importance of the properties of the target antigen to the cytotoxic effects of antibody conjugates as well as the need for caution in experiments using high concentrations of conjugates. They suggest that PLAP may be a suitable target for immunotoxin therapy of human cancer.
Carcinoembryonic antigen immunoscintigraphy complements mammography in the diagnosis of breast carcinoma (2000)

(99)Tc labeled anti-CEA Fab' had high specificity and positive predictive values for breast carcinoma and the majority of false-positive studies were associated with an increased risk of malignancy. Improved imaging techniques, including dedicated gamma cameras for breast and axillary lymph node imaging, will likely improve the test's sensitivity for smaller lesions.
Tumor‐reactive CD8+ T‐cell clones in patients after NY‐ESO‐1 peptide vaccination (2007)

A major objective of peptide vaccination is the induction of tumor-reactive CD8+ T-cells. We have shown that HLA-A2 positive cancer patients frequently develop an antigen-specific CD8+ T-cell response after vaccination with NY-ESO-1 peptides p157-165/p157-167. These T-cells are highly reactive with the peptides used for vaccination, but only rarely recognize HLA-matched, NY-ESO-1 expressing tumor cell lines. To address the apparent lack of tumor recognition of vaccine-induced CD8+ T-cell responses, we used autologous tumor cells for in vitro stimulation and expansion of pre- and postvaccine CD8+ T-cells. In contrast to standard presensitization methods with peptide-pulsed antigen-presenting cells, mixed lymphocyte tumor culture favored the selective expansion of low-frequency tumor-reactive T-cells. In four patients, we were able to demonstrate that antigen-specific and tumor-reactive T-cells are detectable and are indeed elicited as a result of NY-ESO-1 peptide vaccination. Further analyses of postvaccine antigen-specific T-cells at a clonal level show that vaccine-induced antigen-specific T-cells are heterogeneous in functional activity. These results suggest that the methods of immunomonitoring are critical to identify the proportion of tumor-reactive T-cells within the population of vaccine-induced antigen-specific effector cells. Our results show that immunization with NY-ESO-1 peptides leads to strong tumor-reactive CD8+ T-cell responses. Our findings suggest that approaches to peptide vaccination may be improved to induce higher numbers of antigen-specific T-cells and to selectively increase the proportion of CD8+ T-cells that have the capacity to recognize and eliminate tumor cells.
SIK2 Restricts Autophagic Flux To Support Triple-Negative Breast Cancer Survival (2020)

Triple-negative breast cancer (TNBC) is a highly heterogeneous disease with multiple, distinct molecular subtypes that exhibit unique transcriptional programs and clinical progression trajectories. Despite knowledge of the molecular heterogeneity of the disease, most patients are limited to generic, indiscriminate treatment options: cytotoxic chemotherapy, surgery, and radiation. To identify new intervention targets in TNBC, we used large-scale, loss-of-function screening to identify molecular vulnerabilities among different oncogenomic backgrounds. This strategy returned salt inducible kinase 2 (SIK2) as essential for TNBC survival. Genetic or pharmacological inhibition of SIK2 leads to increased autophagic flux in both normal-immortalized and tumor-derived cell lines. However, this activity causes cell death selectively in breast cancer cells and is biased toward the claudin-low subtype. Depletion of ATG5, which is essential for autophagic vesicle formation, rescued the loss of viability following SIK2 inhibition. Importantly, we find that SIK2 is essential for TNBC tumor growth in vivo . Taken together, these findings indicate that claudin-low tumor cells rely on SIK2 to restrain maladaptive autophagic activation. Inhibition of SIK2 therefore presents itself as an intervention opportunity to reactivate this tumor suppressor mechanism.
Long-Term Stabilization of Temporal and Spectral Drifts of a Burst-Mode OPCPA System (2019)

We demonstrate a stabilization system for temporal and spectral drifts of an OPCPA pump-probe laser at the FLASH soft-x-ray FEL-facility. We achieve drifts of 5.7fs rms and 3.2nm rms, respectively over two days. © 2019 The Author(s)
Hydrogen Sulfide Gas Detection via Multivariate Optical Computing (2018)

Hydrogen-sulfide gas is a toxic, colorless gas with a pungent odor that occurs naturally as a decomposition by-product. It is critical to monitor the concentration of hydrogen sulfide. Multivariate optical computing (MOC) is a method that can monitor analytes while minimizing responses to interferences. MOC is a technique by which an analogue calculation is performed entirely in the optical domain, which simplifies instrument design, prevents the drift of a calibration, and increases the strength and durability of spectroscopic instrumentation against physical perturbation when used for chemical detection and identification. This paper discusses the detection of hydrogen-sulfide gas in the ultraviolet (UV) spectral region in the presence of interfering gaseous species. A laboratory spectroscopic measurement system was set up to acquire the UV spectra of H₂S and interference gas mixtures in high-pressure/high-temperature (HPHT) conditions. These spectra were used to guide the design and fabrication of a multivariate optical element (MOE), which has an expected measurement relative accuracy of 3.3% for H₂S, with a concentration in the range of 0⁻150 nmol/mL. An MOC validation system with the MOE was used to test three samples of H₂S and mercaptans mixtures under various pressures, and the relative accuracy of H₂S measurement was determined to be 8.05%.
Biologically Active Compounds through Catalysis: Efficient Synthesis of N‐(Heteroarylcarbonyl)‐N′‐(arylalkyl)piperazines (2004)

A practical route for the synthesis of new biologically active 5-HT(2 A) receptor antagonists has been developed. In only three catalytic steps, this class of central nervous system (CNS) active compounds can be synthesized efficiently with high diversity. As the initial step, an anti-Markovnikov addition of amines to styrenes provides an easy route to N-(arylalkyl)piperazines, which constitute the core structure of the active molecules. Here, base-catalyzed hydroamination reactions of styrenes with benzylated piperazine proceeded in high yield even at room temperature. After catalytic debenzylation, the free amines were successfully carbonylated with different aromatic and heteroaromatic halides and carbon monoxide to yield the desired compounds in good to excellent yields. The two key reactions, base-catalyzed hydroamination of styrenes and palladium-catalyzed aminocarbonylation of haloarenes/heterocycles, showed tolerance towards various functional groups, thereby demonstrating the potential to synthesize a wide variety of new derivatives of this promising class of pharmaceuticals.
Synthesis of Core-shell Type ZnS-CdS Stratified Photocatalyst (2008)

Abstract not Available.
New, highly acidic ionic liquid systems and their application in the carbonylation of tolueneElectronic supplementary information (ESI) available: experimental details. See http://www.rsc.org/suppdata/cc/b4/b403464c/ (2004)

Based on the surprisingly high solubility of AlCl3 in ionic liquids of type [cation][(CF3SO2)2N], a new class of highly acidic, ionic systems has been developed. First tests in toluene carbonylation revealed high potential of these new acidic ionic liquids as catalyst for arene functionaliziation reactions.
Modeling and Evaluating Interoperable Grid Systems (2008)

Grid resource management tools have evolved from manual discovery and job submission to sophisticated brokering solutions. User requirements have created certain properties that resource managers have learned to support. This development is still continuing, and users already find it difficult to distinguish brokers and to migrate their applications when they move to a different grid. Moreover, new architectures are continuously being proposed, such as multi-site and interoperable grid systems. This paper presents the Alvio simulation framework which is designed to evaluate job scheduling strategies in complex HPC infrastructures. The main contribution of this simulator is that it allows modeling from local systems to interoperable grid scenarios. We also present an evaluation of multi-site and grid interoperable systems which shows the effect of job forwarding between different brokers.
Reconstruction of two-dimensional signals from level crossings (1990)

Recent results indicate that reconstruction of two-dimensional signals from crossings of one level requires, in theory and practice, extreme accuracy in positions of the samples. The representation of signals with one-level crossings can be viewed as a tradeoff between bandwidth and dynamic range, in the sense that if the available bandwidth is sufficient to preserve the level crossings accurately, then the dynamic range requirements are significantly reduced. On the other hand, representation of signals by their samples at the Nyquist rate can be considered as requiring relatively small bandwidth and large dynamic range, because, at least in theory, amplitude information at prespecified points is needed, to infinite precision. An overview of existing results in zero crossing representation is presented, and a number of new results on sampling schemes for reconstruction from multiple-level threshold crossing are developed. The quantization characteristics of these sampling schemes appear to lie between those of Nyquist sampling and one-level crossing representations, thus bridging the gap between explicit Nyquist sampling and implicit one-level crossing sampling strategies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: Diels‐Alder Reaction of 2‐Cyano‐1‐aza Dienes. The Effect of Nitrogen Substituents. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The scaling of contact rates with population density for the infectious disease models (2013)

Contact rates and patterns among individuals in a geographic area drive transmission of directly-transmitted pathogens, making it essential to understand and estimate contacts for simulation of disease dynamics. Under the uniform mixing assumption, one of two mechanisms is typically used to describe the relation between contact rate and population density: density-dependent or frequency-dependent. Based on existing evidence of population threshold and human mobility patterns, we formulated a spatial contact model to describe the appropriate form of transmission with initial growth at low density and saturation at higher density. We show that the two mechanisms are extreme cases that do not capture real population movement across all scales. Empirical data of human and wildlife diseases indicate that a nonlinear function may work better when looking at the full spectrum of densities. This estimation can be applied to large areas with population mixing in general activities. For crowds with unusually large densities (e.g., transportation terminals, stadiums, or mass gatherings), the lack of organized social contact structure deviates the physical contacts towards a special case of the spatial contact model - the dynamics of kinetic gas molecule collision. In this case, an ideal gas model with van der Waals correction fits well; existing movement observation data and the contact rate between individuals is estimated using kinetic theory. A complete picture of contact rate scaling with population density may help clarify the definition of transmission rates in heterogeneous, large-scale spatial systems.
Triptolide sensitizes AML cells to TRAIL-induced apoptosis via decrease of XIAP and p53-mediated increase of DR5 (2008)

Acute myeloid leukemia (AML) cells are relatively resistant to tumor necrosis factor alpha-related apoptosis-inducing ligand (TRAIL). We previously reported that triptolide, a potent anticancer agent from a Chinese herb, decreases XIAP in leukemic cells. We evaluated the combination of triptolide and TRAIL and found synergistic promotion of apoptosis in AML cells. XIAP-overexpressing U937 cells (U937XIAP) were more resistant to TRAIL than U937neo cells, and inhibition of XIAP with the small-molecule inhibitor 1396-11 enhanced TRAIL-induced apoptosis, implying XIAP as a resistance factor in AML. Furthermore, triptolide increased DR5 levels in OCI-AML3, while the DR5 increase was blunted in p53-knockdown OCI-AML3 and p53-mutated U937 cells, confirming a role for p53 in the regulation of DR5. In support of this finding, disruption of MDM2-p53 binding with subsequent increase in p53 levels by nutlin3a increased DR5 levels and sensitized OCI-AML3 cells to TRAIL. The combination of 1396-11 plus nutlin3a plus TRAIL was more effective than either the 1396-11 and TRAIL or nutlin3a and TRAIL combinations in OCI-AML3 cells, further supporting the role of triptolide as a sensitizer to TRAIL-induced apoptosis in part by independent modulation of XIAP expression and p53 signaling. Thus, the combination of triptolide and TRAIL may provide a novel strategy for treating AML by overcoming critical mechanisms of apoptosis resistance.
Glyoxylic Acid and MP‐Glyoxylate: Efficient Formaldehyde Equivalents in the 3‐CC of 2‐Aminoazines, Aldehydes, and Isonitriles. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Formation of 4H‐Azepine by the Electrophilic Reaction of a 2‐Methoxyazepinium Ion and Analysis of the Sigmatropic Isomerization (2006)

Abstract 2‐Aryl‐2 H ‐, 3‐aryl‐3 H ‐, and 4‐aryl‐4 H ‐azepine were formed by the novel, electrophilic, π LUMO ‐controlled reaction of the 2‐methoxyazepinium ion, generated in situ by the reaction of TiCl 4 with 2,7‐dialkoxy‐2 H ‐azepine and an aryl compound, for which the kinetic parameters of the sigmatropic hydrogen rearrangement of the 4 H ‐azepine was measured. The substitution and hydrogen shift of the azepinium ion were analyzed with DFT studies. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Computational planning of the synthesis of complex natural products (2020)

Training algorithms to computationally plan multistep organic syntheses has been a challenge for more than 50 years<sup>1-7</sup>. However, the field has progressed greatly since the development of early programs such as LHASA<sup>1,7</sup>, for which reaction choices at each step were made by human operators. Multiple software platforms<sup>6,8-14</sup> are now capable of completely autonomous planning. But these programs 'think' only one step at a time and have so far been limited to relatively simple targets, the syntheses of which could arguably be designed by human chemists within minutes, without the help of a computer. Furthermore, no algorithm has yet been able to design plausible routes to complex natural products, for which much more far-sighted, multistep planning is necessary<sup>15,16</sup> and closely related literature precedents cannot be relied on. Here we demonstrate that such computational synthesis planning is possible, provided that the program's knowledge of organic chemistry and data-based artificial intelligence routines are augmented with causal relationships<sup>17,18</sup>, allowing it to 'strategize' over multiple synthetic steps. Using a Turing-like test administered to synthesis experts, we show that the routes designed by such a program are largely indistinguishable from those designed by humans. We also successfully validated three computer-designed syntheses of natural products in the laboratory. Taken together, these results indicate that expert-level automated synthetic planning is feasible, pending continued improvements to the reaction knowledge base and further code optimization.
Headache and Scalp Edema in Sickle Cell Disease (1996)

In addition to the more common intracranail vaso-occlusive complications, skull infarction should be considered as a cause of newonset headache in patients with sickle cell disease, especially if scalp edema is present.
Toward an interactive article: integrating journals and biological databases (2011)

Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.
Aircraft Design as a Tool in Achieving Educational Objectives for Engineering Concepts in a Core Curriculum (2016)

The U.S. Air Force Academy has a Core Curriculum taken by all cadets as they pursue B.S. degrees in various disciplines. The Core includes a series of engineering courses, including: a freshman engineering course, a sophomore engineering mechanics course, and three junior courses (a course in aeronautics, a course in astronautics, and a course in electrical and computer engineering). In addition, all cadets take an introductory course in computing. Typically these courses are overviews of the various engineering disciplines, and are often also taken by students majoring in the disciplines as an introductory course in their major. The course in aeronautics, Fundamentals of Aeronautics (AE315), has traditionally been taught in lecture mode with regular homework assignments and projects, with student assessment taking place using mid-term and final exams. In order to support the Academy Scholars Program, a new version of AE315 was created for students in the Scholars Program, with the Scholars students using a team-based learning approach. In an approach that was inspired by a sophomore aircraft design course developed at Cal Poly, the Scholars version of AE315 has evolved into an aircraft design course, where the students were asked to perform a conceptual design of an historical aircraft: a multi-role fighter for the U.S. Air Force in 1960. The use of aircraft design as a motivation and basis for learning about aeronautics was successful, with many lessons learned and motivation obtained to expand the course in the future.
A Generalized Proportionate-Type Normalized Subband Adaptive Filter (2019)

We show that a new design criterion, i.e., the least squares on subband errors regularized by a weighted norm, can be used to generalize the proportionate-type normalized subband adaptive filtering (PtNSAF) framework. The new criterion directly penalizes subband errors and includes a sparsity penalty term which is minimized using the damped regularized Newton's method. The impact of the proposed generalized PtNSAF (GPtNSAF) is studied for the system identification problem via computer simulations. Specifically, we study the effects of using different numbers of subbands and various sparsity penalty terms for quasi-sparse, sparse, and dispersive systems. The results show that the benefit of increasing the number of subbands is larger than promoting sparsity of the estimated filter coefficients when the target system is quasi-sparse or dispersive. On the other hand, for sparse target systems, promoting sparsity becomes more important. More importantly, the two aspects provide complementary and additive benefits to the GPtNSAF for speeding up convergence.
13C Nuclear magnetic resonance characterization of poly(propylene) prepared with homogeneous catalysts (1989)

Abstract The minor resonances in the 13 C NMR spectrum of poly(propylene) prepared with soluble Group 4 metallocene/methylalumoxane catalysts are fully characterized. The 13 C shifts for regioirregular sequences, chain‐end structures, and 1,3‐propylene adduct are obtained for both isotactic and atactic components. In both components the dominating mechanism is 1,2‐insertion, with much lower amounts of 2,1‐insertion and 1,3‐insertion depending on the catalysts used. The isotactic component is stereoregular in all insertion modes. In the atactic components random stereosequences are observed. The regiostructures suggest that the propagation step is catalyticsite controlled even for the atactic component.