gebhart/patrepeval huggingface dataset:
MetricForensics: A Multi-Level Approach for Mining Volatile Graphs (2010)

Advances in data collection and storage capacity have made it increasingly possible to collect highly volatile graph data for analysis. Existing graph analysis techniques are not appropriate for such data, especially in cases where streaming or near-real-time results are required. An example that has drawn significant research interest is the cyber-security domain, where internet communication traces are collected and real-time discovery of events, behaviors, patterns and anomalies is desired. We propose MetricForensics, a scalable framework for analysis of volatile graphs. MetricForensics combines a multi-level “drill down" approach, a collection of user-selected graph metrics and a collection of analysis techniques. At each successive level, more sophisticated metrics are computed and the graph is viewed at a finer temporal resolution. In this way, MetricForensics scales to highly volatile graphs by only allocating resources for computationally expensive analysis when an interesting event is discovered at a coarser resolution first. We test MetricForensics on three real-world graphs: an enterprise IP trace, a trace of legitimate and malicious network traffic from a research institution, and the MIT Reality Mining proximity sensor data. Our largest graph has »3M vertices and »32M edges, spanning 4:5 days. The results demonstrate the scalability and capability of MetricForensics in analyzing volatile graphs; and highlight four novel phenomena in such graphs: elbows, broken correlations, prolonged spikes, and strange stars.
X‐ray structural and simulation analysis of a protein mutant: The value of a combined approach (2004)

The effect of the mutation Arg 96 to His on the stability of bacteriophage T4 lysozyme has been previously studied by calorimetric experiments, X-ray crystallography, and free energy simulation techniques. The experimental and calculated values for the difference between the free energy of denaturation of the mutant and the wild type are in reasonable agreement. However, the two approaches led to different explanations for the loss in stability. To analyze the differences, a series of refinements based on the crystallographic data were performed, a number of aspects of the simulations were reexamined, and continuum electrostatic calculations were done to complement the latter. The results of those comparisons provide a better understanding of the origin of the free energy difference in this mutant. Furthermore, they show the importance of the combined use of simulations and crystallography for interpreting the effects of mutations on the energetics of the system.
Targeting S100A9 Reduces Neutrophil Recruitment, Inflammation and Lung Damage in Abdominal Sepsis (2021)

S100A9, a pro-inflammatory alarmin, is up-regulated in inflamed tissues. However, the role of S100A9 in regulating neutrophil activation, inflammation and lung damage in sepsis is not known. Herein, we hypothesized that blocking S100A9 function may attenuate neutrophil recruitment in septic lung injury. Male C57BL/6 mice were pretreated with the S100A9 inhibitor ABR-238901 (10 mg/kg), prior to cercal ligation and puncture (CLP). Bronchoalveolar lavage fluid (BALF) and lung tissue were harvested for analysis of neutrophil infiltration as well as edema and CXC chemokine production. Blood was collected for analysis of membrane-activated complex-1 (Mac-1) expression on neutrophils as well as CXC chemokines and IL-6 in plasma. Induction of CLP markedly increased plasma levels of S100A9. ABR-238901 decreased CLP-induced neutrophil infiltration and edema formation in the lung. In addition, inhibition of S100A9 decreased the CLP-induced up-regulation of Mac-1 on neutrophils. Administration of ABR-238901 also inhibited the CLP-induced increase of CXCL-1, CXCL-2 and IL-6 in plasma and lungs. Our results suggest that S100A9 promotes neutrophil activation and pulmonary accumulation in sepsis. Targeting S100A9 function decreased formation of CXC chemokines in circulation and lungs and attenuated sepsis-induced lung damage. These novel findings suggest that S100A9 plays an important pro-inflammatory role in sepsis and could be a useful target to protect against the excessive inflammation and lung damage associated with the disease.
Benzimidazole analogs as potent hypoxia inducible factor inhibitors: synthesis, biological evaluation, and profiling drug-like properties. (2014)

The potent anti-HIF-1α activity and favorable drug-like properties of compound 3k suggest that it may hold great potential as an adjuvant therapy for cancer treatment through repression of HIF-1α protein expression.
An Efficient Synthesis of Tenofovir (PMPA): A Key Intermediate Leading to Tenofovir-Based HIV Medicines (2020)

&lt;p&gt;Abstract: Herein, we report further improvements to the synthesis of tenofovir &lt;b&gt;1&lt;/b&gt;, the precursor to tenofovir disoproxil fumarate and tenofovir alafenamide fumarate. Starting from acyclic precursor diaminomalononitrile &lt;b&gt;12&lt;/b&gt;, a four-step protocol to tenofovir &lt;b&gt;1 &lt;/b&gt;will allow for vertical integration for more manufacturers. The key transformation is a more convergent one step procedure from &lt;b&gt;6&lt;/b&gt; as compared to the current commercial process, with an improved yield from 59% (two steps) to 70%. Further improvements include eliminating the need for problematic magnesium &lt;i&gt;tert&lt;/i&gt;-butoxide (MTB) and significant solvent reduction by eliminating the need for an intermediate workup. With the costs of HIV/AIDS treatments remaining a barrier for those most in need, lowering the raw material/processing costs and increasing the security of supply can increase patient access.&lt;/p&gt;
Modeling Multitarget Stool DNA Test Results in Asymptomatic Persons With Advanced Precancerous Lesions (2014)

Introduction: In an average-risk population we have previously reported the sensitivity of multitarget stool DNA (sDNA) for colorectal cancer (CRC) (92.4%) and for advanced precancerous lesions (APLs) (42.4%), with increasing sensitivity as advanced precancerous lesion (APL) size increased (p value for trend <0.001) (Imperiale TF, et. al. N Engl J Med 2014). The purpose of the current study was to explore demographic and colonoscopic/histologic features associated with detection of APLs by multitarget sDNA. Methods: Demographic features of age, gender, race/ethnicity, smoking history and colonoscopic/histologic features of lesion location and lesion size, evaluated from 1.0 cm to ≥3.0 cm in 0.5 cm increments, were examined using logistic regression among subjects with CRC and APLs, the latter of which includes tubular adenomas and sessile serrated polyps >1 cm, any size polyp with >25% villous histology or highgrade dysplasia. Results: Sixty-five CRC and 757 APLs were the most advanced findings identified by colonoscopy among 9,989 persons who independently had multitarget sDNA. CRC was uniformly detected irrespective of colonoscopic/histologic features. Overall likelihood ratio goodness of fit was statistically significant for a model for APLs that included both demographic and lesion features. Among APLs, current or former cigarette smoking was associated with higher sensitivity of multitarget sDNA (57.1% vs. 37.1% in never smokers, univariate p<0.001). Adding colonoscopic/histologic features revealed higher test sensitivity for APLs with distal location (adjusted odds ratio [aOR] 2.21; (95% confidence interval [CI] 1.59-3.03), size >1.0 cm (aOR 2.44; CI 1.79-3.33), and current or previous smoking (aOR 1.49; CI 1.10-2.04). Conclusion: Multitarget sDNA sensitivity for APLs increased with lesion size, distal location, and current or former cigarette smoking. Current or former smokers, a group with higher risk for both CRC and APLs, may especially benefit from the observed increase in multitarget sDNA sensitivity observed in this group. Disclosure - Dr. Imperiale - grant support from Exact Sciences Corp. Dr. Lavin - consultant for Exact Sciences Corp. Dr. Lidgard - employee of Exact Sciences Corp. Dr. Berger - employee of Exact Sciences Corp. This research was supported by an industry grant from Eact Sciences Corporation.
Distribution of 2-deoxy-2-fluoro-d-glucose in the coelom of healthy bald eagles (Haliaeetus leucocephalus) (2013)

The study established the biodistribution of (18)FDG in adult eagles, providing a baseline for clinical investigation and future research.
Multiple-frequency calibration of two-dimensional hydrophone arrays for instantaneous beam width measurements of shock-wave lithotripters (2011)

Characterizations of electrohydraulic lithotripters (EHLs) are usually limited to single-point measurements because hydrophone arrays are not readily available, or are prohibitively expensive. Furthermore, beamwidth measurements of peak pressure values made with single-point hydrophones are inaccurate. This inaccuracy comes from the high variability of the acoustic field and the fact that several shocks must be averaged to create a single beamwidth profile when using single-element hydrophones. Previous work demonstrated that characterizing the beam of an EHL with a single-point measurement technique led to an overestimate error of 25% compared to an instantaneous beamwidth measurement using a linear hydrophone array. In this paper, the improvement of our disposable, repeatable, hydrophone array is presented. The geometry was changed to that of a two-dimensional hydrophone array, which allows for the measurement of the instantaneous acoustic field of an EHL and its variation in 2-D. Modifications were made to the hydrophone fabrication methods which improved sensitivity and performance. Finally, a multiple-frequency calibration technique was implemented, allowing absolute pressures to be obtained for each hydrophone element.
Effect of Annealing on the Tolerance of LiCaAlF6 Single Crystals against F2 Laser Irradiation (2004)

The optical tolerance of annealed LiCaAlF 6 single crystals against F 2 laser irradiation was investigated. Annealed LiCaAlF 6 ( t =1.45 mm) shows an improved transmittance at 157 nm, 94.4% after the compensation of the surface reflection loss. Furthermore, after the initial increase by F 2 laser cleaning, transmittance at 157 nm remains almost unchanged even after irradiation with a F 2 laser beam up to 10 5 pulses at a fluence of approximately 160 mJ cm -2 pulse -1 .
A PSCA Promoter Based Avian Retroviral Transgene Model of Normal and Malignant Prostate (2004)

Abstract : The molecular and cellular origins of prostate cancer are poorly understood. Recent evidence from our laboratory suggests that prostate cancer may arise from a basal/luminal precursor cell marked by cell surface expression of PSCA. The evidence supporting this hypothesis is that (I) PSCA marks an intermediate cell population that coexpresses basal and luminal cell cytokeratins (2) this cell population is does not express p63 and is androgen receptor positive, all hallmarks of prostate cancer, and (3) PSCA is highly expressed in HGPIN and prostate cancer and in all animal models of prostate cancer. To test this hypothesis and to develop new models of prostate, we propose to determine whether delivery of oncogenes specifically to the PSCA positive cells of mouse prostate is sufficient to cause cancer. To accomplish this, we will develop a transgenic mouse model in which the retroviral receptor gene tva is expressed in the prostate under control of the PSCA promoter. Virus containing one or more oncogenes will be delivered to the prostate and the resulting phenotype characterized.
Counterdiabatic vortex pump in spinor Bose-Einstein condensates (2017)

Topological phase imprinting is a well-established technique for deterministic vortex creation in spinor Bose-Einstein condensates of alkali-metal atoms. It was recently shown that counterdiabatic quantum control may accelerate vortex creation in comparison to the standard adiabatic protocol and suppress the atom loss due to nonadiabatic transitions. Here we apply this technique, assisted by an optical plug, for vortex pumping to theoretically show that sequential phase imprinting up to 20 cycles generates a vortex with a very large winding number. Our method significantly increases the fidelity of the pump for rapid pumping compared to the case without the counterdiabatic control, leading to the highest angular momentum per particle reported to date for the vortex pump. Our studies are based on numerical integration of the three-dimensional multicomponent Gross-Pitaevskii equation, which conveniently yields the density profiles, phase profiles, angular momentum, and other physically important quantities of the spin-1 system. Our results motivate the experimental realization of the vortex pump and studies of the rich physics it involves.
Electrohydrodynamic Ionization (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Solution Structure, Dimerization, and Dynamics of a Lipophilic α/310-Helical, Cα-Methylated Peptide. Implications for Folding of Membrane Proteins (2001)

The solution structure and the dimerization behavior of the lipophilic, highly C(alpha)-methylated model peptide, mBrBz-Iva(1)-Val(2)-Iva(3)-(alphaMe)Val(4)-(alphaMe)Phe(5)-(alphaMe)Val(6)-Iva(7)-NHMe, was studied by NMR spectroscopy and molecular dynamics simulations. The conformational analysis resulted in a right-handed 3(10)/alpha-helical equilibrium fast on the NMR time scale with a slight preference for the alpha-helical conformation. The NOESY spectrum showed intermolecular NOEs due to an aggregation of the heptapeptide. In addition, temperature-dependent diffusion measurements were performed to calculate the hydrodynamic radius. All these findings are consistent with an antiparallel side-by-side dimerization. The structure of the dimeric peptide was calculated with a simulated annealing strategy. The lipophilic dimer is held together by favorable van der Waals interactions in the sense of a bulge fitting into a groove. The flexibility of the helical conformations concerning an alpha/3(10)-helical equilibrium is shown in a 3 ns molecular dynamics simulation of the resulting dimeric structure. Both overall helical structures of each monomer and the antiparallel mode of dimerization are stable. However, transitions were seen of several residues from a 3(10)-helical into an alpha-helical conformation and vice versa. Hence, this peptide represents a good model in which two often-discussed aspects of hierarchical transmembrane protein folding are present: i <-- i + 3 and i <-- i + 4 local H-bonding interactions cause a specific molecular shape which is then recognized as attractive by other surrounding structures.
Programming Flows in Dense Mobile Environments: A Multi-user Diversity Perspective (2015)

The emergence of OpenFlow and Software Defined Networks brings new perspectives into how we design the next generation networks, where the number of base stations/access points as well as the devices per subscriber will be dramatically higher. In such dense environments, devices can communicate with each other directly and can attach to multiple base stations (or access points) for simultaneous data communication over multiple paths. This paper explores how networks can maximally enable this multi-path diversity through network programmability. In particular, we propose programmable flow clustering and set policies for inter-group as well as intra-group wireless scheduling. Further, we propose programmable demultiplexing of a single network flow onto multiple paths before the congestion areas and multiplexing them together post congestion areas. We show the benefits of such programmability first for legacy applications that cannot take advantage of multi-homing without such programmability. We then evaluate the benefits for smart applications that take advantage of multi-homing by either opening multiple TCP connections over multiple paths or utilizing a transport protocol such as MP-TCP designed for supporting such environments. More specifically, we built an emulation environment over Mininet for our experiments. Our evaluations using synthetic and trace driven channel models indicate that the proposed programmability in wireless scheduling and flow splitting can increase the throughput substantially for both the legacy applications and the current state of the art.
CMOS phase-interpolation DDS for an UWB MB-OFDM Alliance application (2009)

This paper presents a novel concept of using a phase-interpolation direct digital synthesizer for an Ultra Wideband MB-OFDM Alliance application as a low silicon area alternative to state of the art solutions. In particular, an investigation of the spurious tones in such direct digital synthesizer is presented and ways how to reduce their presence are discussed. The design and simulation of the critical blocks made using a 65-nm CMOS process are also presented.
Introduction of two prolines and removal of the polybasic cleavage site leads to optimal efficacy of a recombinant spike based SARS-CoV-2 vaccine in the mouse model (2020)

A vaccine for SARS-CoV-2 is urgently needed. A better understanding of antigen design and attributes that vaccine candidates need to have to induce protective immunity is of high importance. The data presented here validates the choice of antigens that contain the PP mutation and suggests that deletion of the polybasic cleavage site could lead to a further optimized design.
Cyclic prefixing or zero padding for wireless multicarrier transmissions? (2002)

Zero padding (ZP) of multicarrier transmissions has been proposed as an appealing alternative to the traditional cyclic prefix (CP) orthogonal frequency-division multiplexing (OFDM) to ensure symbol recovery regardless of the channel zero locations. In this paper, both systems are studied to delineate their relative merits in wireless systems where channel knowledge is not available at the transmitter. Two novel equalizers are developed for ZP-OFDM to tradeoff performance with implementation complexity. Both CP-OFDM and ZP-OFDM are then compared in terms of transmitter nonlinearities and required power backoff. Next, both systems are tested in terms of channel estimation and tracking capabilities. Simulations tailored to the realistic context of the standard for wireless local area network HIPERLAN/2 illustrate the pertinent tradeoffs.
A Tool for Studying Contact Electrification in Systems Comprising Metals and Insulating Polymers (2003)

We describe an analytical system for in situ measurement of the charge that develops by contact electrification when a ferromagnetic sphere rolls on the surface of a polymer. This system makes it possible to survey the ability of polymeric surfaces to charge by contact electrification. Because the measurement of charge using this tool does not require physical contact of the charged sphere with the measuring electrode, it also enables the kinetics of charging to be examined. The research has focused on the contact charging of spheres having a core-and-shell geometry (a common core of ferromagnetic steel, and a variable shell of thin films of metals, or metals with surface oxides) rolling on the surface of polymeric slabs; it has generated an internally consistent set of data that include the polarity and magnitude of charging for a homologous series of polymers that differ chemically in the pendant group on a polyethylene backbone.
Eine einfache Synthese von (±)-Matrin (1998)

Eine viel kürzere Totalsynthese von (±)-Matrin 1 als die bislang bekannten Verfahren nutzt als Schlüsselschritt eine Radikal-Kaskadenreaktion, in der zwei der vier sechsgliedrigen Ringe und vier neue Bindungen gebildet werden; abschließend wird eine Xanthogenatgruppe übertragen.
Package and board level reliability modeling of advanced CSP pakages for telecommunication applications (2005)

Market for telecommunication products (e.g., mobile phones) is very competitive, demanding products which are more reliable, higher performance, lighter, smaller, cheaper, and shorter time-to-market. These technology requirements are possible with the recent development of advanced Chip Scale Packages (CSPs), such as thin-profile fine-pitch Ball Grid Array (TFBGA), Quad-Flat-No-lead (QFN), and wafer-level CSP (WL-CSP). However, due to limited product development time, these CSPs are usually not tested and studied in detail before introduction to the market. As a result, the package design may not be optimized for various reliability requirements, e.g., popcorn, thermal cycling test, and drop test.
Diffusion-induced line-edge roughness (2003)

As feature dimensions shrink, line edge roughness has become an increasing concern in semiconductor fabrication. There are numerous potential contributors to line edge roughness throughout the lithographic process and any measured roughness value on a printed device feature is, like the feature itself, a convolved function of every processing step. When the full lithographic process is used to study line edge roughness, it can be difficult to isolate the contribution to final roughness from any individual processing step or factor. To gain a more fundamental understanding of roughness generation that is specifically related to photoresist chemistry and formulation it is necessary to design experiments that separate out exposure related issues like mask dimension variation or local dose variation (“shot noise”). This can be accomplished using previously reported experimental protocols for bilayer film stack creation. The bilayer experimental approach has been used to study the effect of variations in such factors as post exposure bake time, photoacid generator loading, and developer concentration on roughness generation. Surface roughness of the developed film stacks is measured via atomic force microscopy. Surface roughness of developed bilayer film stacks may be considered analogous to sidewall roughness of printed features. An acrylate-based 193nm photoresist resin and an APEX-type resin are used in these experiments. In addition to experimental results, results from mesoscale lithographic simulations are used to gain further insight into diffusion induced roughness and how roughness in the latent image is modified during the development step.