gebhart/patrepeval huggingface dataset:
Nonlinear Absorption Initiated Avalanche Breakdown in Dielectric ZrO2 (1988)

We report direct measurements of nonlinear transmission in dielectric ZrO2 prior to the observation of catastrophic damage for nsec laser pulses at 532 nm. The tested cubic zirconia (ZrO2) specimens are stabilized with yttria (Y2O3) having concentrations of 9.4%, 12%, 15%, 18%, and 21%. Transmission measurements were performed for a broad range of pulsewidths from 40 psec to 18 nsec (FWHM) at 532 nm. Our results indicate that the nonlinearity prior to breakdown is mainly attributed to the formation of material defects (color centers) by two-photon absorption (2PA) at high irradiance. These induced color centers appear to be long-lived (the order of hours) but can be bleached by repeated irradiation with relatively low irradiance 532 nm pulses. The accumulated effects of color center absorption during the 2PA measurements makes extraction of the two-photon absorption coefficient difficult. However, the smallest value for the 2PA coefficient (∼0.04 cm/GW) was measured in the ZrO2 sample stabilized with 9.4% Y2O3 for the shortest pulsewidth (40 psec) with which the measurements were performed. The observed nonlinear transmission prior to breakdown is consistent with the interpretation that damage in this material is due to 2PA induced avalanche breakdown.
ChemInform Abstract: SUSTAINED WATER CLEAVAGE BY VISIBLE LIGHT (1982)

Abstract Mit bifunktionellen Redoxkatalysatoren auf TiO 2 ‐Basis (mit feinverteiltem Pt und RuO 2 beladene kolloidale TiO 2 ‐Teilchen) läßt sich in wäßrigen Lösungen eine ununterbrochene H 2 O‐Spaltung zu H 2 und O 2 durch 4 Quanten sichtbaren Lichtes erreichen.
Field Fluctuation Spectroscopy in a Reverberant Cavity with Moving Scatterers (2003)

We report a study of transient ultrasonic waves inside a reverberant cavity containing moving scatterers. We show that the elastic mean free path and the dynamics of the scatterers govern the evolution of the autocorrelation of acoustic wave field. A parallel is established between these results and a closely related technique, diffusing acoustic wave spectroscopy. Excellent agreement is found between experiment and theory for a moving stainless steel ball in a water tank, thereby elucidating the underlying physics, and a potential application, fish monitoring inside aquariums, is demonstrated.
Analyses of inter- and intra-patient variation in the V3 loop of the HIV-1 envelope protein (1991)

The third hypervariable domain of the HIV-1 gp120 envelope protein (V3) has been the focus of intensive sequencing efforts. To date, nearly one thousand V3 loop sequences have been stored in the HIV sequence database. Studies have revealed that the V3 loop elicits potent type-specific immune responses, and that it plays a significant role in cell tropism and fusion . The immunogenic tip of the loop can serve as a type-specific neutralizing antibody epitope, as well as a cytotoxic T-cell epitope. A helper T-cell epitope that lies within the amino terminal half of the V3 loop has also been characterized. Despite the richness of the immunologic response to this region, its potential for variation makes it an elusive target for vaccine design. Analyses of sibling sequence sets (sets of viral sequences derived from one person) show that multiple forms of the immunogenic tip of the loop are found within most HIV-1 infected individuals. Viral V3 sequences obtained from epidemiologically unlinked individuals from North America and Europe show extensive variation. However, some amino acid positions distributed throughout the V3 loop are highly conserved, and there is also conservation of the charge class of amino acid able to occupy certain positions relative to the tip of the loop. By contrast, the sequences obtained from many countries throughout the African continent reveal that V3 is a remarkably fluid region with few absolute constraints on the nature of the amino acids that can occupy most positions in the loop. The high degree of heterogeneity in this region is particularly striking in view of its contribution to biologically important viral functions.
Cystatin C: A Candidate Biomarker for Amyotrophic Lateral Sclerosis (2010)

Amyotrophic lateral sclerosis (ALS) is a fatal neurologic disease characterized by progressive motor neuron degeneration. Clinical disease management is hindered by both a lengthy diagnostic process and the absence of effective treatments. Reliable panels of diagnostic, surrogate, and prognostic biomarkers are needed to accelerate disease diagnosis and expedite drug development. The cysteine protease inhibitor cystatin C has recently gained interest as a candidate diagnostic biomarker for ALS, but further studies are required to fully characterize its biomarker utility. We used quantitative enzyme-linked immunosorbent assay (ELISA) to assess initial and longitudinal cerebrospinal fluid (CSF) and plasma cystatin C levels in 104 ALS patients and controls. Cystatin C levels in ALS patients were significantly elevated in plasma and reduced in CSF compared to healthy controls, but did not differ significantly from neurologic disease controls. In addition, the direction of longitudinal change in CSF cystatin C levels correlated to the rate of ALS disease progression, and initial CSF cystatin C levels were predictive of patient survival, suggesting that cystatin C may function as a surrogate marker of disease progression and survival. These data verify prior results for reduced cystatin C levels in the CSF of ALS patients, identify increased cystatin C levels in the plasma of ALS patients, and reveal correlations between CSF cystatin C levels to both ALS disease progression and patient survival.
Supplementary Table from Nonclinical Characterization of Bexmarilimab, a Clever-1–Targeting Antibody for Supporting Immune Defense Against Cancers (2023)

Supplementary Table from Nonclinical Characterization of Bexmarilimab, a Clever-1–Targeting Antibody for Supporting Immune Defense Against Cancers
High Average Power Diode End-Pumped Composite Nd:YAG Laser Passively Q-switched by Cr4+:YAG Saturable Absorber (2001)

We report a diode end-pumped composite Nd:YAG laser, passively Q-switched by a Cr 4+ :YAG crystal as saturable absorber. The maximum peak power exceeded 16 kW for an average power of 2.6 W, laser pulses of 16.8-ns duration and 272-µJ energy. The maximum average power was 4.2 W with the laser operating at 24.0 kHz repetition frequency and 47.8-ns pulses duration (3.7 kW peak power) at a beam quality of M 2 =1.34. A rate-equation model that considers both the active medium and the saturable absorber dynamics was developed. A good agreement between the experiments and modeling resulted.
Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance (2020)

<i>Pseudomonas putida</i> KT2440 is a promising bacterial chassis for the conversion of lignin-derived aromatic compound mixtures to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to aromatic catabolism and toxicity tolerance of <i>P. putida</i> will be required to achieve industrial relevance. Here, tolerance adaptive laboratory evolution (TALE) was employed with increasing concentrations of the hydroxycinnamic acids <i>p</i>-coumaric acid (<i>p</i>CA) and ferulic acid (FA) individually and in combination (<i>p</i>CA ​+ ​FA). The TALE experiments led to evolved <i>P. putida</i> strains with increased tolerance to the targeted acids as compared to wild type. Specifically, a 37 ​h decrease in lag phase in 20 ​g/L <i>p</i>CA and a 2.4-fold increase in growth rate in 30 ​g/L FA was observed. Whole genome sequencing of intermediate and endpoint evolved <i>P. putida</i> populations revealed several expected and non-intuitive genetic targets underlying these aromatic catabolic and toxicity tolerance enhancements. <i>PP_3350</i> and <i>ttgB</i> were among the most frequently mutated genes, and the beneficial contributions of these mutations were verified via gene knockouts. Deletion of <i>PP_3350,</i> encoding a hypothetical protein, recapitulated improved toxicity tolerance to high concentrations of <i>p</i>CA, but not an improved growth rate in high concentrations of FA. Deletion of <i>ttgB,</i> part of the TtgABC efflux pump, severely inhibited growth in <i>p</i>CA ​+ ​FA TALE-derived strains but did not affect growth in <i>p</i>CA ​+ ​FA in a wild type background, suggesting epistatic interactions. Genes involved in flagellar movement and transcriptional regulation were often mutated in the TALE experiments on multiple substrates, reinforcing ideas of a minimal and deregulated cell as optimal for domesticated growth. Overall, this work demonstrates increased tolerance towards and growth rate at the expense of hydroxycinnamic acids and presents new targets for improving <i>P. putida</i> for microbial lignin valorization.
Genetically Modified L3,7 and L2 Lipooligosaccharides from Neisseria meningitidis Serogroup B Confer a Broad Cross-Bactericidal Response (2009)

Currently available Neisseria meningitidis serogroup B (MenB) vaccines are based on outer membrane vesicles (OMVs) that are obtained from wild-type strains. They are purified with the aim of decreasing the lipooligosaccharide (LOS) content and hence reduce the reactogenicity of the vaccine even though LOS is a potential protective antigen. In <2-year-old children, these MenB vaccines confer protection only against strains expressing homologous PorA, a major and variable outer membrane protein. Our objective was to develop a safe LOS-based vaccine against MenB. To this end, we used modified porA knockout strains expressing genetically detoxified (msbB gene-deleted) L2 and L3,7 LOSs, allowing the production of LOS-enriched OMVs. The vaccine-induced antibodies were found to be bactericidal against nearly all invasive strains, irrespective of capsular serogroup. In addition, we have also demonstrated that LOS lacking the terminal galactose (with a lgtB mutation; truncated L3 LOS), but not LOS produced without the galE gene, induced a bactericidal antibody response in mice similar to that seen for LOS containing the full lacto-N-neotetraose (L3,7 LOS). In conclusion, a bivalent detoxified LOS OMV-based vaccine demonstrated the potential to afford a broad cross-protection against meningococcal disease.
Revani: Revising and Verifying Normative Specifications for Privacy (2016)

Privacy remains a major challenge today, partly because it brings together social and technical considerations. Yet, current software engineering focuses only on the technical aspects. In contrast, the authors' approach, Revani, understands privacy from the standpoint of sociotechnical systems (STSs), with particular attention on the social elements of STSs. They specify STSs via a combination of technical mechanisms and social norms founded on accountability. Revani provides a way to formally represent mechanisms and norms and applies model checking to verify whether specified mechanisms and norms would satisfy stakeholder requirements. Additionally, Revani provides a set of design patterns and a revision tool to update an STS specification as necessary. The authors demonstrate the work of Revani on a healthcare emergency use case pertaining to patient privacy during disasters.
Large area and low power dielectrowetting optical shutter with local deterministic fluid film breakup (2013)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation R. Zhao, B. Cumby, A. Russell, J. Heikenfeld; Large area and low power dielectrowetting optical shutter with local deterministic fluid film breakup. Appl. Phys. Lett. 25 November 2013; 103 (22): 223510. https://doi.org/10.1063/1.4834095 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioApplied Physics Letters Search Advanced Search |Citation Search
Association between the TGFB1 -509C/T and TGFBR2 -875A/G polymorphisms and gastric cancer: a case-control study (2011)

The transforming growth factor-β (TGFβ) pathway plays an important role in various types of human cancer. However, the role of TGFB1 -509C/T and TGFBR2 -875A/G polymorphisms in gastric cancer is controversial. We aimed to investigate the associations between these polymorphisms and gastric cancer susceptibility, clinicopathological parameters and survival. A case-control study was conducted in 1,010 gastric cancer patients and 1,500 healthy controls. Genotypes were determined by PCR-restriction fragment length polymorphism and DNA sequencing. Compared with the TT genotype, the TGFB1 -509 C allele (CT/CC) was significantly associated with a reduced risk of gastric cancer (OR, 0.71; 95% CI, 0.58-0.87; p=0.001) and certain subtypes of gastric cancer including intestinal type (OR, 0.70; 95% CI, 0.57-0.87; p=0.001), poorly differentiated (OR, 0.67; 95% CI, 0.54-0.85; p=0.001) and stage TNM III+IV (OR, 0.73; 95% CI, 0.58-0.92; p=0.008). Compared with the TGFBR2 -875 GG genotype, carriers of the A allele (AA/AG) had a significantly decreased gastric cancer risk (OR, 0.58; 95% CI, 0.62-0.91; P<0.001). A combination of the TGFB1 -509 C and TGFBR2 -875 A alleles was associated with a further decreased risk of gastric cancer (OR, 0.42; 95% CI, 0.32-0.57, p<0.001). No significant correlation was observed between polymorphisms and survival of gastric cancer patients. Our results suggest that both the TGFB1 -509 and TGFBR2 -875 polymorphisms contribute to a decreased gastric cancer risk. The TGFB1 -509 polymorphism affects certain subtypes of gastric cancer according to clinicopathological parameters. A combination of the TGFB1 -509 C and TGFBR2 -875 A alleles conferred a further decreased gastric cancer risk. These findings provide clues to the biological mechanisms that underline tumor heterogeneity.
Targeted volume Correlative Light and Electron Microscopy of environmental marine microorganisms (2023)

EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.
Maximum-Likelihood Sequence Detector for Dynamic Mode High Density Probe Storage (2009)

There is an ever increasing need for storing data in small form factors driven by the ubiquitous use and increased demands of consumer electronics. A new data storage approach that achieves a few Tb per in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> areal densities, utilizes a cantilever probe with a sharp tip that can be used to deform and assess the topography of a polymer medium. The information may be encoded by means of topographic profiles on the medium. The prevalent mode of using the cantilever probe is the static mode that is known to be harsh on the probe and the media. In this paper, the high quality factor dynamic mode operation, which is known to be less harsh on the media and the probe, is analyzed for probe based high density data storage purposes. It is demonstrated that an appropriate level of abstraction is possible that obviates the need for an involved physical model. The read operation is modeled as a communication channel which incorporates the inherent system memory due to the intersymbol interference and the cantilever state that can be identified using training data. Using the identified model, a solution to the maximum likelihood sequence detection problem based on the Viterbi algorithm is devised. Experimental and simulation results demonstrate that the performance of this detector is several orders of magnitude better than the other existing schemes and confirms performance gains that can render the dynamic mode operation feasible for high density data storage purposes.
In situ characterization of hazardous contaminants using prompt gamma neutron activation analysis (1993)

Prompt Gamma Neutron Activation Analysis (PGNAA) has been developed for real-time, in situ measurements of contaminant elements in soil. Pulsed neutron activation coupled with state-of-the-art high count rate throughput electronics and time-sequenced gamma ray energy analysis have been used to obtain sensitivities at the trace level for uranium in soil. The results of detailed neutron dosimetry and prompt neutron-induced gamma ray transport measurements carried out using a soil test matrix will be reported. Initial field deployment of the PGNAA system at a former solution uranium mine in Bruni, Texas will also be described.
Cooling the Tip of a Turbine Blade Using Pressure Side Holes: Part 1 — Adiabatic Effectiveness Measurements (2004)

Sealing and durability for turbine blade tips have been challenging problems since the development of gas turbine engines. Blade tip designs are extremely important in terms of sealing and engine performance. In general, overall engine performance can be improved by increasing turbine inlet temperatures. As a result, cooling methods along the blade tip need to be devised and applied effectively. Film-cooling is typically used as a blade tip cooling method, whereby coolant is supplied through holes placed along the pressure side of a blade. Experiments were conducted in a linear cascade with a scaled-up turbine blade whereby the Reynolds number of the engine was matched. A range of blowing ratios was studied whereby coolant was injected from holes placed along the pressure side tip of the blade as well as from dirt purge holes placed on the blade tip. This paper, which is Part 1 of a two part series, compares adiabatic effectiveness levels measured along a blade tip, while Part 2 combines measured heat transfer coefficients with the adiabatic effectiveness levels to assess the overall cooling benefit of pressure side blowing near a blade tip. The results show better cooling can be achieved for a small tip gap compared with a large tip gap with different flow phenomena occurring for each tip gap setting.
Superior Wear-Resistance of Ti3C2Tx Multilayer Coatings (2021)

Owing to MXenes' tunable mechanical properties induced by their structural and chemical diversity, MXenes are believed to compete with state-of-the-art 2D nanomaterials such as graphene regarding their tribological performance. Their nanolaminate structure offers weak interlayer interactions and an easy-to-shear ability to render them excellent candidates for solid lubrication. However, the acting friction and wear mechanisms are yet to be explored. To elucidate these mechanisms, 100-nm-thick homogeneous multilayer Ti<sub>3</sub>C<sub>2</sub>T<sub><i>x</i></sub> coatings are deposited on technologically relevant stainless steel by electrospraying. Using ball-on-disk tribometry (Si<sub>3</sub>N<sub>4</sub> counterbody) with acting contact pressures of about 300 MPa, their long-term friction and wear performance under dry conditions are studied. MXene-coated specimens demonstrate a 6-fold friction reduction and an ultralow wear rate (4 × 10<sup>-9</sup> mm<sup>3</sup> N<sup>-1</sup> m<sup>-1</sup>) over 100 000 sliding cycles, outperforming state-of-the-art 2D nanomaterials by at least 200% regarding their wear life. High-resolution characterization verified the formation of a beneficial tribolayer consisting of thermally/mechanically degraded MXenes and amorphous/nanocrystalline iron oxides. The transfer of this tribolayer to the counterbody transforms the initial steel/Si<sub>3</sub>N<sub>4</sub> contact to tribolayer/tribolayer contact with low shear resistance. MXene pileups at the wear track's reversal points continuously supply the tribological contact with fresh, lubricious nanosheets, thus enabling an ultra-wear-resistant and low-friction performance.
"Womenomics" and gender-inclusive software: what software engineers need to know (invited talk) (2016)

This short paper is a summary of my keynote at FSE’16, with accompanying references for follow-up.
Community pharmacy interventions for public health priorities: protocol for a systematic review of community pharmacy-delivered smoking, alcohol and weight management interventions (2014)

The review has been registered with PROSPERO (registration no. CRD42013005943). Available at: http://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42013005943.
BibA Induces Opsonizing Antibodies Conferring In Vivo Protection against Group BStreptococcus (2009)

We recently characterized the function of BibA, an immunogenic surface-associated antigen expressed by group B Streptococcus (GBS) that is involved in virulence. In this study, we performed a bibA gene variability analysis on a panel of 72 clinical isolate strains. The bibA gene was present in all the strains analyzed, and 4 allelic variants, correlating with serotype, were identified. Moreover, although the BibA protein was expressed in all strains tested, only 54% of strains demonstrated surface exposure of the antigen in vitro. Importantly, expression of BibA on the bacterial surface was correlated with protection, because mice immunized with BibA were protected against challenge by a GBS strain with high levels of surface exposure of the antigen. In agreement with these findings, serum samples from mice immunized with recombinant BibA induced neutrophil-mediated in vitro opsonophagocytic killing of GBS. In conclusion, we propose BibA as a novel GBS vaccine candidate.
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics (2022)

In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735).
Fascial Sling Correction of Kinked Efferent Limb in Patients With Continent Diversion and Catheterization Difficulty (1996)

Use of the rectus fascial sling in continent urinary diversion enables fixation of the efferent limb to facilitate catheterization and enhance continence.