gebhart/patrepeval huggingface dataset:
Transmission of Influenza Virus via Aerosols and Fomites in the Guinea Pig Model (2009)

Limited data on the relative contributions of different routes of transmission for influenza virus are available. Person-to-person transmission is central to seasonal and pandemic spread; nevertheless, the modes of spread are a matter of ongoing debate. Resolution of this discussion is paramount to the development of effective control measures in health care and community settings. Using the guinea pig model, we demonstrated that transmission of influenza A/Panama/2007/1999 (H3N2) virus through the air is efficient, compared with spread through contaminated environmental surfaces (fomites). We also examined the aerosol transmission efficiencies of 2 human influenza virus A strains and found that A/Panama/2007/1999 influenza virus transmitted more efficiently than A/Texas/36/1991 (H1N1) virus in our model. The data provide new and much-needed insights into the modes of influenza virus spread and strain-specific differences in the efficiency of transmission.
Measuring modal delays of few-mode fibers using frequency-domain method (2021)

A simple and robust frequency-domain method for measuring modal delays of few-mode fibers is presented. The method utilizes the inverse Fourier transform of a measured complex transfer function to determine modal delays between different modes. Through proper treatments of the data, we can de-alias the signal and obtain the accurate values of the time of flights and the modal delays in the right time sequence. The method has been validated through comparing with direct time-domain measurements. A few-mode fiber supporting four modes has been studied in detail with wavelength-resolved time of flights and modal delays obtained. We also illustrate how the new measurement method can provide a way to measure the crosstalk for mode division multiplexing system. The method can be readily used for FMF measurements without obvious limitation on the number of modes involved or measurement wavelength.
Chemotherapeutic Remissions in Wistar Furth Rat Acute Myelogenous Leukemia: A Model for Human AML (1977)

Acute myelogenous leukemia (AML) of the inbred Wistar/Furth (W/Fu) rat is pathophysiologically similar to human AML. Subcutaneous transplantation of 1.0 X 10(6) cells of a clonal tissue culture line of W/Fu AML into 6- to 8-week-old rats produced local myeloblastomas in 8--10 days which progressed to infiltration of regional nodes, replacement of greater than 90% of the bone marrow, ascites, and fatal peripheral blood leukemia with concomitant hyperlysozymemia. Single doses of adriamycin, daunomycin, actinomycin, cytosine arabinoside, or Cytoxan in rats with 1.0 cm myeloblastomas produced complete tumor regression while bu-sulfan, vinblastine, vincristine, dexamethasone, and Methotrexate was relatively ineffective. Responses were associated with delay in progression to peripheral blood leukemia and prolonged survival. Similar results were obtained following treatment of rats with already disseminated leukemia. The demonstration of response to drugs known active against human AML indicates that the W/Fu AML should be a valuable model for rapid evaluation of new chemotherapeutic agents for clinical use.
Separation of gas mixtures using Co(ii) carborane-based porous coordination polymers (2010)

Separations of CO(2)/CH(4), CO(2)/N(2), and O(2)/N(2) mixtures were studied in three porous coordination polymers made of the same carborane ligand and Co(ii) nodes. High selectivities for CO(2) over CH(4) ( approximately 47) and CO(2) over N(2) ( approximately 95) were obtained, especially in the material with coordinated pyridine. Unusual selectivity for O(2) over N(2) (as high as 6.5) was demonstrated in the materials with open Co(ii) sites.
Selection and Characterization of Single-Domain Antibodies for Detection of Lassa Nucleoprotein (2020)

Lassa virus is the etiologic agent of Lassa fever, an acute and often fatal illness endemic to West Africa. It is important to develop new reagents applicable either for the specific diagnosis or as improved therapeutics for the treatment of Lassa fever. Here, we describe the development and initial testing of llama-derived single-domain antibodies that are specific for the Lassa virus nucleoprotein. Four sequence families based on complementarity-determining region (CDR) homology were identified by phage-based enzyme-linked immunosorbent assays, however, the highest affinity clones all belonged to the same sequence family which possess a second disulfide bond between Framework 2 and CDR3. The affinity and thermal stability were evaluated for each clone. A MagPlex-based homogeneous sandwich immunoassay for Lassa virus-like particles was also demonstrated to show their potential for further development as diagnostic reagents.
Fabrication and Validation of Autologous Human Oral Mucosal Epithelial Cell Sheets to Prevent Stenosis after Esophageal Endoscopic Submucosal Dissection (2011)

The method for fabricating epithelial cell sheets shown in this study was suitable for the validation for clinical trials and suggested usability of the fabricated cell sheets.
A one-pot synthesis of polysulfane-bearing block copolymer nanoparticles with tunable size and refractive index (2015)

A one-pot synthesis of sulfur-rich polymer nanoparticles through a ring-opening metathesis polymerization is reported. The nanoparticles are formed in situ from diblock copolymers containing a polynorbornene derivative bearing cyclic polysulfanes. The refractive indices of the resulting nanoparticles are readily controlled in the range from 1.54 to nearly 1.65.
The topological shape of gene expression across the evolution of flowering plants (2022)

Abstract Since they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function. Significance statement A grand challenge in biology is to link gene expression to phenotypes across evolution, development, and the environment, but efforts have been hindered by biological complexity and dataset heterogeneity. Here, we implemented topological data analysis across thousands of gene expression datasets in phylogenetically diverse flowering plants. We created a topological representation of gene expression across plants and observed well-defined gradients of tissues from leaves to seeds, or from healthy to environmentally stressed. Using this framework, we identified a core and deeply conserved expression backbone that defines plant form and function, with key patterns that delineate plant tissues, abiotic, and biotic stresses. Our results highlight the power of topological approaches for analyzing complex biological datasets.
Fast Space-Varying Convolution Using Matrix Source Coding With Applications to Camera Stray Light Reduction (2014)

Many imaging applications require the implementation of space-varying convolution for accurate restoration and reconstruction of images. Here, we use the term space-varying convolution to refer to linear operators whose impulse response has slow spatial variation. In addition, these space-varying convolution operators are often dense, so direct implementation of the convolution operator is typically computationally impractical. One such example is the problem of stray light reduction in digital cameras, which requires the implementation of a dense space-varying deconvolution operator. However, other inverse problems, such as iterative tomographic reconstruction, can also depend on the implementation of dense space-varying convolution. While space-invariant convolution can be efficiently implemented with the fast Fourier transform, this approach does not work for space-varying operators. So direct convolution is often the only option for implementing space-varying convolution. In this paper, we develop a general approach to the efficient implementation of space-varying convolution, and demonstrate its use in the application of stray light reduction. Our approach, which we call matrix source coding, is based on lossy source coding of the dense space-varying convolution matrix. Importantly, by coding the transformation matrix, we not only reduce the memory required to store it; we also dramatically reduce the computation required to implement matrix-vector products. Our algorithm is able to reduce computation by approximately factoring the dense space-varying convolution operator into a product of sparse transforms. Experimental results show that our method can dramatically reduce the computation required for stray light reduction while maintaining high accuracy.
S0648 Clinically Adjusted vs Therapeutic Drug Monitoring Dosing Regimens With Adalimumab in Patients With Moderately to Severely Active Crohn's Disease: Results From the SERENE-CD Maintenance Study (2020)

INTRODUCTION: Adalimumab (ADA) is well-tolerated and effective in patients (pts) with Crohn's disease (CD).1,2 The Serene-CD phase 3 study evaluated higher vs standard dosing regimens of ADA 12-week (Wk) induction and 44Wk maintenance therapy in adults with moderate to severe CD. Outcomes of ADA maintenance therapy using clinically adjusted (CA) dosing or therapeutic drug monitoring (TDM) were explored. METHODS: Safety and efficacy of CA and TDM maintenance regimens at Wk56 were assessed. Clinical responders (N = 184) completing Induction were re-randomized at Wk12 and assigned 1:1 to CA or TDM, both arms initially receiving 40 mg ADA every other wk (EOW). The CA arm could escalate to every wk (EW) based on CDAI (≥220) or high-sensitivity C reactive protein (hs-CRP, ≥10 mg/L). The TDM arm could escalate to EW at Wks 14, 28, or 42 if ADA serum concentration was < 5 µg/mL or 5–10 µg/mL with CDAI≥220 or hs-CRP≥10 mg/L. Once escalated, the pt remained at 40 mg EW. Key exploratory efficacy endpoints at Wk56 included clinical remission and endoscopic response and remission (Table 1). Safety was analyzed in pts receiving at least 1 dose of maintenance study drug. RESULTS: Of re-randomized pts, 76 (82.6%) CA and 79 (85.9%) TDM completed the study. BL characteristics/demographics were well-balanced between treatment arms. In CA and TDM arms, 26 (28.2%) and 36 (39.1%) pts escalated to EW dosing, respectively, with most in both groups escalating at Wk14 (13/26 CA, 21/36 TDM). No difference in proportion of pts achieving Wk56 clinical remission, steroid-free clinical remission among subjects taking corticosteroid at Induction BL, endoscopic response, endoscopic remission, or deep remission between CA vs TDM (Table 1) was found. No significant differences observed between the two groups for sustained clinical remission among Wk12 clinical remitters, or for maintenance of endoscopic response and remission among Wk12 responders and remitters respectively (Table 1). Dose escalation was driven by hs-CRP in CA arm and by serum drug levels in TDM arm. Observed safety profile was similar between groups; no new safety signals or unexpected trends were identified. CONCLUSION: Key efficacy endpoints indicate both CA and TDM maintenance regimens are similar as observed in the SERENE-CD maintenance study. Both dosing regimens were well-tolerated with a similar safety profile.3 TDM used for dose adjustment showed no clinical benefit over use of clinical symptoms and biomarkers alone.Table 1
Lipoprotein(a) levels in a global population with established atherosclerotic cardiovascular disease (2022)

Objective Lipoprotein(a) (Lp(a)) is an important genetically determined risk factor for atherosclerotic vascular disease (ASCVD). With the development of Lp(a)-lowering therapies, this study sought to characterise patterns of Lp(a) levels in a global ASCVD population and identify racial, ethnic, regional and gender differences. Methods A multicentre cross-sectional epidemiological study to estimate the prevalence of elevated Lp(a) in patients with a history of myocardial infarction, ischaemic stroke or peripheral artery disease conducted at 949 sites in 48 countries in North America, Europe, Asia, South America, South Africa and Australia between April 2019 and July 2021. Low-density lipoprotein cholesterol (LDL-C) and Lp(a) levels were measured either as mass (mg/dL) or molar concentration (nmol/L). Results Of 48 135 enrolled patients, 13.9% had prior measurements of Lp(a). Mean age was 62.6 (SD 10.1) years and 25.9% were female. Median Lp(a) was 18.0 mg/dL (IQR 7.9–57.1) or 42.0 nmol/L (IQR 15.0–155.4). Median LDL-C was 77 mg/dL (IQR 58.4–101.0). Lp(a) in women was higher, 22.8 (IQR 9.0–73.0) mg/dL, than in men, 17.0 (IQR 7.1–52.2) mg/dL, p&lt;0.001. Black patients had Lp(a) levels approximately threefold higher than white, Hispanic or Asian patients. Younger patients also had higher levels. 27.9% of patients had Lp(a) levels &gt;50 mg/dL, 20.7% had levels &gt;70 mg/dL, 12.9% were &gt;90 mg/dL and 26.0% of patients exceeded 150 nmol/L. Conclusions Globally, Lp(a) is measured in a small minority of patients with ASCVD and is highest in black, younger and female patients. More than 25% of patients had levels exceeding the established threshold for increased cardiovascular risk, approximately 50 mg/dL or 125 nmol/L. Trial registration number
Adiabatic resonant microring (ARM) modulator (2012)

A high-speed adiabatic resonant microring silicon modulator, which simultaneously enables interior electrical contacts, 4-μm diameter, and 6.9-THz free spectral range, is demonstrated with open eye diagrams up to 12Gb/s, and extinction ratios up to 7.3dB.
Data from Gain of Glucose-Independent Growth upon Metastasis of Breast Cancer Cells to the Brain (2023)

&lt;div&gt;Abstract&lt;p&gt;Breast cancer brain metastasis is resistant to therapy and a particularly poor prognostic feature in patient survival. Altered metabolism is a common feature of cancer cells, but little is known as to what metabolic changes benefit breast cancer brain metastases. We found that brain metastatic breast cancer cells evolved the ability to survive and proliferate independent of glucose due to enhanced gluconeogenesis and oxidations of glutamine and branched chain amino acids, which together sustain the nonoxidative pentose pathway for purine synthesis. Silencing expression of fructose-1,6-bisphosphatases (FBP) in brain metastatic cells reduced their viability and improved the survival of metastasis-bearing immunocompetent hosts. Clinically, we showed that brain metastases from human breast cancer patients expressed higher levels of FBP and glycogen than the corresponding primary tumors. Together, our findings identify a critical metabolic condition required to sustain brain metastasis and suggest that targeting gluconeogenesis may help eradicate this deadly feature in advanced breast cancer patients. &lt;i&gt;Cancer Res; 75(3); 554–65. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
An Epidemiology-inspired Large-scale Analysis of Android App Accessibility (2020)

Accessibility barriers in mobile applications (apps) can make it challenging for people who have impairments or use assistive technology to use those apps. Ross et al.’s epidemiology-inspired framework emphasizes that a wide variety of factors may influence an app's accessibility and presents large-scale analysis as a powerful tool for understanding the prevalence of accessibility barriers (i.e., inaccessibility diseases ). Drawing on this framework, we performed a large-scale analysis of free Android apps, exploring the frequency of accessibility barriers and factors that may have contributed to barrier prevalence. We tested a population of 9,999 apps for seven accessibility barriers: few TalkBack-focusable elements, missing labels, duplicate labels, uninformative labels, editable TextViews with contentDescription , fully overlapping clickable elements, and undersized elements. We began by measuring the prevalence of each accessibility barrier across all relevant element classes and apps. Missing labels and undersized elements were the most prevalent barriers. As a measure of the spread of barriers across apps, we assessed the five most reused classes of elements for missing labels and undersized elements. The Image Button class was among the most barrier-prone of the high reuse element classes; 53% of Image Button elements were missing labels and 40% were undersized. We also investigated factors that may have contributed to the high barrier prevalence in certain classes of elements, selecting examples based on prior knowledge, our analyses, and metrics of reuse and barrier-proneness. These case studies explore: (1) how the few TalkBack-focusable elements accessibility barrier relates to app category (e.g., Education, Entertainment) and the tools used to implement an app, (2) the prevalence of label-based barriers in image-based buttons, (3) design patterns that affect the labeling and size of Radio Buttons and Checkboxes, and (4) accessibility implications of the sizing of third-party plug-in elements. Our work characterizes the current state of Android accessibility, suggests improvements to the app ecosystem, and demonstrates analysis techniques that can be applied in further app accessibility assessments.
Towards photonic time-crystals: observation of a femtosecond time-boundary in the refractive index (2021)

We demonstrate experimentally a time-boundary for photons in a dielectric medium, analogous to a spatial boundary. Such abrupt temporal changes in the permittivity are necessary for observing time-reflections, photonic time-crystals and momentum bandgaps.
Approximation to Nanosecond Optical Switching Based on Commercial Devices (2011)

Optical Packet Switching (OPS) has been proposed as the ultimate solution for Wavelength Division Multiplexing (WDM) core networks, but it has not achieved commercial status due to numerous technological requisites such as packet tunable wavelength conversions, switching times in the order of nanoseconds, and individual wavelength switching. Nevertheless, new OPS paradigms reduce technological complexity by eliminating wavelength conversions and performing joint wavelength switching. Moreover, new interferometric optical devices capable of switching two optical signals in sub-nanosecond times are already commercially available. In this paper, we propose an all-optical switch architecture based on these devices, which switch all wavelengths as a bundle. We also perform a preliminary analysis of this architecture with some simplifications that allow us to set an upper bound on the maximum bit rate attainable in an ideal network (relaxing the need for 3R regeneration and electro-optical conversions).
Multi-Wafer Virtual Probe: Minimum-cost variation characterization by exploring wafer-to-wafer correlation (2010)

In this paper, we propose a new technique, referred to as Multi-Wafer Virtual Probe (MVP) to efficiently model wafer-level spatial variations for nanoscale integrated circuits. Towards this goal, a novel Bayesian inference is derived to extract a shared model template to explore the wafer-to-wafer correlation information within the same lot. In addition, a robust regression algorithm is proposed to automatically detect and remove outliers (i.e., abnormal measurement data with large error) so that they do not bias the modeling results. The proposed MVP method is extensively tested for silicon measurement data collected from 200 wafers at an advanced technology node. Our experimental results demonstrate that MVP offers superior accuracy over other traditional approaches such as VP and EM, if a limited number of measurement data are available.
p38 Inhibitors: beyond pyridinylimidazoles (2005)

Since the discovery of p38 mitogen-activated protein kinase (MAPK) as a potential intracellular modulator that regulates the crucial biosynthesis and functions of pro-inflammatory cytokines (e.g., TNF-α and IL-1β), numerous groups have disclosed their efforts to find small-molecule p38 inhibitors as potential therapeutic agents for the treatment of inflammatory diseases such as rheumatoid arthritis (RA), Crohn’s disease (CD) and psoriasis. Although greater selectivity has been achieved with these newly disclosed series, their safety profile after chronic treatment remains a question to be answered in human clinical trials. The p38 inhibitors that have been disclosed in the recent patent literature (2000 – 2004) are summarised here. These compounds will be classified into series based on their intrinsic structures and by their binding modes, as revealed by either crystallography or molecular modelling.
Impact of a non-conventional PWM strategy on the DC link film capacitor sizing (2015)

In this paper, an analysis of the DC-link voltage ripple for classic and non-conventional Pulse Width Modulation (PWM) strategies such as the Unified-Double Carrier PWM (Uni-DC PWM) is derived. A focus will be held on the case where Film capacitors are applied. The latter have a very low Equivalent Series Resistance (ESR) which is responsible of losses in real capacitors (especially Electrolytic ones) hence, in the frequency range where the PWM harmonics do exist, a Film capacitor can be considered as having a pure capacitive impedance where the DC-link voltage ripple becomes highly dependent on the harmonic frequency distribution. Thus, it is important to determine the exact harmonic components needed for an analysis to be effective and this is where the double Fourier integral provides a mathematically rigorous application for studying PWM characteristics in the frequency domain. Despite the fact that the main objective of the Uni-DC PWM is to reduce the capacitor's RMS current, results show a reverse impact on the DC-link voltage ripple when a Film capacitor is used.
Modeling the suppression of boron transient enhanced diffusion in silicon by substitutional carbon incorporation (2001)

Recent work has indicated that the suppression of boron transient enhanced diffusion (TED) in carbon-rich Si is caused by nonequilibrium Si point defect concentrations, specifically the undersaturation of Si self-interstitials, that result from the coupled out-diffusion of carbon interstitials via the kick-out and Frank–Turnbull reactions. This study of boron TED reduction in Si1−x−yGexCy during 750 °C inert anneals has revealed that the use of an additional reaction that further reduces the Si self-interstitial concentration is necessary to describe accurately the time evolved diffusion behavior of boron. In this article, we present a comprehensive model which includes {311} defects, boron-interstitial clusters, a carbon kick-out reaction, a carbon Frank–Turnbull reaction, and a carbon interstitial-carbon substitutional (CiCs) pairing reaction that successfully simulates carbon suppression of boron TED at 750 °C for anneal times ranging from 10 s to 60 min.