gebhart/patrepeval huggingface dataset:
SU‐F‐I‐10: Spatially Local Statistics for Adaptive Image Filtering (2016)

Purpose: To facilitate adaptive image filtering operations, addressing spatial variations in both noise and signal. Such issues are prevalent in cone‐beam projections, where physical effects such as X‐ray scattering result in spatially variant noise, violating common assumptions of homogeneous noise and challenging conventional filtering approaches to signal extraction and noise suppression. Methods: We present a computational mechanism for probing into and quantifying the spatial variance of noise throughout an image. The mechanism builds a pyramid of local statistics at multiple spatial scales; local statistical information at each scale includes (weighted) mean, median, standard deviation, median absolute deviation, as well as histogram or dynamic range after local mean/median shifting. Based on inter‐scale differences of local statistics, the spatial scope of distinguishable noise variation is detected in a semi‐ or un‐supervised manner. Additionally, we propose and demonstrate the incorporation of such information in globally parametrized (i.e., non‐adaptive) filters, effectively transforming the latter into spatially adaptive filters. The multi‐scale mechanism is materialized by efficient algorithms and implemented in parallel CPU/GPU architectures. Results: We demonstrate the impact of local statistics for adaptive image processing and analysis using cone‐beam projections of a Catphan phantom, fitted within an annulus to increase X‐ray scattering. The effective spatial scope of local statistics calculations is shown to vary throughout the image domain, necessitating multi‐scale noise and signal structure analysis. Filtering results with and without spatial filter adaptation are compared visually, illustrating improvements in imaging signal extraction and noise suppression, and in preserving information in low‐contrast regions. Conclusion: Local image statistics can be incorporated in filtering operations to equip them with spatial adaptivity to spatial signal/noise variations. An efficient multi‐scale computational mechanism is developed to curtail processing latency. Spatially adaptive filtering may impact subsequent processing tasks such as reconstruction and numerical gradient computations for deformable registration. NIH Grant No. R01‐184173
Assessment of an in vitro whole cigarette smoke exposure system: The Borgwaldt RM20S 8-syringe smoking machine (2011)

These results suggest this smoke exposure system is a reliable and repeatable method of generating and exposing ALI in vitro cultures to cigarette smoke. This system will enable the evaluation of future tobacco products and individual components of cigarette smoke and may be used as an alternative in vitro tool for evaluating other aerosols and gaseous mixtures such as air pollutants, inhaled pharmaceuticals and cosmetics.
Kinetics of D–xylose absorption in patients with human immunodeficiency virus enteropathy (1991)

D-Xylose absorption was studied in 12 patients with acquired immunodeficiency syndrome (AIDS) or advanced AIDS-related complex who had had diarrhea for more than 8 weeks, averaged an 11% (range, 3% to 21%) body weight loss during the previous 6 months, and had had negative stool examinations for enteric pathogens. Patients were evaluated by duodenal aspiration and biopsy and received both 25 gm oral and 10 gm intravenous doses of D-xylose. Kinetic analysis of D-xylose absorption was characterized by an absorption rate constant (ka) and a rate constant (ko) reflecting nonabsorptive loss. Extent of D-xylose absorption averaged 18.4% +/- 9.3% (+/- SD) in the 12 patients (normal greater than 60%). Percentage of weight loss during the previous 6 months was negatively correlated with ka (r = -0.69; p = 0.018) in the 11 patients in whom this parameter was reduced but was not correlated with either ko or extent of D-xylose absorption. In these patients with human immunodeficiency virus enteropathy, ka was reduced out of proportion to the minor histologic changes present in the duodenal biopsy specimens.
Synthesis and size-dependent crystallization of colloidal germanium telluridenanoparticles (2009)

Colloidal nanocrystals have long been used to study the dependence of phase stability and transitions on size. Both structural phase stability and phase transitions change dramatically in the nanometre size regime where the surface plays a significant role in determining the overall energetics of the system. We investigate the solid–solid phase transformation of crystallization in amorphous GeTe nanoparticles. We report a colloidal synthetic route to amorphous GeTe nanoparticles. Using in situ X-ray diffraction while heating, we observe the crystallization of the nanoparticles and find a dramatic increase of the crystallization temperature of over 150 °C above the bulk value. Using size-selected nanoparticle films, we show that the crystallization temperature depends strongly on the particle size. In addition, we measure the electrical resistance of nanoparticle films and observe over 5 orders of magnitude lower resistance for the crystalline film compared to the amorphous film. Finally, we discuss the implications of the size-dependence of crystallization in the context of both understanding the behavior of phase stability in the nanosize regime and applications to phase change memory devices.
Data from Lack of <i>p53</i> Augments Antitumor Functions in Cytolytic T Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Repetitive stimulation of T-cell receptor (TCR) with cognate antigen results in robust proliferation and expansion of the T cells, and also imprints them with replicative senescence signatures. Our previous studies have shown that life-span and antitumor function of T cells can be enhanced by inhibiting reactive oxygen species (ROS) or intervening with ROS-dependent JNK activation that leads to its activation-induced cell death. Because tumor suppressor protein &lt;i&gt;p53&lt;/i&gt; is also a redox active transcription factor that regulates cellular ROS generation that triggers downstream factor–mediating apoptosis, we determined if &lt;i&gt;p53&lt;/i&gt; levels could influence persistence and function of tumor-reactive T cells. Using h3T TCR transgenic mice, with human tyrosinase epitope–reactive T cells developed on &lt;i&gt;p53&lt;/i&gt; knockout (KO) background, we determined its role in regulating antitumor T-cell function. Our data show that as compared with h3T cells, h3T-&lt;i&gt;p53&lt;/i&gt; KO T cells exhibited enhanced glycolytic commitment that correlated with increased proliferation, IFNγ secretion, cytolytic capacity, expression of stemness gene signature, and decreased TGF-β signaling. This increased effector function correlated to the improved control of subcutaneously established murine melanoma after adoptive transfer of &lt;i&gt;p53&lt;/i&gt;-KO T cells. Pharmacological inhibition of human TCR-transduced T cells using a combination of &lt;i&gt;p53&lt;/i&gt; inhibitors also potentiated the T-cell effector function and improved persistence. Thus, our data highlight the key role of &lt;i&gt;p53&lt;/i&gt; in regulating the tumor-reactive T-cell response and that targeting this pathway could have potential translational significance in adoptive T-cell therapy. &lt;i&gt;Cancer Res; 76(18); 5229–40. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
EUV for HVM: towards an industrialized scanner for HVM NXE3400B performance update (2018)

With the introduction of its fifth-generation NXE:3400B scanner, ASML brought EUV to High- Volume Manufacturing for 7 nm node lithography and beyond with full support of pellicle. This paper presents an update on lithographic performance results obtained with the NXE:3400B, characterized by an NA of 0.33, a Pupil Fill Ratio (PFR) of 0.2 and throughput capability of 125 wafers per hour. Advances in source power and system availability have enabled a continued increase of productivity. To maximize the number of yielding dies per day excellent Overlay, Focus, and Critical Dimension (CD) control have been realized, combining intrinsic tool stability with holistic control schemes. We will also show matching performance for both Overlay and Imaging, and further improvements in Focus Process Dependencies for the 5nm node.
Simple Direct Measurements of n2 (1985)

A simple direct method for measurements of n2 is described. The method involves measurements of beam distortions in the transmitted, time-integrated spatial profile using an optical multichannel analyzer. A model is described which allows extraction of n2 from fits of experiment to computer generated theoretical spatial profiles. The results for picosecond pulses at 1.06 μm and 0.53 μm are presented for three materials: fused quartz, NaCl, and CS2. Little dispersion in n2 is seen for each material over the wavelength range studied.
Dual blockade of the lipid kinase PIP4Ks and mitotic pathways leads to cancer-selective lethality (2017)

Achieving robust cancer-specific lethality is the ultimate clinical goal. Here, we identify a compound with dual-inhibitory properties, named a131, that selectively kills cancer cells, while protecting normal cells. Through an unbiased CETSA screen, we identify the PIP4K lipid kinases as the target of a131. Ablation of the PIP4Ks generates a phenocopy of the pharmacological effects of PIP4K inhibition by a131. Notably, PIP4Ks inhibition by a131 causes reversible growth arrest in normal cells by transcriptionally upregulating PIK3IP1, a suppressor of the PI3K/Akt/mTOR pathway. Strikingly, Ras activation overrides a131-induced PIK3IP1 upregulation and activates the PI3K/Akt/mTOR pathway. Consequently, Ras-transformed cells override a131-induced growth arrest and enter mitosis where a131's ability to de-cluster supernumerary centrosomes in cancer cells eliminates Ras-activated cells through mitotic catastrophe. Our discovery of drugs with a dual-inhibitory mechanism provides a unique pharmacological strategy against cancer and evidence of cross-activation between the Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways via a Ras˧PIK3IP1˧PI3K signaling network.
Phase 2 randomised trial of oral C5A receptor antagonist CCX168 in ANCA-associated renal vasculitis (2014)

David R.W. Jayne1, Annette Bruchfeld2, Matthias Schaier3, Kazimierz Ciechanowski4, Lorraine Harper5, Michel Jadoul6, Marten Segelmark7, Daina Selga8, Istvan Szombati9, Michael Venning10, Patrick Hamilton10, Christian Hugo11, Paul L.A. Van Daele12, Ondrej Viklicky13, Antonia Potarca14, Thomas J. Schall14 and Pirow Bekker14 Univ of Cambridge, Cambridge, United Kingdom, Karolinska Institute, Stockholm, Sweden, Univ Hosp Heidelberg, Heidelberg, Germany, Pomeranian Medical Univ, Szczecin, Poland, Univ of Birmingham, Birmingham, United Kingdom, Cliniques Saint-Luc, Brussels, Belgium, Linkoping Univ, Linkoping, Sweden, Lund Univ, Lund, Sweden, Budaclinic, Budapest, Hungary, Manchester Univ, Manchester, United Kingdom, Dresden Univ, Dresden, Germany, Erasmus MC Center, Rotterdam, The Netherlands, Instit of Clin and Exp Med, Prague, Czech Republic, ChemoCentryx, Mountain View, CA
The crystallisation of copper(ii) phenylphosphonates (2016)

The crystal structures and syntheses of four different copper(ii) phenylphosphonates, the monophenylphosphonates α-, β-, and γ-Cu(O<sub>3</sub>PC<sub>6</sub>H<sub>5</sub>)·H<sub>2</sub>O (α-CuPhPmH (1) β-CuPhPmH (2) and γ-CuPhPmH (3)), and the diphosphonate Cu(HO<sub>3</sub>PC<sub>6</sub>H<sub>5</sub>)<sub>2</sub>·H<sub>2</sub>O (CuPhP2mH (4)), are presented. The compounds were synthesized from solution at room temperature, at elevated temperature, under hydrothermal conditions, and mechanochemical conditions. The structures of α-CuPhPmH (1) and CuPhP2mH (4) were solved from powder X-ray diffraction data. The structure of β-CuPhPmH (2) was solved by single crystal X-ray analysis. The structures were validated by extended X-ray absorption fine structure (EXAFS) and DTA analyses. Disorder of the crystal structure was elucidated by electron diffraction. The relationship between the compounds and their reaction pathways were investigated by in situ synchrotron measurements.
A Compact, Low-Profile Metasurface-Enabled Antenna for Wearable Medical Body-Area Network Devices (2014)

We propose a compact conformal wearable antenna that operates in the 2.36-2.4 GHz medical body-area network band. The antenna is enabled by placing a highly truncated metasurface, consisting of only a two by two array of I-shaped elements, underneath a planar monopole. In contrast to previously reported artificial magnetic conducting ground plane backed antenna designs, here the metasurface acts not only as a ground plane for isolation, but also as the main radiator. An antenna prototype was fabricated and tested, showing a strong agreement between simulation and measurement. Comparing to previously proposed wearable antennas, the demonstrated antenna has a compact form factor of 0.5 λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ×0.3 λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ×0.028 λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> , all while achieving a 5.5% impedance bandwidth, a gain of 6.2 dBi, and a front-to-back ratio higher than 23 dB. Further numerical and experimental investigations reveal that the performance of the antenna is extraordinarily robust to both structural deformation and human body loading, far superior to both planar monopoles and microstrip patch antennas. Additionally, the introduced metal backed metasurface enables a 95.3% reduction in the specific absorption rate, making such an antenna a prime candidate for incorporation into various wearable devices.
Source Detection via Contact Tracing in the Presence of Asymptomatic Patients (2021)

Inferring the source of a diffusion in a large network of agents is a difficult but feasible task, if a few agents act as sensors revealing the time at which they got hit by the diffusion. A main limitation of current source detection algorithms is that they assume full knowledge of the contact network, which is rarely the case, especially for epidemics, where the source is called patient zero. Inspired by recent contact tracing algorithms, we propose a new framework, which we call Source Detection via Contact Tracing Framework (SDCTF). In the SDCTF, the source detection task starts at the time of the first hospitalization, and initially we have no knowledge about the contact network other than the identity of the first hospitalized agent. We may then explore the network by contact queries, and obtain symptom onset times by test queries in an adaptive way. We also assume that some of the agents may be asymptomatic, and therefore cannot reveal their symptom onset time. Our goal is to find patient zero with as few contact and test queries as possible. We propose two local search algorithms for the SDCTF: the LS algorithm is more data-efficient, but can fail to find the true source if many asymptomatic agents are present, whereas the LS+ algorithm is more robust to asymptomatic agents. By simulations we show that both LS and LS+ outperform state of the art adaptive and non-adaptive source detection algorithms adapted to the SDCTF, even though these baseline algorithms have full access to the contact network. Extending the theory of random exponential trees, we analytically approximate the probability of success of the LS/ LS+ algorithms, and we show that our analytic results match the simulations. Finally, we benchmark our algorithms on the Data-driven COVID-19 Simulator developed by Lorch et al., which is the first time source detection algorithms are tested on such a complex dataset.
Future directions in the molecular breeding of forage and turf (2005)

Forage and turf molecular breeding has now clearly entered the post-genomic era, with a large amount of structural genomics information and genomic resources available for key forage and turf species and relevant model systems. A primary challenge ahead is the conversion of this information into useful functional knowledge for the development of molecular breeding technologies and products. High-throughput approaches for spatial and temporal analysis and the integration of data from the related fields of genomics, transcriptomics, proteomics, metabolomics and phenomics in a systems biology context will be critical for the establishment of stringent gene-function correlations. Translational genomics will allow for results obtained using model plant systems such as Arabidopsis thaliana, rice and Medicago truncatula to have major impact on understanding the molecular basis of plant processes and have direct application to the molecular breeding of forage and turf plants. These developments will be enhanced through applications of transgenesis and functionally associated genetic markers in forage and turf molecular breeding building on genomic and post-genomic discoveries in these target species.
Supplementary Figure 4 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition (2023)

Supplementary Figure 4 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition
Doping in heterostructures, quantum wells, and superlattices (1993)

This chapter is devoted to the role of impurities in semiconductor structures which consist of different types of semiconductor materials. Semiconductor heterostructures, quantum wells and superlattices are structures in which the individual layers have spatial dimensions comparable to the carrier de Broglie wavelength. As a consequence, quantum effects cannot be neglected in such small semiconductor structures. Furthermore, the spatial dimensions of such structures can be comparable to the Bohr radius of impurities. As a consequence, the characteristics of impurities, e.g. ionization energy and wave function, are changed. The area of quantum semiconductor physics has gained much interest since the 1970s. The physical properties of several semiconductor quantum structures are closely related to the doping and to residual impurities in such structures. Among these structures are selectively doped heterostructures, doping superlattices, doped quantum wells, and doped quantum barriers, which will be discussed in this chapter.
RBridges: TRILL Link Data Optimizations (2017)

TRILL (TRansparent Interconnection of Lots of Links) Data frames can
be encoded so as to make more efficient use of communications links
under certain circumstances. This document specifies two such optional
optimizations. One, called Compact Format, improves the compactness of
encoding where a TRILL link is a point-to-point Ethernet link. The
other, called Specific Addressing, optionally decreases the burden on
multi-access TRILL links for multi- destination TRILL Data frames.
This document updates RFC 6325.
Role of DNA polymerase alpha and DNA primase in simian virus 40 DNA replication in vitro. (1986)

The role of DNA polymerase alpha (pol alpha) and DNA primase has been investigated in the simian virus 40 (SV40) DNA replication system in vitro. Removal of pol alpha and primase activities from crude extracts of HeLa cells or monkey cells by use of an anti-pol alpha immunoaffinity column resulted in the loss of replication activity. The addition of purified pol alpha-primase complex isolated from HeLa cells or monkey cells restored the replication activity of depleted extracts. In contrast, the pol alpha-primase complex isolated from either mouse cells or calf thumus did not. Extracts prepared from mouse cells (a source that does not support replication of SV40) did not replicate SV40 DNA. However, the addition of purified pol alpha-primase complex isolated from HeLa cells activated mouse cell extracts. pol alpha and primase from HeLa cells were extensively purified and separated by a one-step immunoaffinity adsorption and elution procedure. Both activities were required to restore DNA synthesis; the addition of pol alpha or primase alone supported replication poorly. Crude extracts of HeLa cells that were active in SV40 replication catalyzed the synthesis of full-length linear double-stranded (RFIII) DNA in reaction mixtures containing poly(dT)-tailed pBR322 RFIII. Maximal activity was dependent on the addition of oligo(dA), ATP, and creatine phosphate and was totally inhibited by aphidicolin. Since pol alpha alone could not replicate this substrate and since there was no degradation of input DNA, we propose that other enzymatic activities associate with pol alpha, displace the non-template strand, and allow the enzyme to replicate through duplex regions.
Poly 3-hydroxybutyrate-co-3-hydroxyhexanoate films can be degraded by the deep-sea microbes at high pressure and low temperature conditions (2019)

We have isolated several poly 3-hydroxybutyrate-co-3-hydroxyhexanoate (PHBH) degradable bacteria from the deep-sea sediment samples. The isolated microbes were involved into α-, γ- Proteobacteria group and the phylum Firmicutes, which were commonly diverged in the ocean environment. Four bacterial strains, Bacillus sp. MH10, Alteromonas sp. MH53, Psychrobacillus sp. PL87 and Rheinheimera sp. PL100, were selected as more active strains for the PHBH bio-degradation at high pressure and cold temperature conditions, and showed that those strains were piezotolerant up to 20–30 MPa. Our findings indicated that the PHBH could be well degraded not only in the ocean environment, but also at the deep-sea bottom, by means of those marine microorganisms.
Molecular and immunologic analysis of a chronic lymphocytic leukemia case with antibodies against human T-cell leukemia virus (1985)

The human T-cell leukemia virus type-I (HTLV-I) is a unique, exogenous, horizontally transmitted retrovirus which is T-cell tropic, and has been associated with a specific type of aggressive leukemia/lymphoma of mature T-cell origin. In a survey of lymphoid malignancies in Jamaica, antibodies to HTLV-I were also found in 6 of 17 patients with chronic lymphocytic leukemia (CLL), raising the possibility of an etiologic relationship. Further studies were undertaken on one of these patients to clarify the nature of the disease and possible virus relationship. Cell surface marker analysis of her peripheral blood cells documented that the majority of circulating lymphocytes were B-cells. DNA-cloned probe analysis with a complete HTLV-I proviral genome of these peripheral malignant B-cells, was negative for integrated virus. A T-cell line was established in culture from her peripheral blood. The presence of HTLV-I in the cultured T-cell line was established by the detection of expressed viral specific gag protein p-19 and proviral DNA. Thus, a B-cell lymphoid malignancy can occur in the presence of HTLV-I infected T-cells, suggesting the possibility of an indirect leukemogenic mechanism.
Synthesis of the First Methylidyne‐Rhodium Cluster by Proton‐Induced H2/CH4‐Elimination from a μ‐Methylene Complex (1980)

The transformation of a μ‐methylene‐dirhodium complex into a μ 3 ‐methylidyne‐trirhodium complex (X‐ray structure analysis) has been accomplished in reaction (1) → (3) . The first step is protonation of (1) to form the (isolable) μ‐hydrido complex (2) . equation image
Discriminative Non-Negative Matrix Factorization For Multiple Pitch Estimation. (2012)

[TODO] Add abstract here.