gebhart/patrepeval huggingface dataset:
Extreme-depth-of-focus imaging with a flat lens (2020)

A lens performs an approximately one-to-one mapping from the object to the image plane. This mapping in the image plane is maintained within a depth of field (or referred to as depth of focus, if the object is at infinity). This necessitates refocusing of the lens when the images are separated by distances larger than the depth of field. Such refocusing mechanisms can increase the cost, complexity, and weight of imaging systems. Here we show that by judicious design of a multi-level diffractive lens (MDL) it is possible to drastically enhance the depth of focus by over 4 orders of magnitude. Using such a lens, we are able to maintain focus for objects that are separated by as large a distance as <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mo>∼</mml:mo> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>6</mml:mn> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">m</mml:mi> </mml:mrow> </mml:math> in our experiments. Specifically, when illuminated by collimated light at <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mi>λ</mml:mi> <mml:mo>=</mml:mo> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>0.85</mml:mn> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mtext>µ</mml:mtext> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">m</mml:mi> </mml:mrow> </mml:mrow> </mml:math> , the MDL produced a beam, which remained in focus from 5 to 1200 mm. The measured full width at half-maximum of the focused beam varied from 6.6 µm (5 mm away from the MDL) to 524 µm (1200 mm away from the MDL). Since the side lobes were well suppressed and the main lobe was close to the diffraction limit, imaging with a horizontal × vertical field of view of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:msup> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>40</mml:mn> </mml:mrow> <mml:mo>∘</mml:mo> </mml:msup> <mml:mo>×</mml:mo> <mml:msup> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>30</mml:mn> </mml:mrow> <mml:mo>∘</mml:mo> </mml:msup> </mml:math> over the entire focal range was possible. This demonstration opens up a new direction for lens design, where by treating the phase in the focal plane as a free parameter, extreme-depth-of-focus imaging becomes possible.
Optical forces on a cylinder induced by surface waves and the conservation of the canonical momentum of light (2021)

Based on rigorous derivations using the electromagnetic energy-momentum tensor, we established a generic relationship between the longitudinal optical force (along the surface wave propagating direction) on a cylinder induced by surface waves and the energy flux of each surface mode supported on the interface between air and a lossless substrate possessing continuous translational symmetry along the longitudinal direction. The longitudinal optical force is completely attributed to the canonical momentum of light. Our theory is valid for generic types of surface waves and lays the theoretical foundation for the research and applications of optical manipulations by surface waves.
A clinical review of the potential role of microaspiration and a dysregulated aerodigestive microbiome in lung disease (2023)

Abstract: When initiated the human microbiome project did not include the lungs and airways in its sampling sites, indicating an under appreciation of the role of the human lung microbiome in health and disease. This paradigm has recently changed through the use of culture independent methods to characterise the human lung microbiome. The original thinking, that the normal lung was essentially sterile, had previously been challenged by findings of microaspiration in normal volunteers and in patients with decreased levels of consciousness. The sterile lung was also questioned by findings of clinically occult infection markers in lung allograft recipients. What is arguably a “rediscovery” of the importance of the human lung microbiome may still underappreciate physiological and patho-physiological inter-relationships between organ systems, studied in separate research disciplines. In particular, microaspiration may be an important, direct mechanism through which the lung microbiome is modulated. As well as aspiration related to gastro-oesophageal reflux and microaspiration the authors feel that the importance of dysphagia in chronic lung disease, will be increasingly recognised in frailty related microbiome exchange between the oropharynx into the lung. This review therefore discusses interconnections in the human microbiome, with a focus on the potential for aerodigestive pathophysiology and microaspiration. Potential connections with human lung disease are discussed and contextualised within a developing literature. This review therefore highlights much needed new targets for translational intervention in lung pathophysiology and underlies the importance of a mixed disciplinary team approach for the future.
Reactivity of Langerhans cells with hybridoma antibody. (1981)

Reactivity of a monoclonal antibody with human Langerhans cells was demonstrated by a double-labeling immunofluorescence technique. Ia-bearing cells of the epidermis (Langerhans cells) were reactive with this antibody both in frozen sections and in cell suspensions prepared from human epidermis. This monoclonal antibody was unreactive with non-Ia-bearing epidermal cells and with peripheral blood B cells, T cells, and monocytes but did not bind to 70% of intrathymic lymphocytes. These observations further distinguish Langerhans cells from classical monocytes. Furthermore, this monoclonal antibody is a highly specific marker for the in vivo identification and in vitro isolation of Langerhans cells.
Correlated In Situ Low‐Frequency Noise and Impedance Spectroscopy Reveal Recombination Dynamics in Organic Solar Cells Using Fullerene and Non‐Fullerene Acceptors (2017)

Abstract Non‐fullerene acceptors based on perylenediimides (PDIs) have garnered significant interest as an alternative to fullerene acceptors in organic photovoltaics (OPVs), but their charge transport phenomena are not well understood, especially in bulk heterojunctions (BHJs). Here, charge transport and current fluctuations are investigated by performing correlated low‐frequency noise and impedance spectroscopy measurements on two BHJ OPV systems, one employing a fullerene acceptor and the other employing a dimeric PDI acceptor. In the dark, these measurements reveal that PDI‐based OPVs have a greater degree of recombination in comparison to fullerene‐based OPVs. Furthermore, for the first time in organic solar cells, 1/ f noise data are fit to the Kleinpenning model to reveal underlying current fluctuations in different transport regimes. Under illumination, 1/ f noise increases by approximately four orders of magnitude for the fullerene‐based OPVs and three orders of magnitude for the PDI‐based OPVs. An inverse correlation is also observed between noise spectral density and power conversion efficiency. Overall, these results show that low‐frequency noise spectroscopy is an effective in situ diagnostic tool to assess charge transport in emerging photovoltaic materials, thereby providing quantitative guidance for the design of next‐generation solar cell materials and technologies.
Supplementary Figures 1-2, Supplementary Tables 1-2 from p53-Reactive T Cells Are Associated with Clinical Benefit in Patients with Platinum-Resistant Epithelial Ovarian Cancer After Treatment with a p53 Vaccine and Gemcitabine Chemotherapy (2023)

&lt;p&gt;Figure S1: Frequency of Tregs does not significantly decline post treatment and does not correlate with p53-reactivity or PFS.; Figure S2: Frequency of MDSC does not significantly differ to healthy controls, does not decline post treatment and does not correlate with p53-reactivity or PFS.; Supplementary Table T1: Multi variation analysis* shows an association between progression free survival and frequency of p53-reactive T cells, disease stage and baseline MDSC. Supplementary Table T2: Correlations (Pearson) of variables included in multi variation analysis.&lt;/p&gt;
Single-cell barcode analysis provides a rapid readout of cellular signaling pathways in clinical specimens (2018)

Serial tissue sampling has become essential in guiding modern targeted and personalized cancer treatments. An alternative to image guided core biopsies are fine needle aspirates (FNA) that yield cells rather than tissues but are much better tolerated and have lower complication rates. The efficient pathway analysis of such cells in the clinic has been difficult, time consuming and costly. Here we develop an antibody-DNA barcoding approach where harvested cells can be rapidly re-stained through the use of custom designed oligonucleotide-fluorophore conjugates. We show that this approach can be used to interrogate drug-relevant pathways in scant clinical samples. Using the PI3K/PTEN/CDK4/6 pathways in breast cancer as an example, we demonstrate how analysis can be performed in tandem with trial enrollment and can evaluate downstream signaling following therapeutic inhibition. This approach should allow more widespread use of scant single cell material in clinical samples.
ADP-ribosylation of human defensin HNP-1 results in the replacement of the modified arginine with the noncoded amino acid ornithine (2009)

Defensins (e.g., human neutrophil peptides, or HNPs) contribute to innate immunity through diverse actions, including microbial killing; high concentrations are present in the lung in response to inflammation. Arginines are critical for HNP activity, which is decreased by their replacement with ornithine. ADP-ribosyltransferases (ARTs) catalyze transfer of ADP-ribose from NAD to an acceptor arginine in a protein substrate, whereas ADP-ribosylarginine hydrolases release ADP-ribose. ART1 on the surface of airway epithelial cells ADP-ribosylated HNP-1 specifically on arginines 14 and 24, with ADP-ribosylation altering biological activity. Di- and mono-ADP-ribosylated HNP-1 were isolated from bronchoalveolar lavage fluid (BALF) of patients with asthma and idiopathic pulmonary fibrosis (IPF), suggesting a role for ADP-ribosylation in disease. In the present study, we observed that ART1-catalyzed ADP-ribosylation of HNP-1 in vitro generated a product with ADP-ribose on arginine 24, and ornithine replacing arginine at position 14. We hypothesized that ADP-ribosylarginine is susceptible to a nonenzymatic hydrolytic reaction yielding ornithine. On incubation of di- or mono-ADP-ribosyl-HNP-1 at 37 degrees C, ADP-ribosylarginine was partially replaced by ornithine, whereas ornithine was not detected by amino acid analysis and mass spectrometry of unmodified HNP-1 incubated under the same conditions. Further, ornithine was produced from the model compound, ADP-ribosylarginine. BALF from an IPF patient contained ADP-ribosyl-HNP-ornithine as well as mono- and di-ADP-ribosylated HNP-1, consistent with in vivo conversion of arginine to ornithine. Targeted ADP-ribosylation of specific arginines by transferases, resulting in their replacement with ornithine, is an alternative pathway for regulation of protein function through posttranslational modification.
Demonstration of oxygen-enriched air staging at Owens-Brockway Glass Containers. Technical progress report, August 1, 1995--July 31, 1996 (1996)

The objective of the program is to demonstrate the use of a previously developed combustion modification technology to reduce NO, emissions from sideport regenerative container glass melters. This technology, known as oxygen-enriched air staging (OEAS), has been demonstrated, and is now being commercialized, for endport container glass furnaces. A 17-month development program has been established with specific objectives to: (1) acquire baseline operating data on the host sideport furnace in Vernon, California, (2) evaluate secondary oxidant injection strategies based on earlier endport furnace results and through modeling of a single port pair, (3) retrofit and test one port pair (the test furnace has six port pairs) with a flexible OEAS system, and select the optimal system configuration, (4) use the results from tests with one port pair to design, retrofit, and test OEAS on the entire furnace (six port pairs), and (5) analyze test results, prepare report, and finalize the business plan to commercialize OEAS for sideport furnaces. The host furnace for testing in this program is an Owens-Brockway 6-port pair sideport furnace in Vernon, California producing 325-ton/d of amber container glass. The baseline NO{sub x} level of this optimized furnace is about 4.0 lb/ton of glass. An anticipated NO{sub x}, reduction of 50% will lower the NO{sub x} production level to below 2 lb/ton. Secondary oxidant staging techniques being considered include oxygen-enriched ambient air staging (OEAS) and oxygen staging (OS).
Observation of Intermolecular Hydrogen Bonding Interactions in Biosynthesized and Biodegradable Poly [(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] in Chloroform and 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP) (2017)

In this work, we describe polymer-solvent interactions in biosynthesized and biodegradable poly[(R)-3-hydroxybutyrate- co-(R)-3-hydroxyhexanoate] (PHBHx) and the atactic homopolymer, poly(3-hydroxybutyrate) (a-PHB), which were studied both as neat polymers and in solutions of chloroform and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). Specifically, infrared frequency shifts of the carbonyl band were observed in semi-crystalline PHBHx, but not in a-PHB, because it cannot form the helical conformation required for crystallization. The carbonyl band of PHBHx exhibited the high frequency associated with amorphous structure in chloroform and the lower frequency traditionally attributed to the helical crystalline structure in HFIP. The same results were obtained for a-PHB, demonstrating that the helical structure is not required for a lower frequency carbonyl-stretching mode. It is proposed that the band shift is due to hydrogen bonding between the carbonyl and hydroxyl hydrogen in HFIP. Therefore, the carbonyl frequency observed upon crystallization is most likely due to hydrogen bonding between the carbonyl and methyl hydrogen of the neighboring polymer chain in the crystal lattice as previously suggested.
America, America! (2008)

This account was written during a four-month stay in Berkeley from May to August 2007. It was partly inspired by a diary published by Simone de Beauvoir after her four-month lecture tour to the US in 1947. We could not resist the temptation of writing a few pages about our impressions. This text is not intended as an essay about anthropological or chemical sciences. We merely tried to understand the conditions of the bubbling creativity that we have so often witnessed in Berkeley. Some of our comments are more or less voluntarily naïve, as if Voltaire's Candide had made a trip to America. Our impressions may appear a bit franchouillardes, and perhaps a trifle rude to our American hosts, whose kindness does not deserve such a harsh treatment.
Direct calculation algorithm for two-dimensional reflector design (2012)

We have developed a fast algorithm to design two-dimensional reflector surfaces that ties together the supporting paraboloids, linear programming, and numerical integration methods. The algorithm builds upon the properties of conics and is shown to be several orders of magnitude faster than the supporting paraboloids and linear programming methods. The scalability and ease of implementation of the algorithm are discussed.
Modulations of ferroptosis in lung cancer therapy (2022)

Introduction Ferroptosis is iron-dependent regulated cell death and is a field of research that has been rapidly growing in recent years. Many preclinical studies show therapeutic benefit of ferroptosis modulation in lung cancers. There are advancements using prognostic ferroptosis-related genes to directly predict outcomes in lung cancer. Targeted therapy using RNA and nanoparticle technology have also shown benefits in ferroptosis induction. Currently, there is limited comprehensive evaluation of how ferroptosis can be used in lung cancer therapy. Thus, the aim of this report is to build an overview of all data on ferroptosis modulation in lung cancer.Areas covered Ferroptotic cell death mechanisms and how ferroptosis is highly distinguished from other forms of cell death, offered insight on the modulations of ferroptosis in killing lung cancer cells in preclinical studies. Search databases included PubMed, Google scholar, and clinicaltrials.gov through the last 10 years.Expert opinion Ferroptosis modulation in lung cancer is a promising therapeutic option, but greater understanding and progression from primarily in vitro studies to animal studies and clinical trials is needed to substantiate its utilization in practice. Future strategies of using ferroptosis modulation adjuvant to first-line therapy may increase its effectiveness and overcome apoptosis-resistance cancers.
Prevention of Physical Property Changes While Being Kept at Room Temperature on the Electrodeposited Copper (2008)

In the electrodeposition of copper, some sort of additives such as brighteners like Bis-(3-sulfopropyl)-disulfide (SPS) are added to the bath to produce a smooth surface. But the deposited copper using this type of bath shows the physical property changes while being kept at room temperature. In this research, an additive that can prevent property changes was searched for and the explanation of why the additive has that effect was investigated.Adding Sodium 2-mercapto-1H-benzoimidazole-5-sulfonate dihydrate (2M-5S) enabled the prevention of physical property changes while keeping the surface smooth. Since the correlation of grain size and tensile strength of the deposited copper using the 2M-5S added bath followed the Hall-Petch equation, the property was thought to be dominated by grain size, and the prevention of property changes was thought to be caused by the prevention of re-crystallization due to the pinning effect of the impurities in the copper.2M-5S was conjectured to react with Diaryl-dimethyl-ammonium-chloride Polymer (DDAC) and adsorb to the cathode together, which was also conjectured to be a possible cause of the increase of impurities incorporated into the copper.
Smart focal-plane technology for micro-instruments and micro-rovers (1993)

It is inevitable that micro-instruments and micro-rovers for space exploration will contain one or more focal-plane arrays for imaging, spectroscopy or navigation. In this paper, we explore the state-of-the-art in focal-plane technology for visible sensors. Also discussed is present research activity in advanced focalplane technology with particular emphasis on the development of smart sensors. The paper concludes with a discussion of possible future directions for the advancement of the technology. Visible focal-plane technology is currently dominated by charge-coupled devices (CCDs). The CCD can be used for both photon detection and as a readout multiplexer since its primary function is the shifting of charge packets. Scientific CCDs typically employ both modes of operation to utilize the maximum amount of chip area for the collection of photons and are routinely made in megapixel array sizes, with the largest demonstrated CCD size being 16 Mpixels. 1 Unfortunately, the electrodes which comprise the CCD and ensure high fidelity of the readout signal also block photons, particularly in the blue and ultraviolet (UV). Thus, separation of the sensor into a photoactive portion and a readout portion is often used to enhance the spectral response. The photoactive region may be a pinned photodiode 2 to obtain high blue response (or a platinum-silicide Schottky diode to obtain infrared response 3). The readout CCD lies between photoactive
YM-359445, an Orally Bioavailable Vascular Endothelial Growth Factor Receptor-2 Tyrosine Kinase Inhibitor, Has Highly Potent Antitumor Activity against Established Tumors (2006)

Our results show that YM-359445 is more potent than orally bioavailable VEGFR2 tyrosine kinase inhibitors, which leads to great expectations for clinical applicability.
Investigating peatland stratigraphy and hydrogeology using integrated electrical geophysics (2002)

Abstract Hydrology has been suggested as the mechanism controlling vegetation and related surficial pore-water chemistry in large peatlands. Peatland hydrology influences the carbon dynamics within these large carbon reservoirs and will influence their response to global warming. A geophysical survey was completed in Caribou Bog, a large peatland in Maine, to evaluate peatland stratigraphy and hydrology. Geophysical measurements were integrated with direct measurements of peat stratigraphy from probing, fluid chemistry, and vegetation patterns in the peatland. Consistent with previous field studies, ground-penetrating radar (GPR) was an excellent method for delineating peatland stratigraphy. Prominent reflectors from the peat-lake sediment and lake sediment-mineral soil contacts were precisely recorded up to 8 m deep. Two-dimensional resistivity and induced polarization imaging were used to investigate stratigraphy beneath the mineral soil, beyond the range of GPR. We observe that the peat is chargeable, and that IP imaging is an alternative method for defining peat thickness. The chargeability of peat is attributed to the high surface-charge density on partially decomposed organic matter. The electrical conductivity imaging resolved glaciomarine sediment thickness (a confining layer) and its variability across the basin. Comparison of the bulk conductivity images with peatland vegetation revealed a correlation between confining layer thickness and dominant vegetation type, suggesting that stratigraphy exerts a control on hydrogeology and vegetation distribution within this peatland. Terrain conductivity measured with a Geonics EM31 meter correlated with confining glaciomarine sediment thickness and was an effective method for estimating variability in glaciomarine sediment thickness over approximately 18 km2. Our understanding of the hydrogeology, stratigraphy, and controls on vegetation growth in this peatland was much enhanced from the geophysical study.
DNA damage intensity in fibroblasts in a 3-dimensional collagen matrix correlates with the Bragg curve energy distribution of a high LET particle (2010)

These 3-D culture systems can be used as a biological substrate to better understand the interaction of heavy charged particles of different energies with tissue and could serve as a basis to model space-radiation-induced cancer initiation and progression.
Optimized fabrication of silicon nanofocusing x-ray lenses using deep reactive ion etching (2007)

The authors describe an improved production route for silicon nanofocusing lenses for hard x rays using e-beam lithography and deep reactive ion etching. As compared to previous prototypes, these optics have a significantly improved from fidelity, reducing spherical aberrations. Close to an ideal performance for the focusing of hard x rays is achieved with these optics, reaching a lateral beam size of about 50nm. The lens profile is checked by scanning electron microscopy.