gebhart/patrepeval huggingface dataset:
Multispectral reflectance enhancement for breast cancer visualization in the operating room (2015)

A color enhancement method to optimize the visualization of breast tumors in cancer pathology is proposed. Light scattering measurements are minimally invasive, and allow the estimation of tissue morphology and composition to guide the surgeon in resection surgeries. The usability of scatter and absorption signatures acquired with a microsampling reflectance spectral imaging system was improved employing an empirical approximation to the Mie theory to estimate the scattering power on a per-pixel basis. The proposed methodology generates a new image with blended color and diagnostic purposes coming from the emphasis or highlighting of specific wavelengths or features. These features can be the specific absorbent tissue components (oxygenated and deoxygenated hemoglobin, etc.), additional parameters as scattering power or amplitude or even the combination of both. The goal is to obtain an improved and inherent tissue contrast working only with the local reflectance of tissue. To this aim, it is provided a visual interpretation of what is considered non-malignant (normal epithelia and stroma, benign epithelia and stroma, inflammation), malignant (DCIS, IDC, ILC) and adipose tissue. Consequently, a fast visualization map of the intracavity area can be offered to the surgeon providing relevant diagnostic information. No labeling or extrinsic indicators are required for proposed methodology and therefore the possibility of transferring absorption and scattering features simultaneously into visualization, fusing their effects into a single image, can guide surgeons efficiently.
A Reciprocal Heuristic Model for Diffuse Scattering From Walls and Surfaces (2023)

Diffuse scattering of electromagnetic waves from natural and artificial surfaces has been extensively studied in various disciplines, including radio wave propagation, and several diffuse scattering models based on different approaches have been proposed over the years, two of the most popular ones being Kirchhoff Theory and the so-called Effective Roughness heuristic model. The latter, although less rigorous than the former, is more flexible and applicable to a wider range of real-world cases, including non-Gaussian surfaces, surfaces with electrically small correlation lengths and scattering from material inhomogeneities that are often present under the surface. Unfortunately, the Effective Roughness model, with the exception of its Lambertian version, does not satisfy reciprocity, which is an important physical-soundness requirement for any propagation model. In the present work, without compromising its effectiveness and its simple and yet sound power-balance approach, we propose a reciprocal version of the Effective Roughness model, which can be easily implemented and replaced to the old version in ray-based propagation models. The new model is analyzed and compared to the old one and to other popular models. Once properly calibrated, it is shown to yield similar - if not better - performance with respect to the old one when checked vs. measurements.
Graphium basitruncatumFungemia in a Patient with Acute Leukemia (2007)

We report the first case of infection caused by Graphium basitruncatum in a man with acute leukemia who developed persistent fungemia and skin lesions. G. basitruncatum, a member of the Microascaceae, is phylogenetically and morphologically distinct from Graphium penicillioides and the opportunistic pathogens Scedosporium apiospermum (Pseudallescheria boydii) and Scedosporium prolificans.
Microwave frequency modulation to enhance Dissolution Dynamic Nuclear Polarization (2014)

Hyperpolarization by Dissolution Dynamic Nuclear Polarization is usually achieved by monochromatic microwave irradiation of the ESR spectrum of free radicals embedded in glasses at 1.2 K and 3.35 T. Hovav et al. (2014) have recently shown that by using frequency-modulated (rather than monochromatic) microwave irradiation one can improve DNP at 3.35 T in the temperature range 10–50 K. We show in this Letter that this is also true under Dissolution-DNP conditions at 1.2 K and 6.7 T. We demonstrate the many virtues of using frequency-modulated microwave irradiation: higher polarizations, faster build-up rates, lower radical concentrations, less paramagnetic broadening, more efficient cross-polarization, and less critical frequency adjustments.
Bioorthogonal Imaging of Aurora Kinase A in Live Cells (2012)

In living color: Aurora kinase A (AKA) was imaged in live cells using a bioorthogonal two-step reaction with a small molecule AKA inhibitor (see scheme) and a fluorescent reporter. The fluorescent molecule was localized to spindle poles and microtubules during metaphase, consistent with the localization of both endogenous and green fluorescent protein tagged AKA. By using this approach, changes in AKA distribution during mitosis were also observed. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Elastic Block Ciphers (2004)

We introduce a new concept of elastic block ciphers, symmetric-key encryption algorithms that for a variable size input do not expand the plaintext, (i.e., do not require plaintext padding), while maintaining the diffusion property of traditional block ciphers and adjusting their computational load proportionally to the size increase. Elastic block ciphers are ideal for applications where length-preserving encryption is most beneficial, such as protecting variable-length database entries or network packets. We present a general algorithmic schema for converting a traditional block cipher, such as AES, to its elastic version, and analyze the security of the resulting cipher. Our approach allows us to "stretch" the supported block size of a block cipher up to twice the original length, while increasing the computational load proportionally to the block size. Our approach does not allow us to use the original cipher as a "black box" (i.e., as an ideal cipher or a pseudorandom permutation as is used in constructing modes of encryption). Nevertheless, under some reasonable conditions on the cipher's structure and its key schedule, we reduce the security of the elastic version to that of the fixed size block cipher. This schema and the security reduction enable us to capitalize on secure ciphers and their already established security properties in elastic designs. We note that we are not aware of previous "reduction type" proofs of security in the area of concrete (i.e., non "black-box") block cipher design. Our implementation of the elastic version of AES, which accepts blocks of all sizes in the range 128 to 255 bits, was measured to be almost twice as fast when encrypting plaintext that is only a few bits longer than a full block (A128 bits), when compared to traditional "pad and block-encrypt" approach.
Targeting the JAK2 Kinase in Hematological Malignancies. (2007)

Abstract JAK2 is an intracellular protein tyrosine kinase whose dysregulation has been implicated in leukemia, lymphoma, and myeloproliferative disorders (MPD). Increased kinase activity of JAK2, caused by point mutation of the JH2 autoinhibitory region or formation of JAK2 fusion proteins, causes increased activation of downstream signaling pathways affecting cell differentiation, proliferation, migration, and apoptosis. Through the use of CLIMB™, our proprietary drug discovery process, the published JAK2 crystal structure was used to build several models that were then used as a substrate for in silico docking of 2.3 million virtual small molecule compounds to generate a subset of leads based on calculated binding energies. These leads were further screened using a number of in silico physicochemical and ADMET prediction algorithms to determine “druggable” leads which were most likely to be successful in a biological context. Lead JAK2 inhibitor candidates exhibit low nanomolar IC50 activity against the JAK2 and JAK2 V617F mutant enzymes. Cancer cell lines expressing either the wild-type or mutant JAK2 enzyme demonstrate sensitivity to these inhibitors resulting in IC50 values in low micromolar to nanomolar range. Consistent with the inhibition of the JAK2 enzyme, activity of downstream signaling partners are severely decreased. The phosphorylation level of STAT5, a downstream modulator of JAK2 signaling, in treated HEL cell lysates was analyzed by western blot analysis. These results showed that lead JAK2 candidates caused an inhibition of STAT5 phosphorylation at a low nanomolar EC50. This series of compounds are currently being tested in in vivo xenograft models. Evaluation of lead candidates in biochemical assays against the hERG and CYP450 enzymes showed that these compounds have little inhibitory activity against these enzymes. SuperGen’s lead selective JAK2 inhibitors exhibit potent inhibition of wild-type and mutant JAK2 kinase activity translating into potent inhibition of cellular signaling pathways and cancer cell proliferation.
Delineating the spectrum of impairments, disabilities, and rehabilitation needs in methylmalonic acidemia (MMA) (2015)

Methylmalonic acidemia patients have complex rehabilitation needs that can be targeted to optimize societal independence and quality of life. Thirty-seven individuals with isolated MMA (28 mut, 5 cblA, 4 cblB), aged 2-33 years, were enrolled in a natural history study, and underwent age-appropriate clinical assessments to characterize impairments and disabilities. Neurological examination and brain imaging studies were used to document movement disorders and the presence of basal ganglia injury. A range of impairments and disabilities were identified by a team of physical medicine experts. Movement disorders, such as chorea and tremor, were common (n = 31, 83%), even among patients without evidence of basal ganglia injury. Joint hypermobility (n = 24, 69%) and pes planus (n = 22, 60%) were frequent and, in many cases, under-recognized. 23 (62%) patients required gastrostomy feedings. 18/31 patients >4 years old (58%) had difficulties with bathing and dressing. 16 of 23 school-aged patients received various forms of educational support. Five of the 10 adult patients were employed or in college; three lived independently. Unmet needs were identified in access to rehabilitation services, such as physical therapy (unavailable to 14/31), and orthotics (unavailable to 15/22). We conclude that patients with MMA are challenged by a number of functional limitations in essential activities of mobility, self-care, and learning, in great part caused by movement disorders and ligamentous laxity. Early assessment, referral, and implementation of age-appropriate rehabilitation services should significantly improve independence and quality of life.
Outbreak of Adverse Reactions Associated with Contaminated Heparin (2008)

Heparin contaminated with OSCS was epidemiologically linked to adverse reactions in this nationwide outbreak. The reported clinical features of many of the cases further support the conclusion that contamination of heparin with OSCS was the cause of the outbreak.
EUV lithography performance of negative-tone chemically amplified fullerene resist (2013)

With Extreme Ultraviolet Lithography (EUVL) emerging as one of the top contenders to succeed from optical lithography for the production of next generation semiconductor devices, the search for suitable resists that combine high resolution, low line edge roughness (LER) and commercially viable sensitivity for high volume production is still ongoing. One promising approach to achieve these goals has been the development of molecular resists. We have previously reported on a molecular negative tone resist for e-beam lithography based on fullerene derivatives. Since then we have developed the system further to adapt it to EUVL. Investigation into the lithographic performance of the resist shows resolution down to 20 nm halfpitch with LERs &lt; 5 nm and sensitivities ~ 20 mJ/cm<sup>2</sup>.
Processing the Interspecies Quorum-sensing Signal Autoinducer-2 (AI-2) (2011)

The molecule (S)-4,5-dihydroxy-2,3-pentanedione (DPD) is produced by many different species of bacteria and is the precursor of the signal molecule autoinducer-2 (AI-2). AI-2 mediates interspecies communication and facilitates regulation of bacterial behaviors such as biofilm formation and virulence. A variety of bacterial species have the ability to sequester and process the AI-2 present in their environment, thereby interfering with the cell-cell communication of other bacteria. This process involves the AI-2-regulated lsr operon, comprised of the Lsr transport system that facilitates uptake of the signal, a kinase that phosphorylates the signal to phospho-DPD (P-DPD), and enzymes (like LsrG) that are responsible for processing the phosphorylated signal. Because P-DPD is the intracellular inducer of the lsr operon, enzymes involved in P-DPD processing impact the levels of Lsr expression. Here we show that LsrG catalyzes isomerization of P-DPD into 3,4,4-trihydroxy-2-pentanone-5-phosphate. We present the crystal structure of LsrG, identify potential catalytic residues, and determine which of these residues affects P-DPD processing in vivo and in vitro. We also show that an lsrG deletion mutant accumulates at least 10 times more P-DPD than wild type cells. Consistent with this result, we find that the lsrG mutant has increased expression of the lsr operon and an altered profile of AI-2 accumulation and removal. Understanding of the biochemical mechanisms employed by bacteria to quench signaling of other species can be of great utility in the development of therapies to control bacterial behavior.
High resistive ELTRAN/sup (R)/ SOI-Epi/sup TM/ wafers for RF application (2002)

We report on highly resistive SOI wafers formed by epitaxial layer transfer (ELTRAN) technology focusing on the final resistivity after formation. The lowering of resistivity in the Si wafer of 200 mm ELTRAN SOI was successfully suppressed by controlling the cleanroom ambient and the location of the bonded interface.
Attosecond Time-Resolved Studies of Electron Dynamics on Surfaces (2010)

We report on time-resolved experiments to investigate the attosecond dynamics of photoelectrons generated by ultra-short XUV pulses on clean metal surfaces and in well-defined adsorbate-metal interfaces.
The Gastrointestinal Adherent Mucous Gel Barrier (2000)

Three phases of production of mucin can be identified in the gastrointestinal (GI) tract on the basis of their location in vivo: the stored, presecreted, intracellular mucin; the gel phase adherent to the epithelial surfaces; and the viscous, mobile mucin, which is largely in soluble form and mixes with the luminal contents. The layer of adherent mucous gel that lines the epithelial surfaces throughout the gut from the stomach to the colon marks the interface between the mucosal epithelium and the fluid luminal environment, which is teeming with nutrients, bacteria, destructive hydrolases, foreign compounds and so on. The adherent mucous gel thus provides a protective barrier and a stable unstirred layer with its own microenvironment, between the mucosal surface and the lumen (,). In the mouth, where salivary mucins are secreted, and the esophagus, there is no discernible adherent mucous gel layer.
Genetic architecture of maize chlorotic mottle virus and maize lethal necrosis through GWAS, linkage analysis and genomic prediction in tropical maize germplasm (2019)

Analysis of the genetic architecture of MCMV and MLN resistance in maize doubled-haploid populations revealed QTLs with major effects on chromosomes 3 and 6 that were consistent across genetic backgrounds and environments. Two major-effect QTLs, qMCMV3-108/qMLN3-108 and qMCMV6-17/qMLN6-17, were identified as conferring resistance to both MCMV and MLN. Maize lethal necrosis (MLN) is a serious threat to the food security of maize-growing smallholders in sub-Saharan Africa. The ability of the maize chlorotic mottle virus (MCMV) to interact with other members of the Potyviridae causes severe yield losses in the form of MLN. The objective of the present study was to gain insights and validate the genetic architecture of resistance to MCMV and MLN in maize. We applied linkage mapping to three doubled-haploid populations and a genome-wide association study (GWAS) on 380 diverse maize lines. For all the populations, phenotypic variation for MCMV and MLN was significant, and heritability was moderate to high. Linkage mapping revealed 13 quantitative trait loci (QTLs) for MCMV resistance and 12 QTLs conferring MLN resistance. One major-effect QTL, qMCMV3-108/qMLN3-108, was consistent across populations for both MCMV and MLN resistance. Joint linkage association mapping (JLAM) revealed 18 and 21 main-effect QTLs for MCMV and MLN resistance, respectively. Another major-effect QTL, qMCMV6-17/qMLN6-17, was detected for both MCMV and MLN resistance. The GWAS revealed a total of 54 SNPs (MCMV-13 and MLN-41) significantly associated (P ≤ 5.60 × 10<sup>-05</sup>) with MCMV and MLN resistance. Most of the GWAS-identified SNPs were within or adjacent to the QTLs detected through linkage mapping. The prediction accuracy for within populations as well as the combined populations is promising; however, the accuracy was low across populations. Overall, MCMV resistance is controlled by a few major and many minor-effect loci and seems more complex than the genetic architecture for MLN resistance.
Organophosphorus Chemistry (2002)

Organophosphorus Chemistry provides a comprehensive annual review of the literature. Coverage includes phosphines and their chalcogenides, phosphonium salts, low coordination number phosphorus compounds, penta- and hexa-coordinated compounds, tervalent phosphorus acids, nucleotides and nucleic acids, ylides and related compounds, and phosphazenes. The series will be of value to research workers in universities, government and industrial research organisations, whose work involves the use of organophosphorus compounds. It provides a concise but comprehensive survey of a vast field of study with a wide variety of applications, enabling the reader to rapidly keep abreast of the latest developments in their specialist areas. Specialist Periodical Reports provide systematic and detailed review coverage of progress in the major areas of chemical research. Written by experts in their specialist fields the series creates a unique service for the active research chemist, supplying regular critical in-depth accounts of progress in particular areas of chemistry. For over 80 years the Royal Society of Chemistry and its predecessor, the Chemical Society, have been publishing reports charting developments in chemistry, which originally took the form of Annual Reports. However, by 1967 the whole spectrum of chemistry could no longer be contained within one volume and the series Specialist Periodical Reports was born. The Annual Reports themselves still existed but were divided into two, and subsequently three, volumes covering Inorganic, Organic and Physical Chemistry. For more general coverage of the highlights in chemistry they remain a 'must'. Since that time the SPR series has altered according to the fluctuating degree of activity in various fields of chemistry. Some titles have remained unchanged, while others have altered their emphasis along with their titles; some have been combined under a new name whereas others have had to be discontinued. The current list of Specialist Periodical Reports can be seen on the inside flap of this volume.
Measurement of Light Intensity Field with a Fluorescent Bead Cantilever (2006)

We propose a light intensity measuring method applicable to near-field measurement as well as far-field measurement. We fabricated a scanning probe composed of a piezoresistive cantilever and a fluorescent bead. The fluorescent bead works as a probe for the light intensity. The bead was attached to the tip of the piezoresistive cantilever, which detected cantilever contact by monitoring strain of the cantilever. Scanning position determination was carried out with accuracy of 100 nm by detecting a contact between the bead and the substrate. The cantilever probe scanned a sub-micron sized aperture to measure intensity distribution in the vicinity of the aperture. This contact detection allowed the probe to scan in near-field region, where distance between the probe and the aperture was within a wavelength.
Multiband Imaging CMOS Image Sensor with Multi-Storied Photodiode Structure † (2018)

We developed a multiband imaging CMOS image sensor (CIS) with a multi-storied photodiode structure, which comprises two photodiode (PD) arrays that capture two different images, visible red, green, and blue (RGB) and near infrared (NIR) images at the same time. The sensor enables us to capture a wide variety of multiband images which is not limited to conventional visible RGB images taken with a Bayer filter or to invisible NIR images. Its wiring layers between two PD arrays can have an optically optimized effect by modifying its material and thickness on the bottom PD array. The incident light angle on the bottom PD depends on the thickness and structure of the wiring and bonding layer, and the structure can act as an optical filter. Its wide-range sensitivity and optimized optical filtering structure enable us to create the images of specific bands of light waves in addition to visible RGB images without designated pixels for IR among same pixel arrays without additional optical components. Our sensor will push the envelope of capturing a wide variety of multiband images.
Stochastic optimization of low-loss optical negative-index metamaterial (2007)

Optical metamaterial consisting of metal-dielectric composites creates a complicated system that is not amenable to analytical solutions. This presents a challenge in optimizing these intricate systems. We present the application of three nature-inspired stochastic optimization techniques in conjunction with fast numerical electromagnetic solvers to yield a metamaterial that satisfies a required design criterion. In particular, three stochastic optimization tools (genetic algorithm, particle swarm optimization, and simulated annealing) are used for designing a low-loss optical negative index metamaterial. A negative refractive index around −0.8+0.2i is obtained at a wavelength of 770 nm. The particle swarm optimization algorithm is found to be the most efficient in this case.
Other MTF Contributions (2021)

We now consider the MTF contributions arising from image motion, image vibration, atmospheric turbulence, and aerosol scattering. We present a first-order analysis of these additional contributions to the system MTF. Our heuristic approach provides a back-of-the-envelope estimate for the imagequality impact of these effects, and a starting point for more advanced analyses.