gebhart/patrepeval huggingface dataset:
Spatially resolved indirect imaging of objects beyond the line of sight (2019)

The nascent field of indirect imaging is concerned with the recovery of information pertaining to objects that are beyond the line-of-sight (LoS) and hidden from view. Current approaches to indirect imaging are either limited in their ability to recover spatially resolved imagery (resolution of few centimeters at 1-meter standoff) or impose severe restrictions on the imaging geometry. The present work examines two approaches that recover spatial detail on hidden objects by exploiting spatial and spectral correlation in the light scattered by the objects. Experiments have demonstrated the ability to discern sub-millimeter spatial detail, on centimeter sized objects positioned 1-meter behind a wall.
Pulsed wave interconnect (2004)

Pulsed wave interconnect is proposed for global interconnect applications. Signals are represented by localized wave-packets that propagate along the interconnect lines at the local speed of light to trigger the receivers. Energy consumption is reduced through charging up only part of the interconnect lines and using the voltage doubling property of the receiver gate capacitances. In a 0.18-/spl mu/m CMOS technology case study, SPICE simulations show that pulsed wave interconnect can save up to 50% of energy and /spl sim/30% of chip area in comparison with the repeater insertion method. A proposed signal splitting structure provides reasonable isolations between different receivers. Measured S-parameters of 3.8-mm interconnect lines fabricated through CMOS foundry showed that the distortion and attenuation of a pico second signal are much less serious than the theoretical predictions. Pulsed wave interconnect also enables time division application of a single line to boost its bit rate capacity. The use of nonlinear transmission lines (NLTL) is also proposed to overcome pulse broadening and attenuation caused by dispersion and frequency-dependent losses. Pulsed waves on an NLTL may be generated, transmitted, split and detected with components realizable in bulk and SOI CMOS technologies. Tapered NLTL can be used for pulse compression. NLTL edge sharpening abilities may be applicable for signal rise time control.
Exposure of turkey sperm to a synthetic peptide before insemination increases fertility (2000)

Effects on fertility and hatch of eggs laid by hens inseminated with sperm exposed to a synthetic peptide were studied. Pooled semen from 40 randomly selected toms was split and held in vitro for 0 or 24 h before use. Just before insemination, sperm (at 8.33x10(9) sperm/mL) were exposed for 5 min to 0.0, 0.05, 0.25, or 0.50 microM peptide. Hens (28 per group) were inseminated within less than 30 min with 250x10(6) in 30 microL. Two inseminations 24 h before onset of lay were followed by weekly inseminations through 22 or 20 wk. For sperm that was fresh or held 24 h, peptide treatment (P<0.02 or 0.01) and week of lay (P<0.01) affected fertility and hatch of total eggs set. There was no effect of peptide treatment on hatchability of fertile eggs. For fresh sperm, use of 0.25 microM peptide, but not 0.05 or 5.0 microM peptide, increased (P<0.05) fertility and hatch of total eggs set compared with the control (0 microM). Values for fertility were 94 vs. 90% and for hatch were 84 vs. 80%. Increases in hatch were especially evident for fresh sperm after approximately 13 wk of lay.
Smart handpumps: a preliminary data analysis (2014)

Groundwater accessed by handpumps is the primary water supply for many people in Africa. This “Smart Water” project considers the study of a region of Kenya where there is significant demand for groundwater, especially among the poor. Some of the engineering aims of this project are to determine if data acquired from accelerometers mounted in hand-pumps can be used to perform three tasks: (i) estimate the depth of the groundwater at the pump, (ii) predict pump failure, and (iii) classify the user of the pump (e.g., as being a man, woman, or child). This paper describes an initial investigation, based on one week of data collection, that demonstrates there is useful information in the accelerometer data collected from handpumps, which can be discovered using machine learning techniques. We show that features derived from the accelerometry data exhibit stable, similar behaviour suggesting that users and pump locations may be characterised. We demonstrate that a machine learning system can classify the data according to person and pump and accurately differentiate between different users. We conclude that our preliminary study suggests that information may exist in accelerometry from handpumps that could allow us to answer the three main questions of the “Smart Water” project, described above, motivating a largescale' data-collection activity.
Differentiation of Mature Eosinophils From Human Embryonic and Induced Pluripotent Stem Cells. (2010)

Abstract Abstract 1594 Eosinophils are multifunctional leukocytes implicated in the pathogenesis of numerous inflammatory processes. As the major effectors, eosinophils function in a variety of biological responses, allergic diseases and helminth infections. It is generally accepted human eosinophils develop through a pathway initially sharing common feature with basophils. However, there lacks a clear chart for early development of human eosinophils, such as during embryonic or fetal stages. We recently established an efficient method for producing eosinophils from human embryonic and induced pluripotent stem cells (hESC/iPSCs). By a two-step induction, we first generated multipotential hematopoietic progenitors by co-culturing hESC/iPSCs with mouse AGM-derived stromal cells for 2 weeks. Then, total co-culture cells were transferred into suspension culture favoring eosinophil development with addition of IL-3 and other factors (SCF, IL-6, TPO, Flt-3 ligand) . The maturation of hESC/iPSC -derived eosinophils was shown in a time-dependent manner, first co-expressing eosinophil-and basophil-specific markers [eosinophil peroxidase (EPO), and 2D7, respectively], then the portion of eosinophil markers gradually increased while that of basophil markers decreased (EPO+ cells from 56.4% at day 7 to 94.4% at day 21, while 2D7+ cells from 62.8% to 25.7%, respectively), typically mimicking the development of eosinophils from human adult hematopoietic progenitors. By flowcytometric analysis, an eosinophil-specific surface marker, Siglec-8, was also expressed on these hESC/iPSC-derived eosinophils in a time-dependent manner (from 10.8% at day 7 to 91.3% at day 21), paralleling to those with EPO. The expression of eosinophil-specific granule cationic proteins (EPO, MBP, ECP, EDN) and IL-5 receptor mRNA was also detected by RT-PCR. Furthermore, transmission electron microscopy (TEM) observation confirmed the eosinophil property. Eosinophils derived from hiPSCs hold similar characteristics as those from hESCs. The function of hES/hiPSC-derived eosinophils is being under investigation. Our study provides an experimental model for exploring early genesis of eosinophils, especially in uncovering the mechanisms controlling the development of the initial innate immune system of human being in normal and diseased individuals. Disclosures: No relevant conflicts of interest to declare.
Mutational Analysis of the Caenorhabditis elegans Cell-Death Gene ced-3 (1999)

Mutations in the gene ced-3, which encodes a protease similar to interleukin-1beta converting enzyme and related proteins termed caspases, prevent programmed cell death in the nematode Caenorhabditis elegans. We used site-directed mutagenesis to demonstrate that both the presumptive active-site cysteine of the CED-3 protease and the aspartate residues at sites of processing of the CED-3 proprotein are required for programmed cell death in vivo. We characterized the phenotypes caused by and the molecular lesions of 52 ced-3 alleles. These alleles can be ordered in a graded phenotypic series. Of the 30 amino acid sites altered by ced-3 missense mutations, 29 are conserved with at least one other caspase, suggesting that these residues define sites important for the functions of all caspases. Animals homozygous for the ced-3(n2452) allele, which is deleted for the region of the ced-3 gene that encodes the protease domain, seemed to be incompletely blocked in programmed cell death, suggesting that some programmed cell death can occur independently of CED-3 protease activity.
Modification of Rice Plant Height by Suppressing the Height-Controlling Gene, D18, in Rice. (2002)

Gibberellin (GA) 3β-hydroxylase catalyzes the final step of active GA synthesis in plants. In rice, the enzyme is encoded by at least two genes (OsGA3ox1 and OsGA3ox2) with differential patterns of expression. Previously, we reported that the OsGA3ox2 gene is identical with the D18 gene. The loss-of-function mutants of D18 designated as d18-AD (Akibare waisei), d18-Id18h (housetsu waisei), and d18-dy (Waito-C) show severe dwarfism caused by the decrease of the level of active GA, GA1. The gene encodes GA 3β-hydroxylase that catalyzes the reaction from GA20 to GA1 and its expression is also regulated by active GA through a feedback mechanism, suggesting that the step catalyzed by the enzyme may be a key step for regulating the level of active GA. To determine the possibility of reducing the height of rice through regulation of the level of active GA, we produced transgenic rice plants expressing the antisense of D18 cDNA. Plants expressing the antisense showed a semi-dwarf phenotype relative to the control plants carrying the vector only. The antisense plants with the semi-dwarf phenotype showed a reduced level of D18 mRNA. In contrast to the reduced level of D18 mRNA, the plants induced a higher expression level of OsGA20ox1, which encodes GA 20-oxidase catalyzing the step from GA53 to GA20 in the GA biosynthetic pathway. These results demonstrate that the height of rice can be controlled by manipulation of the GA 3β-hydroxylase expression through the decrease in the active GA level.
351 INSEMINATION OF HOLSTEIN HEIFERS WITH SEXED SPERM PROCESSED WITH OR WITHOUT EGG YOLK IN THE GLYCEROL-CONTAINING FREEZING MEDIUM (2005)

Preparation of media for use in processing sorted sperm is laborious and expensive. The objective was to determine whether pregnancy rates in heifers following AI of frozen/thawed X chromosome-bearing sperm were equivalent for sperm processed for cryopreservation using glycerol-containing medium with or without egg yolk. X chromosome-bearing sperm from each of two Holstein bulls were isolated on the basis of DNA content using a flow cytometer. Sorted sperm were collected in 50-mL plastic tubes containing 2-mL of 20% egg yolk-TRIS extender without glycerol until each tube contained 12.4 mL and approximately 12 million sperm. Sorted sperm were cooled (5°C) over 90 min before the addition of 12% glycerol-containing TIS medium with or without 20% egg yolk, as two equal volumes (6.5 mL) at 15-min intervals. Tubes containing 25 mL were centrifuged at 850 g for 20 min (5°C). After the supernatant was removed, sperm pellets within treatments and bulls were pooled. Sperm concentration was adjusted to 10 × 106/mL with medium containing 6% glycerol and 20% egg yolk-TRIS. Sorted sperm were packaged and frozen in 0.25 mL-coded straws on freezing racks in LN2 vapor. Straws from each bull-treatment combination were equally packaged in goblets to assure random use. Post-thaw sperm progressive motility, determined with time-lapse photography ('track motility'), was 44% for non-egg yolk and 43% for 20% egg yolk-glycerol-containing media. Nonsynchronized Holstein heifers ( n = 119) were inseminated 4, 12, or 24 h after observed standing estrus. Sperm were deposited into the uterine body anterior to the internal cervical os. Approximately 1 month after insemination, pregnancy was determined using ultrasound. Data were subjected to ANOVA. The pregnancy rate and 95% confidence interval for sorted sperm processed with non-egg yolk-glycerol-containing medium was 56% (49-73; n = 59), and 55% (38-62; n = 60) for the 20% egg yolk-glycerol-containing medium ( P &gt; 0.1). Bull or inseminator effects on pregnancy rates were not significant ( P &gt; 0.01). Pregnancy rates as a function of time of insemination at 4, 12, or 24 h relative to observed estrus were 62% n = 65; 48% n = 48; and 50% n = 6, respectively ( P &gt; 0.1). Even though the scope of the field trial was limited, omission of egg yolk from the glycerol-containing medium did not adversely affect pregnancy rates. Preparation of non-egg yolk-glycerol-containing medium greatly reduces associated time, labor, and expense. This study also resulted in quite acceptable pregnancy rates with insemination doses of 2 × 106 total sorted frozen/thawed sperm.
Three-dimensional mapping and range measurement by means of projected speckle patterns (2008)

We present a novel approach for three-dimensional (3D) measurements that includes the projection of coherent light through ground glass. Such a projection generates random speckle patterns on the object or on the camera, depending if the configuration is transmissive or reflective. In both cases the spatially random patterns are seen by the sensor. Different spatially random patterns are generated at different planes. The patterns are highly random and not correlated. This low correlation between different patterns is used for both 3D mapping of objects and range finding.
Learning MHC I—peptide binding (2006)

Abstract Motivation and results: Motivated by the ability of a simple threading approach to predict MHC I—peptide binding, we developed a new and improved structure-based model for which parameters can be estimated from additional sources of data about MHC-peptide binding. In addition to the known 3D structures of a small number of MHC-peptide complexes that were used in the original threading approach, we included three other sources of information on peptide-MHC binding: (1) MHC class I sequences; (2) known binding energies for a large number of MHC-peptide complexes; and (3) an even larger binary dataset that contains information about strong binders (epitopes) and non-binders (peptides that have a low affinity for a particular MHC molecule). Our model significantly outperforms the standard threading approach in binding energy prediction. In our approach, which we call adaptive double threading, the parameters of the threading model are learnable, and both MHC and peptide sequences can be threaded onto structures of other alleles. These two properties make our model appropriate for predicting binding for alleles for which very little data (if any) is available beyond just their sequence, including prediction for alleles for which 3D structures are not available. The ability of our model to generalize beyond the MHC types for which training data is available also separates our approach from epitope prediction methods which treat MHC alleles as symbolic types, rather than biological sequences. We used the trained binding energy predictor to study viral infections in 246 HIV patients from the West Australian cohort, and over 1000 sequences in HIV clade B from Los Alamos National Laboratory database, capturing the course of HIV evolution over the last 20 years. Finally, we illustrate short-, medium-, and long-term adaptation of HIV to the human immune system. Availability: Contact: jojic@microsoft.com
Unusual Fluorescent Monomeric and Dimeric Dialkynyl Dipyrromethene−Borane Complexes (2006)

Novel monomeric and dimeric dialkynyl borondipyrromethene dyes (E-Bodipy) have been prepared in two different ways, providing systems in which the boron center is attached to either two similar or two dissimilar acetylenic units incorporating chromophores such as pyrene or anthracene. Both families exhibit interesting fluorescence and redox properties in which almost quantitative intramolecular energy transfer occurs.
Type IA Topoisomerases as Targets for Infectious Disease Treatments (2021)

Infectious diseases are one of the main causes of death all over the world, with antimicrobial resistance presenting a great challenge. New antibiotics need to be developed to provide therapeutic treatment options, requiring novel drug targets to be identified and pursued. DNA topoisomerases control the topology of DNA via DNA cleavage-rejoining coupled to DNA strand passage. The change in DNA topological features must be controlled in vital processes including DNA replication, transcription, and DNA repair. Type IIA topoisomerases are well established targets for antibiotics. In this review, type IA topoisomerases in bacteria are discussed as potential targets for new antibiotics. In certain bacterial pathogens, topoisomerase I is the only type IA topoisomerase present, which makes it a valuable antibiotic target. This review will summarize recent attempts that have been made to identify inhibitors of bacterial topoisomerase I as potential leads for antibiotics and use of these inhibitors as molecular probes in cellular studies. Crystal structures of inhibitor-enzyme complexes and more in-depth knowledge of their mechanisms of actions will help to establish the structure-activity relationship of potential drug leads and develop potent and selective therapeutics that can aid in combating the drug resistant bacterial infections that threaten public health.
Heartmate: automated integrated anomaly analysis for effective remote cardiac health management (2017)

Remote cardiac health management is an important healthcare application. We have developed Heartmate that enables basic screening of cardiac health using low cost sensors or smartphone-inbuilt sensors without manual intervention. It consists of robust denoising algorithm along with effective anomaly analytics for physiological signals. Heartmate identifies and eliminates signal corruption as well as detects cardiac anomaly condition from physiological cardiac signals like heart sound or phonocardiogram (PCG) and photoplethysmogram (PPG).
Lipid-free Fluoropolymer-based Propofol Emulsions and Lipid Reversal of Propofol Anesthesia in Rats (2016)

Three of the four novel lipid-free fluoropolymer-based formulations showed efficacy in producing anesthesia, which was comparable to that of Diprivan, and a lipid bolus hastened recovery. These novel propofol formulations have the potential to avoid complications seen with the existing lipid-based formulation.
In Search of the Optimum Information Rate and Symbol Rate in PS-QAM Systems to Enable Highly Efficient Optical Transport Networks (2021)

We demonstrate how optimization of information rates and symbol rates in flexible transponders utilizing Probabilistic Constellation Shaping (PCS) can maximize transmission reach and SE x reach product for high speed optical transmission networks.
Separate density and viscosity measurements of unknown liquid using quartz crystal microbalance (2016)

Aqueous liquids have a wide range of applications in many fields. Basic physical properties like the density and the viscosity have great impacts on the functionalities of a given ionic liquid. For the millions kinds of existing liquids, only a few have been systematically measured with the density and the viscosity using traditional methods. However, these methods are limited to measure the density and the viscosity of an ionic liquid simultaneously especially in processing micro sample volumes. To meet this challenge, we present a new theoretical model and a novel method to separate density and viscosity measurements with single quartz crystal microbalance (QCM) in this work. The agreement of experimental results and theocratical calculations shows that the QCM is capable to measure the density and the viscosity of ionic liquids.
A novel gene mutation that confers abnormal patterns of β‐carotene accumulation in cauliflower (<i>Brassica oleracea</i> var. <i>botrytis</i>) (2001)

The Or gene of cauliflower (Brassica oleracea var. botrytis) causes many tissues of the plant to accumulate carotenoids and turn orange, which is suggestive of a perturbation of the normal regulation of carotenogenesis. A series of experiments to explore the cellular basis of the carotenoid accumulation induced by the Or gene was completed. The Or gene causes obvious carotenoid accumulation in weakly or unpigmented tissues such as the curd, pith, leaf bases and shoot meristems, and cryptically in some cells of other organs, including the roots and developing fruits. The dominant carotenoid accumulated is beta-carotene, which can reach levels that are several hundred-fold higher than those in comparable wild-type tissues. The beta-carotene accumulates in plastids mainly as a component of massive, highly ordered sheets. The Or gene does not affect carotenoid composition of leaves, nor does it alter color and chromoplast appearance in flower petals. Interestingly, mRNA from carotenogenic and other isoprenoid biosynthetic genes upstream of the carotenoid pathway was detected both in orange tissues of the mutant, and in comparable unpigmented wild-type tissues. Thus the unpigmented wild-type tissues are likely to be competent to synthesize carotenoids, but this process is suppressed by an unidentified mechanism. Our results suggest that the Or gene may induce carotenoid accumulation by initiating the synthesis of a carotenoid deposition sink in the form of the large carotenoid-sequestering sheets.
Attenuation Estimation in Reflection: Progress and Prospects (1984)

This monograph presents a tutorial review of the current state-of-the-art in ultrasonic attenuation estimation in reflection. Clinical indications which provide the motivation for attempting in vivo attenuation estimation are discussed. Frequency and time domain techniques and their respective tradeoffs and problems are presented. Finally, current clinical results obtained with the various techniques are summarized and further areas of study are suggested.
Nondestructive Detection of Heavily Shielded Materials by Using Nuclear Resonance Fluorescence with a Laser-Compton Scattering γ-ray Source (2009)

We perform a proof-of-principle experiment for a nondestructive method for detecting the elemental and isotopic composition of materials concealed by heavy shields such as iron plates with a thickness of several centimeters. This method uses nuclear resonance fluorescence (NRF) triggered by an energy-tunable laser-Compton scattering (LCS) γ-ray source. One-dimensional mapping of a lead block hidden behind 1.5-cm-thick iron plates is obtained by measuring an NRF γ-ray of a lead isotope 208Pb. We observe a 5512-keV γ-ray from 208Pb excited by the quasi-monochromatic LCS γ-rays with energies up to 5.7 MeV. The edge position of the lead block is consistent with the exact position within the uncertainty.
Molecular Precision and Enzymatic Degradation: From Readily to Undegradable Polymeric Micelles by Minor Structural Changes (2016)

Studying the enzymatic degradation of synthetic polymers is crucial for the design of suitable materials for biomedical applications ranging from advanced drug delivery systems to tissue engineering. One of the key parameters that governs enzymatic activity is the limited accessibility of the enzyme to its substrates that may be collapsed inside hydrophobic domains. PEG-dendron amphiphiles can serve as powerful tools for the study of enzymatic hydrolysis of polymeric amphiphiles due to the monodispersity and symmetry of the hydrophobic dendritic block, which significantly simplifies kinetic analyses. Using these hybrids, we demonstrate how precise, minor changes in the hydrophobic block are manifested into tremendous changes in the stability of the assembled micelles toward enzymatic degradation. The obtained results emphasize the extreme sensitivity of self-assembly and its great importance in regulating the accessibility of enzymes to their substrates. Furthermore, the demonstration that the structural differences between readily degradable and undegradable micelles are rather minor, points to the critical roles that self-assembly and polydispersity play in designing biodegradable materials.