gebhart/patrepeval huggingface dataset:
Sequence and gene content in 52 kb including and centromeric to the G6PD gene in Xq28 (1995)

A cosmid containing 36.4 kb of high GC human DNA centromeric to the G6PD gene has been analyzed. The sequence was 99.9% precise, based on the comparison of 4.3 kb that overlaps an earlier analysis of 20.1 kb containing G6PD. Properties of the entire 52 kb region that may be characteristic of high GC portions of the genome include a very high density of sixty-two half or full Alu sequences, or 1.2/kb, and an absence of L1 sequences. Other highly repetitive sequences include 11 MER sequences, one of them interrupted at two positions by groups of 3 Alu elements. In segments of unique sequence, computer-aided analysis predicted three possible genes, one of which has thus far been confirmed by the recovery of a corresponding cDNA, both by a direct hybridization method and by a PCR-based method based on a primer pair inferred from the genomic sequence. The cDNA has been sequenced, and is completely concordant with counterpart genomic sequence; it has no resemblance to any previously described gene.
Magnetic First-Order Phase Transition in Single-Crystal MnAs (1963)

This paper describes an experimental and theoretical examination of a 10-\ensuremath{\mu}g $c$-axis-oriented single crystal of MnAs. The critical magnetic field for the first-order transition to the ferromagnetic phase has been measured as a function of temperature (15 to 65\ifmmode^\circ\else\textdegree\fi{}C) and pressure (0 to 1000 bars gauge), using miniature-coil pulsed fields to 110 kOe. Data analysis substantiates the thesis of the recent Bean-Rodbell theory on magnetic first-order phase transitions that the transition in MnAs near 45\ifmmode^\circ\else\textdegree\fi{}C is between ferromagnetic and paramagnetic phases and arises from a sufficiently sensitive dependence of exchange energy on lattice strain and a sufficiently high compressibility. The match between theory and experiment yields a compressibility $K$ of 4.55\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}12}$ ${\mathrm{dyn}}^{\ensuremath{-}1}$ ${\mathrm{cm}}^{2}$, a lattice thermal expansion coefficient $\ensuremath{\alpha}$ of 5.71\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}5}$/\ifmmode^\circ\else\textdegree\fi{}C, an apparent paramagnetic Curie temperature ${{T}_{0}}^{*}$ of 277.1\ifmmode^\circ\else\textdegree\fi{}K, and a Curie-temperature dependence on volume strain, $\ensuremath{\beta}[\ensuremath{\equiv}(\frac{d{T}_{c}}{{T}_{0}}){(\frac{\mathrm{dV}}{{V}_{0}})}^{\ensuremath{-}1}]$, of 18.9, where ${T}_{0}$ is the Curie temperature of the unstrained specimen at 0\ifmmode^\circ\else\textdegree\fi{}K. Discrepancies in the match suggest a primary need to include short-range order in the theory. Auxiliary experiments show the magnetocrystalline anisotropy sum, ${K}_{1}+2{K}_{2}+3{K}_{3}$, to be about -7.6 and -12.0\ifmmode\times\else\texttimes\fi{}${10}^{6}$ ergs/${\mathrm{cm}}^{3}$ at 299 and 77\ifmmode^\circ\else\textdegree\fi{}K, respectively.
Tissue segmentation of computed tomography images using a Random Forest algorithm: a feasibility study (2016)

There is a need for robust, fully automated whole body organ segmentation for diagnostic CT. This study investigates and optimizes a Random Forest algorithm for automated organ segmentation; explores the limitations of a Random Forest algorithm applied to the CT environment; and demonstrates segmentation accuracy in a feasibility study of pediatric and adult patients. To the best of our knowledge, this is the first study to investigate a trainable Weka segmentation (TWS) implementation using Random Forest machine-learning as a means to develop a fully automated tissue segmentation tool developed specifically for pediatric and adult examinations in a diagnostic CT environment. Current innovation in computed tomography (CT) is focused on radiomics, patient-specific radiation dose calculation, and image quality improvement using iterative reconstruction, all of which require specific knowledge of tissue and organ systems within a CT image. The purpose of this study was to develop a fully automated Random Forest classifier algorithm for segmentation of neck-chest-abdomen-pelvis CT examinations based on pediatric and adult CT protocols. Seven materials were classified: background, lung/internal air or gas, fat, muscle, solid organ parenchyma, blood/contrast enhanced fluid, and bone tissue using Matlab and the TWS plugin of FIJI. The following classifier feature filters of TWS were investigated: minimum, maximum, mean, and variance evaluated over a voxel radius of 2 (n) , (n from 0 to 4), along with noise reduction and edge preserving filters: Gaussian, bilateral, Kuwahara, and anisotropic diffusion. The Random Forest algorithm used 200 trees with 2 features randomly selected per node. The optimized auto-segmentation algorithm resulted in 16 image features including features derived from maximum, mean, variance Gaussian and Kuwahara filters. Dice similarity coefficient (DSC) calculations between manually segmented and Random Forest algorithm segmented images from 21 patient image sections, were analyzed. The automated algorithm produced segmentation of seven material classes with a median DSC of 0.86 ± 0.03 for pediatric patient protocols, and 0.85 ± 0.04 for adult patient protocols. Additionally, 100 randomly selected patient examinations were segmented and analyzed, and a mean sensitivity of 0.91 (range: 0.82-0.98), specificity of 0.89 (range: 0.70-0.98), and accuracy of 0.90 (range: 0.76-0.98) were demonstrated. In this study, we demonstrate that this fully automated segmentation tool was able to produce fast and accurate segmentation of the neck and trunk of the body over a wide range of patient habitus and scan parameters.
Construction of infectious potato spindle tuber viroid cDNA clones (1983)

Contiguous restriction fragments from two cloned partial-length potato spindle tuber viroid (PSTV) cDNAs were used to construct recombinant DNAs containing full-length monomeric and dimeric PSTV cDNA. When five different PSTV cDNA plasmids and RNA isolated from E. coli cells harboring these plasmids were tested for infectivity on tomato, plasmid DNAs containing PSTV cDNA dimers were infectious. RNA transcripts containing the sequence of PSTV from these plasmids were also infectious. The sequences of the viroid progeny and the cloned DNA were identical. In vitro mutagenesis of infectious PSTV cDNAs will allow systematic investigation of the role of specific sequences in viroid replication and pathogenesis.
Long-Term Changes in Bone Mineral Density Following Total Knee Replacement (1995)

Bone density was measured using dual photon absorptiometry and dual xray absorptiometry below the tibial component under the medial and lateral plateaus, under the central peg, and distal to the central peg. Measurements of bone density were taken at 1 week, 6 weeks, 6 months, and 1 year after surgery in 31 patients. Seven of these patients also had measurements taken 8 years after surgery. The average age of the patients at surgery was 69 years old. One week after surgery, the mean bone density from all regions was 0.77 g/cm2 in women compared with 1.14 g/cm2 in men. Between 6 weeks and 6 months, the bone density below the tibial component declined inconsistently in most patients, but by 1 year the bone mineral density was statistically equal to the initial bone density at 1 week after surgery. Eight years after total knee arthroplasty, there was a 36.4% decrease in bone mineral density between men and women was not statistically significant. Medial plateau, lateral plateau, under the peg, and distal to the peg bone density changes tended to be the same. Maximum rates of bone resorption in patients with osteoporosis of the same age group have been reported to be between 1% and 2% per year. In this study, after an initial stable period, the bone density of the proximal tibia beneath the tibial component consistently decreased at a rate of 5% per year. Surgeons must consider this relatively large decrease in bone density if they are relying on bone for long-term stable fixation of the prosthesis.(ABSTRACT TRUNCATED AT 250 WORDS)
Understanding radio polarimetry (2000)

Paper II of this series studied the calibration process in mostly qualitative terms. In developing the underlying mathematics this paper completes that analysis and extends it in several directions. It exploits the analogy between scalar and matrix algebras to reformulate the self-calibration method in terms of Jones and coherency matrices. The basic condition that the solutions must satisfy in either case is developed and its consequences are investigated. The fourfold nature of the matrices and the non-commutativity of their multiplication are shown to lead to a number of new effects. In the same way that scalar selfcal leaves the brightness scale undefined, matrix selfcal gives rise to a more complicated indeterminacy. The calibration is far from complete: self-alignment describes more properly what is actually achieved. The true brightness is misrepresented in the image obtained by an unknown brightness-scale factor (as in scalar selfcal) and an undefined poldistortion of the Stokes brightness. The latter is the product of a polrotation of the polvector and a polconversion between unpolarized and polarized brightness. The relation of these concepts to conventional “quasi-scalar” calibration methods is demonstrated. Like scalar selfcal, matrix self-alignment is shown to suppress spatial scattering of brightness in the image, which is a condition for attaining high dynamic range. Poldistortion of the brightness is an in-place transformation, but must be controlled in order to obtain polarimetric fidelity. The theory is applied to reinterpret the quasi-scalar methods of polarimetry including those of Paper II, and to prove two major new assertions: (a.) An instrument calibrated on an unpolarized calibrator measures the degree of polarization correctly regardless of poldistortion; (b.) Under the usual a priori assumptions, a heterogeneous instrument (i.e. one with unequal feeds) can be completely calibrated without requiring a phase-difference measurement.
Use of Antimicrobial Peptides Against Microbial Biofilms: Advantages and Limits (2011)

The formation of surface-attached cellular agglomerates, the so-called biofilms, contributes significantly to bacterial resistance to antibiotics and innate host defenses. Bacterial biofilms are associated to various pathological conditions in humans such as cystic fibrosis, colonization of indwelling medical devices and dental plaque formation involved in caries and periodontitis. Over the last years, natural antimicrobial peptides (AMPs) have attracted considerable interest as a new class of antimicrobial drugs for a number of reasons. Among these, there are the broad activity spectrum, the relative selectivity towards their targets (microbial membranes), the rapid mechanism of action and, above all, the low frequency in selecting resistant strains. Since biofilm resistance to antibiotics is mainly due to the slow growth rate and low metabolic activity of bacteria in such community, the use of AMPs to inhibit biofilm formation could be potentially an attractive therapeutic approach. In fact, due to the prevalent mechanism of action of AMPs, which relies on their ability to permeabilize and/or to form pores within the cytoplasmic membranes, they have a high potential to act also on slow growing or even non-growing bacteria. This review will highlight the most important findings obtained testing AMPs in in vitro and in vivo models of bacterial biofilms, pointing out the possible advantages and limits of their use against microbial biofilm-related infections.
<title>License plate recognition system</title> (1998)

A powerful automated license plate recognition system is presented, which is able to read license numbers of cars, even under non-ideal circumstances. At the front-end of the system, there is a high-speed shutter camera and a frame grabber that delivers the digitized images of cars passing by. In a license plate segmentation step, the approximate positions of the four corner points of the plates are indicated. Due to the perspective view, these corner points may not correspond to a rectangle. By means of resampling, a rectangular license plate with a fixed size of 180 X 40 pixels is reconstructed. After image enhancement steps, the characters are approximately segmented, based on the properties of a vertical projection of the license plate. Next, the separate characters are normalized with respect to contrast, intensity and size. Each character image is projected on a low-dimensional space using the Karhunen- Loeve (KL) transform, containing the relevant information to distinguish it from other characters. A problem with this transformation arises, when the character is not properly segmented. We solved that problem by comparing the inverse KL transformed result with the original character. In case they differ significantly, this may indicate a major segmentation error, for which we can correct. This leads to a much improved segmentation and thus a transformation that holds the needed information for the classification. The KL transformed characters can be classified by several methods. We obtained good results by classifying the transformed characters with the help of the Euclidean distance. A misclassification rate of 0.4% was achieved with a rejection rate of 13%. Further development of the system, for which a number of recommendations are given, is expected to increase the system performance.
Image-storage panels based on field-effect control of conductivity (1968)

Using the principle of field-effect conductivity control, a new method of image storage has been demonstrated. Based on this a new type of solid-state image panel has been developed capable of producing a stored luminescent image. This employs an electroluminescent powder layer for generation of the output image and a ZnO powder layer for control and storage purposes. In operation the exposed ZnO surface is first uniformly corona charged to a negative potential to reduce its conductivity and "erase" old information. Following this the panel is exposed to an optical image which discharges local areas, producing a stored charge pattern on the ZnO surface. In accordance with this charge pattern a conductivity pattern is created in the ZnO layer which in turn controls the luminescent output of corresponding areas of the adjacent phosphor layer. For producing a stored image, approximately one microjoule/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of input radiation in the wavelength range of 3500-4000 Å is required. Reciprocity exists between the exposure time and the radiation level. Stored images have a brightness as high as 20 foot <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> lamberts and a maximum contrast ratio of about 100:1 and exhibit good halftones. Although a hafftone output image can be retained for periods of the order of an hour, it can be rapidly erased when desired by recharging the ZnO surface to a uniform negative potential. Present panels are 12 by 12 inches in size and have a limiting resolution between 400 and 800 TV lines.
A multichannel PWM telemetry system for kinematic gait analysis. (1987)

A multichannel biotelemetry system using pulse-width modulation-frequency modulation (PWM-FM) is described in detail for laboratory construction. Its application in a kinematic gait-analysis system is demonstrated, employing minimally encumbering electrogoniometry and foot-contact switches. The triaxial electrogoniometers sense rotational joint motion, and four foot-switches under the sole of each foot provide information on placement and temporal contact. Signals from the multiple sensors are amplified, encoded by pulse-width modulation, and transmitted at an FM radio frequency of 107 MHz. Received data are decoded and then sampled by a minicomputer for analysis. Results from a comparative study of kinematic gait in five normal subjects and five children with cerebral palsy demonstrate system effectiveness in providing quantitative data and various intrasubject and intersubject gait differences. Factors reviewed in the analysis include swing and stance times; cadence; hip-joint motion in sagittal, coronal, and transverse planes; and sequence of foot placement.
Effect of monensin on rumen metabolism in vitro (1977)

The effect of Monensin (Rumensin, Eli Lilly & Co.) in incubations with mixed rumen microorganisms metabolizing carbohydrate or protein substrates was investigated. Monensin partly inhibited methanogenesis and increased propionate production, although the effect was not always statistically significant. Incubations with substrates specific for methane bacteria suggest that inhibition of methanogenesis by Monensin was not due to a specific toxic action on the methanogenic flora, but rather to an inhibition of hydrogen production from formate. Total and net microbial growth were considerably decreased by addition of Monensin, although the amount of substrate fermented was not altered, resulting in lowered values of microbial growth efficiency. In incubations with casein, Monensin lowered protein degradation in line with a lowered ammonia production, whereas a slight accumulation of alpha-amino nitrogen was observed. The results suggest that besides an influence of Monensin on the rumen carbohydrate fermentation pattern, another reason for the beneficial effects observed in vivo might be decreased food protein degradation in the rumen, altering the final site of protein digestion in the animal. Also, the possibility of a decrease in rumen microbial growth efficiency has to be considered when using Monensin as a food additive.
Control of neuronal pathway selection by the <i>Drosophila</i> LIM homeodomain gene <i>apterous</i> (1995)

The Drosophila apterous gene encodes a LIM homeodomain protein expressed embryonically in a small subset of differentiating neurons. To establish the identity of these neurons and to study the role of apterous in their development, we made apterous promoter fusions to an axon-targeted reporter gene. We found that all apterous-expressing neurons are interneurons that choose a single pathway within the developing central nervous system. In apterous mutants, these neurons choose incorrect pathways and fail to fasciculate with one another. Our results indicate that apterous functions to control neuronal pathway selection and suggest that other vertebrate and invertebrate members of the LIM homeodomain class of proteins may serve similar functions.
Multiscale Color-Texture Image Segmentation with Adaptive Region Merging (2007)

A novel multiscale image segmentation algorithm is presented, which is based on the dominant color and homogeneous texture features (HTF) that are adopted in the MPEG-7 standard. These features are efficiently combined to perform the automatic segmentation. First, the image is roughly segmented into textured and nontextured regions using Gabor decomposition. A multiscale segmentation is then applied to the resulting regions, according to the local texture feature. Finally, a precise boundary refinement procedure is employed to accurately determine the boundaries between textured and nontextured regions. A novel region merging algorithm is introduced with a simple and effective segment classification by using HTF to deal with the over-segmentation problem. Experiments show that our algorithm provides an improved performance compared with JSEG and a watershed algorithm.
Optimized System for D<sup>−</sup>Production from Chargeexchange in Alkali Metals (1982)

Negative ion production for neutral (deuteron) beam injectors is considered for a general system utilizing charge-exchange production in alkali metals. Experimental results provide parameters and show good correlation with calculations using known atomic cross sections, so that beam behavior can be predicted. It is found that coupling into the high voltage accelerator poses significant constraints on optimization of the system, e.g., to determine its minimum size. A typical design for 200-ke V final energy provides D− at 1.5 keV from charge-exchange in rubidium, with an average current density of 23 mA/cm2 and a total current of 20 A.
Chemical and biological adjuvants capable of potentiating tumor cell vaccine. (1978)

With an L1210 tumor vaccine model, three biological and two chemical agents were tested for their ability to act as adjuvants. Adjuvant was administered with irradiated L1210 cells to immunize mice against this poorly immunogenic tumor. Two chemicals, pyran copolymer and glucan, and one biological, Brucella abortus strain 456 ether extract, were shown to be strong stimulators of antitumor immunity. Vaccination with irradiated tumor cells or adjuvant alone did not produce host resistance. Optimal immunity to challenge was produced by concomitant administration of either pyran copolymer, glucan, or B. abortus strain 456 ether extract with L1210 vaccine. Antitumor immunity was maximally expressed when vaccine and adjuvant were administered i.p. Evidence for systemic immunity was demonstrated when challenge was at a distal s.c. site. Mice immune to challenge were found to be refractory to a later rechallenge.
UNIX Time-Sharing System: Document Preparation (1978)

The UNIX∗ operating system provides programs for sophisticated document preparation within the framework of a general-purpose operating system. The document preparation software includes a text editor, programmable text formatters, macro-definition packages for a variety of page layout styles, special processors for mathematical expressions and for tabular material, and numerous supporting programs, such as a spelling-mistake detector. In practice, this collection of facilities has proven to be easy to learn and use, even by secretaries, typists, and other nonspecialists. Experiments have shown that preparation of complicated documents is about twice as fast as on other systems. There are many benefits to using a general-purpose operating system instead of specialized stand-alone terminals or a system dedicated to “word processing.” On the UNIX system, these include an excellent software development facility and the ability to share computing and data resources among a community of users.
Temperature dependence of the optoacoustic transformation efficiency in ex vivo tissues for application in monitoring thermal therapies (2012)

The calibration dependencies of the optoacoustic (OA) transformation efficiency on tissue temperature are obtained for the application in OA temperature monitoring during thermal therapies. Accurate measurement of the OA signal amplitude versus temperature is performed in different ex vivo tissues in the temperature range 25°C to 80°C. The investigated tissues were selected to represent different structural components: chicken breast (skeletal muscle), porcine lard (fatty tissue), and porcine liver (richly perfused tissue). Backward mode of the OA signal detection and a narrow probe laser beam were used in the experiments to avoid the influence of changes in light scattering with tissue coagulation on the OA signal amplitude. Measurements were performed in heating and cooling regimes. Characteristic behavior of the OA signal amplitude temperature dependences in different temperature ranges were described in terms of changes in different structural components of the tissue samples. The accuracy of temperature reconstruction from the obtained calibration dependencies for the investigated tissue types is evaluated.