gebhart/patrepeval huggingface dataset:
JAK2 V617F Mutational Load in Patients with Polycythemia Vera (PV) Measured by Peripheral Blood DNA Is Associated with Disease Severity. (2007)

Abstract Different methods using peripheral blood RNA (Vannucchi AM, et al. Leukemia. 2007,1–8), or archival bone marrow DNA (Tefferi A, et al. Leukemia. 2007,1–2) have yielded varied results correlating allele burden with severity and duration of disease. We therefore aimed to determine whether JAK2V617F allele burden correlated with certain parameters of disease. At our institution, 105 patients were diagnosed according to the criteria of the Polycythemia Vera Study Group. We grouped their JAK2V617F allele burdens into quintiles. DNA from peripheral blood was analyzed using pyrosequencing. For those patients whose allele burden was &amp;lt;5%, a sensitive ARMS (amplification refractory mutation system) assay was performed to demonstrate the presence of the JAK2V617F allele. Duration of disease was assessed from onset of symptoms. Spleen size was measured in cm below the midpoint of the left costal margin in the midclavicular line and categorized as not enlarged, slightly (1–3 cm), moderately (4–9 cm), or grossly enlarged (&amp;gt;9 cm). Thrombotic events were recorded within 5 years of JAK2V617F determination. There were 52 men and 53 women. The patients ranged in age from 35 to 88 years, median 60 years. The median duration of disease was 7.4 years (range: 0.2 - 36.6 years), and the median duration of follow-up after JAK2V617F determination was 12 months year (range: 1 - 43 months). The mean mutant allele burden was 46.0% (s.d. ± 29.7%). The fifth, and highest quintile had a mean mutant allele burden of 90.2% (s.d. ± 5.8%); the lowest quintile had a mean mutant allele burden of 9.9% (s.d. ± 6.3%). JAK2V617F did not correlate with age, gender, hematocrit and platelet count at diagnosis, or rate of phlebotomy prior to cytoreductive therapy. Increasing JAK2V617F burden did correlate with higher WBC at diagnosis (P=0.02), degree of splenomegaly (P&amp;lt;0.0001), presence of marrow fibrosis (P=0.03), and longer duration of disease (P=0.001). There was a trend for a higher JAK2V617F allele burden among patients with venous compared to arterial thrombosis. When the subset of patients who had JAK2V617F testing performed within 5 years of diagnosis (N=35) was examined, trends similar to those we had reported for all 105 patients were found, but no definitive statement can be made because of the small sample size. We noted a JAK2V617F allele burden of more than 80% during the course of the illness was associated with a significant disease phenotype. This is the first report of increased marrow fibrosis associated with high JAK2V617F burden. The importance of using quantitative JAK2V617F for assessing allele burden is stressed because patients with an increased allele burden may be candidates for anti-JAK therapy.
Excess Noise and Avalanche Multiplication in InAlAs (2006)

In recent years, InAlAs avalanche photodiodes (APDs) have reported high sensitivities in high bit rate 10 Gb/s [1] and even 40 Gb/s [2] optical communication applications. InAlAs is able to supersede InP as the multiplication layer in SAM-structure APDs due to its superior ionization characteristics that include larger bandgap and very dissimilar electron and hole ionization coefficients (α and β respectively), while remaining lattice matched to InP substrates. Preliminary studies also suggest relatively small temperature dependence of breakdown voltages compared to InP, which reduces the need for temperature stabilization. The significance of a large electron and hole ionization coefficient ratio is lower excess noise and increased sensitivity, without sacrificing the gain-bandwidth product. Furthermore, InAlAs/InGaAs APDs are electron initiated, which further improves the excess noise performance [3] should there be low-field ionization in the InGaAs absorption layer [4]. Accurate characterization of the InAlAs ionization properties such as excess noise and ionization coefficients are essential when designing and optimizing the InAlAs APD performance using simulators and analytical models. It is therefore surprising that the only data on submicron avalanche structures is by Saleh et al. [5] and even this only reports on electron-initiated multiplication. We present a systematic study of avalanche multiplication and excess noise characteristics of InAlAs on a series of p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -i-n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> and n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -i-p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+<sup/> diodes with nominal intrinsic region widths from 0.1 μm to 2.5 μm.</sup>
Untying Knotted DNA with Elongational Flows (2014)

We present Brownian dynamics simulations of initially knotted double-stranded DNA molecules untying in elongational flows. We show that the motions of the knots are governed by a diffusion-convection equation by deriving scalings that collapse the simulation data. When being convected, all knots displace nonaffinely, and their rates of translation along the chain are topologically dictated. We discover that torus knots "corkscrew" when driven by flow, whereas nontorus knots do not. We show that a simple mechanism can explain a coupling between this rotation and the translation of a knot, explaining observed differences in knot translation rates. These types of knots are encountered in nanoscale manipulation of DNA, occur in biology at multiple length scales (DNA to umbilical cords), and are ubiquitous in daily life (e.g., hair). These results may have a broad impact on manipulations of such knots via flows, with applications to genomic sequencing and polymer processing.
Multiple DNA and protein sequence alignment based on segment-to-segment comparison. (1996)

In this paper, a new way to think about, and to construct, pairwise as well as multiple alignments of DNA and protein sequences is proposed. Rather than forcing alignments to either align single residues or to introduce gaps by defining an alignment as a path running right from the source up to the sink in the associated dot-matrix diagram, we propose to consider alignments as consistent equivalence relations defined on the set of all positions occurring in all sequences under consideration. We also propose constructing alignments from whole segments exhibiting highly significant overall similarity rather than by aligning individual residues. Consequently, we present an alignment algorithm that (i) is based on segment-to-segment comparison instead of the commonly used residue-to-residue comparison and which (ii) avoids the well-known difficulties concerning the choice of appropriate gap penalties: gaps are not treated explicity, but remain as those parts of the sequences that do not belong to any of the aligned segments. Finally, we discuss the application of our algorithm to two test examples and compare it with commonly used alignment methods. As a first example, we aligned a set of 11 DNA sequences coding for functional helix-loop-helix proteins. Though the sequences show only low overall similarity, our program correctly aligned all of the 11 functional sites, which was a unique result among the methods tested. As a by-product, the reading frames of the sequences were identified. Next, we aligned a set of ribonuclease H proteins and compared our results with alignments produced by other programs as reported by McClure et al. [McClure, M. A., Vasi, T. K. & Fitch, W. M. (1994) Mol. Biol. Evol. 11, 571-592]. Our program was one of the best scoring programs. However, in contrast to other methods, our protein alignments are independent of user-defined parameters.
Improved recovery of human islets from young donor pancreases utilizing increased protease dose to collagenase for digesting peri-islet extracellular matrix (2018)

Human islet isolation from young donor pancreases (YDP) utilizing the current purified standard dose of collagenase-protease enzyme mixtures often results in the release of a high percentage of mantled islets. Mantled islets are those surrounded by exocrine tissue and are difficult to purify by density gradient centrifugation, leading to poor islet recovery. Based on difference in extracellular matrix, and total collagen content between YDP and old donor pancreas (ODP, > 35 Y) led us to compare results from islet isolation using increased collagenase combination (ICC) or increased protease combination (IPC), to the standard enzyme combination (SEC) in a "trisected" pancreas model to overcome the donor-to-donor variability. These results showed a reduced percentage of mantled islets (17% ± 7.5%) and higher postpurification islet recovery (83.8% ± 5.6%) with IPC. Furthermore, these results were confirmed in 13 consecutive whole pancreas islet isolations utilizing IPC from VitaCyte, Roche, or SERVA collagenase-protease enzyme mixtures. Results obtained from in vitro and in vivo islet functional assessment indicated that islets isolated using IPC retained normal islet morphology, insulin secretion, and the ability to reverse diabetes after transplantation in diabetic nude mice. This is the first report utilizing trisected pancreas to assess the effectiveness of different enzyme combinations to improve islet recovery from young donor pancreases.
Rigid and remodelled: cerebrovascular structure and function after experimental high‐thoracic spinal cord transection (2015)

High-thoracic or cervical spinal cord injury (SCI) is associated with several critical clinical conditions related to impaired cerebrovascular health, including: 300-400% increased risk of stroke, cognitive decline and diminished cerebral blood flow regulation. The purpose of this study was to examine the influence of high-thoracic (T3 spinal segment) SCI on cerebrovascular structure and function, as well as molecular markers of profibrosis. Seven weeks after complete T3 spinal cord transection (T3-SCI, n = 15) or sham injury (Sham, n = 10), rats were sacrificed for either middle cerebral artery (MCA) structure and function assessments via ex vivo pressure myography, or immunohistochemical analyses. Myogenic tone was unchanged, but over a range of transmural pressures, inward remodelling occurred after T3-SCI with a 40% reduction in distensibility (both P < 0.05), and a 33% reduction in vasoconstrictive reactivity to 5-HT trending toward significance (P = 0.09). After T3-SCI, the MCA had more collagen I (42%), collagen III (24%), transforming growth factor β (47%) and angiotensin II receptor type 2 (132%), 27% less elastin as well as concurrent increased wall thickness and reduced lumen diameter (all P < 0.05). Sympathetic innervation (tyrosine hydroxylase-positive axon density) and endothelium-dependent dilatation (carbachol) of the MCA were not different between groups. This study demonstrates profibrosis and hypertrophic inward remodelling within the largest cerebral artery after high-thoracic SCI, leading to increased stiffness and possibly impaired reactivity. These deleterious adaptations would substantially undermine the capacity for regulation of cerebral blood flow and probably underlie several cerebrovascular clinical conditions in the SCI population.
Fertilization and early embryology: Evaluation of propanediol, ethylene glycol, sucrose and antifreeze proteins on the survival of slow-cooled mouse pronuclear and 4-cell embryos (1995)

Mouse pronuclear and 4-cell embryos were cryopreserved by slow cooling to -33 degrees C in 1.5 M 1,2-propanediol or 1.5 M ethylene glycol, with or without 0.1 M sucrose. Straws were thawed by immersion into a 37 degrees C water bath, immediately after their removal from liquid nitrogen (protocol 1), or after being held in air for 15 (protocol 2) or 30 s (protocol 3). Others were held in air until the ice melted (protocol 4). Embryos which formed blastocysts that hatched and attached to the Petri dish in vitro (plated) were considered viable. The thawing protocol did not significantly influence the viability of embryos frozen in propanediol with 0.1 M sucrose (52-72% of pronuclear and 69-97% of 4-cell embryos plated). In the other solutions tested, propanediol without sucrose and ethylene glycol with/without sucrose, only protocol 2 resulted in uniformly high development of both pronuclear (45-65% plating) and 4-cell embryos (70-97% plating). Thawing protocol 4 significantly reduced development, in particular for embryos frozen in ethylene glycol (0% 1-cell; 0-25% 4-cell plating). The difference between thawing protocols 2 and 4 was reduced by continuing slow cooling of ethylene glycol solutions to lower temperatures (-41 degrees C). Adding antifreeze proteins type I or III did not improve survival or development. Thus, although mouse pronuclear and 4-cell embryos can be frozen-thawed in either ethylene glycol or propanediol without significant loss of viability, an appropriate thawing protocol is essential for embryos frozen in ethylene glycol or propanediol-sucrose.
Pathology of Radiostrontium Exposure in Cats (1972)

Thirty-three cats of two age groups were fed one of three dosage levels of ${}^{89}{\rm Sr}$ for 30 days. Twenty-four died or were killed before 107 days after the experiment was started. Mortality and bone marrow lesions were dose related. All cats had varying degrees of a hemorrhagic disease with hemorrhages most commonly observed in the heart, subcutis and intestines. Histologically, bone marrows of cats dying before 35 days postexposure were depleted of cells. Those dying later had cellular marrows composed predominantly of erythropoietic precursors. Myelofibrosis was seen in 5 cats and myeloid metaplasia, primarily in lymph nodes, developed in 6 cats. Dysplastic lesions occurred in the epiphyseal plate and metaphysis of long bones. Other lesions included atrophy of the thymus and lymphoid tissues and bacterial lesions in several tissues. Ultrastructural studies of bone marrow of 4 cats revealed degenerative changes in mitochondria of plasma cells and the presence of abnormal erythrocyte precursors. C...
Predicting the Discovery Pattern of Publically Known Exploited Vulnerabilities (2020)

Vulnerabilities with publically known exploits typically form 2-7% of all vulnerabilities reported for a given software version. With a smaller number of known exploited vulnerabilities compared with the total number of vulnerabilities, it is more difficult to model and predict when a vulnerability with a known exploit will be reported. In this paper, we introduce an approach for predicting the discovery pattern of publically known exploited vulnerabilities using all publically known vulnerabilities reported for a given software. Eight commonly used vulnerability discovery models (VDMs) and one neural network model (NNM) were utilized to evaluate the prediction capability of our approach. We compared their predictions results with the scenario when only exploited vulnerabilities were used for prediction. Our results show that, in terms of prediction accuracy, out of eight software we analyzed, our approach led to more accurate results in seven cases. Only in one case, the accuracy of our approach was worse by 1.6%.
Ion Channels and Early Development of Neural Cells (1998)

In this review we underscore the merits of using voltage-dependent ion channels as markers for neuronal differentiation from the early stages of uncommitted embryonic blastomeres. Furthermore, a fairly large part of the review is devoted to the descriptions of the establishment of a simple model system for neural induction derived from the cleavage-arrested eight-cell ascidian embryo by pairing a single ectodermal with a single vegetal blastomere as a competent and an inducer cell, respectively. The descriptions are focused particularly on the early developmental processes of various ion channels in neuronal and other excitable membranes observed in this extraordinarily simple system, and we compare these results with those in other significant and definable systems for neural differentiation. It is stressed that this simple system, for which most of the electronic and optical methods and various injection experiments are applicable, may be useful for future molecular physiological studies on the intracellular process of differentiation of the early embryonic cells. We have also highlighted the importance of suppressive mechanisms for cellular differentiation from the experimental results, such as epidermal commitment of the cleavage-arrested one-cell Halocynthia embryos or suppression of epidermal-specific transcription of inward rectifier channels by neural induction signals. It was suggested that reciprocal suppressive mechanisms at the transcriptional level may be one of the key processes for cellular differentiation, by which exclusivity of cell types is maintained.
Static VAR Compensator-Based Voltage Regulation for Variable-Speed Prime Mover Coupled Single-Phase Self-Excited Induction Generator (2005)

In this paper, the single-phase static VAR compensator (SVC) is applied to regulate and stabilize smoothly the generated output voltage of the single-phase self-excited induction generator (single-phase SEIG) driven by a variable-speed prime mover (VSPM) under the conditions of inductive load variations and prime mover speed changes. The conventional fixed gain PI controller-based feedback control scheme is employed to adjust the equivalent capacitance of the single-phase SVC composed of the fixed excitation capacitor (FC) in parallel with the thyristor switched capacitor (TSC) and the thyristor controlled reactor TCR. A PI closed-loop feedback voltage control scheme based on the SVC for the single-phase SEIG coupled by a VSPM prototype set-up is established. The closed-loop feedback output voltage responses in the single-phase SEIG coupled by a VSPM with different inductive load variations using the single-phase SVC with the PI controller are considered and discussed herein. Based on the SVC with the PI controller closed-loop feedback voltage regulation scheme, the experimental results for the single-phase SEIG driven by a VSPM are illustrated and proved its practical effectiveness in terms of the fast response and the high performances.
Joint edge-directed interpolation and adaptive sharpening filter (2013)

In this paper, we present a joint filter that upsamples and adaptively sharpens a video/image simultaneously. The joint filter has been designed by combining a low complexity edge-directed interpolator with an adaptive Laplacian of Gaussian (LoG) filter. The joint filter yields sharp upsampled images, and is demonstrated to have lower computational complexity and similar visual quality when compared to using separate upsampling and sharpening filters.
Synthesis of High Orientated Clay-organic Composites Using Langmuir-Blodgett Technique. (1994)

We reported here the results of the fabrication of clay unit layers/organic molecules multilayers films using a conventional Langmuir-Blodgett technique. Smectite were ultrasonically separated by each unit layer into distilled water. Successively, octadecylamine or nonadecylamine was spread from benzene solution on the water subphases contained clay unit layers at various pH. The monolayers were deposited on an appropriate plate such as glass, silicon etc. at pressures of 25-35dyne. The preferred conditions for making the best multilayers films were systematically examined. The reasonable surface areas were obtained from the π-A curves. According to the XRD patterns, the resulting basal spacing of LB films was estimated to be about 61.3A, which corresponded to the bilayeres of alkylamines. IR spectra demonstrated the existence of hydrogen bonding between the alkylamine and silicate layers. On heating above 60°C, the conformation of alkylamines was stepwisely changed. The possible molecular arrangements within the LB film were discussed.
Body mass index change in gastrointestinal cancer and chronic obstructive pulmonary disease is associated with Dedicator of Cytokinesis 1 (2017)

In sum, one statistically significant common variant in the DOCK1 gene was associated with ΔBMI in GI cancer and COPD cases providing support for at least partially shared aetiology of ΔBMI in complex diseases.
Robust, scalable self-aligned platinum silicide process (2006)

A robust, scalable PtSix process is developed. The process consists of two consecutive annealing steps in a single run; the first is silicidation of Pt films on Si substrates carried out in N2, whereas the second is surface oxidation of the resultant PtSix in O2. By adequately adjusting the temperature during the oxidation step, a protective SiOx hard mask forms on PtSix of different thicknesses and compositions. Such a surface oxidation is absent for Pt on SiO2 isolation, which is crucial for the subsequent selective wet etch for a self-aligned process. Ultralong PtSix nanowires are fabricated using this robust self-aligned process.
p27Kip1 Localizes to Detergent-insoluble Microdomains Within Lymphocyte Membranes (2001)

This study identifies, for the first time, the localization of p27 within a membrane microdomain associated with signaling. Because some cell surface signaling complexes lose p27Kip1 upon cellular activation, p27Kip1 may play a functional role in modulating membrane signaling.
A Perspective of the Comprehensive and Objective Assessment of Analytical Methods Including the Greenness and Functionality Criteria: Application to the Determination of Zinc in Aqueous Samples (2021)

The recently proposed concept of White Analytical Chemistry (WAC), referring to the Red-Green-Blue color model, combines ecological aspects (green) with functionality (red and blue criteria), presenting the complete method as "white". However, it is not easy to carry out an overall quantitative evaluation of the analytical method in line with the WAC idea in an objective manner. This paper outlines the perspective of the future development of such a possibility by attempting to answer selected questions about the evaluation process. Based on the study consisting in the evaluation of selected model methods by a group of 12 independent analysts, it was shown how well individual criteria are assessed, whether the variability of assessments by different people is comparable for each criterion, how large it is, and whether averaging the scores from different researchers can help to choose the best method more objectively.
Improving OFF‐State Bias‐Stress Stability in High‐Mobility Conjugated Polymer Transistors with an Antisolvent Treatment (2022)

Conjugated polymer field-effect transistors are emerging as an enabling technology for flexible electronics due to their excellent mechanical properties combined with sufficiently high charge-carrier mobilities and compatibility with large-area, low-temperature processing. However, their electrical stability remains a concern. ON-state (accumulation mode) bias-stress instabilities in organic semiconductors have been widely studied, and multiple mitigation strategies have been suggested. In contrast, OFF-state (depletion mode) bias-stress instabilities remain poorly understood despite being crucial for many applications in which the transistors are held in their OFF-state for most of the time. Here, a simple method of using an antisolvent treatment is presented to achieve significant improvements in OFF-state bias-stress and environmental stability as well as general device performance for one of the best performing polymers, solution-processable indacenodithiophene-co-benzothiadiazole (IDT-BT). IDT-BT is weakly crystalline, and the notable improvements to an antisolvent-induced, increased degree of crystallinity, resulting in a lower probability of electron trapping and the removal of charge traps is attributed. The work highlights the importance of the microstructure in weakly crystalline polymer films and offers a simple processing strategy for achieving the reliability required for applications in flexible electronics.