gebhart/patrepeval huggingface dataset:
Treatment response assessment of breast masses on dynamic contrast‐enhanced magnetic resonance scans using fuzzy ‐means clustering and level set segmentation (2009)

The goal of this study was to develop an automated method to segment breast masses on dynamic contrast-enhanced (DCE) magnetic resonance (MR) scans and to evaluate its potential for estimating tumor volume on pre- and postchemotherapy images and tumor change in response to treatment. A radiologist experienced in interpreting breast MR scans defined a cuboid volume of interest (VOI) enclosing the mass in the MR volume at one time point within the sequence of DCE-MR scans. The corresponding VOIs over the entire time sequence were then automatically extracted. A new 3D VOI representing the local pharmacokinetic activities in the VOI was generated from the 4D VOI sequence by summarizing the temporal intensity enhancement curve of each voxel with its standard deviation. The method then used the fuzzy c-means (FCM) clustering algorithm followed by morphological filtering for initial mass segmentation. The initial segmentation was refined by the 3D level set (LS) method. The velocity field of the LS method was formulated in terms of the mean curvature which guaranteed the smoothness of the surface, the Sobel edge information which attracted the zero LS to the desired mass margin, and the FCM membership function which improved segmentation accuracy. The method was evaluated on 50 DCE-MR scans of 25 patients who underwent neoadjuvant chemotherapy. Each patient had pre- and postchemotherapy DCE-MR scans on a 1.5 T magnet. The in-plane pixel size ranged from 0.546 to 0.703 mm and the slice thickness ranged from 2.5 to 4.5 mm. The flip angle was 15 degrees, repetition time ranged from 5.98 to 6.7 ms, and echo time ranged from 1.2 to 1.3 ms. Computer segmentation was applied to the coronal T1-weighted images. For comparison, the same radiologist who marked the VOI also manually segmented the mass on each slice. The performance of the automated method was quantified using an overlap measure, defined as the ratio of the intersection of the computer and the manual segmentation volumes to the manual segmentation volume. Pre- and postchemotherapy masses had overlap measures of 0.81 +/- 0.13 (mean +/- s.d.) and 0.71 +/- 0.22, respectively. The percentage volume reduction (PVR) estimated by computer and the radiologist were 55.5 +/- 43.0% (mean +/- s.d.) and 57.8 +/- 51.3%, respectively. Paired Student's t test indicated that the difference between the mean PVRs estimated by computer and the radiologist did not reach statistical significance (p = 0.641). The automated mass segmentation method may have the potential to assist physicians in monitoring volume change in breast masses in response to treatment.
Genetic variations of the midkine (MK) gene in human sporadic colorectal and gastric cancers. (2000)

Midkine (MK), a retinoic acid responsible protein, is regulated during development and may play an important role in tumorigenesis. A search for genetic variations of the MK gene, located on chromosome 11q11.2 in humans, has not yet been conducted in cancers. To examine the entire coding region, as well as 4 regions of the promoter covering all functional motifs, 8 sets of intron-based and promoter region primers were designed. Using these primers, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis of genomic DNA samples from 60 sporadic colorectal and 37 sporadic gastric cancer patients was carried out. This analysis, followed by DNA sequencing, revealed a heterozygous g/t polymorphism at the 62nd base on intron 3 in five colorectal tumors (8.3%) and one gastric tumor (2.7%). In the promoter region, a heterozygous CTT deletion, creating a (CTTTT)2 repeat, in one colorectal cancer sample (1.67%) and a heterozygous 2-bp deletion in the G7 tract in another colorectal cancer patient were detected. A/G and A/A alleles were also detected at nt. -1741 in 36 (97.3%) and one (2.7%) gastric cancer samples, respectively. The A/G alleles were observed in all colorectal cancer patients (100%). All variations observed in the promoter region showed polymorphism. These results suggest that in sporadic colorectal and gastric cancers some gene alterations are present in the MK promoter region, but alterations in the coding region are rare.
Fabrication of Continuous Conducting Gold Wires by Electrospinning (2008)

An innovative approach is developed to electrospin Au polymer wires, dissolving HAuCl4 salt in ethanol followed by addition of poly(acrylic acid) with several modifications in the conventional electrospinning system. The as-prepared Au polymer wires are assembled on the rotating drum in between the spinneret (+ electrode) and the conducting substrate (− electrode). The as-prepared Au polymer wires via sintering transformed to the Au wires comprised of compact Au nanocrystals keeping their one-dimensional identity. By collecting a single Au polymer wire on a gold interdigitated electrode during electrospinning followed by its successive sintering, the conductivity of the single gold wire is measured. Reaction parameters such as the amount of the precursor/polymer, change in the solvent, and change in the wire collecting substrate are optimized. Interestingly, gold dendrites are formed when aluminum foil is used as an Au polymer wire collecting support, which retains its shape even after sintering.
Injecting simulation and modeling upstream in the system engineering process (1996)

This paper describes the application of simulation and modeling to enhance the understanding of a communication networking solution for the Trucking Locator Control System (TLCS) case study at the Johns Hopkins University Masters Program in Technical Management. The four major steps in this process were: developing a model of the TLCS system; generating assumptions about the TLCS system; selecting a simulation tool using a trade-study; and implementing the selected simulation tool. The selected simulation package, COMNET III, was used to establish common understanding about the system under consideration, to provide insight into its performances, and to generate data for further analysis. The same process can be utilized in other System Engineering applications, not only for educational purposes, but also to provide tools for conceptual system design and to enhance the design and integration phase in the System Engineering life-cycle.
Low temperature sensing in tulip (Tulipa gesneriana L.) is mediated through an increased response to auxin (2000)

Tulip (Tulipa gesneriana L.) is a bulbous plant species that requires a period of low temperature for proper growth and flowering. The mechanism of sensing the low temperature period is unknown. The study presented in this paper shows that the essential developmental change in tulip bulbs during cold treatment is an increase in sensitivity to the phytohormone auxin. This is demonstrated using a model system consisting of isolated internodes grown on tissue culture medium containing different combinations of the phytohormones auxin and gibberellin. Using mathematical modelling, equations taken from the field of enzyme kinetics were fitted through the data. By doing so it became apparent that longer periods of low temperature resulted in an increased maximum response at a lower auxin concentration. Besides the cold treatment, gibberellin also enhances the response to auxin in the internodes in this in vitro system. A working model describing the relationship between the cold requirement, gibberellin action and auxin sensitivity is put forward. Possible analogies with other cold-requiring processes such as vernalization and stratification, and the interaction of auxin and gibberellin in the stalk elongation process in other plant species are discussed.
Overview of artificial lift systems (1982)

The purpose of this paper is to provide an ''overview'' of artificial lift systems and give guidelines as to when one system is better suited than another. Advantages and disadvantages are given with examples in the selection of lift methods. Factors that should be considered in the selection of artificial lift equipment are discussed. 3 refs.
KairosVM: Deterministic introspection for real-time virtual machine hierarchical scheduling (2014)

Consolidation and isolation are key technologies that promoted the undisputed popularity of virtualization in most of the computer industry. This popularity has recently led to a growing interest in real-time virtualization, making this technology enter the real-time system market. However, it has several issues due to the strict timing guarantees contracted. Moreover supporting legacy software stacks adds another level of complexity when the software is a black box. We present KairosVM, a latency-bounded, real-time extension to Linux's KVM module. It aims to bridge the lack of communication of the real-time requirements between the guest scheduler and the host scheduler, exploiting virtual machine introspection. The hypervisor captures the real-time requirements of the guest by catching previously added undefined instructions, without the need to do any modification to the guests. Our evaluations show that KairosVM's overhead is negligible when compared to existing introspection solutions thus can be used in real-time.
Antimicrobial Peptides in Human Skin (2005)

Human skin is permanently exposed to a wide variety of potential harmful microorganisms. Despite these microbial threats, skin is surprisingly highly resistant against infections. Various studies in the last decade discovered a chemical cutaneous defense system based on the production of antimicrobial proteins. These antimicrobial proteins act as a first defense line through their broad spectrum of potent antimicrobial activity. In addition to constitutively expressed antimicrobial proteins, production of various antimicrobial proteins in keratinocytes is induced by bacterial compounds as well as proinflammatory cytokines. The resulting local accumulation of antimicrobial proteins offers a fast and very efficient way to prevent microbes from establishing an infection. In this review we summarize the current status of our knowledge of expression of antimicrobial proteins in human skin.
Maltotriose utilization in lager yeast strains: <i>MTT1</i> encodes a maltotriose transporter (2005)

Maltotriose is the second most abundant fermentable sugar in wort and, due to incomplete fermentation, residual maltotriose in beer causes both quality and economic problems in the brewing industry. To identify genes that might improve utilization of maltotriose, we developed a library containing genomic DNA from four lager strains and a laboratory Saccharomyces cerevisiae strain and isolated transformants that could grow on YP/2% maltotriose in the presence of 3 mg/l of the respiratory inhibitor antimycin A. In this way we found a gene which shared 74% similarity with MPH2 and MPH3, 62% similarity with AGT1 and 91% similarity with MAL61 and MAL31, all encoding known maltose transporters. Moreover, the gene shared an even higher similarity (98%) with the uncharacterized Saccharomyces pastorianus mty1 gene (M. Salema-Oom, unpublished; NCBI Accession No. AJ491328). Therefore, we named the gene MTT1 (mty1-like transporter). We showed that the gene was present in four different lager strains but was absent from the laboratory strain CEN.PK113-7D. The ORF in the plasmid isolated from the library lacks 66 base pairs from the 3'-end of MTT1 but instead contains 54 bp of the vector. We named this ORF MTT1alt (NCBI Accession No. DQ010174). 14C-Maltose and repurified 14C-maltotriose were used to show that MTT1 and, especially, MTT1alt, encode maltose transporters for which the ratio between activities to maltotriose and maltose is higher than for most known maltose transporters. Introduction of MTT1 or MTT1alt into lager strain A15 raised maltotriose uptake by about 17% or 105%, respectively.
Testing and spot-checking of data streams (2000)

We consider the tasks of testing and spot-checking for data streams. These testers and spotcheckers are potentially useful in real-time or near real-time applications that process huge datasets. Crucial aspects of the computational model include the space complexity of the testers and spotcheckers (ideally much lower than the size of the input stream) and the number of passes that the tester or spot-checker must make over the input stream (ideally one, because the original stream may be too large to store for a second pass). A sampling-tester [GGR98] for a property P samples some (but usually not all) of its input and, with high probability, outputs PASS if the input has property P and FAIL if the input is far from having P , for an appropriate sense of &quot;far.&quot; A streaming-tester for a property P of one or more input streams takes as input one or more data streams and, with high probability, outputs PASS if the streams have property P and FAIL if the streams are far from havin...
Upconverted Emission from Pyrene and Di-<i>tert</i>-butylpyrene Using Ir(ppy)<sub>3</sub> as Triplet Sensitizer (2006)

Metal-to-ligand charge-transfer sensitized upconverted fluorescence in noncovalent triplet energy transfer assemblies is investigated using Ir(ppy)3 as the sensitizer (ppy=2-phenylpyridine) and pyrene or 3,8-di-tert-butylpyrene as the triplet acceptor/annihilator. Upconverted singlet fluorescence from pyrene or 3,8-di-tert-butylpyrene resulting from triplet-triplet annihilation (TTA) is observed following selective excitation of Ir(ppy)3 in deaerated dichloromethane solutions using 450-nm laser pulses. In both systems, the TTA process is confirmed by the near quadratic dependence of the upconverted fluorescence intensity on incident light power, measured by integrating the upconverted delayed fluorescence kinetic traces as a function of incident excitation power. At the relatively high concentrations of pyrene that were utilized, pyrene excimer formation was detected by its characteristic broad emission centered near 470 nm. In essence, selective excitation of Ir(ppy)3 ultimately resulted in the simultaneous sensitization of both singlet pyrene and pyrene excimers, and the latter degrades the energy stored in the pyrene singlet excited state. Furthermore, in the case of di-tert-butylpyrene/Ir(ppy)3, the formation of excimers is successfully blocked because of the presence of the sterically hindering tert-butyl groups. The current work demonstrates that sensitized TTA is indeed accessible to chromophore systems beyond those previously reported, suggesting the generality of the approach.
A review of machine learning algorithms for identification and classification of non-functional requirements (2019)

Recent developments in requirements engineering (RE) methods have seen a surge in using machine-learning (ML) algorithms to solve some difficult RE problems. One such problem is identification and classification of non-functional requirements (NFRs) in requirements documents. ML-based approaches to this problem have shown to produce promising results, better than those produced by traditional natural language processing (NLP) approaches. Yet, a systematic understanding of these ML approaches is still lacking. This article reports on a systematic review of 24 ML-based approaches for identifying and classifying NFRs. Directed by three research questions, this article aims to understand what ML algorithms are used in these approaches, how these algorithms work and how they are evaluated. (1) 16 different ML algorithms are found in these approaches; of which supervised learning algorithms are most popular. (2) All 24 approaches have followed a standard process in identifying and classifying NFRs. (3) Precision and recall are the most used matrices to measure the performance of these approaches. The review finds that while ML-based approaches have the potential in the classification and identification of NFRs, they face some open challenges that will affect their performance and practical application. The review calls for the close collaboration between RE and ML researchers, to address open challenges facing the development of real-world ML systems. The use of ML in RE opens up exciting opportunities to develop novel expert and intelligent systems to support RE tasks and processes. This implies that RE is being transformed into an application of modern expert systems.
Quantitative Assessment of the SR Ca <sup>2+</sup> Leak-Load Relationship (2002)

Increased diastolic SR Ca2+ leak (J(leak)) could depress contractility in heart failure, but there are conflicting reports regarding the J(leak) magnitude even in normal, intact myocytes. We have developed a novel approach to measure SR Ca2+ leak in intact, isolated ventricular myocytes. After stimulation, myocytes were exposed to 0 Na+, 0 Ca2+ solution +/-1 mmol/L tetracaine (to block resting leak). Total cell [Ca2+] does not change under these conditions with Na+-Ca2+ exchange inhibited. Resting [Ca2+]i declined 25% after tetracaine addition (126+/-6 versus 94+/-6 nmol/L; P<0.05). At the same time, SR [Ca2+] ([Ca2+](SRT)) increased 20% (93+/-8 versus 108+/-6 micromol/L). From this Ca2+ shift, we calculate J(leak) to be 12 micromol/L per second or 30% of the SR diastolic efflux. The remaining 70% is SR pump unidirectional reverse flux (backflux). The sum of these Ca2+ effluxes is counterbalanced by unidirectional forward Ca2+ pump flux. J(leak) also increased nonlinearly with [Ca2+](SRT) with a steeper increase at higher load. We conclude that J(leak) is 4 to 15 micromol/L cytosol per second at physiological [Ca2+](SRT). The data suggest that the leak is steeply [Ca2+](SRT)-dependent, perhaps because of increased [Ca2+]i sensitivity of the ryanodine receptor at higher [Ca2+](SRT). Key factors that determine [Ca2+](SRT) in intact ventricular myocytes include (1) the thermodynamically limited Ca2+ gradient that the SR can develop (which depends on forward flux and backflux through the SR Ca2+ ATPase) and (2) diastolic SR Ca2+ leak (ryanodine receptor mediated).
Richtigkeit und Präzision bei verschiedenen Methoden zum Nachweis von Fructose im Sperma (1972)

Article Richtigkeit und Präzision bei verschiedenen Methoden zum Nachweis von Fructose im Sperma was published on January 1, 1972 in the journal Clinical Chemistry and Laboratory Medicine (CCLM) (volume 10, issue 12).
Polymorphonuclear Leukocyte-Platelet Interactions: Acetyiglyceryl Ether Phosphocholine-Induced Platelet Activation under Stimulation with Chemotactic Peptide1 (1986)

A mixture of rabbit polymorphonuclear leukocytes (PMNs) and platelets at concentrations of 5 X 10(6) PMN and 3.5 X 10(8) platelets/ml Tyrode's solution was stimulated with the chemotactic peptide, formyl-methionyl-leucyl-phenylalanine (FMLP). A micromolar concentration of FMLP elicited an immediate weak aggregation, followed by a strong aggregation with a time lag of about 1 min. Microscopic examination showed that the immediate aggregation was due to PMNs and the delayed one was more complex and involved platelets. The delayed aggregation was dependent upon the concentrations of both the PMNs and FMLP. The delayed aggregation was completely blocked by pretreatment of the PMN-platelet mixture with 8 microM CV-3988, a specific receptor antagonist of 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine (AGEPC), or by the application of platelets desensitized to AGEPC. The time course of AGEPC production by PMNs was well matched to that of the biphasic aggregation response. Furthermore, nordihydroguaiaretic acid inhibited both the AGEPC production by PMNs and the delayed aggregation in a similar dose-dependent manner. These result demonstrate that AGEPC, newly-generated by PMNs under FMLP-stimulation, is of primary importance in platelet aggregation in a PMN-platelet mixed system.
Survival of Mice Receiving Melanoma Transplants Is Promoted by Hydroquinone (1980)

In BALB/c female mice with melanoma transplants, the incidence of "takes" is decreased and survival is increased by hydroquinone, a melanocytolytic agent. The mechanism of drug action is suggested by via DNA. The significant and high degree of positive response to hydroquinone treatment in vivo is encouraging for the clinical management of melanoma with melanocytolytic agents.
Light scattering from a sphere with an irregular inclusion (1995)

The exact solution for the scattering from a sphere with a nonconcentric inclusion of arbitrary shape and optical constants is derived in terms of a vector harmonic expansion. The only information required of the inclusion is its freestanding scattering coefficients, so the inclusion can be composed of multiple refractive indices or be a set of separate inclusions. We then compare the absorption of glycerin host spheres containing small oblate and prolate carbon spheroids in different orientations.
Fundamental Study of KrF Excimer Laser (1995)

The KrF excimer laser is a high power pulsed laser oscillating in the ultraviolet field and able to destroy or amputate molecules of tissue without thermal damage.In order to evaluate the effects of KrF excimer laser irradiation on human mandibular bone, we examined by visual, pathological and SEM observation.The laser irradiation on human mandibular bone resected by oral and maxillofacial surgery had a pulse energy: 65mJ, spot size: 0.80×0.50mm2, energy density: 16J/cm2, water volume: 6.5ml, assist gas (N2): 301/min, frequency: 80Hz, incision speed: 5, 10, 15mm/min.Visual observation: the incisions were sharp without thermal damage, and the depth of the inicions ranged from 0.68 to 2.53mm according to the incision speed.Pathological observation: the inicisions were almost sharp and there was almost no thermal damage layer.SEM observation: the incision section was slightly wavy, but the incision surface was almost clear at 20 magnification. Crystals formed at the incision surface at all incision speeds, and there was no melting of bone tissue at 5000 magnification.
ELECTROMAGNETIC DETERMINATION OF REGIONAL BLOOD FLOW IN UNANESTHETIZED ANIMALS (1957)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Region-based coding of motion fields for low-bitrate video compression (2005)

Low-bitrate video compression requires a compact encoding of motion fields. We encode motion fields by segmenting them into regions of homogeneous motion. Each region is formed by a collection of blocks. The segmentation is represented by the connectedness relationship between adjacent blocks. To reduce the amount of connectedness information, blocks may be of variable size, as determined by a quadtree structure. We use context-based binary arithmetic coding to further reduce the amount of bits required to code the segmentation. A segmentation algorithm based on rate-distortion optimization is presented. Simulations show that such a motion-field coding scheme achieves coding efficiency comparable to the state-of-the-art H.264 codec with modest improvements.