gebhart/patrepeval huggingface dataset:
Investigation of the use of X-ray CT images for attenuation compensation in SPECT (1994)

This study investigates the general use of single-beam X-ray computed tomography (CT) images for generating attenuation maps for compensation of photon attenuation in SPECT images. A 3D mathematical thorax phantom is used to simulate both emission and transmission projection data for monoenergetic (radionuclide) and polyenergetic (X-ray) sources. Polyenergetic transmission projection data are simulated for a standard X-ray spectrum and fan-beam geometry. The projection data are reconstructed using filtered backprojection to form an X-ray CT image which is then scaled to produce an estimate of the attenuation map at the energy of the emission radionuclide. Emission projection data are simulated for a fan-beam geometry at the energies of /sup 201/Tl and /sup 99m/Tc, two radionuclides commonly used in cardiac SPECT. Detector response and scatter are not included in the model. Noiseless, emission projection data are iteratively reconstructed using the ML-EM algorithm with nonuniform attenuation compensation and attenuation maps derived from both the simulated X-ray CT image and from a simulated monoenergetic transmission CT image. The attenuation maps generated from the X-ray CT images accurately estimate the attenuation coefficient for muscle and lung tissues, but not for bone tissues, which show error in the attenuation coefficient of 21-42% for spinal bone and 34-58% for rib bone. However, despite the inaccurate estimate of bone attenuation, the reconstructed SPECT images provide estimates of myocardial radioactivity concentration to within 9% and show few artifacts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data (2013)

The rat has been widely used as a disease model in a laboratory setting, resulting in an abundance of genetic and phenotype data from a wide variety of studies. These data can be found at the Rat Genome Database (RGD, http://rgd.mcw.edu/), which provides a platform for researchers interested in linking genomic variations to phenotypes. Quantitative trait loci (QTLs) form one of the earliest and core datasets, allowing researchers to identify loci harboring genes associated with disease. These QTLs are not only important for those using the rat to identify genes and regions associated with disease, but also for cross-organism analyses of syntenic regions on the mouse and the human genomes to identify potential regions for study in these organisms. Currently, RGD has data on >1,900 rat QTLs that include details about the methods and animals used to determine the respective QTL along with the genomic positions and markers that define the region. RGD also curates human QTLs (>1,900) and houses>4,000 mouse QTLs (imported from Mouse Genome Informatics). Multiple ontologies are used to standardize traits, phenotypes, diseases, and experimental methods to facilitate queries, analyses, and cross-organism comparisons. QTLs are visualized in tools such as GBrowse and GViewer, with additional tools for analysis of gene sets within QTL regions. The QTL data at RGD provide valuable information for the study of mapped phenotypes and identification of candidate genes for disease associations.
Chromosomal beta-lactam resistance in enterobacteria. (1986)

Most enterobacterial species carry a chromosomal ampC beta-lactamase gene. In Escherichia coli and Shigella, expression from ampC is non-inducible and the beta-lactamase is synthesized at low levels. Mutations leading to increased beta-lactamase synthesis occur rather infrequently, making resistance to modern cephalosporins a rare event in these species. In other enterobacteria and Pseudomonas, ampC beta-lactamase synthesis is induced by beta-lactams. In Enterobacter cloacae, Citrobacter freundii and probably also in other species with inducible beta-lactamase expression, ampC is regulated by at least two genes, ampR and ampD. Mutations affecting ampR abolish beta-lactamase inducibility, and mutants devoid of ampR, produce ampC beta-lactamase at low constitutive levels. Mutations in ampD lead to constitutive overproduction of inducible beta-lactamase if an intact ampR protein is present in the cell. The latter type of mutations occur at a high frequency and result in clinical resistance to several third-generation cephalosporins.
Dideoxy linear PCR on a commercial fluorescent automated DNA sequencer. (1992)

The use of automated fluorescent DNA sequencer systems and PCR-based DNA sequencing methods play an important role in the actual effort to improve the efficiency of large-scale DNA analysis. Here we show the application of the linear PCR using a single fluorescent primer and dideoxynucleotide terminators in four separate sequencing reactions on the EMBL/Pharmacia's fluorescent automated DNA sequencer. We have used dideoxy/deoxynucleoside triphosphate ratios and linear amplification cycle conditions to obtain an accurate sequencing response of up to, and over, 500 bases from just 400 ng of double-stranded DNA template without chemical denaturation. The sequencing protocol described in this paper is effectively suited for enhancement of sensitivity and performance of the automated DNA sequencing system.
Preliminary Results from a Phase I Study of Revlimid® (Lenalidomide) in Combination with Vidaza® (Azacitidine) in Patients with Advanced Myelodysplastic Syndromes (MDS). (2007)

Abstract Background: Early MDS becomes more advanced as immature myeloid cells proliferate, angiogenesis increases, genetic lesions accumulate, and tumor suppressor genes become inactivated through hypermethylation. Progression to acute myeloid leukemia (AML) may be prevented by targeting these defects through combination therapy, using an immunomodulatory, anti-angiogenic agent, lenalidomide (LEN), and a hypomethylating drug, azacitidine (AZA). Methods: We conducted a multicenter, Phase I trial in patients (pts) with advanced MDS (IPSS score ≥1.5, or FAB or WHO classification with ≥5% myeloblasts) starting in 6/06, with results reported through 7/07. Pts were enrolled using a “3+3” design (See Table), and could not receive LEN or AZA previously. Cycles lasted 28 days, to a maximum of 7 cycles of therapy. The primary endpoint was to determine the maximum tolerated dose (MTD) and dose-limiting toxicities (DLTs, defined as Grade 3/4 non-hematologic toxicity or &gt;50% neutrophil (ANC) or platelet (plt) drop without recovery by Day 56) of the combination. A secondary endpoint was response as defined by the Modified International Working Group. Dose Level AZA Schedule LEN Schedule 1 75 mg/m2 SC days 1–5 5 mg PO days 1–14 2 75 mg/m2 SC days 1–5 5 mg PO days 1–21 3 75 mg/m2 SC days 1–5 10 mg PO days 1–21 4 50 mg/m2 SC days 1–5, 8–12 5 mg PO days 1–14 5 50 mg/m2 SC days 1–5, 8–12 5 mg PO days 1–21 6 50 mg/m2 SC days 1–5, 8–12 10 mg PO days 1–21 Results: Seven patients have been enrolled, 6 are evaluable for toxicity data. Median age was 64 years (range 52–70), 1 pt was female, and median follow-up is 5.5 months (range 1.5–13). All pts had RAEB-2; IPSS scores were 1.5 (4), 2.0 (2), and 3.0 (1), with IPSS cytogenetic risk categories of poor (1), intermediate (1), and good (5). No pt had a del (5q) lesion. Median time from MDS diagnosis was 3.5 wks (range 2–106). No DLTs occurred in Dose Levels 1 or 2, and MTD has not yet been reached. Grade 1/2 non-hematologic toxicities (n=6) included fatigue (4), injection site reaction (6), rash (3), pruritis (3), constipation or diarrhea (6), dizziness (1), and mucositis (1). Grade 3/4 non-hematologic toxicities included febrile neutropenia (1). Median ANC drop was 16.4% and plt drop was 10.4%. Although one patient was delayed 1 week in starting cycle 2 for neutropenia, there were no dose-reductions for toxicities. Four pts are evaluable for response: 2 had a complete response, 1 an erythroid response, and 1 progressive disease. Conclusions: The combination of LEN and AZA is well-tolerated and early results suggest efficacy in advanced MDS. Responses and toxicity data from higher Dose Levels will be presented.
IBCIS: Intelligent blood cell identification system (2008)

The analysis of blood cells in microscope images can provide useful information concerning the health of patients. There are three major blood cell types, namely, erythrocytes (red), leukocytes (white), and platelets. Manual classification is time consuming and susceptible to error due to the different morphological features of the cells. This paper presents an intelligent system that simulates a human visual inspection and classification of the three blood cell types. The proposed system comprises two phases: The image preprocessing phase where blood cell features are extracted via global pattern averaging, and the neural network arbitration phase where training is the first and then classification is carried out. Experimental results suggest that the proposed method performs well in identifying blood cell types regardless of their irregular shapes, sizes and orientation, thus providing a fast, simple and efficient rotational and scale invariant blood cell identification system which can be used in automating laboratory reporting.
Postexposure chemoprophylaxis with ZDV or ZDV combined with interferon-alpha: failure after inoculating rhesus monkeys with a high dose of SIV. (1991)

Presently, no information is available regarding the efficacy of chemoprophylaxis in controlled human trials following accidental exposure to the human immunodeficiency virus (HIV). Using the closely related simian immunodeficiency virus (SIV) in rhesus monkeys, which develop a disease closely resembling human AIDS, we tested the efficacy of either single-agent 3'-azido-3'-deoxythymidine (ZDV) or the combination of ZDV plus recombinant human interferon-alpha (IFN-alpha). Treatment was started 3 h following inoculation of a high dose of SIV and continued for 21 days. SIV-inoculated control animals remained untreated. Virus was recovered from all monkeys on day 8, and by week 7 all had seroconverted. In contrast to monkeys treated with ZDV alone, animals given combination therapy had lower levels of p27 gag antigen compared to untreated controls on day 8 (p = 0.043). We conclude that neither treatment regimen could prevent infection after high-dose virus exposure; however, combination therapy may have depressed the level of virus replication more effectively than ZDV alone.
Wireless interfaces for IEEE 1451 sensor networks (2002)

NIST started working with industry and the Institute of Electrical and Electronics Engineers (IEEE) in the mid 90's to develop a standardized interface to network smart sensors. With the spread of wireless technology, more industries are looking to incorporate wireless communications into their products and manufacturing processes. This paper discusses the IEEE 1451 standard interface for smart sensors, emerging wireless communication technologies, and possible solutions for creating a wireless interface for the IEEE 1451 standard.
The Endocardium (1989)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
High performance NdFeB magnets (invited) (1996)

Although the production and applications of NdFeB magnets have increased enormously in the last decade because of their outstanding magnetic properties at room temperature, some applications were limited because of poor thermal stability and corrosion resistance. To address these problems, there have been many efforts and much progress. In many instances, the alloy modifications produced an improvement of some characteristics but only at the expense of other characteristics. It is therefore necessary to find a method (or alloy) for improving the thermal stability, coercivity, and corrosion resistance without sacrificing performance. We have found that the proper control of very small amounts of Cu, Co, and O in (Nd, Dy)FeB alloys substantially improves the coercivity, high-temperature capabilities, and corrosion resistance without a reduction of remanence. As a result, a high performance NdFeB magnet with excellent temperature stability and corrosion resistance was developed.
Influence of Culvert Shape on Outlet Scour (1987)

A flume study is conducted to determine culvert shape influence on the scour geometry at culvert outlets. Twenty-six experiments are performed in which flows discharged for 316 minutes through circular, arch, square and rectangular shaped culverts and the resulting scour holes are documented. The scour hole dimensions for the arch, square and rectangular shaped culverts are normalized and compared to the scour hole dimensions for the circular culvert. Culvert shape significantly influenced the scour dimensions compared to the scour dimensions determined using the circular shape culvert. A series of expressions are developed correlating the dimensionless scour hole parameters of depth, width, length and volume to the modified discharge intensity. The denominator of the modified discharge intensity parameter, termed the culvert shape factor, compensates for shape differences for comparison.
Object/rule integration in CLIPS (1994)

Abstract: This paper gives a brief overview of the C Language Integrated Production System (CLIPS) with a focus on the object‐oriented features. The advantages of an object data representation over the traditional working memory element (WME), i.e. facts, are discussed and the implementation of the Rete inference algorithm in CLIPS is presented in detail. A few methods for achieving pattern‐matching on objects with the current inference engine are given and, finally, the paper examines the modifications necessary to the Rete algorithm to allow direct object pattern‐matching.
Controlled Elemental Depth Profile in Sol–Gel‐Derived PZT Films (2006)

Elemental depth profiles of PZT films prepared by two sol–gel formulations, differing in the zirconium precursor stabilization, were investigated by SIMS analysis. Early decomposition of the zirconium precursor yielded opposing gradients of zirconium and titanium, while simultaneous late decomposition of zirconium and titanium precursors provided profile uniformity. The gradients formed during initial crystallization are irreversible. Both types of films showed excellent hysteresis; however, uniform films exhibited a much higher dielectric constant, indicating superior piezoelectric properties. Non‐uniform films displayed a complex CV pattern, consistent with an inhomogeneous structure. Finally, thermal decomposition of the individual metal precursors is crucial for controlling film uniformity.
Insulin Resistance, Obesity and the Metabolic Syndrome. Is there a Therapeutic Role for Endothelin-1 Antagonists? (2005)

There is increasing evidence to suggest that chronic activation of the endothelin-1 system can lead to heterologous desensitization of the glucose-regulatory and mitogenic actions of insulin with subsequent development of glucose intolerance, hyperinsulinemia, impaired endothelial function and exacerbation of cardiovascular disease. Effects are mediated through a variety of mechanisms that include attenuation of key insulin signalling pathways and decreased tyrosine phosphorylation of insulin receptor substrates IRS-1, SHC and G alpha q/11. Other actions involve hemodynamic changes leading to reduced delivery of insulin and glucose to peripheral tissues as well as enhanced hepatic glycogenolysis, decreased glucose-transporter translocation and modulation of various adipokines that regulate insulin action. Overall the data suggest that ET-1 antagonists may provide an effective means of improving cardiac dysfunction and favourably influencing glucose tolerance in obese humans and patients with early insulin sensitivity where there is clear evidence for activation of the ET-1 system. Although most effects of ET-1 that modulate mechanisms leading to glucose intolerance appear to involve the ETA receptor subtype recent data indicates that combined ETA/ETB receptor antagonists may function as effectively as selective ETA blockers. Prospective trials are needed to assess whether ET-1 antagonists, either alone or in combination, are superior to other more conventional therapies such as insulin sensitizers and to evaluate effects of combined treatments on the development of insulin resistance and the progression of diabetes. Early screening of patients at risk for evidence of ET-1 activation would help to identify subjects who may benefit most from such treatment.
Performance evaluation of a six-axis generalized force-reflecting teleoperator (1991)

Recent work in real-time distributed computation and control has culminated in a prototype force-reflecting telemanipulation system having dissimilar master (cable-driven force-reflecting hand controller) and slave (PUMA 560 robot with custom controller), extremely high sampling rate (1000 Hz), and low loop computation delay (5 ms). In a series of experiments with this system and five trained test operators covering more than 100 h of teleoperation, performance in a series of generic and application-driven tasks with and without force feedback was measured, and with control shared between teleoperation and local sensor referenced control. Measurements defining task performance include 100-Hz recording of six-axis force-torque information, task completion time, and visual observation of predefined task errors. It is shown that all performance measures improved as capability was added along a spectrum of capabilities ranging from pure position control through force-reflecting teleoperation and shared control. Performance was maximal for the barehanded operator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
NMR-Based Biosensing with Optimized Delivery of Polarized <sup>129</sup>Xe to Solutions (2005)

Laser-enhanced (LE) 129Xe nuclear magnetic resonance (NMR) is an exceptional tool for sensing extremely small physical and chemical changes; however, the difficult mechanics of bringing polarized xenon and samples of interest together have limited applications, particularly to biological molecules. Here we present a method for accomplishing solution 129Xe biosensing based on flow (bubbling) of LE 129Xe gas through a solution in situ in the NMR probe, with pauses for data acquisition. This overcomes fundamental limitations of conventional solution-state LE 129Xe NMR, e.g., the difficulty in transferring hydrophobic xenon into aqueous environments, and the need to handle the sample to refresh LE 129Xe after an observation pulse depletes polarization. With this new method, we gained a factor of >100 in sensitivity due to improved xenon transfer to the solution and the ability to signal average by renewing the polarized xenon. Polarized xenon in biosensors was detected at very low concentrations, </=250 nanomolar, while retaining all the usual information from NMR. This approach can be used to simultaneously detect multiple sensors with different chemical shifts and is also capable of detecting signals from opaque, heterogeneous samples, which is a unique advantage over optical methods. This general approach is adaptable for sensing minute quantities of xenon in heterogeneous in vitro samples, in miniaturized devices and should be applicable to certain in-vivo environments.
Speaking the same language: improving evaluation of patient-focused outcomes using standardized terminology. (2000)

As the practice of medicine grows in complexity and the public calls for demonstrated value at decreased cost, the need for increasing effectiveness of both providing care and evaluating patient outcomes becomes paramount. This paper will demonstrate the success of utilizing a standardized taxonomy within an automated patient record to provide cues to clinicians regarding individual, patient-focused outcomes as well as timely evaluation of aggregated patient outcomes data. A case study will be used to illustrate dynamic evaluation of clinical outcomes following cardiac surgery.
[Loss of heterozygosity at different chromosomes in patients with breast cancer]. (1994)

The loss of heterozygosity (LOH) at chromosomes 3p24, 7q31, 16q24.3 and 17p13.1 was measured in 15 patients with breast cancer by means of polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) or PCR-CA repeat analysis. In 36%, 36%, 50% and 56% of the informative cases, LOH was detected at 3p24, 7q31, 16q24.3 and 17p13.1 loci, respectively. All the LOH at 3p24 or 7q31 happened in stage II or III, 67% of the LOH at 3p24 or 7q31 happened in the cases with lymph node metastasis, and 67% of the LOH at 3p24 or 7q31 were found in estrogen receptor negative patients. This finding shows that the measurement of LOH at 3p24 and 7q31 may be an useful predicting marker for the prognosis of patients with breast cancer. The high percent of LOH at these four loci may also indicate the possibility of the existence of tumor suppressor genes for breast cancer.
Elementary Number Theory, Group Theory and Ramanujan Graphs (2001)

This text is a self contained treatment of expander graphs and in particular their explicit construction. Expander graphs are both highly connected but sparse, and besides their interest within combinatorics and graph theory, they also find various applications in computer science and engineering. The reader needs only a background in elementary algebra, analysis and combinatorics; the authors supply the necessary background material from graph theory, number theory, group theory and representation theory. The text can therefore be used as a brief introduction to these subjects as well as an illustration of how such topics are synthesised in modern mathematics.
Proteins of the 14-3-3 Family Associate with Raf and Contribute to Its Activation (1994)

The Raf serine/threonine kinase is activated in a Ras-dependent manner during mitogenic cell signaling (Avruch et al. 1994). Ras proteins in their active, GTP-bound states bind to Raf (Finney et al. 1993; Moodie et al. 1993; Van Aelst et al. 1993; Vojtek et al. 1993; Warne et al. 1993; Zhang et al. 1993; Hallberg et al. 1994) and translocate it to the plasma membrane (Leevers et al. 1994; Traverse et al. 1993; Stokoe et al. 1994). Once in the membrane, Raf kinase becomes activated through mechanisms that are poorly understood. A number of phosphorylation sites on Raf have been identified that appear necessary for the activation process (Fabian et al. 1993; Morrison et al. 1993), and indeed, protein kinase C can activate Raf in cells under certain conditions (Kolch et al. 1993; Carroll and May 1994). However, the precise role of these phosphorylation events is not yet clear; nor is...