gebhart/patrepeval huggingface dataset:
Size–strain line-broadening analysis of the ceria round-robin sample (2004)

The results of both a line-broadening study on a ceria sample and a size–strain round robin on diffraction line-broadening methods, which was sponsored by the Commission on Powder Diffraction of the International Union of Crystallography, are presented. The sample was prepared by heating hydrated ceria at 923 K for 45 h. Another ceria sample was prepared to correct for the effects of instrumental broadening by annealing commercially obtained ceria at 1573 K for 3 h and slowly cooling it in the furnace. The diffraction measurements were carried out with two laboratory and two synchrotron X-ray sources, two constant-wavelength neutron and a time-of-flight (TOF) neutron source. Diffraction measurements were analyzed by three methods: the model assuming a lognormal size distribution of spherical crystallites, Warren–Averbach analysis and Rietveld refinement. The last two methods detected a relatively small strain in the sample, as opposed to the first method. Assuming a strain-free sample, the results from all three methods agree well. The average real crystallite size, on the assumption of a spherical crystallite shape, is 191 (5) Å. The scatter of results given by different instruments is relatively small, although significantly larger than the estimated standard uncertainties. The Rietveld refinement results for this ceria sample indicate that the diffraction peaks can be successfully approximated with a pseudo-Voigt function. In a common approximation used in Rietveld refinement programs, this implies that the size-broadened profile cannot be approximated by a Lorentzian but by a full Voigt or pseudo-Voigt function. In the second part of this paper, the results of the round robin on the size–strain line-broadening analysis methods are presented, which was conducted through the participation of 18 groups from 12 countries. Participants have reported results obtained by analyzing data that were collected on the two ceria samples at seven instruments. The analysis of results received in terms of coherently diffracting, both volume-weighted and area-weighted apparent domain size are reported. Although there is a reasonable agreement, the reported results on the volume-weighted domain size show significantly higher scatter than those on the area-weighted domain size. This is most likely due to a significant number of results reporting a high value of strain. Most of those results were obtained by Rietveld refinement in which the Gaussian size parameter was not refined, thus erroneously assigning size-related broadening to other effects. A comparison of results with the average of the three-way comparative analysis from the first part shows a good agreement.
Investigation and reduction of metal voids post-CMP in dual damascene process (2008)

Copper void density post copper CMP and defect reduction methods were investigated on 300 mm wafers of 65 nm node in this work. Effects of copper seed thickness, post-plating anneal temperature, FAB ambient and FOUP cleanliness on metal voids were examined. It was found that thinner seed thickness, lower anneal temperature with longer time post plating, high temperature de-gas or water rinse before copper plating, N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> purge and special FOUP all resulted in reduced metal line void density.
A 27 mW CMOS fractional-N synthesizer/modulator IC (2002)

A 1.8GHz transmitter supports a data rate of 2.5Mb/s using GFSK with BT=0.5, the same modulation method used in DECT. The architecture increases, by over an order of magnitude, the achievable data rate for the transmitter method, in which phase/frequency modulation is by dithering the divide value within a phase locked loop (PLL). This design avoids mixers and D/A converters to generate I and Q waveforms, so that simplicity and power savings are achieved. The system was built using a custom, CMOS fractional-N synthesizer that contains several key circuits. Included are an on-chip, continuous-time filter that requires no tuning or external components, a digital MASH /spl Sigma//spl delta/ converter that achieves low-power operation through pipelining, and a 64-modulus divider that supports any divide value between 32 and 63.5 in half cycle increments. Also included is a phase/frequency detector (PFD) that avoids dead-zone problems.
Discontinuous Nanoporous Membranes Reduce Non‐Specific Fouling for Immunoaffinity Cell Capture (2013)

The microfluidic isolation of target cells using adhesion-based surface capture has been widely explored for biology and medicine. However, high-throughput processing can be challenging due to interfacial limitations such as transport, reaction, and non-specific fouling. Here, it is shown that antibody-functionalized capture surfaces with discontinuous permeability enable efficient target cell capture at high flow rates by decreasing fouling. Experimental characterization and theoretical modeling reveal that "wall effects" affect cell-surface interactions and promote excess surface accumulation. These issues are partially circumvented by reducing the transport and deposition of cells near the channel walls. Optimized microfluidic devices can be operated at higher cell concentrations with significant improvements in throughput.
Gas-source molecular beam epitaxial growth, characterization, and light-emitting diode application of InxGa1−xP on GaP(100) (1993)

Highly lattice-mismatched InxGa1−xP (x≤0.38) layers were grown on GaP substrates by gas-source molecular beam epitaxy. A relatively thin, compositionally linear-graded buffer layer was used to reduce the number of threading dislocations. Studies by double-crystal x-ray diffraction and transmission electron microscopy show this buffer layer to be 97% strain-relaxed along both 〈110〉 directions with dislocations well confined within the graded buffer and the substrate. Threading dislocation densities in the top layers were less than 1×107 cm−2. Room-temperature photoluminescence, ranging from 560 to 600 nm, is achieved. Heterojunction p-i-n diodes emitting at 560 nm at 300 K exhibit good rectifying and reverse breakdown characteristics.
Overexpression of Bcl-XL by cytotoxic drug exposure confers resistance to ionizing radiation-induced internucleosomal DNA fragmentation. (1995)

Acquired resistance to diverse chemotherapeutic agents has been associated with overexpression of the P-glycoprotein. We have selected human U-937 cells for clones resistant to the cytotoxic agents doxorubicin (U-A20) and vincristine (U-V20). The results demonstrate that P-glycoprotein-positive U-A20 and U-V20 cells exhibit resistance to inducers of internucleosomal DNA fragmentation. Although parental U-937 cells responded to ionizing radiation with the DNA laddering characteristic of physiological cell death, the drug-resistant lines were insensitive to this effect. The U-A20 and U-V20 clones were also resistant to endonucleolytic DNA cleavage associated with exposure to tumor necrosis factor or ceramide. Previous work has demonstrated that physiological cell death is inhibited by overexpression of the Bcl-2 protein. However, analysis of Bcl-2 revealed similar levels in the parental and drug-resistant cells. In contrast, we show that U-A20 and U-V20 cells overexpress the Bcl-2-related protein, Bcl-xL. Moreover, studies with a U-937 cell line transfected with a Bcl-XL expression vector confirm resistance to ionizing radiation-induced DNA fragmentation and cell killing. These findings suggest that, unlike Bcl-2, Bcl-XL may be constitutively overexpressed as a result of selection for cytotoxic drug resistance and that Bcl-XL participates in an acquired form of multimodality resistance to chemotherapeutic agents and radiation.
Knowledge‐based segmentation of thoracic computed tomography images for assessment of split lung function (2000)

The assessment of differential left and right lung function is important for patients under consideration for lung resection procedures such as single lung transplantation. We developed an automated, knowledge-based segmentation algorithm for purposes of deriving functional information from dynamic computed tomography (CT) image data. Median lung attenuation (HU) and area measurements were automatically calculated for each lung from thoracic CT images acquired during a forced expiratory maneuver as indicators of the amount and rate of airflow. The accuracy of these derived measures from fully automated segmentation was validated against those from segmentation using manual editing by an expert observer. A total of 1313 axial images were analyzed from 49 patients. The images were segmented using our knowledge-based system that identifies the chest wall, mediastinum, trachea, large airways and lung parenchyma on CT images. The key components of the system are an anatomical model, an inference engine and image processing routines, and segmentation involves matching objects extracted from the image to anatomical objects described in the model. The segmentation results from all images were inspected by the expert observer. Manual editing was required to correct 183 (13.94%) of the images, and the sensitivity, specificity, and accuracy of the knowledge-based segmentation were greater than 98.55% in classifying pixels as lung or nonlung. There was no significant difference between median lung attenuation or area values from automated and edited segmentations (p > 0.70). Using the knowledge-based segmentation method we can automatically derive indirect quantitative measures of single lung function that cannot be obtained using conventional pulmonary function tests.
Transforming growth factor beta: potential autocrine growth inhibitor of estrogen receptor-negative human breast cancer cells. (1988)

Transforming growth factor beta (TGF beta), a two-subunit Mr 25,000 polypeptide, inhibits growth of several epithelial human cancer cell lines and has been proposed as an autocrine growth inhibitor. TGF beta activity has been found in conditioned media from some breast cancer cell lines, and TGF beta mRNA has been detected in breast cancer cell lines and human breast cancer specimens. In the present study we attempted to characterize the interaction of TGF beta with breast cancer cells by examining the biological activity, receptor binding, and secretion of this polypeptide by a panel of estrogen receptor (ER)-positive and ER-negative human breast cancer cell lines. Growth of the four ER-negative lines, MDA231, MDA330, HS578T, and BT20, was exquisitely sensitive to TGF beta. Dose-dependent inhibition of monolayer growth, anchorage-independent growth, and of [3H]thymidine incorporation was observed with TGF beta concentrations ranging from 1 to 100 pM. Growth of the four ER-positive lines, T47D, ZR75-1, and two MCF7 lines from different laboratories, was unaffected by similar concentrations of TGF beta. In receptor-binding studies using 125I-TGF beta, the four ER-negative lines exhibited specific high affinity TGF beta receptors. Binding was a time- and temperature-dependent process. Scatchard analysis of the binding data showed between 2800 and 12900 receptor sites per cell and a Kd between 29 and 160 pM. Epidermal growth factor, insulin, insulin-like growth factors I and II, and transforming growth factor alpha did not compete for 125I-TGF beta binding. Chemical cross-linking studies with ER-negative breast cancer cells revealed three specific TGF beta receptors with molecular weights approximating 400,000, 92,000, and 69,000. The four ER-positive lines had no detectable TGF beta binding. Using a radioreceptor assay with A549 cells and a NRK bioassay, TGF beta activity was detectable in the conditioned media from the four ER-negative cell lines; media from the ER-positive lines had low levels of TGF beta activity. In summary, ER-negative, estrogen-independent cultured human breast cancer cells have receptors for, are inhibited by, and secrete TGF beta activity, suggesting the possibility that this polypeptide may function as an autocrine growth inhibitor or as a paracrine growth factor for tumor stromal cells.
Immunological Effects of Yeast- and Mushroom-Derived β -Glucans (2008)

Glucans have a long history as nonspecific biological modulators. We compared the effects of three different glucans on immune reactions. Using two different administrations (intraperitoneal and oral) and two different animal models, we showed that yeast-derived Betamune (Biorigin, São Paulo, Brazil) caused significant stimulation of phagocytic activity as well as potentiation of synthesis and release of interleukin (IL)-1, IL-2, IL-4, IL-6, IL-8, IL-13, and tumor necrosis factor-alpha. In addition, Betamune inhibited growth of tumor cells in vivo and affected expression of several important genes in breast cancer cells. Compared to adult mice, young animals showed different sensitivity to glucan action.
Glutathione S-transferase mu genotype, diet, and smoking as determinants of sister chromatid exchange frequency in lymphocytes. (1995)

Polymorphisms in inherited metabolic traits and intake of dietary antioxidants have been reported to be associated with risk for the development of lung cancer in smokers. This increased risk of lung cancer is presumably attributable to the accumulation of DNA damage. We conducted a study to investigate whether genetic metabolic variants and antioxidant consumption affected the sister chromatid exchange (SCE) level in lymphocytes. Study subjects were 78 friends and spouses of cases from a case-control study of lung cancer designed to investigate the association of metabolic polymorphisms with lung cancer. The metabolic traits studied included glutathione S-transferase class mu and variants of P-450 isoenzymes CYP1A1 and CYP2D6. Intake of antioxidants including vitamins A, C, and E and selenium was determined through the administration of a validated, semiquantitative food frequency questionnaire. Detailed information on smoking, family history of cancer, medical history, and environmental and occupational exposures was also obtained in an interviewer-administered questionnaire. Smoking status was found to be significantly associated with SCE frequency. In addition SCE frequency decreased with the period of time since quitting smoking. The presence of one or more glutathione S-transferase class mu alleles was associated with significantly lower SCE. Higher intake of vitamin A and selenium was also inversely associated with SCE level. Thus, the results suggest that glutathione S-transferase class mu and the intake of vitamin A and selenium may modulate the accumulation of chromosomal damage in lymphocytes.
Physical mapping of the mec region of an American methicillin-resistant Staphylococcus aureus strain (1991)

We mapped part of the mec region of a locally prevalent strain of Staphylococcus aureus. The mec region was found to harbor an insert of the transposon Tn554, which encodes spectinomycin and macrolide-lincosamide-streptogramin B resistance, and a 4.6-kb segment of DNA that contains the kanamycin resistance gene aadD. This 4.6-kb segment appears to be an integrated form of a previously described plasmid, pUB110, and is flanked by copies of the insertion sequence IS257. The integration event may be an example of processes that have led to accretion of resistance determinants in the mec region of S. aureus.
Statistical properties of the simulated time horizon in conservative parallel discrete-event simulations (2002)

We investigate the universal characteristics of the simulated time horizon of the basic conservative parallel algorithm when implemented on regular lattices. This technique [1, 2] is generically applicable to various physical, biological, or chemical systems where the underlying dynamics is asynchronous. Employing direct simulations, and using standard tools and the concept of dynamic scaling from non-equilibrium surface/interface physics, we identify the universality class of the time horizon and determine its implications for the asymptotic scalability of the basic conservative scheme. Our main finding is that while the simulation converges to an asymptotic nonzero rate of progress, the statistical width of the time horizon diverges with the number of PEs in a power law fashion. This is in contrast with the findings of Ref. [3]. This information can be very useful, e.g., we utilize it to understand optimizing the size of a moving "time window" to enforce memory constraints.
Managing update conflicts in Bayou, a weakly connected replicated storage system (1995)

Bayou is a replicated, weakly consmtent storage system designed for a mobile computing environment that includes portable machines with less than ideal network connectivity. To maximize availabdity, users can read and write any accessible replica. Bayou's design has focused on supporting apphcation-specific mechanisms to detect and resolve the update conflicts that naturally arise in such a system, ensuring that replicas move towards eventual consistency, and defining a protocol by which the resolution of update conflicts stabilizes, It includes novel methods for confhct detection, called dependency checks, and per-write conflict resolution based on client-provided merge procedures. To guarantee eventual consistency, Bayou servers must be able to rollback the effects of previously executed writes and redo them according to a global serialization order. Furthermore, Bayou permits clients to observe the results of all writes received by a server, mchrding tentative writes whose conflicts have not been ultimately resolved. This paper presents the motivation for and design of these mechanisms and describes the experiences gained with an initial implementation of the system.
Cardiac Myocyte Cell Cycle Control in Development, Disease, and Regeneration (2007)

Cardiac myocytes rapidly proliferate during fetal life but exit the cell cycle soon after birth in mammals. Although the extent to which adult cardiac myocytes are capable of cell cycle reentry is controversial and species-specific differences may exist, it appears that for the vast majority of adult cardiac myocytes the predominant form of growth postnatally is an increase in cell size (hypertrophy) not number. Unfortunately, this limits the ability of the heart to restore function after any significant injury. Interest in novel regenerative therapies has led to the accumulation of much information on the mechanisms that regulate the rapid proliferation of cardiac myocytes in utero, their cell cycle exit in the perinatal period, and the permanent arrest (terminal differentiation) in adult myocytes. The recent identification of cardiac progenitor cells capable of giving rise to cardiac myocyte-like cells has challenged the dogma that the heart is a terminally differentiated organ and opened new prospects for cardiac regeneration. In this review, we summarize the current understanding of cardiomyocyte cell cycle control in normal development and disease. In addition, we also discuss the potential usefulness of cardiomyocyte self-renewal as well as feasibility of therapeutic manipulation of the cardiac myocyte cell cycle for cardiac regeneration.
In-Vivo Evaluation of an In Situ Polymer Precipitation Delivery System for a Novel Natriuretic Peptide (2013)

This study reports on the release of a novel natriuretic peptide, CD-NP, from an in situ polymer precipitation delivery system. Following extensive screening of in-vitro release profiles, an in-vivo evaluation of the efficacy of the delivery system was carried out in Wistar rats. Gel injection was performed subcutaneously on the back of the rats. A secondary messenger, cyclic Guanosine 3'5' Monophosphate (cGMP), was tested for verification of CD-NP bioactivity, in addition to direct measurements of CD-NP levels in plasma and urine using a radio-immuno assay. Plasma evaluation showed an elevated level of CD-NP over 3 weeks' duration. Unexpectedly, plasma cGMP level followed a decreasing trend over the same duration despite high CD-NP level. Loss of drug bioactivity was ruled out as a high level of CD-NP and cGMP excretion was observed in the treatment group as compared to baseline readings. This unexpected low-plasma cGMP levels and high-urinary cGMP excretion suggest that there might be other compensatory responses to regulation of the CDNP bioactivity as a result of the high drug dosing. The results stress the importance of assessing the overall bioactivity of released drug (in-vivo) concurrently in addition to measuring its concentrations, to determine the correct release profile.
L 1  FePt–MgO perpendicular thin film deposited by alternating sputtering at elevated temperature (2006)

FePt – MgO two phase thin films have been obtained by an alternating sputtering method at elevated temperatures. It is found that the L10 FePt grains grow in a columnar manner through the thickness of the film and possess a (001) perpendicular texture promoted by the (200)-textured crystalline MgO underlayer. The amorphous MgO in the two phase mixture forms uniform separation walls between FePt grains. The microstructure is similar to that of Co-alloy/oxide granular media.
Subretinally Transplanted Embryonic Stem Cells Rescue Photoreceptor Cells from Degeneration in the RCS Rats (2001)

The Royal College of Surgeons (RCS) rat is an animal model for retinal degeneration such as the age-related macular degeneration. The RCS rat undergoes a progressive retinal degeneration during the early postnatal period. A potential treatment to prevent this retinal degeneration is the transplantation into the subretinal space of cells that would replace functions of the degenerating retinal pigment epithelium (RPE) cells or may form neurotrophic factors. In this study we have investigated the potential of subretinally transplanted embryonic stem cells to prevent the genetically determined photoreceptor cell degeneration in the RCS rat. Embryonic stem cells from the inner cell mass of the mouse blastocyst were allowed to differentiate to neural precursor cells in vitro and were then transplanted into the subretinal space of 20-day-old RCS rats. Transplanted and sham-operated rats were sacrificed 2 months following cell transplantation. The eyes were enucleated and photoreceptor degeneration was quantified by analyzing and determining the thickness of the outer nuclear layer by light and electron microscopy. In the eyes transplanted with embryonic cells up to 8 rows of photoreceptor cell nuclei were observed, whereas in nontreated control eyes the outer nuclear layer had degenerated completely. Transplantation of embryonic stem cells appears to delay photoreceptor cell degeneration in RCS rats.
Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients (2015)

Blinded to tumor genotype, this plasma NGS approach detected a broad range of targetable genomic alterations in NSCLC with no false positives including complex mutations like rearrangements and unexpected resistance mutations such as EGFR C797S. Through use of widely available vacutainers and a desktop sequencing platform, this assay has the potential to be implemented broadly for patient care and translational research.
Performance status and sensitivity to first‐line chemotherapy are significant prognostic factors in patients with recurrent small cell lung cancer receiving second‐line chemotherapy (2008)

Both PS and sensitivity to initial chemotherapy were found to be significant prognostic factors for survival in recurrent SCLC patients treated with second-line chemotherapy. These 2 factors should therefore be used as stratification factors in future clinical trials.