gebhart/patrepeval huggingface dataset:
Investigation into the surface morphology of nanosized silicate and hybrid films by optical and atomic-force microscopy (2007)

This paper reports on the results of investigations into the surface morphology of hybrid organic-inorganic films prepared by the sol-gel method on single-crystal semiconductor silicon. The spin-on-glass films are coated from sols based on tetraethoxysilane. The chemical composition of the films is modified by introducing inorganic compounds (dopants), namely, boric acid and gadolinium nitrate, into the sols. For the purpose of increasing the film thickness, the sols are modified by small amounts (∼1 wt %) of polyols that have linear and branched structures, different molecular weights, and different numbers of active functional groups. A substantial change in the surface morphology of the spin-coated films, i.e., the formation of a specific structure of the films under the action of the above dopants and modifiers, is revealed using optical and atomic-force microscopy.
Fast Transforms for Acoustic Imaging—Part II: Applications (2011)

In Part I ["Fast Transforms for Acoustic Imaging-Part I: Theory," IEEE Transactions on Image Processing], we introduced the Kronecker array transform (KAT), a fast transform for imaging with separable arrays. Given a source distribution, the KAT produces the spectral matrix which would be measured by a separable sensor array. In Part II, we establish connections between the KAT, beamforming and 2-D convolutions, and show how these results can be used to accelerate classical and state of the art array imaging algorithms. We also propose using the KAT to accelerate general purpose regularized least-squares solvers. Using this approach, we avoid ill-conditioned deconvolution steps and obtain more accurate reconstructions than previously possible, while maintaining low computational costs. We also show how the KAT performs when imaging near-field source distributions, and illustrate the trade-off between accuracy and computational complexity. Finally, we show that separable designs can deliver accuracy competitive with multi-arm logarithmic spiral geometries, while having the computational advantages of the KAT.
A sensitivity-guided algorithm for automated determination of IMRT objective function parameters (2006)

Optimizing intensity-modulated radiotherapy (IMRT) plans involves tradeoffs that balance normal-tissue objectives against each other and against tumor objectives. Adjusting the parameters that determine the appropriate contributions of individual anatomic structures to the objective functions through trial and error is time consuming and may not produce the best achievable plans. We have developed a sensitivity-guided parameter optimization (SGPO) method to assist in the automatic determination of parameters to drive the IMRT optimization to better achieve, or even exceed, specified planning goals. The method is based on the trade-off relationships among multiple objectives: In a globally optimal plan (or within a convex subspace of the plan objectives), any attempt to improve the achievement of goals for a structure will result in sacrificing the goals for at least one other structure. However, different objectives may have different sensitivities to the overall goal of an IMRT plan. For instance, changes in dose distribution, hence the subscore corresponding to an objective for a given normal structure, may minimally impact the target dose distribution. Stated differently, the target coverage is insensitive to the changes in dose distribution of the specific normal structure. A lung cancer treatment plan designed with the SGPO method was used to demonstrate that IMRT plans could be designed to favor a structure with the highest target sensitivity and spare the structures with the least target sensitivity without compromising the target coverage. Using one case each of prostate and paranasal sinus cancers, we also demonstrated that several alternative optimal solutions could be designed with the SGPO algorithm favoring different structures. Finally, we applied the method to eight oropharyngeal cancer cases to obtain objective function parameters that satisfied the Radiation Therapy Oncology Group RTOG-H-0022 protocol. The eight plans optimized using the computer-generated objective function parameters met the protocol's scoring criteria with no or only minor protocol violations. Our preliminary study indicates that the SGPO method may be an effective and practical way to improve IMRT planning.
Enantioseparation of chiral drugs and current status of electromigration techniques in this field (2001)

In keeping with the expanded scope of the Journal of Separation Science, this short review summarizes current trends in the development and use of chiral drugs and reports the author's insight into the role of separation science in this field. In keeping with the thematic character of this special issue, electromigration techniques such as capillary electrophoresis and capillary electrochromatography are stressed. The most recent developments in the field of micropreparative enantioseparations based on various electromigration techniques are also summarized.
Systematic review of genome-wide gene expression studies of bipolar disorder (2013)

We provided an up-to-date summary of results from gene expression studies of the brain in BP. Our analyses focused on the highest quality data available and provided results by brain region so that similarities and differences can be examined relative to disease status. The results are available for closer inspection on-line at Metamoodics [http://metamoodics.igm.jhmi.edu/], where investigators can look up any genes of interest and view the current results in their genomic context and in relation to leading findings from other genomic experiments in bipolar disorder.
Registration of Radar and Optical Satellite Images Using Multiscale Filter Technique and Information Measure (2010)

The experimental results showed that proposed scheme can be capable to register radar and optical satellite images such as PALSAR and ASTER images. Compared to the traditional manual method, the scheme using multiscale filter technique and information measure can greatly enhance the registration process. The hybrid search/optimization approach is relatively less sensitive to initial guess, and make the registration process robust. Meanwhile, our method maintains comparable accuracy comparing with the traditional manual method. Except for the computing time, the scheme might encounter difficulties when the two images with very time differences. Future work should include two parts. The first one is to conduct many more experiments on different regions. The other one is to incorporate some feature based technique to speed up the search process.
Two genes encoding an endoglucanase and a cellulose-binding protein are clustered and co-regulated by a TTA codon in <i>Streptomyces halstedii</i> JM8 (1997)

Streptomyces halstedii JM8 Cel2 is an endoglucanase of 28 kDa that is first produced as a protein of 42 kDa (p42) and is later processed at its C-terminus. Cel2 displays optimal activity towards CM-cellulose at pH6 and 50 degrees C and shows no activity against crystalline cellulose or xylan. The N-terminus of p42 shares similarity with cellulases included in family 12 of the beta-glycanases and the C-terminus shares similarity with bacterial cellulose-binding domains included in family II. This latter domain enables the precursor to bind so tightly to Avicel that it can only be eluted by boiling in 10% (w/v) SDS. Another open reading frame (ORF) situated 216 bp downstream from the p42 ORF encodes a protein of 40 kDa (p40) that does not have any clear hydrolytic activity against cellulosic or xylanosic compounds, but shows high affinity for Avicel (crystalline cellulose). The p40 protein is processed in old cultures to give a protein of 35 kDa that does not bind to Avicel. Translation of both ORFs is impaired in Streptomyces coelicolor bldA mutants, suggesting that a TTA codon situated at the fourth position of the first ORF is responsible for this regulation. S1 nuclease protection experiments demonstrate that both ORFs are co-transcribed.
High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq (2011)

Hypoxia-inducible factor (HIF) regulates the major transcriptional cascade central to the response of all mammalian cells to alterations in oxygen tension. Expression arrays indicate that many hundreds of genes are regulated by this pathway, controlling diverse processes that in turn orchestrate both oxygen delivery and utilization. However, the extent to which HIF exerts direct versus indirect control over gene expression together with the factors dictating the range of HIF-regulated genes remains unclear. Using chromatin immunoprecipitation linked to high throughput sequencing, we identify HIF-binding sites across the genome, independently of gene architecture. Using gene set enrichment analysis, we demonstrate robust associations with the regulation of gene expression by HIF, indicating that these sites operate over long genomic intervals. Analysis of HIF-binding motifs demonstrates sequence preferences outside of the core RCGTG-binding motif but does not reveal any additional absolute sequence requirements. Across the entire genome, only a small proportion of these potential binding sites are bound by HIF, although occupancy of potential sites was enhanced approximately 20-fold at normoxic DNAse1 hypersensitivity sites (irrespective of distance from promoters), suggesting that epigenetic regulation of chromatin may have an important role in defining the response to hypoxia.
Synthesis of Polymerized Thin Films for Immobilized Ligand Display in Proteomic Analysis (2003)

We describe a new material for the display of biomolecular ligands for use in proteomic analysis. We report here on the construction of the first functionalized polymerized diacetylene thin films (PDTFs) for use in displaying immobilized ligands and their application in mass spectral proteomic analysis. Functionalized polymerized thin film surfaces were constructed with diacetylene-containing biotin lipid monomers designed for the capture of proteins (streptavidin) from a complex cellular lysate and detection with mass spectrometry (MS). These materials serve as a prototype for ligand-based spotted arrays amenable to high throughput screening. Functionalized PDTFs can be easily manufactured for customized microarrays and demonstrate high protein specificity and low nonspecific protein adsorption, and the resulting microarrays constructed from these materials are compatible with several different protein analysis platforms. Our results suggest that these materials have broad potential applications for use in mass spectral-based proteomic analysis.
Effect of radial temperature profiles on yields in steam cracking (2004)

Abstract Radial temperature profiles during steam cracking result in radial nonuniformities in the product yields due to radial variations in the concentration of the radicals. The effect of using a 1‐D or a 2‐D reactor model on the calculated product yields is evaluated for the cracking of ethane. With a 2‐D reactor model the simulated ethylene yield decreases. Ethylene formed at the high‐temperature zone near the hot wall diffuses to the center where secondary reactions are favored, generating C 3 and C 4 olefins. This effect is confirmed by the calculation of a reactor of a Kellogg Millisecond Furnace. In this small‐diameter reactor the 1‐D behavior is more pronounced, resulting in higher ethylene yields at comparable conversions. The effect of the radial gradients on the coking rate calculated with a fundamental kinetic coking model based on elementary reaction steps is even more pronounced. Only when the coke model is coupled to a 2‐D reactor model, a good agreement with the reference data is observed. In order to obtain accurate simulation results the more detailed 2‐D reactor model is required, even if this increases the computational effort. © 2004 American Institute of Chemical Engineers AIChE J, 50: 173–183, 2004
Aberrant 11beta-hydroxysteroid dehydrogenase-1 activity in the cpk mouse: implications for regulation by the Ke 6 gene. (1996)

Glucocorticoids have been used to create experimental polycystic kidney disease in rodents and to induce cysts in embryonic kidneys cultures. In addition, the plasma corticosterone levels are higher in a heritable murine model of polycystic kidney disease, cpk mice, in the first postnatal week. Previously, we had shown that the 11beta-hydroxysteroid dehydrogenase-1 (11betaHSD-1) gene is down-regulated in the cpk mice in a coordinated pattern with the Ke 6 gene. In this study, we measured the level of 11betaHSD-1 activity in kidney and liver tissues of cpk homozygote mice and found a reduction in its activity only in the kidney, not in the liver. The activity of the 11betaHSD-1 enzyme appears to be tightly correlated to the level of Ke 6 protein in these tissues. We discuss the possibility that the activity of the 11betaHSD-1 enzyme may be regulated by the Ke 6 enzyme. Ke 6 gene expression has been located to the outer stripe region of rodent kidneys, which is the same region of expression as that for the 11betaHSD-1 gene. These results suggest that down-regulation of the Ke 6 gene may lead to elevated corticosterone levels, mediated through an inhibition of 11betaHSD-1 activity.
Network management by delegation (2010)

Network management systems built on a client/server model centralize responsibilities in client manager processes, with server agents playing restrictive support roles. As a result, managers must micro-manage agents through primitive steps, resulting in ineffective distribution of management responsibilities, failure-prone management bottlenecks, and limitations for real time responsiveness. We present a more flexible paradigm, the Manager-Agent Delegation (MAD) framework. It supports the ability to extend the functionality of servers (agents) at execution time, allowing flexible distribution of management responsibilities in a distributed environment. MAD can store and instantiate delegated scripts, and provides a concurrent runtime environment, where they can execute asynchronously without requiring the manager's intervention. A delegation protocol allows a manager to transfer programs, create process instances, and control their execution. We describe the delegation model, its application to network management, and the design of a prototype implementation.
Macro Power from Micro Machinery (1997)

S. D. Senturia Typical turbine engines generate about 100 MW of power. Scaled down to millimeter size, a turbine could generate tens of watts, enough for powering micromachinery. In their Perspective, Epstein and Senturia review past progress and recent developments in micromotor engineering.
Opioids Depress Cortical Centers Responsible for the Volitional Control of Respiration (2009)

Respiratory depression limits provision of safe opioid analgesia and is the main cause of death in drug addicts. Although opioids are known to inhibit brainstem respiratory activity, their effects on cortical areas that mediate respiration are less well understood. Here, functional magnetic resonance imaging was used to examine how brainstem and cortical activity related to a short breath hold is modulated by the opioid remifentanil. We hypothesized that remifentanil would differentially depress brain areas that mediate sensory-affective components of respiration over those that mediate volitional motor control. Quantitative measures of cerebral blood flow were used to control for hypercapnia-induced changes in blood oxygen level-dependent (BOLD) signal. Awareness of respiration, reflected by an urge-to-breathe score, was profoundly reduced with remifentanil. Urge to breathe was associated with activity in the bilateral insula, frontal operculum, and secondary somatosensory cortex. Localized remifentanil-induced decreases in breath hold-related activity were observed in the left anterior insula and operculum. We also observed remifentanil-induced decreases in the BOLD response to breath holding in the left dorsolateral prefrontal cortex, anterior cingulate, the cerebellum, and periaqueductal gray, brain areas that mediate task performance. Activity in areas mediating motor control (putamen, motor cortex) and sensory-motor integration (supramarginal gyrus) were unaffected by remifentanil. Breath hold-related activity was observed in the medulla. These findings highlight the importance of higher cortical centers in providing contextual awareness of respiration that leads to appropriate modulation of respiratory control. Opioids have profound effects on the cortical centers that control breathing, which potentiates their actions in the brainstem.
Naloxone reverses inhibitory effect of electroacupuncture on sympathetic cardiovascular reflex responses (1999)

Acupuncture and electroacupuncture (EA) have been used in traditional Chinese medicine to treat a wide range of diseases and conditions, including angina pectoris and myocardial infarction. In a feline model of reflex-induced reversible myocardial ischemia, electrical stimulation of the median nerves to mimic EA (Neiguan acupoint) significantly improved ischemic dysfunction, secondary to an inhibitory effect of EA on reflex pressor effects evoked by bradykinin (BK). The central mechanism of EA's inhibitory effect in this model is unknown. Accordingly, in alpha-chloralose-anesthetized cats, BK (10 micrograms/ml) was applied to the gallbladder to elicit a cardiovascular reflex response that significantly (P < 0.05) increased arterial blood pressure and heart rate; normalized systolic wall thickening (%WTh) of the left ventricle, measured by ultrasonic single-crystal sonomicrometer, increased by 31 +/- 11% (P < 0.05). After ligation of a side branch of the left anterior descending coronary artery, the reflex pressor response to BK resulted in a significant decrease of %WTh (-32 +/- 6%) in the ischemic region. When bilateral EA of the Neiguan acupoints was performed, the pressor response to BK was inhibited and regional myocardial function was significantly improved (+19 +/- 20%). The inhibitory effects of EA on blood pressure and %WTh were reversed by intravenous injection of naloxone (0.4 mg/kg; n = 9) or microinjection of naloxone (10 nM in 0.1 microliter/site; n = 14) into the rostral ventrolateral medulla (rVLM). Thus %WTh with intravenous naloxone was reduced to -13 +/- 29% (P<0.05) during stimulation of the gallbladder. Our results indicate that the inhibitory effect of EA on the BK-induced pressor response and the consequent improvement of ischemic dysfunction is dependent on the activation of opioid receptors, specifically receptors located in the rVLM.
Six Hundred Years of Autopsies (1971)

Six Hundred Years of Autopsies Get access Frederick Stenn, M.D. Frederick Stenn, M.D. Frederick Stenn, M.D., is Professor of Medicine, Northwestern University Medical School, Chicago. Search for other works by this author on: Oxford Academic PubMed Google Scholar Laboratory Medicine, Volume 2, Issue 1, 1 January 1971, Pages 21–25, https://doi.org/10.1093/labmed/2.1.21 Published: 01 January 1971
A polymorphic dinucleotide repeat in intron 1 of the human tissue plasminogen activator gene (1992)

Journal Article A polymorphic dinucleotide repeat in intron 1 of the human tissue plasminogen activator gene Get access W. Thomas, W. Thomas Department of Molecular Biology, Genentech IncSouth San Francisco, CA 94080, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar D. Drayna D. Drayna Department of Molecular Biology, Genentech IncSouth San Francisco, CA 94080, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 1, Issue 2, May 1992, Page 138, https://doi.org/10.1093/hmg/1.2.138-a Published: 01 May 1992
Targeted agents in non-small cell lung cancer therapy: What is there on the horizon? (2013)

Lung cancer is a heterogeneous group of diseases. There has been much research in lung cancer over the past decade which has advanced our ability to treat these patients with a more personalized approach. The scope of this paper is to review the literature and give a broad understanding of the current molecular targets for which we currently have therapies as well as other targets for which we may soon have therapies. Additionally, we will cover some of the issues of resistance with these targeted therapies. The molecular targets we intend to discuss are epidermal growth factor receptor (EGFR), Vascular endothelial growth factor (VEGF), anaplastic large-cell lymphoma kinase (ALK), KRAS, C-MET/RON, PIK3CA. ROS-1, RET Fibroblast growth factor receptor (FGFR). Ephrins and their receptors, BRAF, and immunotherapies/vaccines. This manuscript only summarizes the work which has been done to date and in no way is meant to be comprehensive.
Adaptive reconstruction algorithm for reducing transmission errors on digital holograms (2008)

We examine the effects of transmission error on the digital holograms in phase-shifting digital holography. It is evident that the reconstruction object image is vulnerable to transmission errors from the noise channel. An estimation-based reconstruction algorithm is used to detect the error points and the largest-error hologram of the error points. Based on the detection result, the adaptive algorithm reconstructs the digital hologram by removing the noise effect on the largest-error hologram. With accurate detection, the proposed algorithm is able to reconstruct an object image from a digital hologram with severe transmission errors.
Effect of ex vivo culture duration on phenotype and cytokine production by mature dendritic cells derived from peripheral blood monocytes (2008)

Extended initial culture of DCs in GM-CSF/IL-4 does not affect yield or viability of subsequently matured DCs, but can adversely affect their ability to homogeneously express high levels of functionally important surface molecules such as CD83 and CCR7 and to produce IL-12.
Effect of light ray overlap between neighboring parallax images in autostereoscopic 3D displays (2009)

A display system with lens arrays at the front of a high-resolution LCD has been known as a method to realize an autostereoscopic three-dimensional (3D) display. In these displays, a light ray overlap between neighboring parallax images affects the image quality. In this study, the overlap effects were investigated for the one-dimensional (horizontal parallax only) integral imaging (1D-II) method. We fabricated samples of 1D-II displays with different levels of light ray overlaps and evaluated the 3D image by subjective assessment. It is found that the 1D-II display utilizing the proper parallax overlaps can eliminate banding artifact and have good 3D image quality within the wide range of a viewing area.
The oscilloscope: A stabilized cathode-ray: Oscillograph with linear time-axis (1927)

A method is described for using a cathode-ray oscillograph for the simultaneous observation of a number of variable quantities by means of a distributor. A linear time-axis, obtained by means of a gas-discharge lamp connected to a source of direct-current through a resistance or thermionic tube, is stabilized by introducing into this circuit a small e. m. f. derived from the same source that supplies the unknown quantities under observation. By making stabilization definitive rather than casual, distortion is avoided. The unknown quantities are thus shown in a form convenient for observation, appearing as stationary curves plotted with time as abscissa. The curves may be superposed about a common zero line, or displaced with reference to each other with separate zero lines. The name oscilloscope is applied to the apparatus here described, assembled as an instrument.