gebhart/patrepeval huggingface dataset:
Study of Local Structure in Selected Organic–Inorganic Perovskites in the <i>Pm</i>3<i>m</i> Phase (2008)

The local structures of the inorganic component of selected organic–inorganic perovskites (OIPs) are studied by analyzing the X-ray pair distribution function. Whereas the long-range structure of each perovskite is the untilted Pm3̅m phase, all the OIPs showed significant internal distortion of the octahedra. Varying the halide has a significant impact on the lattice constant. There is evidence of local lone-pair distortions for certain compositions. The most complex case of disorder appears to be that of CH3NH3SnBr3.
Increased expression of S100A4 and its prognostic significance in esophageal squamous cell carcinoma (2001)

S100A4 has been implicated in invasion and metastasis of cancer, but prognostic significance of its expression in esophageal squamous cell carcinoma remains unclear. In this study, we examined the expression of S100A4 by Western blot analysis and immunohistochemistry in surgically resected esophageal squamous cell carcinoma. The relationship between S100A4 tissue status and clinicopathological findings was analyzed to assess the prognostic significance of S100A4 in esophageal squamous cell carcinoma. The S100A4 protein level was significantly higher in tumor tissue than in corresponding normal esophageal mucosa (p<0.05) in 22 cases of esophageal carcinoma by Western blot analysis. S100A4 expression was detected in 25% of 52 cases of esophageal squamous cell carcinoma by immunohistochemistry and correlated with the depth of invasion (p<0.05). Patients with S100A4-positive carcinoma had significantly poorer prognosis than those with S100A4-negative carcinoma, which was also true in the cases with deep invasion of the primary cancer (T3, T4) (p<0.01 and p<0.05, respectively). Moreover, S100A4 tissue status remained the only independent prognostic parameter in the multivariate analysis. Our results suggest that S100A4 may play a key role in the progression of esophageal carcinoma and that immunohistochemical detection of S100A4 in the primary tumor may be useful for the prediction of a poor prognosis.
The World in an Eye (2004)

This paper provides a comprehensive analysis of exactly what visual information about the world is embedded within a single image of an eye. It turns out that the cornea of an eye and a camera viewing the eye form a catadioptric imaging system. We refer to this as a corneal imaging system. Unlike a typical catadioptric system, a corneal one is flexible in that the reflector (cornea) is not rigidly attached to the camera. Using a geometric model of the cornea based on anatomical studies, its 3D location and orientation can be estimated from a single image of the eye. Once this is done, a wide-angle view of the environment of the person can be obtained from the image. In addition, we can compute the projection of the environment onto the retina with its center aligned with the gaze direction. This foveated retinal image reveals what the person is looking at. We present a detailed analysis of the characteristics of the corneal imaging system including field of view, resolution and locus of viewpoints. When both eyes of a person are captured in an image, we have a stereo corneal imaging system. We analyze the epipolar geometry of this stereo system and show how it can be used to compute 3D structure. The framework we present in this paper for interpreting eye images is passive and non-invasive. It has direct implications for several fields including visual recognition, human-machine interfaces, computer graphics and human affect studies. 1. What do Eyes Reveal?
A complete genome screen for genes predisposing to severe bipolar disorder in two Costa Rican pedigrees (1996)

Bipolar mood disorder (BP) is a debilitating syndrome characterized by episodes of mania and depression. We designed a multistage study to detect all major loci predisposing to severe BP (termed BP-I) in two pedigrees drawn from the Central Valley of Costa Rica, where the population is largely descended from a few founders in the 16th-18th centuries. We considered only individuals with BP-I as affected and screened the genome for linkage with 473 microsatellite markers. We used a model for linkage analysis that incorporated a high phenocopy rate and a conservative estimate of penetrance. Our goal in this study was not to establish definitive linkage but rather to detect all regions possibly harboring major genes for BP-I in these pedigrees. To facilitate this aim, we evaluated the degree to which markers that were informative in our data set provided coverage of each genome region; we estimate that at least 94% of the genome has been covered, at a predesignated threshold determined through prior linkage simulation analyses. We report here the results of our genome screen for BP-I loci and indicate several regions that merit further study, including segments in 18q, 18p, and 11p, in which suggestive lod scores were observed for two or more contiguous markers. Isolated lod scores that exceeded our thresholds in one or both families also occurred on chromosomes 1, 2, 3, 4, 5, 7, 13, 15, 16, and 17. Interesting regions highlighted in this genome screen will be followed up using linkage disequilibrium (LD) methods.
Handbook of Surface Plasmon Resonance (2008)

Surface plasmon resonance (SPR) plays a dominant role in real-time interaction sensing of biomolecular binding events. This book focuses on a total system description including optics, fluidics and sensor surfaces. It covers all commercial SPR systems in the market. It is the first of its kind and fills a gap in the technical literature as no other handbook on SPR is currently available. The final chapter discussed new trends and a vision is given for future developments and needs of the SPR market. This excellent handbook provides comprehensive information with easy to use, stand-alone chapters and will be of great use to anyone one working with or affiliated to the technology.
Techniques for software thread integration in real-time embedded systems (2002)

This paper presents details of how to perform thread integration to provide low-cost concurrency for general-purpose microcontrollers and microprocessors. A post-pass compiler interleaves multiple threads of control at the machine instruction level for concurrent execution on a uniprocessor and provides very fine-grain multithreading without context switching overhead. Such efficient concurrency allows implementation of real-time functions in software rather than dedicated peripheral hardware. We investigate a set of code transformations which allow systematic integration of a real-time guest thread into a host thread, producing an integrated thread which meets all real-time requirements. The thread integration concept and the associated code transformations have been applied to example functions chosen from three application domains to evaluate the method's feasibility.
Organization of fibroblasts in the heart (2004)

Cardiac fibroblasts are organized into a three-dimensional network in the heart. This organization follows the endomysial weave network that surrounds groups of myocytes. Reverse transcriptase-polymerase chain reaction, Western blots, and immunohistochemistry were used to show that discoidin domain receptor 2 (DDR2) was specific for cardiac fibroblasts and not expressed on endothelial cells, smooth muscle cells, or cardiac myocytes. DDR2 is expressed early in development and in the adult heart. High voltage electron microscopy (HVEM), scanning electron microscopy, and laser scanning confocal microscopy document the three-dimensional organization of fibroblasts in the heart. Antibodies against connexin 43 and 45 showed different patterns but confirmed, along with HVEM, that fibroblasts are connected to each other as well as cardiac myocytes. The implications of this arrangement of fibroblasts can be important to cardiac function. The signaling of DDR2 and the expression of matrix metalloproteinase 2 in relation to collagen turnover and remodeling is discussed.
A Novel Approach for Characterizing Protein Ligand Complexes:  Molecular Basis for Specificity of Small-Molecule Bcl-2 Inhibitors (2002)

The increasing diversity of small molecule libraries has been an important source for the development of new drugs and, more recently, for unraveling the mechanisms of cellular events-a process termed chemical genetics.(1) Unfortunately, the majority of currently available compounds are mechanism-based enzyme inhibitors, whereas most of cellular activity regulation proceeds on the level of protein-protein interactions. Hence, the development of small molecule inhibitors of protein-protein interactions is important. When screening compound libraries, low-micromolar inhibitors of protein interactions can be routinely found. The enhancement of affinities and rationalization of the binding mechanism require structural information about the protein-ligand complexes. Crystallization of low-affinity complexes is difficult, and their NMR analysis suffers from exchange broadening, which limits the number of obtainable intermolecular constraints. Here we present a novel method of ligand validation and optimization, which is based on the combination of structural and computational approaches. We successfully used this method to analyze the basis for structure-activity relationships of previously selected (2) small molecule inhibitors of the antiapoptotic protein Bcl-xL and identified new members of this inhibitor family.
Follistatin modulates activin activity in a cell- and tissue-specific manner. (1993)

The high affinity activin-binding protein, follistatin, has recently been shown to block activin-stimulated activities in several in vitro systems. In the present study we sought to extend these observations and investigate the effects of follistatin on the activity of activin in stimulating the re-aggregation of Sertoli cell monolayers and proliferation of testicular germ cells, as measured by incorporation of [3H]-thymidine in vitro. Germ-Sertoli cell cocultures prepared from 21 day old rats were treated with media alone or media containing recombinant human (rh) activin A or rh activin B with or without follistatin, the low affinity activin-binding protein, alpha 2 macroglobulin, or a monoclonal antibody (mAB) known to block activin B activity. Follistatin blocked the ability of activin A to stimulate reaggregation of Sertoli cell monolayers when present at a 2-fold ratio (wt/wt) to activin. However, in these same cultures, follistatin had no effect on the ability of activin A to stimulate [3H]-thymidine incorporation. In activin B-treated cultures, both responses could be blocked by the addition of a neutralizing mAB directed against activin B. These results suggest that follistatin can modulate activin action in a cell-type specific fashion, and that this protein may play an important role in regulating the bioavailability of activin.
Rice Resistance to Planthoppers and Leafhoppers (2012)

For over 50 years, host-plant resistance has been regarded as an efficient method to reduce yield losses to rice caused by delphacid and cicadelid hoppers. Already a number of resistant rice varieties have been developed and deployed throughout Asia. To date, over 70 hopper resistance genes have been identified in rice; however, less than 10 genes have been deliberately introduced to commercial rice varieties. Currently, due to recent brown planthopper (Nilaparvata lugens [Stål]) and whitebacked planthopper (Sogatella furcifera [Horvath]) outbreaks occurring at an unprecedented scale, researchers are working toward a second generation of resistant varieties using newly identified gene loci and applying new molecular breeding methods. This paper reviews advances in the identification of resistance genes and QTLs against hoppers in rice. It collates all published information on resistance loci and QTLs against the major rice planthoppers and leafhoppers and presents information on gene locations, genetic markers, differential varieties, and wild rice species as sources of resistance. The review indicates that, whereas progress in the identification of genes has been rapid, considerable tidying of the information is required, especially regarding gene nomenclature and resistance spectra. Furthermore, sound information on gene functioning is almost completely lacking. However, hopper responses to resistance mechanisms are likely to be similar because a single phenotyping technique has been applied by most national and international breeding programs during germplasm screening. The review classifies genes occurring at two chromosome regions associated with several identified resistance loci and highlights these (Chr4S: BphR-R and Chr12L: BphR-R) as general stress response regions. The review calls for a greater diversity of phenotyping methods to enhance the durability of resistant varieties developed using marker-aided selection and emphasizes a need to anticipate the development of virulent hopper populations in response to the field deployment of genes.
New insights into pulmonary inflammation in cystic fibrosis (2006)

Persistent lower airway infection with inflammation is the major cause of morbidity and mortality in cystic fibrosis. This review examines the recent advances in the understanding of airway inflammation in cystic fibrosis, and focuses on the evidence that pulmonary inflammation is, under some circumstances, disassociated from infection, and the potential implications for therapeutic intervention.
The Production and Evaluation of Contrast-Carrying Liposomes Made with an Automatic High-Pressure System (1987)

An automatic, high-pressure system (Microfluidizer) has been found useful for producing contrast-carrying liposomes on an industrial scale. The goal of this investigation was to determine the feasibility of using this new microemulsification process to manufacture contrast-carrying microemulsified liposomes (MELs). Seven contrast media (three ionic, four nonionic) were encapsulated into the MELs. Light and electron microscopy, light scattering, radioisotope, and CT scan techniques were used to characterize these MELs, and the contrast entrapments among the studied media were compared. The contrast-carrying MELs had good properties for imaging normal reticuloendothelial tissues, selectively. They had a narrow size range (0.1-3.0 micron), a single bilayer wall, high liver and spleen upake, and low leakage rates. The nonionic media were significantly more effectively entrapped in the MELs than the ionic media (P less than .05). The iodine-to-lipid weight ratio was about 1:16 for ionic media and 1:4 for nonionic media. Physical properties of the contrast media such as osmotic pressure and charge appeared to affect contrast entrapment. It was concluded that the microemulsification process is a useful system for producing contrast-carrying liposomes continuously, on a large scale and in a reproducible manner.
HIV-1 Protein Nef Inhibits Activity of ATP-binding Cassette Transporter A1 by Targeting Endoplasmic Reticulum Chaperone Calnexin (2014)

HIV-infected patients are at increased risk of developing atherosclerosis, in part due to an altered high density lipoprotein profile exacerbated by down-modulation and impairment of ATP-binding cassette transporter A1 (ABCA1) activity by the HIV-1 protein Nef. However, the mechanisms of this Nef effect remain unknown. Here, we show that Nef interacts with an endoplasmic reticulum chaperone calnexin, which regulates folding and maturation of glycosylated proteins. Nef disrupted interaction between calnexin and ABCA1 but increased affinity and enhanced interaction of calnexin with HIV-1 gp160. The Nef mutant that did not bind to calnexin did not affect the calnexin-ABCA1 interaction. Interaction with calnexin was essential for functionality of ABCA1, as knockdown of calnexin blocked the ABCA1 exit from the endoplasmic reticulum, reduced ABCA1 abundance, and inhibited cholesterol efflux; the same effects were observed after Nef overexpression. However, the effects of calnexin knockdown and Nef on cholesterol efflux were not additive; in fact, the combined effect of these two factors together did not differ significantly from the effect of calnexin knockdown alone. Interestingly, gp160 and ABCA1 interacted with calnexin differently; although gp160 binding to calnexin was dependent on glycosylation, glycosylation was of little importance for the interaction between ABCA1 and calnexin. Thus, Nef regulates the activity of calnexin to stimulate its interaction with gp160 at the expense of ABCA1. This study identifies a mechanism for Nef-dependent inactivation of ABCA1 and dysregulation of cholesterol metabolism.
Differential Splicing Alters Subcellular Localization of the Alpha but not Beta Isoform of the MIER1 Transcriptional Regulator in Breast Cancer Cells (2012)

MIER1 was originally identified in a screen for novel fibroblast growth factor activated early response genes. The mier1 gene gives rise to multiple transcripts encoding protein isoforms that differ in their amino (N-) and carboxy (C-) termini. Much of the work to date has focused on the two C-terminal variants, MIER1α and β, both of which have been shown to function as transcriptional repressors. Our previous work revealed a dramatic shift in MIER1α subcellular localization from nuclear in normal breast tissue to cytoplasmic in invasive breast carcinoma, suggesting that loss of nuclear MIER1α may play a role in breast cancer development. In the present study, we investigated whether alternative splicing to include a cassette exon and produce an N-terminal variant of MIER1α affects its subcellular localization in MCF7 breast carcinoma cells. We demonstrate that this cassette exon, exon 3A, encodes a consensus leucine-rich nuclear export signal (NES). Inclusion of this exon in MIER1α to produce the MIER1-3Aα isoform altered its subcellular distribution in MCF7 cells from 81% nuclear to 2% nuclear and this change in localization was abrogated by mutation of critical leucines within the NES. Treatment with leptomycin B (LMB), an inhibitor of the nuclear export receptor CRM1, resulted in a significant increase in the percentage of cells with nuclear MIER1-3Aα, from 4% to 53%, demonstrating that cytoplasmic localization of this isoform was due to CRM1-dependent nuclear export. Inclusion of exon 3A in MIER1β to produce the N-terminal variant MIER1-3Aβ however had little effect on the nuclear targeting of this isoform. Our results demonstrate that alternative splicing to include exon 3A specifically affects the localization pattern of the α isoform.
LAG-3, a novel lymphocyte activation gene closely related to CD4. (1990)

We have identified a novel human gene of the Ig superfamily, designated LAG-3. Expression of this gene is undetectable in resting PBL, while it is found (a 2-kb message) in activated T and NK cells. The LAG-3 gene includes eight exons; the corresponding cDNA encodes a 498-amino acid membrane protein with four extracellular IgSF domains. The first one belongs to the V-SET; it is particular since it includes an extra loop in the middle of the domain and an unusual intrachain disulphide bridge. The three other domains belong to the C2-SET. Strong internal homologies are found in the LAG-3 molecule between domains 1 and 3, as well as between domains 2 and 4. It is therefore likely that LAG-3 has evolved by duplication of a pre-existing gene encoding a two IgSF-domain structure. The compared analysis of LAG-3 and CD4, with respect to both their peptidic sequence as well as their exon/intron organization, indicated that the two molecules are closely related. This point is strengthened by the finding that both genes are located on the distal part of the short arm of chromosome 12.
III–V multijunction solar cells for concentrating photovoltaics (2008)

Concerns about the changing environment and fossil fuel depletion have prompted much controversy and scrutiny. One way to address these issues is to use concentrating photovoltaics (CPV) as an alternate source for energy production. Multijunction solar cells built from III–V semiconductors are being evaluated globally in CPV systems designed to supplement electricity generation for utility companies. The high efficiency of III–V multijunction concentrator cells, with demonstrated efficiency over 40% since 2006, strongly reduces the cost of CPV systems, and makes III–V multijunction cells the technology of choice for most concentrator systems today. In designing multijunction cells, consideration must be given to the epitaxial growth of structures so that the lattice parameter between material systems is compatible for enhancing device performance. Low resistance metal contacts are crucial for attaining high performance. Optimization of the front metal grid pattern is required to maximize light absorption and minimize I2R losses in the gridlines and the semiconductor sheet. Understanding how a multijunction device works is important for the design of next-generation high efficiency solar cells, which need to operate in the 45%–50% range for a CPV system to make better economical sense. However, the survivability of solar cells in the field is of chief concern, and accelerated tests must be conducted to assess the reliability of devices during operation in CPV systems. These topics are the focus of this review.
Design of Energy- and Cost-Efficient Massive MIMO Arrays (2015)

Large arrays of radios have been exploited for beamforming and null steering in both radar and communication applications, but cost and form factor limitations have precluded their use in commercial systems. This paper discusses how to build arrays that enable multiuser massive multiple-input-multiple-output (MIMO) and aggressive spatial multiplexing with many users sharing the same spectrum. The focus of the paper is the energy- and cost-efficient realization of these arrays in order to enable new applications. Distributed algorithms for beamforming are proposed, and the optimum array size is considered as a function of the performance of the receiver, transmitter, frequency synthesizer, and signal distribution within the array. The effects of errors such as phase noise and synchronization skew across the array are analyzed. The paper discusses both RF frequencies below 10 GHz, where fully digital techniques are preferred, and operation at millimeter (mm)-wave bands where a combination of digital and analog techniques are needed to keep cost and power low.
Genetic Analysis of Regulatory Mutants Affecting Synthesis of Extracellular Proteinases in the Yeast <i>Yarrowia lipolytica</i>: Identification of a <i>RIM101/pacC</i> Homolog (1997)

Depending on the pH of the growth medium, the yeast Yarrowia lipolytica secretes both an acidic proteinase and an alkaline proteinase, the synthesis of which is also controlled by carbon, nitrogen, and sulfur availability, as well as by the presence of extracellular proteins. Recessive mutations at four unlinked loci, named PAL1 to PAL4, were isolated which prevent alkaline proteinase derepression under conditions of carbon and nitrogen limitation at pH 6.8. These mutations markedly affect mating and sporulation. A dominant suppressor of all four PAL mutations was isolated from a wild-type genomic library, which turned out to be a C-terminally truncated form of a 585-residue transcriptional factor of the His2Cys2 zinc finger family, which we propose to call YlRim101p. Another C-terminally truncated version of YlRim101p (419 residues) is encoded by the dominant RPH2 mutation previously isolated as expressing alkaline protease independently of the pH. YlRim101p is homologous to the transcriptional activators Rim101p of Saccharomyces cerevisiae, required for entry into meiosis, and PacC of Aspergillus nidulans and Penicillium chrysogenum, which were recently shown to mediate regulation by ambient pH. YlRim101p appears essential for mating and sporulation and for alkaline proteinase derepression. YlRIM101 expression is autoregulated, maximal at alkaline pH, and strongly impaired by PAL mutations.