gebhart/patrepeval huggingface dataset:
Small molecular organic photovoltaic cells with exciton blocking layer at anode interface for improved device performance (2011)

We demonstrate enhanced power conversion efficiency (ηPCE) for small molecular-based organic photovoltaic cells with an exciton blocking layer (ExBL) at the anode/donor interface. Although poly(3,4-ethylenedioxythiophene):poly(4-styrene sulfonate) (PEDOT:PSS) films are widely used as anodic buffer layers, they also act as exciton quenchers. To prevent exciton quenching, we introduced a tris[4-(5-phenyl thiophen-2-yl)phenyl]amine layer between the donor and the PEDOT:PSS layer and clarified its effect. By a combination of dual ExBLs at both the anode and cathode sides, we achieved significantly enhanced short circuit current and ηPCE values; the highest ηPCE = 5.24% was obtained by optimizing the device parameters.
A genetic strategy to identify targets for the development of drugs that prevent bacterial persistence (2013)

Antibacterial drug development suffers from a paucity of targets whose inhibition kills replicating and nonreplicating bacteria. The latter include phenotypically dormant cells, known as persisters, which are tolerant to many antibiotics and often contribute to failure in the treatment of chronic infections. This is nowhere more apparent than in tuberculosis caused by Mycobacterium tuberculosis, a pathogen that tolerates many antibiotics once it ceases to replicate. We developed a strategy to identify proteins that Mycobacterium tuberculosis requires to both grow and persist and whose inhibition has the potential to prevent drug tolerance and persister formation. This strategy is based on a tunable dual-control genetic switch that provides a regulatory range spanning three orders of magnitude, quickly depletes proteins in both replicating and nonreplicating mycobacteria, and exhibits increased robustness to phenotypic reversion. Using this switch, we demonstrated that depletion of the nicotinamide adenine dinucleotide synthetase (NadE) rapidly killed Mycobacterium tuberculosis under conditions of standard growth and nonreplicative persistence induced by oxygen and nutrient limitation as well as during the acute and chronic phases of infection in mice. These findings establish the dual-control switch as a robust tool with which to probe the essentiality of Mycobacterium tuberculosis proteins under different conditions, including those that induce antibiotic tolerance, and NadE as a target with the potential to shorten current tuberculosis chemotherapies.
Protective immunity against herpes simplex virus (HSV) type 1 following oral administration of recombinant Salmonella typhimurium vaccine strains expressing HSV antigens. (1997)

Salmonella typhimurium strains expressing foreign antigens of various pathogens are capable of eliciting antigen-specific humoral and cellular immune responses. Attenuated S. typhimurium strain chi4550 (delta(cya) delta(crp) delta(asd)) was used as an expression vector for herpes simplex virus (HSV) antigens. Genes encoding glycoprotein D (gD) and the immediate-early protein ICP27 of HSV-1 were cloned and expressed in plasmid pYA292 (asd+) and subsequently placed into chi4550. Following two oral immunizations, the protective efficacy of recombinant strains against zosteriform challenge with HSV-1 was measured in 3-4-week-old BALB/c mice. Levels of protection observed were 77% with the ICP27 construct but only 31% with the gD construct. Zosteriform protection correlates with a CD4+-mediated delayed-type hypersensitivity (DTH) reaction against HSV. Accordingly, significant DTH was observed only in mice immunized orally with the S. typhimurium ICP27 construct. ELISA analysis of antigen-specific humoral responses failed to detect serum antibody responses following oral administration although recombinant S. typhimurium were isolated from spleens of orally dosed mice up to day 30. Intravenous (i.v.) immunization with the gD-expressing construct did, however, induce detectable serum antibody responses. Some humoral IgA responses against gD in faecal samples were detected as early as 3 weeks post-oral immunization while those induced by the i.v. route were slightly lower. These data suggest that recombinant S. typhimurium HSV antigens are capable of inducing immunity against HSV, some aspects of which are protective against HSV challenge.
Genetic regulation of gibberellin deactivation in Pisum (1995)

Summary The regulation of gibberellin (GA) deactivation was examined using the sin (slender) mutation in the garden pea ( Pisum sativum L.). This mutation blocks the deactivation of GA 20 , the precursor of the bioactive GA 1 . Firstly, crosses were made to combine sin with the GA biosynthesis mutations na , lh i and le‐3 . The combination sin na produced a novel phenotype, with long (‘slender’) basal internodes and extremely short (‘nana’) upper internodes. In contrast, the double mutant sin lh i was phenotypically dwarf. The mutation sin causes an accumulation of GA 20 in maturing seeds, and this was unaffected by na , since the na mutation is not expressed in seeds. In contrast, lh i seeds did not accumulate GA 20 , since lh i imposes an early block on GA biosynthesis. Secondly, the effects of sin on several steps in GA deactivation were investigated. In maturing seeds, the mutation sin blocks two steps in GA 20 metabolism, namely, GA 20 to GA 29 , and GA 29 to GA 29 ‐catabolite. In the vegetative plant, on the other hand, sin blocked the step GA 20 to GA 29 , but not GA 29 to GA 29 ‐catabolite; the steps GA 20 to GA 81 and GA 20 to GA 1 were also not impaired in this mutant. It is clear that the effects of sin , like those of na , are strongly organ‐specific. The presence of separate enzymes for the steps GA 20 to GA 29 and GA 29 to GA 29 ‐catabolite was suggested by the observation that GA 8 inhibited the latter step, but not the former, and by the inability of GA 20 and GA 29 to inhibit each other's metabolism. It is suggested that the Sin gene may be a regulatory gene controlling the expression of two structural genes involved in GA deactivation.
Toward β-Amino Acid Proteins:  Design, Synthesis, and Characterization of a Fifteen Kilodalton β-Peptide Tetramer (2008)

A 28 residue "retro" beta-peptide has been designed to self-assemble as a tetramer, successfully recapitulating the octameric beta-peptide bundle complex Zwit-1F. Z28, the largest beta-peptide synthesized to date, was achieved in a linear, microwave-assisted synthesis in 19% isolated yield and high purity. Z28 forms the expected tetrameric complex and is more stable and cooperative in its folding than Zwit-1F. The successful design and synthesis of Z28 is an important step toward true beta-amino acid proteins.
$Ka$-Band Miniaturized Quasi-Planar High-$Q$ Resonators (2007)

Air-filled copper Ka-band resonators with heights between 250-700 mum are demonstrated with measured unloaded Q factors between 440-829. The low-profile quasi-planar resonators are fabricated using a sequential metal deposition process. Miniaturization of up to 70% with respect to a TE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">101</sub> quasi-planar resonator is accomplished by reducing the footprint of the resonator while maintaining the height. Finite-element simulations predict the measured resonant frequency within less than 1%. Due to fabrication imperfections, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">un</sub> is measured to be approximately 15% less than predicted. The resonators are compatible with air-filled rectangular microcoaxial feed lines fabricated in the same metal-deposition process.
Acute Myeloid Leukemia (AML): Different Treatment Strategies Versus a Common Standard Arm—Combined Prospective Analysis by the German AML Intergroup (2012)

A strictly prospective comparison of different treatment strategies in patients with AML did not show clinically relevant outcome differences when compared through a common standard treatment arm. The results provide a representative basis for further therapeutic approaches.
Pluripotent stem cells reveal the developmental biology of human megakaryocytes and provide a source of platelets for clinical application (2012)

Human pluripotent stem cells [PSCs; including human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] can infinitely proliferate in vitro and are easily accessible for gene manipulation. Megakaryocytes (MKs) and platelets can be created from human ESCs and iPSCs in vitro and represent a potential source of blood cells for transfusion and a promising tool for studying the human thrombopoiesis. Moreover, disease-specific iPSCs are a powerful tool for elucidating the pathogenesis of hematological diseases and for drug screening. In that context, we and other groups have developed in vitro MK and platelet differentiation systems from human pluripotent stem cells (PSCs). Combining this co-culture system with a drug-inducible gene expression system enabled us to clarify the novel role played by c-MYC during human thrombopoiesis. In the next decade, technical advances (e.g., high-throughput genomic sequencing) will likely enable the identification of numerous gene mutations associated with abnormal thrombopoiesis. Combined with such technology, an in vitro system for differentiating human PSCs into MKs and platelets could provide a novel platform for studying human gene function associated with thrombopoiesis.
In-silico analysis of kallikrein gene expression in pancreatic and colon cancers. (2004)

Human kallikreins are a cluster of 15 serine protease genes located in the chromosomal band 19q13.4, a non-randomly rearranged region in many solid tumors, including pancreatic cancer. We utilized the SAGE and EST databases of the Cancer Genome Anatomy Project to perform in-silico analysis of kallikrein gene expression in normal and cancerous pancreatic and colon tissues and cell lines using virtual Northern blotting (VNB), digital differential display (DDD) and X-profiler. At least two kallikreins, KLK6 and KLK10, are significantly up-regulated in pancreatic cancer. We probed 2 normal and 6 pancreatic cancer SAGE libraries with gene-specific tags for each of these kallikreins. KLK6 was found to be expressed in 5/6 cancer libraries and showed the most marked (5-fold) increase in average expression levels in cancer vs. normal. These data were verified by screening the EST databases, where all mRNA clones isolated were from cancerous libraries, with no clones detected in normal pancreatic tissues or cell lines. X-profiler comparison of two pools of normal and cancerous pancreatic libraries further verified the significant increase of KLK6 expression levels in pancreatic cancer. DDD data showed a 13-fold increase in KLK10 expression in pancreatic cancer. Three kallikrein genes, KLK6, 8 and 10 are overexpressed in colon cancer compared to normal colon, while one kallikrein, KLK1, is down-regulated. While no expression of KLK6 was detected in normal colon, KLK6-specific tags were detectable in 2 cancer libraries. Similar results were obtained by EST screening; no KLK6 clones were detected in any of the 28 normal libraries examined, while 10 KLK6 EST clones were found in colon adenocarcinoma. KLK10 was not detectable in normal colon. Gene-specific tags were, however, detectable with high density in colon cancer and 7 EST clones were found to be expressed in colon Adenocarcinoma.
Synthesis of stereoscopic views from monocular endoscopic videos (2010)

Recent studies have shown that 3D imaging provides some unique advantages over traditional 2D imaging for minimal invasive surgery. However, most existing endoscopes still use single-lens cameras, and the use of dual-lens 3D imaging techniques is still limited. This paper proposes an approach to enabling 3D imaging from a single-lens endoscope by automatically synthesizing stereoscopic views from monocular images captured by the endoscope. We first formulate the problem by introducing the notion of normalized disparity, based on which we show that affine reconstruction is sufficient for stereoscopic view synthesis. With this formulation and exploiting other domain-specific constraints, we then propose a robust structure-from-motion algorithm for a sparse set of feature points and a fast, linear interpretation algorithm for creating a dense disparity field for synthesizing stereoscopic views from original monocular video. Both synthetic images and real endoscopic videos are used to evaluate the proposed method. The results demonstrate the feasibility and effectiveness of the proposed method.
VLSI fabrication principles : silicon and gallium arsenide (1994)

Material Properties. Phase Diagrams and Solid Solubility. Crystal Growth and Doping. Diffusion. Epitaxy. Ion Implantation. Native Films. Deposited Films. Etching and Cleaning. Lithographic Processes. Device and Circuit Fabrication. Appendix. Index.
Towards a Detailed Understanding of Bacterial Metabolism—Spectroscopic Characterization of Staphylococcus Epidermidis (2006)

Bacteria are a major cause of infection. To fight disease and growing resistance, research interest is focused on understanding bacterial metabolism. For a detailed evaluation of the involved mechanisms, a precise knowledge of the molecular composition of the bacteria is required. In this article, various vibrational spectroscopic techniques are applied to comprehensively characterize, on a molecular level, bacteria of the strain Staphylococcus epidermidis, an opportunistic pathogen which has evolved to become a major cause of nosocomial infections. IR absorption spectroscopy reflects the overall chemical composition of the cells, with major focus on the protein vibrations. Smaller sample volumes-down to a single cell-are sufficient to probe the overall chemical composition by means of micro-Raman spectroscopy. The nucleic-acid and aromatic amino-acid moieties are almost exclusively explored by UV resonance Raman spectroscopy. In combination with statistical evaluation methods [hierarchical cluster analysis (HCA), principal component analysis (PCA), linear discriminant analysis (LDA)], the protein and nucleic-acid components that change during the different bacterial growth phases can be identified from the in vivo vibrational spectra. Furthermore, tip-enhanced Raman spectroscopy (TERS) provides insight into the surface structures and follows the dynamics of the polysaccharide and peptide components on the bacterial cells with a spatial resolution below the diffraction limit. This might open new ways for the elucidation of host-bacteria and drug-bacteria interactions.
Affinity Purification of Human τ Proteins and the Construction of a Sensitive Sandwich Enzyme‐Linked Immunosorbent Assay for Human τ Detection (1992)

Immunoaffinity chromatography with a monoclonal antibody produced against bovine tau protein was used to purify tau proteins from human brain. Fifty grams of brain tissue yielded approximately 2 mg of pure tau proteins. The affinity-purified human tau was used to produce a high-titered rabbit anti-human tau serum. The monoclonal anti-tau antibody and the polyclonal rabbit anti-tau serum were then used to construct a sandwich enzyme-linked immunosorbent assay for detection of human tau proteins, with a sensitivity of 1 ng/ml.
STK33 plays an important positive role in the development of human large cell lung cancers with variable metastatic potential (2015)

Serine/threonine kinase 33 (STK33) is a novel protein that has attracted considerable interest in recent years. Previous research has revealed that STK33 expression plays a special role in cancer cell proliferation. However, the mechanisms of STK33 induction of cancer cells remain largely unknown. In this study, it is demonstrated that STK33 expression varies in NL9980 and L9981 cells which are homogeneous cell lines with similar genetic backgrounds. STK33 can promote cell migration and invasion and suppress p53 gene expression in the NL9980 and L9981 cells. In addition, this protein also promotes epithelial-mesenchymal transition (EMT). Moreover, STK33 knockdown decreases tumor-related gene expression and inhibits cell migration, invasion, and EMT, suggesting that STK33 may be a mediator of signaling pathways that are involved in cancer. In conclusion, our results suggest that STK33 may be an important prognostic marker and a therapeutic target for the metastatic progression of human lung cancer.
Cloning and functional comparison of kappa and delta opioid receptors from mouse brain. (1993)

While trying to identify new members of the somatostatin receptor family of G protein-coupled receptors, we isolated cDNAs from a mouse brain library encoding two related receptor-like proteins, designated msl-1 and msl-2, of 380 and 372 amino acids, respectively. There was 61% identity and 71% similarity between the sequences of msl-1 and msl-2. Among members of the G protein-coupled receptor superfamily, the sequences of both msl-1 and msl-1 were most closely related to those of the somatostatin receptors (SSTRs), having approximately 35% identity with the sequence of SSTR1. Transient expression in COS-1 cells showed that msl-1 and msl-2 did not bind somatostatin. Rather they bound opioids selectively and with high affinity and had the pharmacological properties of kappa and delta opioid receptors, respectively. Indeed, the sequence of msl-2 was identical to that of a delta opioid receptor recently cloned by other workers. Functional characterization of kappa/msl-1 and delta/msl-2 opioid receptors showed that they were coupled to G proteins and mediated opioid receptor class-specific agonist inhibition of forskolin-stimulated cAMP formation. RNA blotting studies and in situ hybridization histochemistry showed that kappa opioid receptor mRNA was expressed at high levels in brain in the neocortex, hippocampus, amygdala, medial habenula, hypothalamus (arcuate and paraventricular nuclei), locus ceruleus, and parabrachial nucleus, suggesting that this receptor may play a role in arousal and regulation of autonomic and neuroendocrine functions.
Properties and regulation of the minK potassium channel protein (1997)

The minK gene encodes a protein of 130 amino acids that has a single transmembrane segment and is expressed in many tissues including heart, uterus, and kidney. When Xenopus oocytes are injected with minK mRNA, a very slowly activating voltage-dependent potassium current is induced in these cells. The induced channels appear to result from the interaction of the minK protein with other channel-forming subunits such as the KvLQT1 channel. The minK protein is intimately associated with the structure of the resultant channels, and mutations in minK can alter ion selectivity and modulation by second messengers. Strong candidates for native currents regulated by the minK protein include the slow component of the cardiac delayed rectifier and potassium currents recorded across epithelial cells in vestibular organs and cochlea.
Potential cellular receptors involved in hepatitis C virus entry into cells (2005)

Hepatitis C virus (HCV) infects hepatocytes and leads to permanent, severe liver damage. Since the genomic sequence of HCV was determined, progress has been made towards understanding the functions of the HCV-encoded proteins and identifying the cellular receptor(s) responsible for adsorption and penetration of the virus particle into the target cells. Several cellular receptors for HCV have been proposed, all of which are associated with lipid and lipoprotein metabolism. This article reviews the cellular receptors for HCV and suggests a general model for HCV entry into cells, in which lipoproteins play a crucial role.
Membrane potential difference and intracellular cation concentrations in human placental trophoblast cells in culture. (1996)

1. The electrochemical gradients for Na+ and K+ were assessed in a cell culture model of trophoblast differentiation. 2. Membrane potential difference (Em), intracellular water and Na+ and K+ contents were measured in choriocarcinoma cells (JAr cell line; 96% of which are undifferentiated trophoblast cells) and in mononucleate and multinucleate (differentiated) cytotrophoblast cells isolated from the human placenta at term. 3. There was a significant fall in Em from -57 mV in JAr cells, to -48 and -40 mV in mono-and multinucleate cytotrophoblast cells, respectively. Treatment with ouabain (1 mM for 15 min) depolarized the JAr cell membrane by 15 mV but did not affect cytotrophoblast cell membrane potential. 4. Intracellular K+ concentration was similar in JAr, mono- and multinucleate cytotrophoblast cells but Na+ concentration was higher in mononucleate cytotrophoblast cells compared with JAr cells. 5. Ouabain treatment (3 mM for 15 min) caused a small increase (4.5%) in cell water in mononucleate cytotrophoblast cells but lowered K+ (approximately 30%) and increased Na+ concentration (approximately 125%) in all the trophoblast cells studied. 6. The K+ equilibrium potential (EK) was more negative than Em in all cells and the difference between EK and Em was smaller in JAr cells (-25 mV) than in mono- and multinucleate cytotrophoblast cells (-33 and -43 mV, respectively). 7. The Na+ equilibrium potential (ENa) was positive in the trophoblast cells and the difference between ENa and Em was 122, 100 and 100 mV in JAr, mono- and multinucleate cytotrophoblast cells, respectively. 8. These results suggest that the electrochemical gradient for K+ is affected by the stage of trophoblast cell differentiation. In contrast, the electrochemical gradient for Na+ is similar in mono- and multinucleate cytotrophoblast cells.
Invertible finite elements for robust simulation of large deformation (2004)

We present an algorithm for the finite element simulation of elastoplastic solids which is capable of robustly and efficiently handling arbitrarily large deformation. In fact, our model remains valid even when large parts of the mesh are inverted. The algorithm is straightforward to implement and can be used with any material constitutive model, and for both volumetric solids and thin shells such as cloth. We also provide a mechanism for controlling plastic deformation, which allows a deformable object to be guided towards a desired final shape without sacrificing realistic behavior. Finally, we present an improved method for rigid body collision handling in the context of mixed explicit/implicit time-stepping.
GP-GAN: Towards Realistic High-Resolution Image Blending (2017)

It is common but challenging to address high-resolution image blending in the automatic photo editing application. In this paper, we would like to focus on solving the problem of high-resolution image blending, where the composite images are provided. We propose a framework called Gaussian-Poisson Generative Adversarial Network (GP-GAN) to leverage the strengths of the classical gradient-based approach and Generative Adversarial Networks. To the best of our knowledge, it's the first work that explores the capability of GANs in high-resolution image blending task. Concretely, we propose Gaussian-Poisson Equation to formulate the high-resolution image blending problem, which is a joint optimization constrained by the gradient and color information. Inspired by the prior works, we obtain gradient information via applying gradient filters. To generate the color information, we propose a Blending GAN to learn the mapping between the composite images and the well-blended ones. Compared to the alternative methods, our approach can deliver high-resolution, realistic images with fewer bleedings and unpleasant artifacts. Experiments confirm that our approach achieves the state-of-the-art performance on Transient Attributes dataset. A user study on Amazon Mechanical Turk finds that the majority of workers are in favor of the proposed method.