gebhart/patrepeval huggingface dataset:
The use of transgenic and naturally occurring mutants to understand and manipulate tomato fruit ripening (1994)

ABSTRACT In the years since we last reviewed the use of mutants to study tomato fruit ripening ( Grierson et al. 1987 ), considerable information has been gained by the cloning, sequencing and identification of many mRNAs implicated in this developmental process. Genes involved in cell wall degradation, colour change and ethylene synthesis have been cloned, and antisense techniques have been developed and used to produce genetically engineered mutant fruit deficient in these aspects of ripening (see Gray et al. 1992 ). Recently, a previously cloned ripening gene has been used to complement a naturally occurring fruit colour mutant, yellow flesh ( Fray &amp; Grierson 1993a ), and a ripening impaired mutant, ripening inhibitor , has been used to identify several new ripening‐related mRNAs ( Picton et al. 1993b ). The chromosomal region bearing the ripening inhibitor mutation has been subjected to high‐resolution mapping ( Churchill, Giovannoni &amp; Tanksley 1993 ) and chromosome walking experiments are in progress to identify this gene.
PPDB: The Paraphrase Database (2013)

We present the 1.0 release of our paraphrase database, PPDB. Its English portion, PPDB:Eng, contains over 220 million paraphrase pairs, consisting of 73 million phrasal and 8 million lexical paraphrases, as well as 140 million paraphrase patterns, which capture many meaning-preserving syntactic transformations. The paraphrases are extracted from bilingual parallel corpora totaling over 100 million sentence pairs and over 2 billion English words. We also release PPDB:Spa, a collection of 196 million Spanish paraphrases. Each paraphrase pair in PPDB contains a set of associated scores, including paraphrase probabilities derived from the bitext data and a variety of monolingual distributional similarity scores computed from the Google n-grams and the Annotated Gigaword corpus. Our release includes pruning tools that allow users to determine their own precision/recall tradeoff. 1
Mechanics of hemispherical electronics (2009)

A simple analytical model is established for the development of hemisphere electronics, which has many important applications in electronic-eye cameras and related curvilinear systems. The photodetector arrays, made in planar mesh layouts with conventional techniques, are deformed and transferred onto a hemisphere. The model gives accurately the positions of photodetectors on the hemisphere, and has been validated by experiments and finite element analysis. The results also indicate very small residual strains in the photodetectors. The model provides a tool to define a pattern of photodetectors in the planar, as-fabricated layout to yield any desired spatial configuration on the hemisphere.
Recombination in the Hemagglutinin Gene of the 1918 "Spanish Flu" (2001)

When gene sequences from the influenza virus that caused the 1918 pandemic were first compared with those of related viruses, they yielded few clues about its origins and virulence. Our reanalysis indicates that the hemagglutinin gene, a key virulence determinant, originated by recombination. The "globular domain" of the 1918 hemagglutinin protein was encoded by a part of a gene derived from a swine-lineage influenza, whereas the "stalk" was encoded by parts derived from a human-lineage influenza. Phylogenetic analyses showed that this recombination, which probably changed the virulence of the virus, occurred at the start of, or immediately before, the pandemic and thus may have triggered it.
Thrombin-Activatable Microbubbles as Potential Ultrasound Contrast Agents for the Detection of Acute Thrombosis (2017)

Acute deep vein thrombosis (DVT) is the formation of a blood clot in the deep veins of the body that can lead to fatal pulmonary embolism. Acute DVT is difficult to distinguish from chronic DVT by ultrasound (US), the imaging modality of choice, and is therefore treated aggressively with anticoagulants, which can lead to internal bleeding. Here we demonstrate that conjugating perfluorobutane-filled (PFB-filled) microbubbles (MBs) with thrombin-sensitive activatable cell-penetrating peptides (ACPPs) could lead to the development of contrast agents that detect acute thrombosis with US imaging. Successful conjugation of ACPP to PFB-filled MBs was confirmed by fluorescence microscopy and flow cytometry. Fluorescein-labeled ACPP was used to evaluate the efficiency of thrombin-triggered cleavage by measuring the mean fluorescence intensity of ACPP-labeled MBs (ACPP-MBs) before and after incubation at 37 °C with thrombin. Lastly, control MBs and ACPP-MBs were infused through a tube containing a clot, and US contrast enhancement was measured with or without the presence of a thrombin inhibitor after washing the clot with saline. With thrombin activity, 91.7 ± 14.2% of the signal was retained after ACPP-MB infusion and washing, whereas only 16.7 ± 4% of the signal was retained when infusing ACPP-MBs in the presence of hirudin, a potent thrombin inhibitor.
Isolation, Structure Elucidation, and Synthesis of a Macrophage Stimulatory Lipopeptide from Mycoplasma fermentans Acting at Picomolar Concentration (1997)

Macrophages are typically stimulated by components of microbial cell walls. Surprisingly, cell wall-less mycoplasmas can also very efficiently stimulate macrophages. We showed recently that mycoplasma-derived lipopeptides constitute the active principle. We have now isolated a clone of Mycoplasma fermentans expressing mainly one macrophage-stimulating lipopeptide. This lipopeptide was detergent-extracted and isolated by reversed-phase high-performance liquid chromotography, using nitric oxide release from C3H/HeJ mouse macrophages as bioassay for detection. In contrast to "conventional" bacterial lipoproteins, this lipopeptide had a free NH2 terminus. Amino acid composition, sequence, and the molecular weight of 2,163. 3 are consistent with the following structure: S-(2, 3-bisacyloxypropyl)cysteine-GNNDESNISFKEK with one mole C16:0, and a further mole of a mixture of C18:0 and C18:1 fatty acid per lipopeptide molecule. The sequence could not be found in either the protein identification resource nor the Swiss Prot data bank. We named this 2-kD lipopeptide, macrophage-activating lipopeptide-2 (MALP-2). Synthetic dipalmitoyl MALP-2 and mycoplasma-derived MALP-2 were compared with the bioassay. Both lipopeptides showed an identical dose dependency with a half-maximal response at 10(-11) M concentration. MALP-2 may be one of the most potent natural macrophage stimulators besides endotoxin.
Cloning of the Complete DNA Genomes of Four Bean-Infecting Geminiviruses and Determining Their Infectivity by Electric Discharge Particle Acceleration (1991)

Geminiviruses are small plant viruses that encapsidate a single-stranded circular DNA and form double-stranded DNAs in infected plants. Infection of economically important hosts with cloned DNAs of geminiviruses frequently has been difficult. Four isolates of bipartite bean-infecting geminiviruses (bean golden mosaic geminivirus isolates from Brazil [BGMV-BZ], Guatemala [BGMV-GA], and the Dominican Republic [BGMV-DR]; and bean dwarf mosaic geminivirus from Colombia [BDMV-CO]) were cloned; full-length cloned double-stranded DNA components A and B of each isolate were not infectious when mechanically coinoculated onto bean primary leaves by surface abrasion but were infectious when coinoculated into radicles of beans (Phaseolus vulgaris) by electric discharge particle acceleration. This novel method for the introduction of cloned geminiviral DNA into plants was extremely efficient and resulted in symptom expression in as few as 7 days. Moreover, infection of beans by cloned DNAs of BGMV-BZ, which has never been mechanically transmitted as virions or cloned DNAs, indicated that this procedure circumvents plant barriers to mechanical transmission. Three engineered mutants of BGMV-GA component A were constructed and separately introduced into beans with wild-type BGMV-GA component B, and disease phenotypes determined. Soybeans (Glycine max) also were infected with cloned DNAs of BGMV-BZ, BGMV-GA, and BDMV-CO, demonstrating a potentially important alternate host for these viruses. Particle acceleration will facilitate genetic analysis of bean-infecting geminiviruses and may allow for the efficient introduction of viral nucleic acids or virions of other viruses into hosts that are refractory to mechanical transmission.
High-resolution functional proteomics by active-site peptide profiling (2005)

Characterization and functional annotation of the large number of proteins predicted from genome sequencing projects poses a major scientific challenge. Whereas several proteomics techniques have been developed to quantify the abundance of proteins, these methods provide little information regarding protein function. Here, we present a gel-free platform that permits ultrasensitive, quantitative, and high-resolution analyses of protein activities in proteomes, including highly problematic samples such as undiluted plasma. We demonstrate the value of this platform for the discovery of both disease-related enzyme activities and specific inhibitors that target these proteins.
Brief Report: A Differential Transcriptomic Profile of Ex Vivo Expanded Adult Human Hematopoietic Stem Cells Empowers Them for Engraftment Better than Their Surface Phenotype (2017)

Abstract Transplantation of small cord blood (CB) units, or of autologous ex vivo-genetically modified adult hematopoietic stem cells (HSC), face the common challenge of suboptimal HSC doses for infusion and impaired engraftment of the transplanted cells. Ex vivo expansion of HSCs, using either cell-based coculture approaches or especially small molecules have been successfully tested mainly in CB and in prolonged cultures. Here, we explored whether innovative combinations of small molecules can sufficiently, after short culture, expand adult HSCs while retaining their functionality in vivo. We found that 5-day cultured cells, in the presence of the small molecule combinations tested, achieved higher engraftment levels in NSG mice than both their uncultured and their cytokine only-cultured counterparts. Surprisingly, the engraftment levels were neither concordant to the numbers of phenotypically similar HSCs expanded under different small molecule combinations, nor explained by their distinct companion cells present. Transcriptomic comparative analysis of sorted, phenotypically similar, ex vivo generated HSCs transplanted in equal numbers, suggested that HSCs generated under expansion conditions that maintain low expression of the Rap1/Ras/PI3K-AKT pathway exhibit a superior functional profile in vivo.
Describing Videos by Exploiting Temporal Structure (2015)

Recent progress in using recurrent neural networks (RNNs) for image description has motivated the exploration of their application for video description. However, while images are static, working with videos requires modeling their dynamic temporal structure and then properly integrating that information into a natural language description model. In this context, we propose an approach that successfully takes into account both the local and global temporal structure of videos to produce descriptions. First, our approach incorporates a spatial temporal 3-D convolutional neural network (3-D CNN) representation of the short temporal dynamics. The 3-D CNN representation is trained on video action recognition tasks, so as to produce a representation that is tuned to human motion and behavior. Second we propose a temporal attention mechanism that allows to go beyond local temporal modeling and learns to automatically select the most relevant temporal segments given the text-generating RNN. Our approach exceeds the current state-of-art for both BLEU and METEOR metrics on the Youtube2Text dataset. We also present results on a new, larger and more challenging dataset of paired video and natural language descriptions.
Percutaneous Left Atrial Appendage Occlusion (PLAATO) for Preventing Cardioembolism (2002)

Transcatheter LAA occlusion is simple and feasible. At the follow-up study, the device remained in the LAA, with benign healing and no evidence of new thrombus or damage to surrounding structures. This new strategy may provide an alternative treatment for patients with nonvalvular atrial fibrillation who are less than optimal candidates for warfarin.
Intermittent Administration of Inhaled Tobramycin in Patients with Cystic Fibrosis (1999)

In a 24-week study of patients with cystic fibrosis, intermittent administration of inhaled tobramycin was well tolerated and improved pulmonary function, decreased the density of P. aeruginosa in sputum, and decreased the risk of hospitalization.
Differential interactions of heparin and heparan sulfate glycosaminoglycans with the selectins. Implications for the use of unfractionated and low molecular weight heparins as therapeutic agents. (1998)

The selectins are calcium-dependent C-type lectins that bind certain sialylated, fucosylated, sulfated glycoprotein ligands. L-selectin also recognizes endothelial proteoglycans in a calcium-dependent manner, via heparan sulfate (HS) glycosaminoglycan chains enriched in unsubstituted glucosamine units. We now show that these HS chains can also bind P-selectin, but not E-selectin. However, while L-selectin binding requires micromolar levels of free calcium, P-selectin recognition is largely divalent cation-independent. Despite this, HS chains bound to P-selectin are eluted by ethylenediamine tetraacetic acid (EDTA), but only at high concentrations. Porcine intestinal mucosal (mast cell-derived) heparin (PIM-heparin) shows similar properties, with no binding to E-selectin, calcium-dependent binding of a subfraction to L-selectin and to P-selectin, and calcium-independent binding of a larger fraction to P-selectin, the latter being disrupted by high EDTA concentrations. Analysis of defined heparin fragment pools shows a size dependence for interaction, with tetradecasaccharides showing easily detectable binding to L- and P-selectin affinity columns. L-selectin binding fragments include more heavily sulfated and epimerized regions and, as with the endothelial HS chains, they are enriched in free amino groups. The P-selectin binding component includes this fraction as well as some less highly modified regions. Thus, endothelium-derived HS chains and mast cell-derived heparins could play a role in modulating the biology of selectins in vivo. Notably, P- and L-selectin binding to sialyl-Lewisx and to HL-60 cells (which are known to carry the native ligand PSGL-1) is inhibited by unfractionated pharmaceutical heparin preparations at concentrations 12-50-fold lower than those recommended for effective anticoagulation in vivo. In contrast, two low molecular weight heparins currently considered as clinical replacements for unfractionated heparin are much poorer inhibitors. Thus, patients undergoing heparin therapy for other reasons may be experiencing clinically significant inhibition of L- and P-selectin function, and the current switchover to low-molecular weight heparins may come at some loss of this effect. Low-dose unfractionated heparin should be investigated as a treatment option for acute and chronic diseases in which P- and L-selectin play pathological roles.
Glymes as versatile solvents for chemical reactions and processes: from the laboratory to industry (2013)

Glymes, also known as glycol diethers, are saturated non-cyclic polyethers containing no other functional groups. Most glymes are usually less volatile and less toxic than common laboratory organic solvents; in this context, they are more environmentally benign solvents. However, it is also important to point out that some glymes could cause long-term reproductive and developmental damages despite their low acute toxicities. Glymes have both hydrophilic and hydrophobic characters that common organic solvents are lack of. In addition, they are usually thermally and chemically stable, and can even form complexes with ions. Therefore, glymes are found in a broad range of laboratory applications including organic synthesis, electrochemistry, biocatalysis, materials, and Chemical Vapor Deposition (CVD), etc. In addition, glyme are used in numerous industrial applications, such as cleaning products, inks, adhesives and coatings, batteries and electronics, absorption refrigeration and heat pumps, as well as pharmaceutical formulations, etc. However, there is a lack of comprehensive and critical review on this attractive subject. This review aims to accomplish this task by providing an in-depth understanding of glymes' physicochemical properties, toxicity and major applications.
849. Syntheses in the quinazolone series. Part IV. The conversion of N-aroylorthanilamides into 2-arylquinazol-4-ones (1956)

H. Stephen and G. Wadge, J. Chem. Soc., 1956, 4420 DOI: 10.1039/JR9560004420
Beta (β) tungsten thin films: Structure, electron transport, and giant spin Hall effect (2015)

We use a simple magnetron sputtering process to fabricate beta (β) tungsten thin films, which are capable of generating giant spin Hall effect. As-deposited thin films are always in the metastable β-W phase from 3.0 to 26.7 nm. The β-W phase remains intact below a critical thickness of 22.1 nm even after magnetic thermal annealing at 280 °C, which is required to induce perpendicular magnetic anisotropy (PMA) in a layered structure of β-W/Co40Fe40B20/MgO. Intensive annealing transforms the thicker films (&amp;gt;22.1 nm) into the stable α-W phase. We analyze the structure and grain size of both β- and α-W thin films. Electron transport in terms of resistivity and normal Hall effect is studied over a broad temperature range of 10 K to at least 300 K on all samples. Very low switching current densities are achieved in β-W/Co40Fe40B20/MgO with PMA. These basic properties reveal useful behaviors in β-W thin films, making them technologically promising for spintronic magnetic random access memories and spin-logic devices.
Nothing Else Matters: Model-Agnostic Explanations By Identifying Prediction Invariance (2016)

At the core of interpretable machine learning is the question of whether humans are able to make accurate predictions about a model's behavior. Assumed in this question are three properties of the interpretable output: coverage, precision, and effort. Coverage refers to how often humans think they can predict the model's behavior, precision to how accurate humans are in those predictions, and effort is either the up-front effort required in interpreting the model, or the effort required to make predictions about a model's behavior. In this work, we propose anchor-LIME (aLIME), a model-agnostic technique that produces high-precision rule-based explanations for which the coverage boundaries are very clear. We compare aLIME to linear LIME with simulated experiments, and demonstrate the flexibility of aLIME with qualitative examples from a variety of domains and tasks.
Modulation of Paired Immunoglobulin-Like Type 2 Receptor Signaling Alters the Host Response toStaphylococcus aureus-Induced Pneumonia (2010)

Paired immunoglobulin-like type 2 receptors (PILRs) inhibitory PILRalpha and activating PILRbeta are predominantly expressed on myeloid cells. Their functions in host defense and inflammation are largely unknown, and in this study, we evaluated their roles in an acute Staphylococcus aureus pneumonia model. Compared to their respective controls, Pilrb(-/-) mice or mice in which PILRalpha was activated with an agonistic antibody showed improved clearance of pulmonary staphylococci and improved survival. These mice had reduced serum or bronchoalveolar lavage fluid levels of interleukin-1beta (IL-1beta), tumor necrosis factor alpha (TNF-alpha), and IL-6 and elevated levels of gamma interferon (IFN-gamma), IL-12, and IL-10. In contrast, mice in which PILRbeta was activated had increased lung bacterial burdens and higher mortality coupled with an intense proinflammatory response with highly elevated levels of IL-1beta, TNF-alpha, and IL-6. Treatment groups with reduced bacterial burdens had higher levels of Keratinocyte-derived chemokine (KC), macrophage inflammatory protein 2 (MIP-2), and MIP-1alpha in bronchoalveolar lavage fluid and an increased influx of neutrophils and macrophages to the lungs. Consistent with our in vivo findings, bone marrow-derived macrophages from Pilrb(-/-) mice released significantly less IL-1beta and TNF-alpha and more IFN-gamma and IL-12 than did the wild-type macrophages when directly stimulated with heat-killed S. aureus. To our knowledge, this is the first evidence that S. aureus directly interacts with PILRbeta. It provides a mechanism by which manipulating the balance in favor of an inhibitory PILR signal, by activation of PILRalpha or deletion of PILRbeta, helps to control acute S. aureus-mediated pneumonia and attenuate the inflammatory response. These results highlight the importance of PILRs in innate immunity and the control of inflammation.
Modal analysis of a small surface emitting laser with a selectively oxidized waveguide (1995)

We describe studies of an index-guided ∼4×3 μm2 vertical cavity surface emitting laser with a cw, room temperature 133 μA threshold current and 53% slope efficiency fabricated using selective wet thermal oxidation to provide optical and electrical confinement. While the device operates strictly single mode, a large number of transverse modes are evident in the subthreshold luminescence observed in both vertical and lateral directions. Despite the lumped nature of the index region, the transverse mode wavelengths agree very well with those predicted for a conventional distributed waveguide structure. Waveguide dimensions and an effective index step of 2% between the active and cladding region are determined by fitting the modal data.
Pathophysiology of Acute Ischaemic Stroke: An Analysis of Common Signalling Mechanisms and Identification of New Molecular Targets (2006)

Stroke continues to be a major cause of death and disability. The currently available therapies have proven to be highly unsatisfactory (except thrombolysis) and attempts are being made to identify and characterize signalling proteins which could be exploited to design novel therapeutic modalities. The pathophysiology of stroke is a complex process. Delaying interventions from the first hours to days or even weeks following blood vessel occlusion may lead to worsening or impairment of recovery in later stages. The objective of this review is to critically evaluate the major mechanisms underlying stroke pathophysiology, especially the role of cell signalling in excitotoxicity, inflammation, apoptosis, neuroprotection and angiogenesis, and highlight potential novel targets for drug discovery.