gebhart/patrepeval huggingface dataset:
Salt Marsh Values: Retrospection from the end of the Century (2005)

Two of the greatest problems in coastal waters are eutrophicaton and rapid decline in populations of important fish species. Salt marshes are important in combating both these problems. A paradigm for salt marsh function: marshes import inorganic nutrients and export organic nutrients and, as a result, grow fish. As ground and tidal water flow through salt-water wetlands, plants, bacteria and algae produce or transform the organic matter of the food chain that supports fish and shellfish populations. While salt marshes modify the principal plant nutrients, N and P, some of the pathways result in removal of nutrients from biologically active systems. Nitrogen is removed primarily either by being trapped in refractory organic matter that contributes to marsh maintenance through accretion or through loss to the atmosphere (as N2) by denitrification. Salt marshes along the Atlantic coast of the United States have changed during the past century; the number of hectares has declined and the nutrient loading per hectare has increased. We examine data on the correlation between fish catch and various marsh features from Long Island, New York in 1880. We review research on the ways salt marshes reduce both the level and rate of eutrophication of coastal waters by intercepting nitrate in discharging groundwater. Finally, we consider how these functions have changed with the decrease in area of salt marshes along the Atlantic coast from Georgia to Maine.
Contextual conditional models for smartphone-based human mobility prediction (2012)

Human behavior is often complex and context-dependent. This paper presents a general technique to exploit this "multidimensional" contextual variable for human mobility prediction. We use an ensemble method, in which we extract different mobility patterns with multiple models and then combine these models under a probabilistic framework. The key idea lies in the assumption that human mobility can be explained by several mobility patterns that depend on a sub-set of the contextual variables and these can be learned by a simple model. We showed how this idea can be applied to two specific online prediction tasks: what is the next place a user will visit? and how long will he stay in the current place?. Using smartphone data collected from 153 users during 17 months, we show the potential of our method in predicting human mobility in real life.
Redox Stimulation of Human THP‐1 Monocytes in Response to Cold Physical Plasma (2015)

In plasma medicine, cold physical plasma delivers a delicate mixture of reactive components to cells and tissues. Recent studies suggested a beneficial role of cold plasma in wound healing. Yet, the biological processes related to the redox modulation via plasma are not fully understood. We here used the monocytic cell line THP-1 as a model to test their response to cold plasma in vitro. Intriguingly, short term plasma treatment stimulated cell growth. Longer exposure only modestly compromised cell viability but apparently supported the growth of cells that were enlarged in size and that showed enhanced metabolic activity. A significantly increased mitochondrial content in plasma treated cells supported this notion. On THP-1 cell proteome level, we identified an increase of protein translation with key regulatory proteins being involved in redox regulation (hypoxia inducible factor 2α), differentiation (retinoic acid signaling and interferon inducible factors), and cell growth (Yin Yang 1). Regulation of inflammation is a key element in many chronic diseases, and we found a significantly increased expression of the anti-inflammatory heme oxygenase 1 (HMOX1) and of the neutrophil attractant chemokine interleukin-8 (IL-8). Together, these results foster the view that cold physical plasma modulates the redox balance and inflammatory processes in wound related cells.
Preparations of Anthraquinone and Naphthoquinone Derivatives and Their Cytotoxic Effects (2011)

Chrysophanol and 1,8-di-O-hexylchrysophanol derivatives having nucleic acid bases at position 5 were synthesized. Furthermore, derivatives of menadione substituted at position 11 (type A naphthoquinone derivatives) or methylmenadione substituted at position 7 (type B naphthoquinone derivatives) modified with nucleic acid bases, amines and thiocyano, selenocyano or thioacetyl groups were synthesized. The cytotoxic effects of these derivatives on HCT 116 cells, which poorly express P-glycoprotein (P-gp), and Hep G2 cells, which stably express P-gp, were evaluated by performing 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Results were compared with those obtained using 5-fluorouracil (5-FU), which has been used clinically. Several of these derivatives exhibited markedly higher potent cytotoxic effects not only on HCT cancer cells but also Hep G2 cancer cells as compared with 5-FU.
Forging of Heat-Resistant Alloys (2005)

Abstract This article provides a discussion on forging methods, melting procedures, forging equipment, forging practices, grain refinement, and critical factors considered in forging process. It describes the different types of solid-solution-strengthened and precipitation-strengthened superalloys, namely, iron-nickel superalloys, nickel-base alloys, cobalt-base alloys, and powder alloys. The article discusses the microstructural mechanisms during hot deformation and presents processing maps for various superalloys. It concludes with a discussion on heat treatment of wrought heat-resistant alloy forgings.
Picosecond time-gated microscopy of UV-damaged plant tissue (2002)

We demonstrate that picosecond time-gated fluorescence microscopy can be used to monitor subtle changes in the kinetics and spatial distribution of perturbations to the molecular and cellular structure of plant tissue caused by ultraviolet radiation. Single-molecule experiments on Photosystem II and chloroplast preparations give picosecond fluorescence decay kinetics that are similar to those obtained previously on bulk samples. For green plant leaves, localized and well-defined cellular structure is seen for normal material whereas relatively diffuse and non-specific features are seen after UV-irradiation indicating significant UV-induced rupture of the cellular structure. The changes in the chlorophyll fluorescence decay kinetics indicate uncoupling of chlorophyll molecules in the light-harvesting system leading to inhibition of energy reorganization and transfer in the antennae and subsequent exciton transfer to the reaction centers.
Alkaline serine proteinase from <i>Thermomonospora fusca</i> YX. Stability to heat and denaturants (1990)

The serine proteinase isolated from Thermomonospora fusca YX shows considerable thermal stability up to 80 degrees C, and progressive inactivation occurs at higher temperatures. Lyotropic salts affected the thermal stability of the enzyme at 85 degrees C, suggesting that disruption of hydrophobic interactions play an important role in the decreased thermal stability of the enzyme above 80 degrees C. Thermal stability is highly pH-dependent; above pH 6.0-6.5 there is a sharp decrease in the stability of the enzyme, reflecting increased autolysis. Although some stabilization occurs upon increasing ionic strength, Ca2+ binding does not appear to play a role in thermal stability. Denaturants, i.e. 8 M-urea, 6 M-guanidinium chloride or 1% SDS, had no significant effect on the activity of the enzyme after 24 h at 25 degrees C.
SiamRPN++: Evolution of Siamese Visual Tracking With Very Deep Networks (2019)

Siamese network based trackers formulate tracking as convolutional feature cross-correlation between target template and searching region. However, Siamese trackers still have accuracy gap compared with state-of-the-art algorithms and they cannot take advantage of feature from deep networks, such as ResNet-50 or deeper. In this work we prove the core reason comes from the lack of strict translation invariance. By comprehensive theoretical analysis and experimental validations, we break this restriction through a simple yet effective spatial aware sampling strategy and successfully train a ResNet-driven Siamese tracker with significant performance gain. Moreover, we propose a new model architecture to perform depth-wise and layer-wise aggregations, which not only further improves the accuracy but also reduces the model size. We conduct extensive ablation studies to demonstrate the effectiveness of the proposed tracker, which obtains currently the best results on four large tracking benchmarks, including OTB2015, VOT2018, UAV123, and LaSOT. Our model will be released to facilitate further studies based on this problem.
Synthesis of End-Functionalized Polymers by Means of Living Anionic Polymerization. 8. Reactions of Living Anionic Polymers with α,ω-Dihaloalkanes (1997)

In order to prepare well-defined polymers with halogen end groups, anionic living polymers of isoprene and styrene were allowed to react with excess amounts of α,ω-dihaloalkanes in THF at −78 °C. The monosubstitution reactions of 1,3-dichloropropane with these anionic living polymers proceeded cleanly to afford quantitatively the polymers with chlorine end groups that possessed controllable molecular weights and narrow molecular weight distributions. On the other hand, the reactions of the anionic living polymers with either α,ω-dibromoalkanes or α,ω-diiodoalkanes proceeded competitively with side reactions leading to dimer formation of the starting living polymers. Thus, the bromine- and iodine-terminated polymers were obtained in 12−93% yields along with undesirable dimers. As side reaction candidates, we speculated on metal−halogen interchange and/or single electron transfer pathways followed by coupling reactions between the reaction intermediates generated by both pathways. By end-capping the polystyryl anion with 1,1-diphenylethylene, one could almost suppress the dimer formation, and the end-functionalized polystyrenes with bromine and iodine were successfully obtained in more than 95% yield.
Recent Advances in NMR Expanding its Role in Rational Drug Design (2001)

The technology of nuclear magnetic resonance spectroscopy continues to advance at a rapid pace. Recent improvements in gradient technology and the coupling of NMR to various chromatography methods will provide new opportunities in drug discovery. These opportunities include rapid high throughput screening to determine the receptor-bound conformations of small organic ligands. NMR coupled to liquid chromatography has opened a new door to the quantitative and qualitative analysis of complex mixtures including metabolites extracted from body fluids and extracts containing various natural products. This review will focus on the following four advances in NMR technology: 1) pulse-field gradient (PFG) NMR, 2) SAR (structure activity relationship) by NMR, 3) LC-NMR (liquid chromatography), and 4) application of membrane models for the study of neuropeptides. The information content available to medicinal chemists from each experiment will be discussed.
Synthesis of (.+-.)-fredericamycin A (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of (.+-.)-fredericamycin AT. Ross. Kelly, Naohito. Ohashi, Rosemary J. Armstrong-Chong, and Stephen H. BellCite this: J. Am. Chem. Soc. 1986, 108, 22, 7100–7101Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://pubs.acs.org/doi/10.1021/ja00282a042https://doi.org/10.1021/ja00282a042research-articleACS PublicationsRequest reuse permissionsArticle Views532Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A novel electronically scanned white-light interferometer using a Mach-Zehnder approach (1996)

A theoretical analysis and experimental evaluation of a novel Mach-Zehnder interferometer (MZI), used as a recovery interferometer in an electronically scanned white-light interferometer is reported. This modified version of a MZI has the advantages of being very simple and compact, with high stability and does not introduce any spatial "misoverlapping" of the beams. In addition, since only one beamsplitter is employed in the interferometer (instead of the usual two used in a conventional MZI), the system is relatively easy to implement and at low cost. Furthermore, this configuration can be simply set to cover a wide range of optical path difference values by simply changing the angle and position of one of the mirrors. This gives the interferometer the advantage of being easily adapted far a range of different measurement applications.
Physionet Challenge 2011: Improving the quality of electrocardiography data collected using real time QRS-complex and T-Wave detection (2011)

The Physionet Challenge [1] focused on discerning between usable and unusable electrocardiography (ECG) data tele-medically from mobile embedded devices. Based on our publications [2,3,4], we have designed a method to determine the quality of ECG data and its usability using an adaptation of the Tompkins et al [5] real time QRS detection algorithm. With our modifications to the algorithm to cater to a very short length of data, out method is able to differentiate with accuracy the usability of ECG data in training set A as well as test set B.
An Improved Least-Squares Method for Designing Function-Generating Mechanisms (1975)

An improved general theory for the least-squares synthesis of function-generating mechanisms is developed. This theory leads to a rapidly converging iterative-type algorithm, the use of which is illustrated by two planar four-bar examples. The theory and associated algorithms may be applied to the synthesis of any planar or spatial function-generating linkage.
Motif Mining in Weighted Networks (2012)

Unexpectedly frequent subgraphs, known as motifs, can help in characterizing the structure of complex networks. Most of the existing methods for finding motifs are designed for unweighted networks, where only the existence of connection between nodes is considered, and not their strength or capacity. However, in many real world networks, edges contain more information than just simple node connectivity. In this paper, we propose a new method to incorporate edge weight information in motif mining. We think of a motif as a subgraph that contains unexpected information, and we define a new significance measurement to assess this subgraph exceptionality. The proposed metric embeds the weight distribution in subgraphs and it is based on weight entropy. We use the g-trie data structure to find instances of k-sized subgraphs and to calculate its significance score. Following a statistical approach, the random entropy of subgraphs is then calculated, avoiding the time consuming step of random network generation. The discrimination power of the derived motif profile by the proposed method is assessed against the results of the traditional unweighted motifs through a graph classification problem. We use a set of labeled ego networks of co-authorship in the biology and mathematics fields. The new proposed method is shown to be feasible, achieving even slightly better accuracy. Since it does not require the generation of random networks, it is also computationally faster, and because we are able to use the weight information in computing the motif importance, we can avoid converting weighted networks into unweighted ones.
The future of our specialty: Critical care medicine a decade from now (2006)

From the Departments of Critical Care Medicine, Surgery, and Pharmacology, University of Pittsburgh School of Medicine, Pittburgh, PA (MPF); and the Service of Surgical Intensive Care, University of Geneva, Geneva, Switzerland (PMS).
SIMS Studies of Semi‐Insulating InP Amorphized by Mg and Si (1982)

Using secondary ion mass spectrometry (SIMS) the annealing characteristics of amorphizing implants of Mg and Si in semi‐insulating have been examined. Substantial redistribution of Mg and Fe occurs during 30 min anneals of implanted with 1015 cm−2, 250 keV Mg. Atomic profiles indicate that Mg and Fe are gettered out of the amorphous zone into an implant damaged, bulk region. Examination of electron channelling patterns (ECP) from samples annealed for 30 min at 550° and 650°C show no discernible patterns at the surface or at depths near the theoretical damage profile peak. Weak channelling patterns are visible at the calculated peak damage depth, however, in samples annealed at 750°C for 30 and 60 min. Flat tails of Mg extending over a distance of about 1 μm are seen in the bulk. Little redistribution of Si occurs during 30 min, 750°C anneals of , 240 keV Si implants. Redistribution of Fe is observed in these Si implanted samples, however, resulting in an accumulation region near the implanted Si peak.
Alkylation of isopentane with isopentene in the presence of concentrated sulphuric acid (1948)

Abstract Alkylation of isopentene with isopentane and sulphuric acid can be accomplished in two minutes reaction time, provided that the reacting substances are emulsified during the reaction. The most favourable ratio of the reacting substances (volumes) is about 5 of isoparaffin; 2 1/2 of sulphuric acid; 1 of olefin. If the reaction conditions are favourable to the formation of polymer hydrocarbons from the olefin (bad mixing) a long reaction time is required to obtain a “good alkylate”. The formation of products with an anomalous number of carbon atoms proceeds simultaneously with the formation of pure alkylate (C 10 ). With isopentene the formation of polymer‐sulphuric acid esters is the first step in the formation of alkylate.
Effect of Growth State on Transcription Levels of Genes Encoding Major Secreted Antigens of <i>Mycobacterium tuberculosis</i> in the Mouse Lung (2004)

Arrest of the multiplication of Mycobacterium tuberculosis caused by expression of adaptive immunity in mouse lung was accompanied by a 10- to 20-fold decrease in levels of mRNAs encoding the secreted Ag85 complex and 38-kDa lipoprotein. esat-6 mRNA levels were high throughout infection. The data imply that multiplying and nonreplicating tubercle bacilli have different antigen compositions.
Pancreatic Islet Culture and Preservation Strategies: Advances, Challenges, and Future Outlook (2010)

Postisolation islet survival is a critical step for achieving successful and efficient islet transplantation. This involves the optimization of islet culture in order to prolong survival and functionality in vitro. Many studies have focused on different strategies to culture pancreatic islets in vitro through manipulation of culture media, surface modified substrates, and the use of various techniques such as encapsulation, embedding, scaffold, and bioreactor culture strategies. This review aims to present and discuss the different methodologies employed to optimize pancreatic islet culture in vitro as well as address their respective advantages and drawbacks.
Algebra-Assisted Construction of Quasi-Cyclic LDPC Codes for 5G New Radio (2018)

Quasi-cyclic LDPC (QC-LDPC) codes have been accepted as the standard codes of 5G enhanced mobile broadband data channel. These standard codes are designed to support multiple lifting sizes and possess rate-compatible property, which can help adapt various information lengths and code rates well. In this paper, we propose an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">algebra-assisted</i> method for constructing QC-LDPC codes with such properties. We will first review the encoding mechanism and requirements of 5G LDPC codes, and present <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cycle analysis</i> for such emerging codes. We then propose a metric, referred to as <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">weighted average number of cycles</i> (WANC), from the perspective of cycle structure for constructing the QC-LDPC codes that can support <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">multiple lifting sizes</i> . Based on the WANC metric and algebraic methods, we develop a simple and practical algorithm to construct this kind of QC-LDPC codes. We finally apply the proposed algorithm to construct the exponent matrices for cases of 5G LDPC codes and the standard LDPC codes of consultative committee for space data systems, respectively. Simulation results show that the proposed WANC metric and designed algorithm are feasible and effective, and thus can be utilized to design other similar QC-LDPC codes.
Functional genomics: technological challenges and opportunities (1999)

In April, the Merck Genome Research Institute and the National Cancer Institute's Cancer Genome Anatomy Project, both supporters of functional genomics technology development and research, brought together a group of 27 scientists working at the forefront of this new field. Here we report on the presentations, discussions, and outcomes from this highly interactive and stimulating meeting held at the Banbury Center.
Genomic insights that advance the species definition for prokaryotes (2005)

To help advance the species definition for prokaryotes, we have compared the gene content of 70 closely related and fully sequenced bacterial genomes to identify whether species boundaries exist, and to determine the role of the organism's ecology on its shared gene content. We found the average nucleotide identity (ANI) of the shared genes between two strains to be a robust means to compare genetic relatedness among strains, and that ANI values of approximately 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition. At the 94% ANI cutoff, current species includes only moderately homogeneous strains, e.g., most of the >4-Mb genomes share only 65-90% of their genes, apparently as a result of the strains having evolved in different ecological settings. Furthermore, diagnostic genetic signatures (boundaries) are evident between groups of strains of the same species, and the intergroup genetic similarity can be as high as 98-99% ANI, indicating that justifiable species might be found even among organisms that are nearly identical at the nucleotide level. Notably, a large fraction, e.g., up to 65%, of the differences in gene content within species is associated with bacteriophage and transposase elements, revealing an important role of these elements during bacterial speciation. Our findings are consistent with a definition for species that would include a more homogeneous set of strains than provided by the current definition and one that considers the ecology of the strains in addition to their evolutionary distance.