gebhart/patrepeval huggingface dataset:
Herbicide-tolerant Transgenic Soybean over 15 Years of Cultivation: Pesticide Use, Weed Resistance, and Some Economic Issues. The Case of the USA (2011)

Genetically modified (GM) herbicide-tolerant (HT) crops have been largely adopted where they have been authorized. Nevertheless, they are fiercely criticized by some, notably because of the herbicide use associated with them. However, how much herbicide is applied to GMHT crops compared to conventional crops, and what impacts does the use of herbicide have? The paper first presents some factors explaining the predominance of GMHT crops. Then, trends in the use of herbicide for GM crops are studied in the case of the most widespread HT crop: HT soybean in the USA. The trends in the toxicity of herbicides applied to HT soybean are also addressed, as well as the appearance of glyphosate-resistant (GR) weeds. Lastly, the paper examines the spread of GR weeds and its impact. How are farmers, weed scientists, and the industry coping with this development, and what are the prospects of glyphosate-tolerant crops given weed resistance? In conclusion, some issues of sustainability and innovation governance raised by genetically modified herbicide-tolerant crops are discussed.
Seismic traveltime equations for azimuthally anisotropic and isotropic media; estimation of interval elastic properties (1991)

Abstract I derive analytical expressions giving traveltime-offset curves for multilayered weakly azimuthally isotropic and anisotropic media on terms of the elastic properties of each layer. This method is based upon an approximate skewed hyperbolic moveout formula involving three measured bulk velocities for each reflector. The primary benefits of this technique are: (1) it allows for fast traveltime computation; (2) it makes possible an extremely rapid estimation of the interval elastic parameters; and (3) it provides physical insight into the wave propagation in anisotropic media.I establish a traveltime inversion algorithm which allows the estimation of the five elastic constants together with the orientation of the axis of symmetry for each layer. In the isotropic limit, this algorithm reduces to the conventional one used for determining the interval velocities from stacking velocity measurements in isotropic media. The inversion technique is applied to surface seismic measurements and VSP field surveys. In both cases, the method provides very good estimates of these six parameters, even in highly anisotropic materials. The results also show that the orientation of the horizontal axis of symmetry, for a given azimuthally anisotropic layer at depth, can be obtained using only quasi-P-wave information. This technique can be easily incorporated into conventional velocity analysis algorithms. Interval anisotropic properties can then be estimated with little additional effort.
[A comparative evaluation of the cardioprotective and antianginal actions of energy-providing agents]. (1993)

The limitation of a myocardial necrotic area by some energy-yielding compounds in rat coronary occlusion and their capacity to elevate the ischemia threshold in conscious rabbits were studied. Sodium malate, ascorbic acid and phosphoenolpyruvate were demonstrated to reduce the sizes of necrotic areas and increase the ischemia threshold, whereas cytochrome C and fructose-1,6-diphosphate were effective solely in limiting the infection area. It was concluded that the preventive antianginal effect of energy-yielding and electron-accepting compounds depended on their capacity to accumulate in intact cardiomyocytes.
Microglial Immunoreceptor Tyrosine-Based Activation and Inhibition Motif Signaling in Neuroinflammation (2010)

Elimination of extracellular aggregates and apoptotic neural membranes without inflammation is crucial for brain tissue homeostasis. In the mammalian central nervous system, essential molecules in this process are the Fc receptors and the DAP12-associated receptors which both trigger the microglial immunoreceptor tyrosine-based activation motif- (ITAM-) Syk-signaling cascade. Microglial triggering receptor expressed on myeloid cells-2 (TREM2), signal regulatory protein-beta1, and complement receptor-3 (CD11b/CD18) signal via the adaptor protein DAP12 and activate phagocytic activity of microglia. Microglial ITAM-signaling receptors are counter-regulated by immunoreceptor tyrosine-based inhibition motif- (ITIM-) signaling molecules such as sialic acid-binding immunoglobulin superfamily lectins (Siglecs). Siglecs can suppress the proinflammatory and phagocytic activity of microglia via ITIM signaling. Moreover, microglial neurotoxicity is alleviated via interaction of Siglec-11 with sialic acids on the neuronal glycocalyx. Thus, ITAM- and ITIM-signaling receptors modulate microglial phagocytosis and cytokine expression during neuroinflammatory processes. Their dysfunction could lead to impaired phagocytic clearance and neurodegeneration triggered by chronic inflammation.
Neutralization of SARS-CoV-2 pseudovirus using ACE2-engineered extracellular vesicles (2021)

The spread of coronavirus disease 2019 (COVID-19) throughout the world has resulted in stressful healthcare burdens and global health crises. Developing an effective measure to protect people from infection is an urgent need. The blockage of interaction between angiotensin-converting enzyme 2 (ACE2) and S protein is considered an essential target for anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) drugs. A full-length ACE2 protein could be a potential drug to block early entry of SARS-CoV-2 into host cells. In this study, a therapeutic strategy was developed by using extracellular vesicles (EVs) with decoy receptor ACE2 for neutralization of SARS-CoV-2. The EVs embedded with engineered ACE2 (EVs-ACE2) were prepared; the EVs-ACE2 were derived from an engineered cell line with stable ACE2 expression. The potential effect of the EVs-ACE2 on anti-SARS-CoV-2 was demonstrated by both <i>in vitro</i> and <i>in vivo</i> neutralization experiments using the pseudovirus with the S protein (S-pseudovirus). EVs-ACE2 can inhibit the infection of S-pseudovirus in various cells, and importantly, the mice treated with intranasal administration of EVs-ACE2 can suppress the entry of S-pseudovirus into the mucosal epithelium. Therefore, the intranasal EVs-ACE2 could be a preventive medicine to protect from SARS-CoV-2 infection. This EVs-based strategy offers a potential route to COVID-19 drug development.
Efficiently Observing Internet of Things Resources (2012)

The Constrained Application Protocol (CoAP) is a lightweight protocol that enables the implementation of Restful embedded web services. Observe is one of the CoAP extensions, which allow servers to send every resource state change to interested clients. In this paper we present an interesting extension to the observe option, called conditional observation, where clients specify notification criteria along their observation request. We evaluate the feasibility of implementing this on a constrained device and evaluate the correct operation for a simple scenario. It is shown that the use of conditional observations can result in a reduced number of packets and power consumption compared to normal observe in combination with client-side filtering.
Effects of instrumentation, irrigation and dressing with calcium hydroxide on infection in pulpless teeth with periapical bone lesions (2002)

Although a calcium hydroxide paste was placed in the prepared canals, the number of positive canals had increased in the period between visits. However, the number of microorganisms had only increased to 0.93% of the original number of CFU (sample 1). It is concluded that a calcium hydroxide and sterile saline slurry limits but does not totally prevent regrowth of endodontic bacteria.
Control of in vivo differentiation of myeloid leukemic cells. (1988)

The differentiation of leukemic cells in vivo can be a useful approach to therapy. In vivo differentiation of myeloid leukemic cells was studied in intraperitoneally implanted diffusion chambers, containing different soluble antigens. The presence of these antigens in the chambers induced differentiation of myeloid leukemic cells and this was inhibited in immune-deficient mice. Transfer of normal spleen cells enriched for T-lymphocytes or antigen-specific helper T lymphocyte cell lines to mice in which differentiation of leukemic cells was inhibited, restored in vivo differentiation of the leukemic cells. Antigen-specific helper T cells produce myeloid regulatory proteins and can accumulate at a site that contains the specific antigen. It is suggested that migration in response to antigen of helper T cells producing regulatory proteins may play an important role in inducing in vivo differentiation of leukemic cells. We have identified a class of myeloid leukemic cells that can be induced to differentiate in vitro by incubation with pure MGI-1GM (GM-CSF) or IL-3, but not with MGI-1G (G-CSF). Experiments with pure recombinant proteins have shown that MGI-1GM and IL-3, but not MGI-1G, can also induce these myeloid leukemic cells to differentiate in vivo. These results and our previous studies on the myeloid cell differentiation-inducing protein MGI-2, demonstrate the potential use of normal hematopoietic regulatory proteins not only in regulation of normal hematopoiesis, but also in the treatment of myeloid leukemia by in vivo induction of terminal cell differentiation.
Mechanisms of inflammation in gout (2010)

An acute attack of gout is a paradigm of acute sterile inflammation, as opposed to pyogenic inflammation. Recent studies suggest that the triggering of IL-1beta release from leucocytes lies at the heart of a cascade of processes that involves multiple cytokines and mediators. The NLRP3 inflammasome appears to have a specific role in this regard, but the biochemical events leading to its activation are still not well understood. We review the known mechanisms that underlie the inflammatory process triggered by urate crystals and suggest areas that require further research.
A beginner's guide to radiation damage (2009)

Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with this comes an expanding literature, and, to the new breed of protein crystallographer who is not really interested in X-ray physics or radiation chemistry but just wants to solve a biologically relevant structure, the technical nature and breadth of this literature can be daunting. The purpose of this paper is to serve as a rough guide to radiation damage issues, and to provide references to the more exacting and detailed work. No attempt has been made to report precise numbers (a factor of two is considered satisfactory), and, since there are aspects of radiation damage that are demonstrably unpredictable, the 'worst case scenario' as well as the 'average crystal' are discussed in terms of the practicalities of data collection.
Ethyl Pyrrole‐2‐Carboxylate (2003)

Abstract Ethyl pyrrole‐2‐carboxylate intermediate: 2‐ Pyrrolyl trichloromethyl ketone product: ethyl pyrrole‐2‐carboxylate
Science on the Web: Students Online in a Sixth-Grade Classroom (2000)

Abstract Publications from newspapers to research journals are filled with claims about the Internet and its value for education, yet research is just beginning to evaluate uses of these new information resources in the classroom. As part of the University of Michigan Digital Library Project, this research was undertaken as a first step in designing tools for secondary students to access a digital library. The Web offered an initial site for learning how students interact with digital resources and use standard tools. The Web can be seen as a site for student inquiry in science, using it as an information resource that opens the boundaries of the classroom and creates the possibility for students to pursue questions of personal interest. This study looks at students in 6th-grade science classes as they use the Web to carry out an inquiry-based assignment. Their understanding and enactment of their assignment to do research on the Web, their engagement in information seeking, and their use of Web technologies are explored and analyzed. Findings include evidence that students use Web technologies easily but simplistically; that information seeking is a complex and difficult process for these students, who seek to reduce the task to finding an obvious answer or finding a good Web site; and that developing students' understanding of content through use of the Web is a challenge for students and teachers.
How to interpret the results of a sleep study (2014)

With an increased level of awareness of sleep disorders among the public, there has been an increase in requests for sleep studies, and consequently, more referrals made to sleep specialists by primary care physicians and other health care providers. Understanding technical and clinical information provided in the sleep study report is crucial. It offers significant insight in to sleep pathophysiology in relation to patient symptoms. The purpose of this article is to provide a simple and easy method to interpret the reported results of polysomnography for primary care physicians. This will facilitate better understanding and management of patients with sleep disorders and related complications.
Methods for Use of Peptide-MHC Tetramers in Tumor Immunology (2003)

Direct analysis of T-cells of defined specificity and phenotype, without in vitro manipulation that accompanies limiting dilution analysis or other restimulation protocols for evaluating precursor frequency, provides the most accurate representation possible of in vivo events. The natural ligand of the T-cell receptor (TCR), the peptide-major histocompatibility, could be used to identify T-cells of a given specificity, but the use of a single peptide-MHC would fail because the affinity of the peptide-MHC for its TCR ligand is characterized by a very fast dissociation rate (1,2). A tetrameric peptide-MHC, however, exhibits sufficient affinity for its TCR ligand to permit its use as a staining reagent in flow cytometry so that peptide-specific T-cells can be visualized by fluorescent markers conjugated to the tetramer (3,4). By combining this approach with fluorescent antibodies staining phenotypic markers or intra- cellular cytokines, this novel and powerful technology now provides a more rapid and informative assessment of antigen-specific T-cells in a given population. Furthermore, sorting individual tetramer+ cells provides an expeditious means for detailed single cell analysis or sorting followed by in vitro expansion. We and others have demonstrated that peptide-MHC tetramers can be used for the purposes discussed in the next sections.
Statistical profiling and visualization for detection of malicious insider attacks on computer networks (2004)

The massive volume of intrusion detection system (IDS) alarms generated on large networks, and the resulting need for labor-intensive security analysis of the text-based IDS alarm logs, has recently brought into question the cost-effectiveness of IDSs. In particular, when host-based IDSs are used to monitor an organization's internal networks, the majority of the resulting alarms represent legitimate, automated system administration. Because of the absence of ground truth about known attacks, we propose an unsupervised, anomaly-based method for automatically distinguishing alarms that are potentially generated by malicious insider attacks, from the repetitive and temporally structured legitimate system-administration alarms. The majority of previous work in this area has used heuristic and statistical filtering techniques to discard a relatively large proportion of alarms in the final presentation to the security analyst, which is a potentially dangerous practice. Instead, we demonstrate the use of a typicality measure to visualize the apparent risk associated with alarms, while retaining information about the temporal context of the entire alarm stream for the analyst to view. The relevance of the statistical method is examined by comparing the results to a set of analyst-curated alarms from an operational environment.
Insulin increases fatty acid synthase gene transcription in human adipocytes (1998)

The purpose of this study was to investigate the molecular mechanism whereby insulin increases expression of a key de novo lipogenic gene, fatty acid synthase (FAS), in cultured human adipocytes and hepatoma cells. RNA isolated from cultured adipocytes or from Hep G2 cells treated with or without insulin (20 nM) was analyzed. In addition, run-on transcription assays and measurements of RNA half-life were performed to determine the controlled step in FAS gene regulation by insulin. We demonstrated that FAS mRNA was expressed in both Hep G2 cells and human adipocytes. Insulin induced an approximately five- and three-fold increase in FAS mRNA content in adipocytes and hepatoma cells, respectively. Similar regulation of FAS was observed in adipocytes from lean and obese human subjects. Furthermore, we demonstrated that the induction of human FAS expression by insulin was due to increased transcription rate of the FAS gene in human adipocytes, whereas mRNA stabilization accounted for increased FAS mRNA content in hepatoma cells. In conclusion, we report here for the first time expression of human FAS mRNA and its specific transcriptional induction by insulin in cultured human adipocytes.
Improving the Lethal Effect of Cpl-7, a Pneumococcal Phage Lysozyme with Broad Bactericidal Activity, by Inverting the Net Charge of Its Cell Wall-Binding Module (2013)

Phage endolysins are murein hydrolases that break the bacterial cell wall to provoke lysis and release of phage progeny. Recently, these enzymes have also been recognized as powerful and specific antibacterial agents when added exogenously. In the pneumococcal system, most cell wall associated murein hydrolases reported so far depend on choline for activity, and Cpl-7 lysozyme constitutes a remarkable exception. Here, we report the improvement of the killing activity of the Cpl-7 endolysin by inversion of the sign of the charge of the cell wall-binding module (from -14.93 to +3.0 at neutral pH). The engineered variant, Cpl-7S, has 15 amino acid substitutions and an improved lytic activity against Streptococcus pneumoniae (including multiresistant strains), Streptococcus pyogenes, and other pathogens. Moreover, we have demonstrated that a single 25-μg dose of Cpl-7S significantly increased the survival rate of zebrafish embryos infected with S. pneumoniae or S. pyogenes, confirming the killing effect of Cpl-7S in vivo. Interestingly, Cpl-7S, in combination with 0.01% carvacrol (an essential oil), was also found to efficiently kill Gram-negative bacteria such as Escherichia coli and Pseudomonas putida, an effect not described previously. Our findings provide a strategy to improve the lytic activity of phage endolysins based on facilitating their pass through the negatively charged bacterial envelope, and thereby their interaction with the cell wall target, by modulating the net charge of the cell wall-binding modules.
Companion to the 23rd ACM SIGPLAN conference on Object-oriented programming systems languages and applications (2008)

It's a pleasure to welcome you to OOPSLA 2008, the 23rd Annual Conference on Object-Oriented Programming, Systems, Languages, and Applications. Originally devoted to object-oriented programming, OOPSLA has grown in scope to encompass programming, practices and paradigms addressing current software challenges, such as programmer productivity, security & reliability, ultra-large scale systems and evolving hardware platforms.

OOPSLA is the premier forum for practitioners, researchers, educators and students in diverse disciplines whose common threads are objects and related technologies. From its inception, OOPSLA has served as an incubator for advanced technologies and practices. Dynamic compilation and optimization, patterns, refactoring, aspect-oriented software development, agile methods, service-oriented architectures and model-driven development (to name just a few) all have OOPSLA roots.

OOPSLA 2008 continues and strengthens that tradition. It features an exciting roster of researchers, practitioners and educators from around the world coming to showcase their latest work in a highly diverse set of venues that meet the needs of our equally diverse audience. Presentations from invited speakers dovetail with technical papers, practitioner reports, expert panels, demonstrations, formal and informal educational symposia, workshops, and tutorials from world-class lecturers. Bend your head around some out-of-the box thinking at the ever-popular Onward! track. Discuss late-breaking results with the researchers themselves at poster sessions, which culminate in the ACM Student Research Competition. Get some hands-on design experience at the DesignFest®. Gather together with like-minded people at Open Space and Birds-of-a-Feather sessions to discuss shared topics of interest. Or just let us know what's on your mind at the Lightning Talks, where anyone can speak to the community on just about anything at all.
Toward Hypoxia-Selective DNA-Alkylating Agents Built by Grafting Nitrogen Mustards onto the Bioreductively Activated, Hypoxia-Selective DNA-Oxidizing Agent 3-Amino-1,2,4-benzotriazine 1,4-Dioxide (Tirapazamine) (2014)

Tirapazamine (3-amino-1,2,4-benzotriazine 1,4-dioxide) is a heterocyclic di-N-oxide that undergoes enzymatic deoxygenation selectively in the oxygen-poor (hypoxic) cells found in solid tumors to generate a mono-N-oxide metabolite. This work explored the idea that the electronic changes resulting from the metabolic deoxygenation of tirapazamine analogues might be exploited to activate a DNA-alkylating species selectively in hypoxic tissue. Toward this end, tirapazamine analogues bearing nitrogen mustard units were prepared. In the case of the tirapazamine analogue 18a bearing a nitrogen mustard unit at the 6-position, it was found that removal of the 4-oxide from the parent di-N-oxide to generate the mono-N-oxide analogue 17a did indeed cause a substantial increase in reactivity of the mustard unit, as measured by hydrolysis rates and DNA-alkylation yields. Hammett sigma values were measured to quantitatively assess the magnitude of the electronic changes induced by metabolic deoxygenation of the 3-amino-1,2,4-benzotriazine 1,4-dioxide heterocycle. The results provide evidence that the 1,2,4-benzotiazine 1,4-dioxide unit can serve as an oxygen-sensing prodrug platform for the selective unmasking of bioactive agents in hypoxic cells.
Long-term pervaporation performance of microporous methylated silica membranesElectronic Supplementary Information (ESI) available: details of the sol synthesis; GPC and NMR measurements; and additional SEM micrographs. See http://www.rsc.org/suppdata/cc/b4/b401496k/ (2004)

The incorporation of methyl groups in microporous silica membranes was proven to enhance the service time in the dehydration of a butanol-water mixture at 95 degrees C from a few weeks to more than 18 months with a water flux of about 4 kg m(-2) h(-1) and a selectivity between 500 and 20 000.