gebhart/patrepeval huggingface dataset:
Microbial Communities Associated with Zones of Elevated Magnetic Susceptibility in Hydrocarbon-Contaminated Sediments (2015)

Recent studies suggest that magnetic susceptibility (MS) measurements can play an important role in identifying zones where microbial-mediated iron mineral transformations are occurring. Here we investigated the microbial community variations within zones of elevated MS in a petroleum hydrocarbon-contaminated aquifer near Bemidji, Minnesota, USA. Our main objective was to 1) identify the key microbial populations that may play a role in hydrocarbon degradation, 2) analyze which microbial populations could be connected to the elevated MS and 3) explore the use of non-destructive geophysical techniques as a tool to guide microbial sampling. Clone libraries based on the 16S rRNA gene revealed the presence of iron-reducing β-Proteobacteria in the vadose zone, whereas the free petroleum phase on the water table was characterized by a methanogenic consortium, in which the syntrophic δ-proteobacterium Smithella and the hydrogenotrophic Methanoregula predominated. Nonmetric multidimensional scaling (NMDS) found a close relationship between elevated MS values and the methanogenic hydrocarbon-degrading consortium. Our results suggest that magnetic susceptibility measurements can guide microbiologists to zones of active microbial biodegradation in aged petroleum spills.
Gender inequalities among authors who contributed equally (2019)

We analyzed 2898 scientific papers published between 1995 and 2017 in which two or more authors shared the first author position. For papers in which the first and second authors made equal contributions, mixed-gender combinations were most frequent, followed by male-male and then female-female author combinations. For mixed-gender combinations, more male authors were in the first position, although the disparity decreased over time. For papers in which three or more authors made equal contributions, there were more male authors than female authors in the first position and more all-male than all-female author combinations. The gender inequalities observed among authors who made equal contributions are not consistent with random or alphabetical ordering of authors. These results raise concerns about female authors not receiving proper credit for publications and suggest a need for journals to request clarity on the method used to decide author order among those who contributed equally.
Abstract 292: PTC596 combination therapy for sarcoma (2019)

Sarcomas are rare cancers derived from mesenchymal tissues. Although rare, there are approximately 15,000 new cases of sarcoma diagnosed each year in the United States. Certain soft tissue sarcomas are treated with doxorubicin and olaratumabas first line, gemcitabine as second line, and often dacarbazine (DTIC) as third line. PTC596 is a first-in-class, oral investigational new drug that reduces levels of BMI1, a protein required for cancer stem cell survival. PTC596 acts by binding to tubulin causing a G2M cell cycle arrest. PTC596 lowers levels of BMI1 in preclinical tumor models and is generally well tolerated as a monotherapy at doses that result in preclinical target plasma concentrations. Efficacy of PTC596 was evaluated in a series of preclinical models. PTC596 delayed tumor growth as monotherapy and significantly enhanced, in combination, the activity of standard chemotherapeutics including gemcitabine, doxorubicin/ doxil, dacarbazine (DTIC), and other tubulin binding agents. Based on these results, a Ph1b clinical trial in patients with relapsed refractory leiomyosarcoma is to be initiated. It is a dose escalation study of a combination regimen of dacarbazine and PTC596 with the dose-limiting toxicity (DLT) to be determined using a continuous reassessment methodology. Previously, a Phase I multi-center dose escalation study was conducted in patients with advanced solid tumors. PTC596 was administered as an oral monotherapy in 4-week cycles using bodyweight-adjusted twice-per-week (biw) dosing. A maximum tolerated dose (MTD) was not determined though a well-tolerated recommended Phase 2 dose of 7mg/kg biw was identified. The most relevant toxicities observed were neutropenia, nausea, and vomiting which were generally mild to moderate, manageable and reversible.Citation Format: Marla Weetall, Art Branstrom, John Baird, Liang Cao, Josephine Sheedy, Kylie O'Keefe, Matthew Ingham, Gary K. Schwartz, Robert Spiegel, Edward O'Mara. PTC596 combination therapy for sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 292.
Genetic Control of High Oleic Acid Seed Content in Soybean (2008)

BACHLAVA, ELENI. Genetic Control of High Oleic Acid Seed Content in Soybean. (Under the direction of Andrea J. Cardinal and Ralph E. Dewey)\n\nThe increase of oleic acid concentration in soybean [Glycine max (L.) Merr.] oil improves its nutritional value and oxidative stability; therefore, the incorporation of the high oleate trait in soybean germplasm is required for the commercial success of soybean oil. Little is known, however, about the response to selection for higher oleate content, which is dependent on its heritability in breeding populations, and the correlated responses of other fatty acids and agronomic traits to selection for oleate content, which depends on their genetic correlations with oleate. Furthermore, the lack of knowledge on the genetic factors underlying oleate variation in soybean oilseeds hampers the use of marker assisted selection for high oleate content in soybean breeding programs. The results of this study suggested that oleate heritability was sufficiently high that early generation selection can be effective when practiced on unreplicated lines grown at a single environment. Moreover, this study indicated that selection for higher oleate will result in lower linoleate, linolenate and palmitate content in soybean oil. Also, the significant negative correlation between oleate content and yield implied that the development of high oleate germplasm may be hindered by lower yields. The isoforms of FAD2 gene, which catalyze the desaturation of oleate to linoleate during fatty acid biosynthesis, were mapped in order to investigate their cosegregation with the oleate quantitative trait loci (QTLs) identified. FAD2-1A and FAD2-1B mapped on linkage groups O and I, respectively, while the closely linked FAD2-2A and FAD2-2B isoforms mapped on linkage group L of soybean genome. An oleate QTL with moderate effects was reported in the proximity of FAD2-1B on linkage group I. Also, an oleate QTL with moderate effects was detected on linkage group F, which interacted epistatically with the QTL on linkage group I. In conclusion, no major oleate QTLs were identified and the FAD2-1A, FAD2-1B and FAD2-2B did not encode for the major oleate genes that contribute to the elevated oleate content of the experimental lines used in this study.
Kernelized Hashcode Representations for Relation Extraction (2019)

Kernel methods have produced state-of-the-art results for a number of NLP tasks such as relation extraction, but suffer from poor scalability due to the high cost of computing kernel similarities between natural language structures. A recently proposed technique, kernelized locality-sensitive hashing (KLSH), can significantly reduce the computational cost, but is only applicable to classifiers operating on kNN graphs. Here we propose to use random subspaces of KLSH codes for efficiently constructing an explicit representation of NLP structures suitable for general classification methods. Further, we propose an approach for optimizing the KLSH model for classification problems by maximizing an approximation of mutual information between the KLSH codes (feature vectors) and the class labels. We evaluate the proposed approach on biomedical relation extraction datasets, and observe significant and robust improvements in accuracy w.r.t. state-ofthe-art classifiers, along with drastic (orders-of-magnitude) speedup compared to conventional kernel methods.
AZD3199: A fast acting β2-receptor agonist with a long duration of action (2011)

Background: AZD3199 is a novel, ultra long acting β 2 -agonist (uLABA) designed to combine 24 hour duration of action with a fast onset of action similar to formoterol, as well as low systemic exposure. Its in vivo profile was evaluated in the guinea pig. Methods: Bronchoconstriction was elicited in anesthetized guinea pigs by histamine administration. Dose-response curves for AZD3199 given via the inhaled and intra-tracheal (i.t.) routes were constructed and sub-maximal doses used to define duration of action from 2–72 hours. The b-antagonist propranolol was administered after histamine-challenge to show the level of β 2 efficacy at each dose and time point. Blood samples were taken throughout and plasma K + concentrations used as a marker of systemic β 2 effects. Satellite groups were used to monitor lung and plasma AZD3199 levels. The pharmacodynamic and pharmacokinetic profiles of AZD3199 were compared to formoterol and salmeterol. Results: Sub-maximal doses of AZD3199 given i.t. inhibited bronchoconstriction for 24 hours; equi-effective doses of formoterol and salmeterol had significant effects for 12 hours. AZD3199 had the longest lung PK half-life. Inhalation of sub-maximal doses of nebulized AZD3199 gave bronchoprotection lasting 24 hours, with no significant effects on blood K + levels. An equi-effective inhaled dose of formoterol bronchoprotected for 8 hours with decreases in blood K + seen at 2 hours. The reduced systemic effects for AZD3199 relative to formoterol are consistent with its high lung to plasma concentration ratio. Conclusion: AZD3199 is a novel uLABA with a fast onset of action and a longer duration of action than conventional LABAs, and also has a low potential for systemic effects.
Packing the meeting summarization knapsack (2008)

Despite considerable work in automatic meeting summarization over the last few years, comparing results remains difficult due to varied task conditions and evaluations. To address this issue, we present a method for determining the best possible extractive summary given an evaluation metric like ROUGE. Our oracle system is based on a knapsack-packing framework, and though NP-Hard, can be solved nearly optimally by a genetic algorithm. To frame new research results in a meaningful context, we suggest presenting our oracle results alongside two simple baselines. We show oracle and baseline results for a variety of evaluation scenarios that have recently appeared in this field.
An adaptive scheduling scheme for dynamic service time allocation on a shared resource (2003)

A scheduling scheme that allows a number of customers to share a common resource in an efficient and fair way is presented. Each customer is allowed to use the resource for an amount of time that does not exceed a certain limit, the limit being a function of the waiting time elapsed between the time of its last request and the time of access to the resource. After expiration of the service time allocated to a customer, if more service is still needed, the customer has to re-enter the request queue and issue a new service request. The scheme combines the advantages of both processor-sharing and first-come, first-served disciplines in a dynamic way. The applicability and the advantages of the scheme in both open and closed system environments are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Laser-Assisted Machining of a Fiber Reinforced Metal Matrix Composite (2009)

Metal matrix composites due to their excellent properties of high specific strength, fracture resistance and corrosion resistance are highly sought after over their non-ferrous alloys, but these materials also present difficulty in machining. Excessive tool wear and high tooling costs of diamond tools makes the cost associated with machining of these composites very high. This paper is concerned with machining of high volume fraction long-fiber MMC’s, which has seldom been studied. The composite material considered for this study is an Al-2%Cu aluminum matrix composite reinforced with 62% by volume fraction alumina fibers (Al-2%Cu/Al2O3). Laser-machining is utilized to improve the tool life and the material removal rate while minimizing the sub-surface damage. The effectiveness of the laser-assisted machining process is studied by measuring the cutting forces, specific cutting energy, surface roughness, sub-surface damage and tool wear under various material removal temperatures. A multi-phase finite element model is developed in ABAQUS/Standard to identify and assist in selection of cutting parameters such as; tool rake angle, cutting speed and material removal temperature. The multi-phase model is also successful in predicting the damage depth on machining. The optimum material removal temperature is established as 300°C at a cutting speed of 30 m/min. LAM provides a 65% reduction in the surface roughness, specific cutting energy, the tool wear rate and minimum sub-surface damage over conventional machining using the same cutting conditions.
Crystallization and characterization of the recombinant human Clara cell 10‐kDa protein (1994)

Crystals of recombinant human Clara cell 10-kDa protein were grown both from ammonium sulfate and polyethylene glycol (PEG) solutions. Crystals grown from ammonium sulfate solution have been characterized by X-ray diffraction studies as monoclinic with the space group C2 and lattice constants a = 69.2 A, b = 83.0 A, c = 58.3 A, and beta = 99.7 degrees. The monoclinic crystals diffract to beyond 2.5 A. Some of the crystals grown from PEG were of a similar habit to those grown from ammonium sulfate, but others were triclinic with the space group P1 and cell constants a = 40.3 A, b = 46.3 A, c = 51.3 A, alpha = 117.7 degrees, beta = 102.3 degrees, and gamma = 71.4 degrees. These crystals diffract to beyond 3.2 A.
Micromechanics of Fibroblast Contraction of a Collagen-Gag Matrix (2001)

Abstract Contractile fibroblasts play a major role in the synthesis and remodeling of scar tissue following dermal injury. Inhibition of dermal wound contraction by contractile fibroblasts, using a collagen-GAG matrix, has been linked to the blocking of scar formation[1]. Scar tissue is mechanically and functionally inferior to the dermal tissue which it replaces. Specifically, scar tissue is weaker, physically disfiguring, and can lead to restricted joint mobility.
Data from Tumor Detection by Imaging Proteolytic Activity (2023)

&lt;div&gt;Abstract&lt;p&gt;The cell surface protease membrane-type serine protease-1 (MT-SP1), also known as matriptase, is often upregulated in epithelial cancers. We hypothesized that dysregulation of MT-SP1 with regard to its cognate inhibitor hepatocyte growth factor activator inhibitor-1 (HAI-1), a situation that increases proteolytic activity, might be exploited for imaging purposes to differentiate malignant from normal tissue. In this study, we show that MT-SP1 is active on cancer cells and that its activity may be targeted &lt;i&gt;in vivo&lt;/i&gt; for tumor detection. A proteolytic activity assay with several MT-SP1–positive human cancer cell lines showed that MT-SP1 antibodies that inhibit recombinant enzyme activity &lt;i&gt;in vitro&lt;/i&gt; also bind and inhibit the full-length enzyme expressed on cells. In contrast, in the same assay, MT-SP1–negative cancer cell lines were inactive. Fluorescence microscopy confirmed the cell surface localization of labeled antibodies bound to MT-SP1–positive cells. To evaluate &lt;i&gt;in vivo&lt;/i&gt; targeting capability, 0.7 to 2 nmoles of fluorescently labeled antibodies were administered to mice bearing tumors that were positive or negative for MT-SP1. Antibodies localized to MT-SP1–positive tumors (&lt;i&gt;n&lt;/i&gt; = 3), permitting visualization of MT-SP1 activity, whereas MT-SP1–negative tumors (&lt;i&gt;n&lt;/i&gt; = 2) were not visualized. Our findings define MT-SP1 activity as a useful biomarker to visualize epithelial cancers using a noninvasive antibody-based method. Cancer Res; 70(4); 1505–12&lt;/p&gt;&lt;/div&gt;
Acute effect of tumor necrosis factor-alpha is minimal on mechanics but significant on energetics in blood-perfused canine left ventricles (1999)

TNF-alpha minimally alters left ventricular mechanics, but significantly changes energetics. The latter effect may result from changes in intracellular calcium handling.
Reduction of Streptococcus pneumoniae in upper respiratory tract cultures and a decreased incidence of related acute otitis media following introduction of childhood pneumococcal conjugate vaccines in a Swedish county (2016)

After introduction of PCV in 2009, we have observed a significantly decreased number of pneumococcal isolates in the upper respiratory tract, a shift to non-PHiD-CV10 serotypes, and a reduction of complicated AOM. Our findings may have implications for future vaccine design.
Anti-PEG Antibodies Boosted in Humans by SARS-CoV-2 Lipid Nanoparticle mRNA Vaccine (2022)

ABSTRACT Humans commonly have low level antibodies to poly(ethylene) glycol (PEG) due to environmental exposure. Lipid nanoparticle (LNP) mRNA vaccines for SARS-CoV-2 contain small amounts of PEG but it is not known whether PEG antibodies are enhanced by vaccination and what their impact is on particle–immune cell interactions in human blood. We studied plasma from 130 adults receiving either the BNT162b2 (Pfizer-BioNTech) or mRNA-1273 (Moderna) mRNA vaccines, or no SARS-CoV-2 vaccine for PEG-specific antibodies. Anti-PEG IgG was commonly detected prior to vaccination and was significantly boosted a mean of 13.1-fold (range 1.0 to 70.9) following mRNA-1273 vaccination and a mean of 1.78-fold (range 0.68 to 16.6) following BNT162b2 vaccination. Anti-PEG IgM increased 68.5-fold (range 0.9 to 377.1) and 2.64-fold (0.76 to 12.84) following mRNA-1273 and BNT162b2 vaccination, respectively. The rise in PEG-specific antibodies following mRNA-1273 vaccination was associated with a significant increase in the association of clinically relevant PEGylated LNPs with blood phagocytes ex vivo . PEG antibodies did not impact the SARS-CoV-2 specific neutralizing antibody response to vaccination. However, the elevated levels of vaccine-induced anti-PEG antibodies correlated with increased systemic reactogenicity following two doses of vaccination. We conclude that PEG-specific antibodies can be boosted by LNP mRNA-vaccination and that the rise in PEG-specific antibodies is associated with systemic reactogenicity and an increase of PEG particle–leukocyte association in human blood. The longer-term clinical impact of the increase in PEG-specific antibodies induced by lipid nanoparticle mRNA-vaccines should be monitored.
ChemInform Abstract: Production, Isolation and Structure Determination of Novel Fluoroindolocarbazoles from Saccharothrix aerocolonigenes ATCC 39243. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
CRISPR-targeted transposable element insertion for efficient plant genome engineering (2023)

<title>Abstract</title> The current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone, and this inefficiency hampers genome editing approaches to develop improved crops. Often considered genome ‘parasites’, transposable elements (TEs) evolved to insert their DNA seamlessly into genomes. TEs select their site of insertion based on preferences for chromatin contexts, which differ for each TE type. We developed a genome engineering tool that controls the TE insertion site and cargo delivered, taking advantage of the TE’s natural ability to precisely insert into the genome. Inspired by CRISPR-associated transposases (CASTs) that target transposition in a programmable manner in bacteria, we generated a synthetic CAST by fusing the rice <italic>Pong </italic>TE transposase protein to the Cas9 or CPF1 programmable nucleases. We demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancer elements, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis. We additionally translated this system into soybean, a major global crop in need of targeted insertion technology. We have engineered a TE ‘parasite’ into a usable and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
Reliability-Aware Proactive Energy Management in Hard Real-Time Systems (2010)

Advanced technologies such as sub-45nm CMOS and 3D integration are known to have more accelerated and increased number of reliability failure mechanisms. Classical reliability assessment methodology, which assumes ad-hoc failure criteria and worst-case for all influencing dynamic aspects, is no longer viable in these technologies. In this paper, the authors advocate that managing temperature and reliability at run-time is necessary to overcome this reliability-wall without incurring significant cost penalty. Nonlinear nature of modern systems, however, makes the run-time control very challenging. The authors suggest that full cost-consciousness requires a truly proactive controller that can efficiently manage system slack with future in perspective. This paper introduces the concept of “gas-pedal,” which enhances the effectiveness of the proactive controller in minimizing the cost without sacrificing the hard guarantees required by the constraints. Reliability-aware dynamic energy management of a processor running AVC motion compensation task is used as a motivational case study to illustrate the proposed concepts.
CacheSack: Theory and Experience of Google’s Admission Optimization for Datacenter Flash Caches (2023)

This article describes the algorithm, implementation, and deployment experience of CacheSack, the admission algorithm for Google datacenter flash caches. CacheSack minimizes the dominant costs of Google’s datacenter flash caches: disk IO and flash footprint. CacheSack partitions cache traffic into disjoint categories, analyzes the observed cache benefit of each subset, and formulates a knapsack problem to assign the optimal admission policy to each subset. Prior to this work, Google datacenter flash cache admission policies were optimized manually, with most caches using the Lazy Adaptive Replacement Cache algorithm. Production experiments showed that CacheSack significantly outperforms the prior static admission policies for a 7.7% improvement of the total cost of ownership, as well as significant improvements in disk reads (9.5% reduction) and flash wearout (17.8% reduction).