gebhart/patrepeval huggingface dataset:
Mutations in the flhD gene of Escherichia coli K-12 do not cause the reported effect on cell division (2010)

The hetero-oligomeric FlhD/FlhC complex is a global regulator of transcription in Escherichia coli. FlhD alone, independent of FlhC, has also been reported to control when E. coli cells stop dividing and enter the stationary phase. This work is frequently cited as evidence that FlhD regulates cell division; however, our data indicate that this is not the case. The results presented here show that the previously observed phenotype is not due to the flhD locus, but is instead due to differences in the thyA alleles present in the flhD(+) and flhD(-) strains used in the original studies. We find that when the strains being compared have the same thyA allele (wild type or mutant), flhD mutations have no effect on growth.
An estimation algorithm for vision-based exploration of small bodies in space (2005)

This paper summarizes a methodology for designing on-board state estimators in support of spacecraft exploration of small bodies such as asteroids and comets. This paper focuses on an estimation algorithm that incorporates two basic computer-vision measurement types: a landmark table and a paired feature table. Several innovations are developed to incorporate these measurement types into the on-board state estimation algorithm. Simulations are provided to demonstrate the feasibility of the approach.
Five Things You Didn’t Want to Know about Hydraulic Fractures (2013)

It is common to envision and design hydraulic fractures as if they were simple, planar features that are relatively consistent in width and durable in their flow capacity. Production forecasting is frequently based on a simplified description of the reservoir as a homogeneous single productive layer. In rare instances the pay intervals may be simulated with as many as a dozen layered strata, but even the most meticulous reservoir engineer may mistakenly assign each layer a highly conductive, durable connection with the wellbore. When analyzing the resulting production data, similar assumptions are made, which can erroneously reinforce these misconceptions.
Kinetics and Specificity of Peptide Uptake by the Oligopeptide Transport System of Lactococcus lactis (1998)

To obtain amino acids for growth, Lactococcus lactis uses a proteolytic system to degrade exogenous proteins such as caseins. The extracellular cell wall-attached proteinase PrtP and the oligopeptide transport system Opp mediate the first two steps in the utilization of caseins. beta-Casein is degraded by PrtP to fragments of 5-30 amino acid residues, and only a limited number of peptides are selected from this pool for uptake via Opp. To study the specificity of Opp and the kinetics of peptide uptake in L. lactis in detail, we used the following strategy: (i) the Opp system was overexpressed; (ii) a 4-fold peptidase mutant was used that is unable to degrade KYGK; (iii) iodinated KYGK was used as the reporter peptide; (iv) libraries of peptides, in which one amino acid position is systematically varied, were used as competitive peptides; and (v) peptides were synthesized on the basis of the beta-casein degradation products, their inhibition of KYGK uptake was determined, and the uptake of these peptides was followed by high-performance liquid chromatography (HPLC). These studies indicate that (i) the Opp system can transport a broad range of peptides from 4 up to at least 18 residues with very little preference for particular side chains and (ii) the kinetics of peptide uptake differ for different substrates tested. Whereas class I peptides such as KYGK exhibit normal Michaelis-Menten kinetics, the level of uptake of the majority of peptides (class II) increases sigmoidally with concentration. Different models for explaining the apparent cooperative effects that are observed for peptide uptake are discussed.
Analytic studies of foam cells from breast cancer precursors (1984)

A preliminary study of foam cells from nipple aspirate fluid demonstrated the ability of image analysis to discriminate categories of breast disease. Foam cell images numbering 471 were collected from nipple aspirate samples representing three to six cases of each of the four following disease categories based on breast tissue diagnosis: benign, nonproliferative; hyperplasia; atypical hyperplasia; and cancer. Twenty-two shape and density parameters were measured for each cell image. Using multivariate analysis, eight nuclear and three cytoplasmic parameters showed significant differences (P less than 0.005) when tested among cell populations from the breast disease categories. Linear stepwise discriminant analysis enabled construction of a three-parameter model that was optimal for distinguishing among cell populations from the four categories of breast disease. The means of all twenty-three parameters were then evaluated on a per-patient basis. A second three-parameter model was constructed that distinguished, with 100% accuracy, patients with proliferative disease from those with nonproliferative disease. Grouping disease categories and comparing patients whose diagnosis was benign or hyperplasia versus atypical hyperplasia or malignant, the model placed patients in the correct group 83% of the time.
Farnesyltransferase inhibitors induce cytochrome c release and caspase 3 activation preferentially in transformed cells (1998)

Farnesyltransferase inhibitors (FTIs) represent a new class of anticancer drugs that show promise in blocking the growth of tumors. Here, we report that FTIs are capable of inducing apoptosis of transformed but not untransformed cells. Treatment of v-K-ras-transformed normal rat kidney (KNRK) cells with FTIs leads to the induction of apoptotic cell morphology, chromatin condensation and DNA fragmentation. In addition, fluorescence-activated cell sorter analysis of FTI-treated KNRK cells shows a sub-G1 apoptotic peak (chromosome content of <2 N). This FTI-induced apoptosis is evident only when the cells are grown in low serum conditions (0.1% fetal calf serum) and is observed selectively with transformed KNRK cells and not with untransformed NRK cells. Further analysis of the mechanism underlying this apoptosis has shown that FTI treatment of KNRK cells results in the activation of caspase 3 but not caspase 1. Moreover, the addition of Z-DEVD-fmk, an agent that interferes with caspase 3 activity, can inhibit FTI-induced apoptosis in a dose-dependent manner. Introduction of the CASP-3 gene into MCF7 cells, which lack caspase 3 activity, results in a significant increase of FTI-induced apoptosis. Furthermore, FTI induces the release of cytochrome c into the cytosol. This release is an important feature of caspase 3-mediated apoptosis. These results suggest that FTIs induce apoptosis through the release of cytochrome c from the mitochondria resulting in caspase 3 activation.
Association Between Lowering LDL-C and Cardiovascular Risk Reduction Among Different Therapeutic Interventions (2016)

In this meta-regression analysis, the use of statin and nonstatin therapies that act via upregulation of LDL receptor expression to reduce LDL-C were associated with similar RRs of major vascular events per change in LDL-C. Lower achieved LDL-C levels were associated with lower rates of major coronary events.
Activity of erlotinib when dosed below the maximum tolerated dose for EGFR‐mutant lung cancer: Implications for targeted therapy development (2016)

At doses below the MTD, erlotinib treatment results in a high response rate and a prolonged median PFS. Review of the literature indicates that 15 of 30 small-molecule inhibitors that are approved or in late-stage development for cancer therapy have recommended doses below the MTD. When the toxicities of MTD dosing are a concern, an investigation of small-molecule inhibitors at doses below the MTD is warranted. Cancer 2016;122:3456-63. © 2016 American Cancer Society.
The relation of platelet density to platelet age: survival of low- and high-density 111indium-labeled platelets in baboons (1986)

Abstract The relationship between platelet density and platelet age has been studied using continuous linear Percoll density gradients and 111In- labeling of autologous platelets in baboons. To investigate changes in platelet density during senescence in the circulation, baboons were infused with 111In-labeled autologous platelets, and blood was collected at one hour postinfusion and twice daily thereafter for six days. Platelets were isolated from these samples in high yield (greater than 95%) and separated in continuous linear Percoll density gradients following density equilibrium centrifugation. Although at one hour postinfusion the density distribution of radiolabeled platelets coincided closely with the distribution of the total platelet population, a detectable symmetrical shift toward higher densities was observed after five days. The relative specific radioactivity (RSR) of high-density platelets (1.064 to 1.067 g/mL) decreased at a slower rate than that of the total platelet population (platelets of all densities), whereas the RSR of low-density platelets (1.053 to 1.056 g/mL) showed a more immediate and rapid decrease. These results give rise to one of two interpretations: (1) low-density platelets have a shorter survival time than more dense platelets and are therefore cleared from the circulation at a faster rate, or (2) platelets of all densities increase in density upon aging in the circulation. To determine the explanation for changing RSR of different density fractions we studied the in vivo disappearance characteristics of low- and high-density 111In-labeled platelets. There were no significant differences between the mean survival times of low-density platelets (5.0 +/- 0.49 days, +/- 1 SD, n = 6), high-density platelets (4.9 +/- 0.56 days, n = 6), or control platelets representing platelets of all densities (4.9 +/- 0.38 days, n = 6). Although a slight increase in the density of all platelets during platelet senescence is indicated by these studies, we conclude that platelet density heterogeneity is not primarily a consequence of age-related changes in platelet density.
Better Substrates for Bacterial Transglycosylases (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTBetter Substrates for Bacterial TransglycosylasesXiang-Yang Ye, Mei-Chu Lo, Livia Brunner, Deborah Walker, Daniel Kahne, and Suzanne WalkerView Author Information Department of Chemistry, Princeton University Princeton, New Jersey 08544 Cite this: J. Am. Chem. Soc. 2001, 123, 13, 3155–3156Publication Date (Web):March 9, 2001Publication History Received3 January 2001Published online9 March 2001Published inissue 1 April 2001https://pubs.acs.org/doi/10.1021/ja010028qhttps://doi.org/10.1021/ja010028qrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1864Altmetric-Citations138LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Assays,Lipids,Mathematical methods,Membranes,Peptides and proteins Get e-Alerts
Physiology and pathophysiology of bone remodeling. (1999)

The skeleton is a metabolically active organ that undergoes continuous remodeling throughout life. This remodeling is necessary both to maintain the structural integrity of the skeleton and to subserve its metabolic functions as a storehouse of calcium and phosphorus. These dual functions often come into conflict under conditions of changing mechanical forces or metabolic and nutritional stress. The bone remodeling cycle involves a complex series of sequential steps that are highly regulated. The "activation" phase of remodeling is dependent on the effects of local and systemic factors on mesenchymal cells of the osteoblast lineage. These cells interact with hematopoietic precursors to form osteoclasts in the "resorption" phase. Subsequently, there is a "reversal" phase during which mononuclear cells are present on the bone surface. They may complete the resorption process and produce the signals that initiate formation. Finally, successive waves of mesenchymal cells differentiate into functional osteoblasts, which lay down matrix in the "formation" phase. The effects of calcium-regulating hormones on this remodeling cycle subserve the metabolic functions of the skeleton. Other systemic hormones control overall skeletal growth. The responses to changes in mechanical force and repair of microfractures, as well as the maintenance of the remodeling cycle, are determined locally by cytokines, prostaglandins, and growth factors. Interactions between systemic and local factors are important in the pathogenesis of osteoporosis as well as the skeletal changes in hyperparathyroidism and hyperthyroidism. Local factors are implicated in the pathogenesis of the skeletal changes associated with immobilization, inflammation, and Paget disease of bone.
Superhydrophilic and Superwetting Surfaces: Definition and Mechanisms of Control (2010)

The term superhydrophobicity was introduced in 1996 to describe water-repellent fractal surfaces, made of a hydrophobic material, on which water drops remain as almost perfect spheres and roll off such surfaces leaving no residue. Today, superhydrophobic surfaces are defined as textured materials (and coatings) on (nonsmooth) surfaces on which water forms contact angles 150° and larger, with only a few degrees of contact angle hysteresis (or sliding angle). The terms superhydrophilicity and superwetting were introduced a few years after the term superhydrophobicity to describe the complete spreading of water or liquid on substrates. The definition of superhydrophilic and superwetting substrates has not been clarified yet, and unrestricted use of these terms sometimes stirs controversy. This Letter briefly reviews the superwetting phenomenon and offers a suggestion on defining superhydrophilic and superwetting substrates and surfaces.
Hyperostosis–Hyperphosphatemia Syndrome: A Congenital Disorder of O-Glycosylation Associated With Augmented Processing of Fibroblast Growth Factor 23 (2006)

The primary defect in HHS is impairment of glycosylation of FGF23 resulting from mutations in GALNT3 and leading to augmented processing of FGF23. These changes in FGF23 abolish its phosphaturic effect and lead to severe persistent hyperphosphatemia. This study provides the pathogenetic mechanism of the first mucin-type O-glycosylation defect identified.
PTPN2 negatively regulates oncogenic JAK1 in T-cell acute lymphoblastic leukemia (2011)

We have recently reported inactivation of the tyrosine phosphatase PTPN2 (also known as TC-PTP) through deletion of the entire gene locus in ∼ 6% of T-cell acute lymphoblastic leukemia (T-ALL) cases. T-ALL is an aggressive disease of the thymocytes characterized by the stepwise accumulation of chromosomal abnormalities and gene mutations. In the present study, we confirmed the strong association of the PTPN2 deletion with TLX1 and NUP214-ABL1 expression. In addition, we found cooperation between PTPN2 deletion and activating JAK1 gene mutations. Activating mutations in JAK1 kinase occur in ∼ 10% of human T-ALL cases, and aberrant kinase activity has been shown to confer proliferation and survival advantages. Our results reveal that some JAK1 mutation-positive T-ALLs harbor deletions of the tyrosine phosphatase PTPN2, a known negative regulator of the JAK/STAT pathway. We provide evidence that down-regulation of Ptpn2 sensitizes lymphoid cells to JAK1-mediated transformation and reduces their sensitivity to JAK inhibition.
Overview of natural history, pathology, molecular genetics and management of HNPCC (Lynch syndrome) (1996)

Hereditary non-polyposis colorectal cancer (HNPCC) predisposes to cancers of the colon, endometrium and several other extra-colonic sites in the absence of premonitory physical stigmata (Muir-Torre syndrome excepted). Discovery of the several DNA mismatch repair genes (hMSH2, hMLH1, hPMS1, hPMS2) holds the potential for determining the cancer destiny of patients, theoretically in utero. Pre-symptomatic DNA testing is now possible in patients from HNPCC families and will be clinically available once inexpensive and simple tests for these germ-line mutations have been effected. Genetic counseling will be mandatory, given the myriad socio-psychological, insurance, and potentially other personal issues which may impact this knowledge. New findings in the pathology of HNPCC, particularly an increased frequency of interval cancers and the likely accelerated rate of the adenoma to cancer sequence, indicate the need for more frequent colonoscopic surveillance with an option for prophylactic subtotal colectomy in germ-line-positive individuals.
Microbial Fuel Cells Generating Electricity from Rhizodeposits of Rice Plants (2008)

Living plants transport substantial amounts of organic material into the soil. This process, called rhizodeposition, provides the substrate for the rhizospheric microbial community. In this study, a laboratory-scale sediment microbial fuel cell, of which the anode is positioned in the rhizosphere of the rice plants, is used to microbially oxidize the plant-derived organics. An electrical current was generated through the in situ oxidation of rhizodeposits from living rice plants. The electrical power output of a sediment microbial fuel cell was found to be a factor 7 higher in the presence of actively growing plants. This process offers the potential of light-driven power generation from living plants in a nondestructive way. Sustainable power productions up to 330 W ha(-1) could be attributed to the oxidation of the plant-derived compounds.
Large-Scale Discovery of Induced Point Mutations With High-Throughput TILLING (2003)

TILLING (Targeting Induced Local Lesions in Genomes) is a general reverse-genetic strategy that provides an allelic series of induced point mutations in genes of interest. High-throughput TILLING allows the rapid and low-cost discovery of induced point mutations in populations of chemically mutagenized individuals. As chemical mutagenesis is widely applicable and mutation detection for TILLING is dependent only on sufficient yield of PCR products, TILLING can be applied to most organisms. We have developed TILLING as a service to the Arabidopsis community known as the Arabidopsis TILLING Project (ATP). Our goal is to rapidly deliver allelic series of ethylmethanesulfonate-induced mutations in target 1-kb loci requested by the international research community. In the first year of public operation, ATP has discovered, sequenced, and delivered >1000 mutations in >100 genes ordered by Arabidopsis researchers. The tools and methodologies described here can be adapted to create similar facilities for other organisms.
Hemicellulose and hemicellulases (1993)

Chemistry of hemicelluloses: relationship between hemicellulose structure and enzymes required for its hydrolysis, J. Puls and J. Schuseil biochemical aspects of the production of microbial hemicellulases, P. Biely enzymological aspects of microbial hemicelluloses with emphasis on fungal systems, M.P. Coughlan et al Feruloyl and p-courmaroyl esterases from the anaerobic fungus Neocallimastix strain MC-2 - properties and functions in plant cell wall degradation, W. Scott Bomeman et al molecular biology of hemicellulases, G.P. Hazlewood and H.J. Gilbert applications of hemicelluloses in biopulping, bio-bleaching, food, feed and pulp and paper industries, K.K.Y. Wong and J.N. Saddler.
Boundary effects on the optical properties of InGaN multiple quantum wells (2003)

We examine the issues of spontaneous and piezoelectric polarization discontinuity on the optical properties of 3.0-nm-thick indium gallium nitride (InGaN) multiple quantum wells (MQWs). A quench of band-edge emission from the cap GaN layer is observed when the photoexcitation source is changed from a 355- to a 248-nm laser. The interband transitions from the InGaN wells exhibit a linear dependence on the 1) spectral blue shift of ∼8.5×10/sup -18/ meV /spl middot/ cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and 2) change of the internal field of ∼3×10/sup -14/ meV /spl middot/ cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with the injected carrier density up to N/sub inj/∼10/sup 19/ cm/sup -3/ at 77 K. These observations are attributed to the redistribution of photogenerated carriers in the InGaN wells due to the polarization discontinuity at the QW interface and the surface band bending effect. By incorporating an additional boundary condition of surface Fermi-level pinning into the Poisson equation and the band-structure analysis, it is shown the emission from the InGaN-GaN MQWs is dominant by the recombination between the high-lying subbands and the screening of internal field effects.
Musketeer (2015)

Many systems for the parallel processing of big data are available today. Yet, few users can tell by intuition which system, or combination of systems, is "best" for a given workflow. Porting workflows between systems is tedious. Hence, users become "locked in", despite faster or more efficient systems being available. This is a direct consequence of the tight coupling between user-facing front-ends that express workflows (e.g., Hive, SparkSQL, Lindi, GraphLINQ) and the back-end execution engines that run them (e.g., MapReduce, Spark, PowerGraph, Naiad).
Acidic Alkali Metal Salts and Ammonium Salts of Keggin-type Heteropolyacids as Efficient Solid Acid Catalysts for Liquid-phase Friedel-Crafts Reactions (1992)

Abstract Acidic salts of the Keggin-type heteropolytungstic acids prepared through partial neutralization with alkali metal carbonates or ammonium hydroxide had relatively large surface areas, and showed high catalytic efficiency as insoluble solid acid catalysts in Friedel-Crafts alkylation and acylation using benzyl chloride, benzoyl chloride, benzoic anhydride, benzoic acid, acetic anhydride, and acetic acid as electrophiles.