gebhart/patrepeval huggingface dataset:
Action of Polymyxin B on Bacterial Membranes: Morphological Changes in the Cytoplasm and in the Outer Membrane of Salmonella typhimurium and Escherichia coli B (1975)

Though the primary action of the cationic antibiotic polymyxin B is against the membrane of susceptible bacteria, severe morphological changes are detected in the cytoplasm. Using fluorescence microscopy and a mono-N-dansyl-polymyxin B derivative, we could demonstrate aggregations of the antibiotic with cellular material, possibly nucleic acids and/or ribosomes. These aggregations were only produced by minimum inhibitory or higher concentrations of the antibiotic as shown with Salmonella and Escherichia strains differing in their polymyxin susceptibility. The outer membrane of Salmonella typhimurium revealed characteristic blebs when treated with polymyxin B. This was investigated by the gentle methods of spray-freezing and freeze-etching. The obtained electron micrographs suggest that the polymyxin-induced blebs are projections of the outer monolayer of the outer membrane. A possible mechanism of penetration of polymyxin B through the cell envelope of gram-negative bacteria is presented.
Inhibition of retinal angiogenesis by peptides derived from thrombospondin-1. (2000)

Thrombospondin (TSP)1 is a tumor suppressor with activity that is associated with its ability to inhibit neovascularization. Previous studies have mapped this antiangiogenic activity to the type 1 repeats and the amino-terminal portion of the molecule within the procollagen-like domain. The present study was performed to investigate the ability of TSP-1 and peptides derived from the type 1 repeats to inhibit retinal angiogenesis.TSP-1 and peptides with tryptophan-rich, heparin-binding sequences and transforming growth factor (TGF)-beta1 activation sequences were evaluated in two models of retinal angiogenesis: a retinal explant assay and a rat model of retinopathy of prematurity (ROP).Platelet-derived TSP-1 inhibited angiogenesis in both experimental models. Peptides from the native TSP-1 sequence, which contained both the tryptophan-rich repeat and the TGF-beta1 activation sequence, were the most potent inhibitors of endothelial cell outgrowth in the retinal explant assay. In contrast, a peptide containing only the tryptophan-rich, heparin-binding sequence was most active in inhibiting neovascular disease in the rat ROP model.These results indicate that the type 1 repeats of TSP-1 contain two subdomains that may independently influence the process of neovascularization, and that peptides derived from these type 1 repeats may be promising pharmacologic agents for treatment of retinal angiogenesis.
Story Segmentation and Topic Detection in the Broadcast News Domain (1999)

In this paper we present algorithms for story segmentation and topic detection. Both algorithms are online algorithms and use a combination of machine learning, statistical natural language processing and information retrieval techniques. The story segmentation algorithm is a two stage algorithm that uses a decision tree based probabilistic model in the first stage and incorporates aspects of our detection system via an information-retrieval based refinement scheme in the second stage. The topic detection algorithm is an incremental clustering algorithm that employs a novel dynamic clusterdependent similarity measure between documents and clusters. Cseg and topic-weighted Cdet for these algorithms on the 1998 TDT2 Evaluation are 0.1651 and 0.0042. 1. Introduction Automatic segmentation of a text stream, possibly the output of a speech recognizer, into its constituent stories and the detection of new topics and their clustering are important components in applications dealing with mu...
CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data (2008)

CMA is a user-friendly comprehensive package for classifier construction and evaluation implementing most usual approaches. It is freely available from the Bioconductor website at (http://bioconductor.org/packages/2.3/bioc/html/CMA.html).
How Well Can Passage Meaning be Derived without Using Word Order? A Comparison of Latent Semantic Analysis and Humans (1997)

How much of the meaning of a naturally occurring English passage is derivable from its combination of words without considering their order? An exploratory approach to this question was provided by asking humans to judge the quality and quantity of knowledge conveyed by short student essays on scientific topics and comparing the inter-rater reliability and predictive accuracy of their estimates with the performance of a corpus-based statistical model that takes no account of word order within an essay. There was surprisingly little difference between the human judges and the model.
Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter (2004)

Reversing the spread of antibiotic multiresistant bacteria is hampered by ignorance of the natural history of resistance genes, the mobile elements carrying them, and the bacterial hosts harboring them. Using traditional cultivation and cultivation-independent molecular techniques, we quantified antibiotic resistance genes and mobile elements called integrons in poultry house litter from commercial poultry farms. Unexpectedly, the major reservoir for Class 1 integrons in poultry litter is not their previously identified hosts, Gram-negative Enterobacteriaceae such as Escherichia coli. Rather, integrons and associated resistance genes abound in several genera of Gram-positive bacteria that constitute >85% of the litter community compared with Enterobacteriaceae that comprise <2% of this ecosystem. This finding warrants reexamination of our assumptions about the persistence and spread of antibiotic resistance genes.
Chemokines and the Arrest of Lymphocytes Rolling Under Flow Conditions (1998)

Circulating lymphocytes are recruited from the blood to the tissue by rolling along the endothelium until being stopped by a signaling event linked to the Gialpha subunit of a heterotrimeric GTP-binding protein; that event then triggers rapid integrin-dependent adhesion. Four chemokines are now shown to induce such adhesion to intercellular adhesion molecule-1 and to induce arrest of rolling cells within 1 second under flow conditions similar to those of blood. SDF-1 (also called PBSF), 6-C-kine (also called Exodus-2), and MIP-3beta (also called ELC or Exodus-3) induced adhesion of most circulating lymphocytes, including most CD4+ T cells; and MIP-3alpha (also called LARC or Exodus-1) triggered adhesion of memory, but not naïve, CD4+ T cells. Thus, chemokines can regulate the arrest of lymphocyte subsets under flowing conditions, which may allow them to control lymphocyte-endothelial cell recognition and lymphocyte recruitment in vivo.
Growing tips of type I collagen fibrils formed in vitro are near-paraboloidal in shape, implying a reciprocal relationship between accretion and diameter. (1992)

Collagen fibrils generated in vitro at 37 degrees C by enzymic removal of C-terminal propeptides from type I pC-collagen (an intermediate in the normal processing of type I procollagen to collagen containing the C-terminal propeptides but not the N-terminal propeptides) display shape polarity, with one tip fine tapered and the other coarse tapered. Mass measurements by scanning transmission electron microscopy show that the mass per unit length along both kinds of tip increases roughly linearly over distances of approximately 100 D periods from the fibril end [D (axial periodicity) = 67 nm]. The fine tips of fibrils of widely differing lengths exhibit near-identical mass distributions, the mass in all cases increasing at the rate of approximately 17 molecules per D period, irrespective of fibril length. Coarse tips display less regular behavior. These results show that (i) the shape of a fine tip is not conical but resembles more closely a paraboloid of revolution, and (ii) for this shape to be maintained throughout growth, accretion (rate of mass uptake per unit area) cannot everywhere be the same on the surface of the tip but must decrease as the diameter increases. To a first approximation, accretion alpha (diameter)-1.
Observation of Classical-Quantum Crossover of 1/f Flux Noise and Its Paramagnetic Temperature Dependence (2017)

By analyzing the dissipative dynamics of a tunable gap flux qubit, we extract both sides of its two-sided environmental flux noise spectral density over a range of frequencies around 2k_{B}T/h≈1 GHz, allowing for the observation of a classical-quantum crossover. Below the crossover point, the symmetric noise component follows a 1/f power law that matches the magnitude of the 1/f noise near 1 Hz. The antisymmetric component displays a 1/T dependence below 100 mK, providing dynamical evidence for a paramagnetic environment. Extrapolating the two-sided spectrum predicts the linewidth and reorganization energy of incoherent resonant tunneling between flux qubit wells.
Structure–Activity Relationship of a Broad-Spectrum Insect Odorant Receptor Agonist (2012)

Agonism of insect odorant receptor (OR) cation channels may represent a new strategy for the manipulation of destructive insect olfactory-driven behaviors. We have explored the chemical space around VUAA1, the first in class agonist of the obligate OR co-receptor ion channel (Orco), and describe novel compound analogues with increased potency across insect taxa. Functional analyses reveal several of these VUAA1 structural analogues display significantly greater potency as compared to the activity of the previously described active compounds in mobility-based behavioral assays on mosquito larvae.
Organization and heterogeneity of sequences within a repeating unit of human Y chromosome deoxyribonucleic acid (1979)

Fragments of 3.4 kilobases (kb) are released from DNA of human males, but not DNA of human females, by cleavage with restriction endonucleases HaeIII, EcoRI, or EcoRII. Most, if not all, reiterated DNA which is specific for the Y chromosome (it-Y DNA) is present within these male-specific 3.4-kb molecules. Although such 3.4-kb molecules are themselves localized to the Y chromosome, this is not true for all sequences within them. At least two distinguishable types of reiterated sequences are found within each 3.4-kb molecule. One type consists of at least two families which are highly reiterated and are not confined to the Y chromosome. The other type is composed of an estimated minimum of 39 families, each moderately reiterated and localized to the Y chromosome. Y-specific and non-Y-specific sequences are interspersed with one another in the same 3.4-kb molecule. In the average 3.4-kb molecule, three 800 nucleotide lengths of Y-specific sequences alternate with four 250 nucleotide lengths of non-Y-specific sequences. Since the total number of families of Y-specific sequences, calculated on the basis of reiteration frequency and total abundance in a male genome, greatly exceeds the number of Y -specific sequences present in a single 3.4-kb molecule, it necessarily follows that the population of these 3.4-kb molecules is heterogeneous.
Mutual injection locking: a new architecture for high-power solid-state laser arrays (2005)

In this paper, bidirectional (mutual) injection locking is demonstrated with solid-state lasers, producing significant improvements over traditional single-direction injection locking. Each laser element shares part of its output with other elements in bidirectional locking, distinct from single-direction (traditional) injection locking where one master laser provides the locking signal for a number of slaves. In a phase-locked array, the individual laser outputs add coherently, and the brightness of the entire array scales with the square of the number of elements, as if the active material diameter were increasing. Benefits of bidirectional locking, when compared to traditional injection locking, include reduced laser threshold, better output beam quality, and improved scaling capability. Experiments using two Nd:YVO/sub 4/ lasers confirmed that mutual injection locking reduced lasing threshold by a factor of at least two and increased the output beam quality significantly. The injection-locking effects began with 0.03% coupling between lasers and full-phase locking for coupling exceeding 0.5%. The 0.5% requirement for full-phase locking is significantly lower than the requirement for traditional injection locking. The large coupling requirement limits traditional injection-locked arrays to fewer than 20 elements, whereas mutually injection-locked arrays have no such limit. Mutual injection locking of an array of lasers can lead to a new architecture for high-power laser systems.
Nuclear Factor-Kappa B1 is Associated With Gastric Cancer in a Chinese Population (2014)

Activated nuclear factor-κB (NF-κB) is associated with the pathogenesis of numerous cancers, such as gastric cancer (GC). Genetic polymorphisms in the genomic region containing nuclear factor-κB1 (NFKB1) have a plausible role in modulating the risk of GC. To identify markers contributing to the genetic susceptibility to GC, we analyzed 15 single nucleotide polymorphisms (SNPs, rs28362491, rs3774932, rs1598856, rs230531, rs230530, rs230528, rs230521, rs230498, rs230539, rs1005819, rs3774956, rs4648055, rs3774964, rs4648068, and rs3774968) in the genomic region containing NFKB1. The participants included 401 patients with GC and 433 healthy controls. The allelic or genotypic frequencies of the rs28362491 (located in the promoter region of NFKB1), rs230521 (NFKB1 intron 4), and rs4648068 (NFKB1 intron 12) polymorphisms in the patients with GC were significantly different from those in the healthy controls. Strong linkage disequilibrium was observed in 4 blocks (D'>0.9). Significantly more A-T haplotypes (block 1, P=0.0005), A-C haplotypes (block 2, P=0.0001) and G-A-A haplotypes (block 4, P=0.016) were found in the patients with GC. Significantly more A-C haplotypes (block 1, P=0.005) and A-G haplotypes (block 2, P=0.0004) were found in the healthy controls. These findings suggest a role for NFKB1 polymorphism in GC among a Han Chinese population and may be informative for future genetic studies on gastric cancer.
Fatal Salmonella septicemia after platelet transfusion (1987)

A thrombocytopenic, leukopenic patient with multiple myeloma who was given 7 units of platelets died 6 days later from complications of Salmonella heidelberg septicemia. A platelet donor who was asymptomatic at the time of donation had group B Salmonella on stool culture. His clinical history and the results of serologic studies and stool culture were consistent with a mild Salmonella gastroenteritis 5 days before donation. Antibiotic sensitivity patterns and plasmid profiles indicated that the organism (S. heidelberg) isolated from the donor's stool was identical to that isolated from the patient's blood and from the platelet bags. It is believed that low-grade, asymptomatic bacteremia in the donor was the source of infection in the recipient. Food and Drug Administration records contain reports of six septic deaths due to platelet transfusions since 1979, compared with none in the preceding 4 years. Increased use of platelet products and the standard practice of storage at room temperature may contribute to the risk of sepsis after platelet transfusion, particularly in immunocompromised patients.
Software-managed address translation (2002)

In this paper we explore software-managed address translation. The purpose of the study is to specify the memory management design for a high clock-rate PowerPC implementation in which a simple design is a prerequisite for a fast clock and a short design cycle. We show that software-managed address translation is just as efficient as hardware-managed address translation and it is much more flexible. Operating systems such as OSF/1 and Mach charge between 0.10 and 0.28 cycles per instruction (CPI) for address translation using dedicated memory-management hardware. Software-managed translation requires 0.05 CPI. Mechanisms to support such features as shared memory, superpages, sub-page protection, and sparse address spaces can be defined completely in software, allowing much more flexibility than in hardware-defined mechanisms.
Mapping of the 5' termini of two adeno-associated virus 2 RNAs in the left half of the genome (1982)

The left 45% of the adeno-associated virus 2 genome was sequenced. The 5' termini of two adeno-associated virus-specific RNAs were mapped at the nucleotide level within this region of the genome (nucleotides 286 to 288 and 871 to 874). Both of these 5' termini map 31 +/- 2 nucleotides downstream from the start of "TATA' boxes.
Endometriosis: The prevalence of endometrial immunoglobulin G antibodies in patients with endometriosis (1995)

The purpose of this study was to investigate the frequency of antibodies in the serum of patients with endometriosis reacting with endometrial, ovarian, thyroid and skeletal muscle antigens. A total of 55 fertile patients with pelvic pain who had endometriosis diagnosed by laparoscopy and confirmed by histology formed the study group, while 43 fertile patients without pelvic pain and undergoing tubal sterilization formed the control group. Eutopic endometrial membrane antigen was prepared from biopsies taken from patients or controls by an ultracentrifugation technique and used in an enzyme-linked immunosorbent assay (ELISA) for immunoglobulin (Ig) G, IgA and IgM endometrial antibodies. Ovarian, thyroid and skeletal muscle antigens were prepared similarly and used in an ELISA. There was a significant difference in the prevalence of IgG antibodies to eutopic endometrial antigens derived from either control or endometriosis patients (P < 0.05). IgA or IgM antibodies against endometrial antigens were not detected. Endometrial antibodies were detectable in both the luteal and the follicular phases of the menstrual cycle. Immunoblot analysis demonstrated the presence of endometrial antigens with molecular weights of 60 and 66 kDa in the eutopic endometrium of patients with endometriosis. Antibodies to thyroid, ovary or skeletal muscle were not detected in these patients. These findings indicate that endometrial antibodies of the IgG class can be detected in approximately 50% of patients with endometriosis but it remains unclear whether these represent a pathologically distinct subgroup of such patients.
Identification by HPLC-MS of Carotenoids of theThraustochytriumCHN-1 Strain Isolated from the Seto Inland Sea (2003)

The orange-pigmented Thraustochytrium, CHN-1 strain was found to contain astaxanthin as the main carotenoid pigment. Echinenone, canthaxanthin, phoenicoxanthin and beta-carotene were also identified by high-performance liquid chromatography (HPLC) and HPLC-mass spectrometry. The total extractable carotenoid level was found to increase with culture age.
Introduction to general, organic, and biological chemistry (1988)

Introduction to general, organic, and biological chemistry , Introduction to general, organic, and biological chemistry , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Multi-robot coordination using generalized social potential fields (2009)

We present a novel approach to compute collision-free paths for multiple robots subject to local coordination constraints. More specifically, given a set of robots, their initial and final configurations, and possibly some additional coordination constraints, our goal is to compute a collision-free path between the initial and final configuration that maintains the constraints. To solve this problem, our approach generalizes the social potential field method to be applicable to both convex and nonconvex polyhedra. Social potential fields are then integrated into a “physics-based motion planning” framework which uses constrained dynamics to solve the motion planning problem. Our approach is able to plan for over 200 robots while averaging about 110 ms per step in a variety of environments.
Spreadsheet table transformations from examples (2011)

Every day, millions of computer end-users need to perform tasks over large, tabular data, yet lack the programming knowledge to do such tasks automatically. In this work, we present an automatic technique that takes from a user an example of how the user needs to transform a table of data, and provides to the user a program that implements the transformation described by the example. In particular, we present a language of programs TableProg that can describe transformations that real users require.We then present an algorithm ProgFromEx that takes an example input and output table, and infers a program in TableProg that implements the transformation described by the example. When the program is applied to the example input, it reproduces the example output. When the program is applied to another, potentially larger, table with a 'similar' layout as the example input table, then the program produces a corresponding table with a layout that is similar to the example output table. A user can apply ProgFromEx interactively, providing multiple small examples to obtain a program that implements the transformation that the user desires. Moreover, ProgFromEx can help identify 'noisy' examples that contain errors. To evaluate the practicality of TableProg and ProgFromEx, we implemented ProgFromEx as a module for the Microsoft Excel spreadsheet program. We applied the module to automatically implement over 50 table transformations specified by endusers through examples on online Excel help forums. In seconds, ProgFromEx found programs that satisfied the examples and could be applied to larger input tables. This experience demonstrates that TableProg and ProgFromEx can significantly automate the tasks over tabular data that users need to perform.
TPAP-Catalyzed Direct Oxidation of Primary Alcohols to Carboxylic Acids through Stabilized Aldehyde Hydrates (2011)

We present a simple, mild, and highly effective method for the direct conversion of primary alcohols to carboxylic acids. TPAP serves as the catalyst, and NMO·H(2)O plays a dual role, acting as the co-oxidant and as a reagent for aldehyde hydrate stabilization. This previously unknown stabilizing effect of geminal diols by N-oxides is the key for the efficiency of the overall transformation.
Rate control for advance video coding (AVC) standard (2003)

Rate control plays a very important role in constant bit rate (CBR) coding. AVC standard is jointly developed by ISO and ITU-T, which contains several inter and intra prediction modes. Rate distortion optimization (RDO) based on prerequisite quantization parameters determines the optimal prediction of each macroblock. This makes the current AVC software difficult to adopt the existing rate control techniques. This paper proposes an efficient rate control algorithm at macroblock level for AVC standard by considering both rate control and optimal prediction selection. Firstly, a quantization parameter estimated from neighboring macroblock is used in selecting an initial prediction and calculating the activity. Secondly, the estimated quantization parameter is refined according to the activity and virtual buffer occupancy. At last, the prediction mode is determined with the refined quantization parameter. Experimental results show that the proposed rate control algorithm can accurately achieve the target bit rate. Furthermore, the coding efficiency is similar to or even better than that of variable bit rate (VBR) coding.