gebhart/patrepeval huggingface dataset:
Sparse solution of underdetermined linear equations by stagewise orthogonal matching pursuit (2006)

Finding the sparsest solution to underdetermined systems of linear equations y = Φx is NP-hard in general. We show here that for systems with ‘typical’/‘random ’ Φ, a good approximation to the sparsest solution is obtained by applying a fixed number of standard operations from linear algebra. Our proposal, Stagewise Orthogonal Matching Pursuit (StOMP), successively transforms the signal into a negligible residual. Starting with initial residual r0 = y, at the s-th stage it forms the ‘matched filter ’ Φ T rs−1, identifies all coordinates with amplitudes exceeding a specially-chosen threshold, solves a least-squares problem using the selected coordinates, and subtracts the leastsquares fit, producing a new residual. After a fixed number of stages (e.g. 10), it stops. In contrast to Orthogonal Matching Pursuit (OMP), many coefficients can enter the model at each stage in StOMP while only one enters per stage in OMP; and StOMP takes a fixed number of stages (e.g. 10), while OMP can take many (e.g. n). StOMP runs much faster than competing proposals for sparse solutions, such as ℓ1 minimization and OMP, and so is attractive for solving large-scale problems. We use phase diagrams to compare algorithm performance. The problem of recovering a k-sparse vector x0 from (y, Φ) where Φ is random n × N and y = Φx0 is represented by a point (n/N, k/n)
Communicating police misconduct: alleged, variably reported, and/or real? (2003)

With the passing of the tenth anniversary of the Rodney King affair in addition to recent media reports of excessive force (such as the arrest of Donovan Jackson video-taped by Mitchell Crooks), the issue of police brutality has again been placed at the forefront of media coverage.Lawrence and Ross (L&R) highlight the importance of these issues and provide a beginning to the much-needed research in this area.Both these books examine major American newspaper portrayals of police use of force from the late 1970s through the early 90s.They take the position, independently, not only that excessive use of force by law enforcement occurs far more often than is reported, but also that it is a widespread social problem affecting the lives of ordinary (and especially ethnic minority) people in large cities.Compelling data in this regard provided by Ross relate to the thousands of complaints about police brutality submitted to civil rights agencies per annum in New York City and the contrasting handful of allegations that make it into the media.In addition, Lawrence refers to out-of-court settlements of police misconduct by the New York Police Department of many millions of dollars that could be averaged out, from 1987to 1992, to $400 per Officer.(Needless to say, even such captivating statistics as these
Influence of spacecraft outgassing on the exploration of tenuous atmospheres with in situ mass spectrometry (2010)

In situ mass spectrometry has been a powerful tool in many space missions to investigate atmospheres and exospheres of different bodies in the solar system. Applying new technologies, the mass spectrometers have become increasingly more sensitive. In this study, we show that spacecraft outgassing, which can never be completely prevented, will be the limiting factor in future missions that investigate very tenuous atmospheres and exospheres of moons, asteroids, or comets at large heliocentric distances. The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) instrument on the European Space Agency Rosetta mission has monitored spacecraft outgassing for 6 years during the cruise phase with unprecedented instrument sensitivity. It is shown that diffusion of gas from materials and from the spacecraft interior plays an important role in maintaining a relatively permanent thin gas cloud around the spacecraft for many years. The density and composition of this gas cloud depends on location on the spacecraft, maneuvers, and payload activity. The main contaminants are water, which is adsorbed on cold surfaces, and organics from the spacecraft structure, electronics, and insulations. Decomposed lubricant material can give a significant contribution to the total background. Fortunately for Rosetta, outgassing of the spacecraft will play a minor role when the comet is close to perihelion; only in the early phase of the mission the outgassing may be larger than the cometary signature.
Depolarization of light backscattered by randomly oriented nonspherical particles (1995)

We derive theoretically and validate numerically general relationships for the elements of the backscattering matrix and for the linear, δL, and circular, δC, backscattering depolarization ratios for nonspherical particles in random orientation. For the practically important case of randomly oriented particles with a plane of symmetry or particles and their mirror particles occurring in equal numbers and in random orientation, δC = 2δL/(1 − δL). Extensive T-matrix computations for randomly oriented spheroids demonstrate that, although both δL and δC are indicators of particle nonsphericity, they cannot be considered a universal measure of the departure of particle shape from that of a sphere and have no simple dependence on particle size and refractive index.
Purification of the human NF-E2 complex: cDNA cloning of the hematopoietic cell-specific subunit and evidence for an associated partner. (1993)

The human globin locus control region-binding protein, NF-E2, was purified by DNA affinity chromatography. Its tissue-specific component, p45 NF-E2, was cloned by use of a low-stringency library screen with murine p45 NF-E2 cDNA (N. C. Andrews, H. Erdjument-Bromage, M. B. Davidson, P. Tempst, and S. H. Orkin, Nature [London] 362:722-728, 1993). The human p45 NF-E2 gene was localized to chromosome 12q13 by fluorescent in situ hybridization. Human p45 NF-E2 and murine p45 NF-E2 are highly homologous basic region-leucine zipper (bZIP) proteins with identical DNA-binding domains. Immunoprecipitation experiments demonstrated that p45 NF-E2 is associated in vivo with an 18-kDa protein (p18). Because bZIP proteins bind DNA as dimers, we infer that native NF-E2 must be a heterodimer of 45- and 18-kDa subunits. Although AP-1 and CREB copurified with NF-E2, no evidence was found for heterodimer formation between p45 NF-E2 and proteins other than p18. Thus, p18 appears to be the sole specific partner of p45 NF-E2 in erythroid cells. Cloning of human p45 NF-E2 should permit studies of the role of NF-E2 in globin gene regulation and erythroid differentiation.
Entropy-Based Tests of Uniformity (1981)

Abstract The power properties of an entropy-based test are investigated when used for testing uniformity on [0, 1]. Percentage points and power against seven alternatives are reported. Compared with other tests of uniformity, the entropy-based test possesses good power properties for many alternatives. Some asymptotic null and alternative distributions are derived. For sample sizes up to 100 the table of percentage points provides a practical guide for using this test. A theory of entropy-based tests of distributional hypotheses other than uniformity is outlined.
Studies of acetylation and deacetylation in high mobility group proteins. Identification of the sites of acetylation in high mobility group proteins 14 and 17. (1981)

Duck erythrocytes were incubated with [3H]acetate both in the presence and absence of sodium butyrate. Subsequent perchloric acid extraction of the nuclei, followed by selective acetone precipitation, CM-Sephadex ion exchange chromatography, and gel filtration yielded radioactively labeled high mobility group (HMG) proteins HMG-14 and HMG-17 in pure form. Extensive enzymatic degradation of the proteins followed by amino acid analysis of the digests yielded a significant amount of material eluting in the position of epsilon-N-acetyllysine. Furthermore, automated Edman degradation of intact 3H-labeled HMG-14 and HMG-17 identified the specific sites of acetylation of these proteins. In both erythrocyte HMGs isolated from cells not exposed to butyrate, the lysine residue at position 2 was the only one found to be labeled. However, one additional site in HMG-14 and two additional sites in HMG-17 were found in the proteins from cells incubated in butyrate. Finally, studies of the enzymatic deacetylation of HMG-14 and HMG-17 confirmed that both nuclear proteins serve as deacetylase substrates and that butyrate inhibits their deacetylation, just as in the case of other HMG proteins and nucleosomal core histones.
Achieving Highly Efficient Nonfullerene Organic Solar Cells with Improved Intermolecular Interaction and Open‐Circuit Voltage (2017)

A new acceptor-donor-acceptor-structured nonfullerene acceptor ITCC (3,9-bis(4-(1,1-dicyanomethylene)-3-methylene-2-oxo-cyclopenta[b]thiophen)-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d':2,3-d']-s-indaceno[1,2-b:5,6-b']-dithiophene) is designed and synthesized via simple end-group modification. ITCC shows improved electron-transport properties and a high-lying lowest unoccupied molecular orbital level. A power conversion efficiency of 11.4% with an impressive V <sub>OC</sub> of over 1 V is recorded in photovoltaic devices, suggesting that ITCC has great potential for applications in tandem organic solar cells.
ATP Synthesis in Cotyledons of Cucumber and Mung Bean Seeds during the First Hours of Imbibition (1988)

ATP concentration increased rapidly during the first 6h of imbibition in cotyledons of cucumber and mung bean seeds. The increase was strongly inhibited by 1-h treatment of tissues with cyanide in both species. Carbonylcyanide m-chlorophenylhydrazone, an uncoupler of oxidative phosphorylation, showed little effect during the first hour of the treatment, but its inhibitory effect on ATP synthesis became significant after 3 h. Mitochondrial fractions prepared from 6-h-old cucumber cotyledons were capable of phosphorylating ADP to ATP. These results suggest that mitochondrial oxidative phosphorylation may be involved in ATP synthesis during the early hours of imbibition in both cucumber and mung bean seeds.
A generalized orthonormal basis for linear dynamical systems (1995)

In many areas of signal, system, and control theory, orthogonal functions play an important role in issues of analysis and design. In this paper, it is shown that there exist orthogonal functions that, in a natural way, are generated by stable linear dynamical systems and that compose an orthonormal basis for the signal space l/sub 2sup n/. To this end, use is made of balanced realizations of inner transfer functions. The orthogonal functions can be considered as generalizations of, for example, the pulse functions, Laguerre functions, and Kautz functions, and give rise to an alternative series expansion of rational transfer functions. It is shown how we can exploit these generalized basis functions to increase the speed of convergence in a series expansion, i.e., to obtain a good approximation by retaining only a finite number of expansion coefficients. Consequences for identification of expansion coefficients are analyzed, and a bound is formulated on the error that is made when approximating a system by a finite number of expansion coefficients.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Logo Retrieval in Document Images (2012)

This paper presents a scalable algorithm for segmentation free logo retrieval in document images. The contributions include the use of the SURF feature for logo retrieval, a novel indexing algorithm for efficient retrieval and a method to filter results using the orientation of local features and geometric constraints. Results demonstrate that logo retrieval can be performed with high accuracy and efficiently scaled to a large datasets.
Lecithin-retinol Acyltransferase Is Essential for Accumulation of All-trans-Retinyl Esters in the Eye and in the Liver (2004)

Lecithin-retinol acyltransferase (LRAT), an enzyme present mainly in the retinal pigmented epithelial cells and liver, converts all-trans-retinol into all-trans-retinyl esters. In the retinal pigmented epithelium, LRAT plays a key role in the retinoid cycle, a two-cell recycling system that replenishes the 11-cis-retinal chromophore of rhodopsin and cone pigments. We disrupted mouse Lrat gene expression by targeted recombination and generated a homozygous Lrat knock-out (Lrat-/-) mouse. Despite the expression of LRAT in multiple tissues, the Lrat-/- mouse develops normally. The histological analysis and electron microscopy of the retina for 6-8-week-old Lrat-/- mice revealed that the rod outer segments are approximately 35% shorter than those of Lrat+/+ mice, whereas other neuronal layers appear normal. Lrat-/- mice have trace levels of all-trans-retinyl esters in the liver, lung, eye, and blood, whereas the circulating all-trans-retinol is reduced only slightly. Scotopic and photopic electroretinograms as well as pupillary constriction analyses revealed that rod and cone visual functions are severely attenuated at an early age. We conclude that Lrat-/- mice may serve as an animal model with early onset severe retinal dystrophy and severe retinyl ester deprivation.
LAS, a novel selective estrogen receptor modulator with chemopreventive and therapeutic activity in the N-nitroso-N-methylurea-induced rat mammary tumor model. (2001)

The N-nitroso-N-methylurea-induced rat mammary tumor model was used to conduct two types of studies: a prevention study designed to test the ability of the novel selective estrogen receptor modulator lasofoxifene (LAS) to inhibit the development of mammary tumors, and a treatment study designed to test the inhibitory effect of LAS on the growth of established tumors. The prevention study indicated that LAS markedly delayed the emergence of N-nitroso-N-methylurea-induced tumors to an extent similar to that obtained by the established antiestrogen tamoxifen (TAM). At the highest dose administered, both TAM and LAS reduced tumor incidence by 75% and total tumor number by 90% relative to the controls. LAS also reduced the multiplicity of tumors, i.e., the mean number of tumors per rat, and resulted in substantially smaller total tumor burden. In the treatment study, LAS significantly inhibited tumor growth compared with the controls. In addition, whereas none of the untreated tumors regressed completely over the experimental period, 40% of LAS-treated tumors regressed by >50% at the highest dose (10 mg/kg daily). The results of this study in a rat mammary tumor model indicate that LAS has both chemopreventive and chemotherapeutic effects quantitatively comparable with those of TAM.
Chapter X: Polarity and Translational Punctuation (1970)

INTRODUCTION The three structural proteins of the lac operon are produced in different molar ratios. While the mechanism which gives rise to this natural polarity is still unknown, the complex phenomena of mutational polarity, with its relationship to polypeptide initiation and termination, seems to be the most likely direction from which an understanding of natural polarity will come. In this chapter the current status of work on the mechanism of polypeptide initiation and termination will be reviewed briefly. Then I will discuss in detail the phenomena of mutational polarity in the lac operon and its relationship to polypeptide initiation and termination. INITIATION Each separate polypeptide chain synthesized by an operon has an initiation code sequence. A complex mechanism is required to recognize this sequence and initiate polypeptide synthesis at the correct site and rate and in the right reading frame. The nature of the code sequence and the mechanism of initiation is under very active study using a variety of techniques. The current status of this work is summarized in the scheme shown in Fig. 1 (see Kolakofsky, Dewey, and Thach, 1969 for more detailed review and bibliography). A 30 S ribosomal subunit, an F-met charged tRNA f , and a messenger RNA react in the presence of GTP and 3 protein factors f1, f2 and f3. The GTP is split in the reaction and the product is a multi-molecular complex containing 30 S ribosome-F-met-tRNA f -mRNA-f1. In the second step of the initiation reaction a 50 S ribosomal subunit is added to this...
The structure of the human tissue-type plasminogen activator gene: correlation of intron and exon structures to functional and structural domains. (1984)

A genomic clone carrying the human tissue-type plasminogen activator (t-PA) gene was isolated from a cosmid library, and the gene structure was elucidated by restriction mapping, Southern blotting, and DNA sequencing. The cosmid contained all the coding parts of the mRNA, except for the first 58 bases in the 5' end of the mRNA, and had a total length of greater than 20 kilobases. It was separated into at least 14 exons by at least 13 introns, and the exons seemed to code for structural or functional domains. Thus, the signal peptide, the propeptide, and the domains of the heavy chain, including the regions homologous to growth factors, and to the "finger" structure of fibronectin, are all encoded by separate exons. In addition, the two kringle regions of t-PA were both coded for by two exons and were cleaved by introns at identical positions. The region coding for the light chain, comprising the serine protease part of the molecule was split by four introns, revealing a gene organization similar to other serine proteases.
Impeding Xist Expression from the Active X Chromosome Improves Mouse Somatic Cell Nuclear Transfer (2010)

Cloning mammals by means of somatic cell nuclear transfer (SCNT) is highly inefficient because of erroneous reprogramming of the donor genome. Reprogramming errors appear to arise randomly, but the nature of nonrandom, SCNT-specific errors remains elusive. We found that Xist, a noncoding RNA that inactivates one of the two X chromosomes in females, was ectopically expressed from the active X (Xa) chromosome in cloned mouse embryos of both sexes. Deletion of Xist on Xa showed normal global gene expression and resulted in about an eight- to ninefold increase in cloning efficiency. We also identified an Xist-independent mechanism that specifically down-regulated a subset of X-linked genes through somatic-type repressive histone blocks. Thus, we have identified nonrandom reprogramming errors in mouse cloning that can be altered to improve the efficiency of SCNT methods.
Abnormalities of Immunoregulatory T Cells in Disorders of Immune Function (1979)

We studied a five-year-old girl with several autoimmune disorders and a 16-year-old boy with acquired agammaglobulinemia to determine whether aberrations of immunoregulatory T cells could explain some instances of immunodeficiency or autoimmunity. The normal peripheral blood T-cell population, as defined by specific heteroantiserums, is 20 per cent TH2+ and 80 per cent TH2-. Human suppressor cells are TH2+, whereas helper cells are TH2-. In addition, each subset expresses Ia antigens upon activation. Our patient with autoimmune disease had no demonstrable TH2+ cells, and her lymphocytes could not be induced to suppress. Her circulating T cells were of an activated-helper phenotype, i.e., TH2-,Ia+. In contrast, in the boy with agammaglobulinemia, the T-cell population was predominantly of an activated-suppressor phenotype, i.e., TH2+,Ia+. This patient's T cells abrogated both his own and his histoidentical brother's B-cell secretion of immunoglobulins. We conclude that the characterization of T cells may provide insight into the causes of a number of abnormal immune states in man.
SLIP1, a Factor Required for Activation of Histone mRNA Translation by the Stem-Loop Binding Protein (2007)

Replication-dependent histone mRNAs are the only eukaryotic cellular mRNAs that are not polyadenylated, ending instead in a conserved stem-loop. The 3' end of histone mRNA is required for histone mRNA translation, as is the stem-loop binding protein (SLBP), which binds the 3' end of histone mRNA. We have identified five conserved residues in a 15-amino-acid region in the amino-terminal portion of SLBP, each of which is required for translation. Using a yeast two-hybrid screen, we identified a novel protein, SLBP-interacting protein 1 (SLIP1), that specifically interacts with this region. Mutations in any of the residues required for translation reduces SLIP1 binding to SLBP. The expression of SLIP1 in Xenopus oocytes together with human SLBP stimulates translation of a reporter mRNA ending in the stem-loop but not a reporter with a poly(A) tail. The expression of SLIP1 in HeLa cells also stimulates the expression of a green fluorescent protein reporter mRNA ending in a stem-loop. RNA interference-mediated downregulation of endogenous SLIP1 reduces the rate of translation of endogenous histone mRNA and also reduces cell viability. SLIP1 may function by bridging the 3' end of the histone mRNA with the 5' end of the mRNA, similar to the mechanism of translation of polyadenylated mRNAs.
Serum Adalimumab Concentration and Clinical Remission in Patients with Crohnʼs Disease (2013)

A positive association between serum adalimumab concentration and remission was identified at several time points. A threshold concentration reliably associated with remission was not identified. Further prospective evaluations are needed before recommendations for adalimumab concentration monitoring can be made.
Association of CXCL13 and CCL21 expression with the progressive organization of lymphoid‐like structures in Sjögren's syndrome (2005)

The acquisition of lymphoid features by inflammatory foci in SS is critically associated with the enlargement of the inflammatory foci and with the expression of CXCL13 and CCL21 within the infiltrate, but is not associated with their expression by epithelial cells. These data strongly support an active participation of CXCL13 and CCL21 in regulating the progressive organization and maintenance of periductal foci.
Fuzzy matching of Web queries to structured data (2010)

Recognizing the alternative ways people use to reference an entity, is important for many Web applications that query structured data. In such applications, there is often a mismatch between how content creators describe entities and how different users try to retrieve them. In this paper, we consider the problem of determining whether a candidate query approximately matches with an entity. We propose an off-line, data-driven, bottom-up approach that mines query logs for instances where Web content creators and Web users apply a variety of strings to refer to the same Web pages. This way, given a set of strings that reference entities, we generate an expanded set of equivalent strings for each entity. The proposed method is verified with experiments on real-life data sets showing that we can dramatically increase the queries that can be matched.
An allosteric synthetic DNA (1999)

Allosteric DNA oligonucleotides are potentially useful diagnostic reagents. Here we develop a model system for the study of allosteric interactions in DNAs. A DNA that binds either Cibacron blue or cholic acid was isolated and partially characterized. Isolation was performed using a multi-stage SELEX. First, short oligos that bind either Cibacron blue or cholic acid were enriched from random oligonucleotide pools. Then, members of the two pools were fused to form longer oligos, which were then selected for theability to bind Cibacron blue columns and elute with cholic acid. One resulting isolate (A22) was studied. Dye- and cholate-binding functions can be separated on sequences from the 5'- and 3'-regions, respectively. Ligand-column affinity assays indicate that each domain binds only its respective ligand. However, the full-length A22 will bind either dye or cholate columns and elute with the other ligand, as if binding by the ligands is mutually exclusive. Furthermore, S1 nuclease protection assays show that Cibacron blue causes a structural change in A22 and that cholic acid inhibits this change. This system will be useful for elucidating mechanisms of allosteric interactions in synthetic DNAs.