gebhart/patrepeval huggingface dataset:
Wide & Deep Learning for Recommender Systems (2016)

Generalized linear models with nonlinear feature transformations are widely used for large-scale regression and classification problems with sparse inputs. Memorization of feature interactions through a wide set of cross-product feature transformations are effective and interpretable, while generalization requires more feature engineering effort. With less feature engineering, deep neural networks can generalize better to unseen feature combinations through low-dimensional dense embeddings learned for the sparse features. However, deep neural networks with embeddings can over-generalize and recommend less relevant items when the user-item interactions are sparse and high-rank. In this paper, we present Wide & Deep learning---jointly trained wide linear models and deep neural networks---to combine the benefits of memorization and generalization for recommender systems. We productionized and evaluated the system on Google Play, a commercial mobile app store with over one billion active users and over one million apps. Online experiment results show that Wide & Deep significantly increased app acquisitions compared with wide-only and deep-only models. We have also open-sourced our implementation in TensorFlow.
Fundamental Limits of Cooperation (2013)

Cooperation is viewed as a key ingredient for interference management in wireless networks. This paper shows that cooperation has fundamental limitations. First, it is established that in systems that rely on pilot-assisted channel estimation, the spectral efficiency is upper-bounded by a quantity that does not depend on the transmit powers; in this framework, cooperation is possible only within clusters of limited size, which are subject to out-of-cluster interference whose power scales with that of the in-cluster signals. Second, an upper bound is also shown to exist if the cooperation extends to an entire (large) system operating as a single cluster; here, pilot-assisted transmission is necessarily transcended. Altogether, it is concluded that cooperation cannot in general change an interference-limited network to a noise-limited one. Consequently, the existing literature that routinely assumes that the high-power spectral efficiency scales with the log-scale transmit power provides only a partial characterization. The complete characterization proposed in this paper subdivides the high-power regime into a degree-of-freedom regime, where the scaling with the log-scale transmit power holds approximately, and a saturation regime, where the spectral efficiency hits a ceiling that is independent of the power. Using a cellular system as an example, it is demonstrated that the spectral efficiency saturates at power levels of operational relevance.
Capillary electrophoresis of inorganic ions: An update (2004)

This review as a sequel of three earlier similar reports gives a summary of the progress and significant methodological developments, starting from 2002, in the use of capillary electrophoresis (CE) for inorganic ion analysis. As substantiated by the illustrative number of relevant references, improvements in sensitivity achieved both in and outside a CE system, advances in manipulating the separation selectivity, novel hardware configurations, and system performance innovations are continually being reported over the review period. Specifically viewed are the recent advancements in elemental (bio)speciation analysis, which remains one of the most fertile areas of CE research, as well as in three recently booming research topics: contactless conductivity detection, separations on microchips, and transient isotachophoretic preconcentration. A state-of-the-art picture of technique's potentialities within the field of interest presented here demonstrates that CE has become recognized and is growing in acceptance as a reliable alternative to traditional analytical methods such as high-performance liquid chromatography (HPLC).
Carbon starvation of Salmonella typhimurium does not cause a general increase of mutation rates (1997)

Mutation rates in bacteria can vary depending on the genetic target studied and the specific growth conditions of the cells. Here, two different methods were used to determine how rates of mutation to antibiotic resistance, auxotrophy, and prototrophy were influenced by carbon starvation on agar plates. The rate of mutation to rifampin resistance was increased by starvation as measured by fluctuation tests, similar to what has been reported previously for Escherichia coli. In contrast, the rates of mutation to various types of auxotrophy were unaffected or decreased as measured by both fluctuation tests and a repeated-streaking procedure. Similarly, the rates of reversion to prototrophy of his and lac nonsense and missense mutations were unaffected by starvation. Thus, mutation rates of different genetic targets can be affected differently by starvation and we conclude that carbon starvation is not generally mutagenic in Salmonella typhimurium.
Signal interception: performance advantages of cyclic-feature detectors (1992)

The problem of detecting the presence of spread-spectrum phase-shift-keyed signals in variable noise and interference backgrounds is considered, and the performances of four detectors are evaluated and compared. The detectors include the optimum radiometer, the optimum modified radiometer that jointly estimates the noise level and detects the signal, and the maximum-SNR spectral-line regenerator for spectral-line frequencies equal to the chip rate and the doubled carrier frequency. It is concluded that the spectral-line regenerators can outperform both types of radiometers by a wide margin. The performance advantages are quantified in terms of receiver operating characteristics for several noise and interference environments and receiver collection times.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interaction of Fibrin(ogen) with Heparin:  Further Characterization and Localization of the Heparin-Binding Site (2003)

The beta chain 15-42 sequence of the fibrin(ogen) E region was implicated in heparin binding [Odrljin et al. (1996) Blood 88, 2050-2061]; whether heparin binds to other fibrin(ogen) regions remains to be clarified. To address this question, we studied the interaction of heparin with fibrinogen, fibrin, and their major fragments D(1), D-D, E(1), E(3), and alphaC, which together cover the entire structure of the molecule, by ligand blotting, surface plasmon resonance, and fluorescence. All three techniques revealed that at physiological ionic conditions only fibrin(ogen) and the E(1) fragment bind heparin, indicating that the only physiologically relevant heparin-binding site of fibrin(ogen) is located in its E region. To test whether the beta15-42 sequence is sufficient to form this site or some additional sequences are also involved, we tested the interaction of heparin with a number of beta15-42-containing fragments. The synthetic beta15-42 peptide bound heparin weakly (K(d) = 44.5 microM) while the recombinant beta15-57 and beta15-64 fragments exhibited almost 7-fold higher affinity (K(d) = 6.4 and 7.1 microM, respectively), indicating that the beta43-57 region is also important for heparin binding. At the same time the recombinant dimeric disulfide-linked (beta15-66)(2) fragment which mimics the dimeric arrangement of the beta chains in fibrin bound heparin with high affinity (K(d) = 66 nM), almost 100-fold higher than that for the monomeric fragments. This affinity was similar to those determined for fibrin and the E(1) fragment (K(d) = 72 and 70 nM, respectively) suggesting that (beta15-66)(2) mimics well the heparin-binding properties of the latter two. Altogether, these results indicate that the only heparin-binding site in fibrin(ogen) is formed by NH(2)-terminal portions of the beta chains, including residues beta15-57, and that dimerization is essential for high-affinity binding.
Separation and evaluation of changing pattern of glycosaminoglycans in 3-methyl cholanthrene induced fibrosarcoma. (1989)

The present study evaluates the glycosaminoglycans (GAGs) pattern associated with transplantable rat fibrosarcoma induced by 3-methylcholanthrene. The quantitative analysis of fractionation of GAGs in fibrosarcoma and fetal tissues was performed by enzymatic digestion. The average value of total GAGs in fibrosarcoma and fetal tissue was found to be 4 times higher than its value in the tissue of origin. GAG content showed a steady increase from 7th day onward to 25th day. Hyaluronic acid content in tumor tissue was observed to increase markedly (8-fold) against that of the normal tissue and was equivalent to that of the fetal tissue. Chondroitin sulfate level was also increased in the tumor as well as fetal tissue. The increase in the chondroitin sulfate and hyaluronic acid contents might possibly be due to the abnormal GAG metabolism in the increased production of both sulfated and nonsulfated GAGs.
Regulation of the large ( 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn (2004)

Most cases of Angelman syndrome (AS) result from loss or inactivation of ubiquitin protein ligase 3A (UBE3A), a gene displaying maternal-specific expression in brain. Epigenetic silencing of the paternal UBE3A allele in brain appears to be mediated by a non-coding UBE3A antisense (UBE3A-ATS). In human, UBE3A-ATS extends approximately 450 kb to UBE3A from the small nuclear ribonucleoprotein N (SNURF/SNRPN) promoter region that contains a cis-acting imprinting center (IC). The concept of a single large antisense transcript is difficult to reconcile with the observation that SNURF/SNRPN shows a ubiquitous pattern of expression while the more distal part of UBE3A-ATS, which overlaps UBE3A, is brain specific. To address this problem, we examined murine transcripts initiating from several alternative exons dispersed within a 500 kb region upstream of Snurf/Snrpn. Similar to Ube3a-ATS, these upstream (U) exon-containing transcripts are expressed at neuronal stages of differentiation in a cell culture model of neurogenesis. These findings suggest the novel hypothesis that brain-specific transcription of Ube3a-ATS is regulated by the U exons rather than Snurf/Snrpn exon 1 as previously suggested from human studies. In support of this hypothesis, we describe U-Ube3a-ATS transcripts where U exons are spliced to Ube3a-ATS with the exclusion of Snurf-Snrpn. We also show that the murine U exons have arisen by genomic duplication of segments that include elements of the IC, suggesting that the brain specific silencing of Ube3a is due to multiple alternatively spliced IC-Ube3a-ATS transcripts.
Insulin Receptors and Insulin Resistance (1983)

Resistance to the action of insulin plays a central role in many important disease states, including diabetes and obesity. Many insights into the mechanism and significance of insulin resistance in these and other disorders have followed upon our expanding knowledge regarding insulin receptors. In this article, we review our current understanding of insulin receptors and their regulation, and we assess the role of insulin receptor pathology in the various syndromes characterized by insulin resistance.
Complement Activation Determines the Therapeutic Activity of Rituximab In Vivo (2003)

Rituximab is an anti-CD20 chimeric mAb effective for the treatment of B-NHL. It can lyse lymphoma cells in vitro through both C- and Ab-dependent cellular cytotoxicity. The mechanism of action of rituximab in vivo is however still unclear. We have set up a new in vivo model in nonimmunodeficient mice by stable transduction of the human CD20 cDNA in the murine lymphoma line EL4. Animals injected i.v. with the EL4-CD20(+) lymphoma cells died within 30 days with evident liver, spleen, and bone marrow involvement, confirmed by immunohistochemistry and PCR analysis. A single injection of rituximab or the murine anti-CD20 Ab 1F5, given i.p. 1 day after the tumor, cured 100% of the animals. Indeed, at week 4 after tumor cell inoculation, CD20(+) cells were undetectable in all organs analyzed in rituximab-treated animals, as determined by immunohistochemistry and PCR. Rituximab had no direct effect on tumor growth in vitro. Depletion of either NK cells or neutrophils or both in tumor-injected animals did not affect the therapeutic activity of the drug. Similarly, rituximab was able to eradicate tumor cells in athymic nude mice, suggesting that its activity is T cell independent. In contrast, the protective activity of rituximab or the 1F5 Ab was completely abolished in syngeneic knockout animals lacking C1q, the first component of the classical pathway of C (C1qa(-/-)). These data demonstrate that C activation is fundamental for rituximab therapeutic activity in vivo.
Efficient gene editing in adult mouse livers via adenoviral delivery of CRISPR/Cas9 (2014)

We developed an adenovirus-based CRISPR/Cas9 system for gene editing in vivo. In the liver, we demonstrated that the system could reach the level of tissue-specific gene knockout, resulting in phenotypic changes. Given the wide spectrum of cell types susceptible to adenoviral infection, and the fact that adenoviral genome rarely integrates into its host cell genome, we believe the adenovirus-based CRISPR/Cas9 system will find applications in a variety of experimental settings.
Differential radioactive quantification of protein abundance ratios between benign and malignant prostate tissues: Cancer association of annexin A3 (2007)

A differential quantitative protein expression study, comparing matched prostate cancerous and benign tissues from 31 patients, revealed proteins newly associated with prostate cancer. Average effects for 17 proteins whose abundance was significantly different (p<0.01) across patients ranged from 1.5- to 6.1-fold, and included a number of known cancer markers. The most differentially abundant proteins between cancer and benign samples were isopeptidase T, serum amyloid P (SAP), annexin A3 (ANXA3) and mitochondrial enoyl coenzyme-A hydratase. SAP is restricted to stroma in healthy tissue, and the lower abundance in tumours may be explained by the reduced stromal content. ANXA3 is present in healthy epithelial cells, exhibits strong staining in precancerous prostatic intraepithelial neoplasia, and is relatively less abundant in individual tumour cells of increasing Gleason pattern (GP), despite exhibiting higher overall tissue abundance in tumours. ANXA3 staining was predominantly cytoplasmic, yet nuclear localization was also observed. Strongly staining single cells, possibly phagocytes, were interspersed in highly dedifferentiated GP5 tumour areas among tumour cells without measurable ANXA3. Local recurrent androgen ablation therapy-resistant tumours exhibit heterogenous low levels of ANXA3 staining. Results are discussed focussing on the potential implications for tumour tissues.
Medial Localization of Mineralization-Regulating Proteins in Association With Monckeberg’s Sclerosis (1999)

These data indicate that medial calcification in MS lesions is an active process potentially orchestrated by phenotypically modified VSMCs.
Mouse Lysozyme-M Knockout Mice Reveal How the Self-Determinant Hierarchy Shapes the T Cell Repertoire against This Circulating Self Antigen in Wild-Type Mice (2004)

We have studied T cell tolerance to defined determinants within ML-M using wild-type (WT; ML-M(+/+)) and LysMcre (ML-M(-/-)) C3H (H-2(k)) mice to determine the relative contribution of ML-M-derived epitopes vs those from other self Ags in selection of the ML-M-specific T cell repertoire. ML-M was totally nonimmunogenic in WT mice, but was rendered immunogenic in LysMcre mice. Most of the response to ML-M in LysMcre mice was directed to the immunodominant determinant region 105-119. This determinant is spontaneously displayed (without adding exogenous ML-M) by macrophages of WT, but not LysMcre, mice and is stimulatory for peptide 105-119 (p105-119)-primed T cells. Moreover, neonatal tolerization of LysMcre mice with p105-119 or ML-M abrogated the T cell response to subsequent challenge with ML-M or p105-119. Furthermore, p95-109 and p110-125 of ML-M were immunogenic in LysMcre mice, but not in WT mice, thereby representing subdominant, tolerance-inducing epitopes of ML-M. As expected, the T cell repertoire to cryptic ML determinants in WT mice was also intact in LysMcre mice. Furthermore, the pattern of response to the related homologue of ML-M, hen eggwhite lysozyme, was similar in these two groups of mice. Thus, several codominant T cell determinants within ML-M contribute significantly to tolerance induction, and the anti-cryptic T cell repertoire to ML-M was positively selected on non-ML-M self ligands. These results reveal that the induction of self tolerance to a multideterminant protein follows the quantitative hierarchy of self-determinant expression and are of relevance in understanding the pathogenesis of autoimmunity.
A retrospective study of the prognostic impact of cytokine secretion in mixed lymphocyte culture on long-term graft function following allogeneic renal transplantation (2005)

We have previously shown that in vitro measurement of cytokine production prior to renal transplantation can provide predictive information on the risk of acute rejection. Our earlier studies demonstrated that patients who secreted high levels of interferon-gamma (IFN-gamma) in OKT3-stimulated or mixed lymphocyte culture had a significantly increased risk of acute rejection compared with patients who secreted lower levels. In this study, we performed a retrospective analysis of the same cohort of patients in order to determine the prognostic value of cytokine profiles and other variables on long-term graft function. Our results show that high levels of IFN-gamma in pretransplant mixed lymphocyte culture are a highly significant predictor of poorer creatinine levels at 18, 24 and 36 months post-transplant.
d‐glufosinate as a male sterility agent for hybrid seed production (2010)

A chemical male sterility system based on anther-localized conversion of the inactive D-enantiomer of the herbicide, glufosinate (2-amino-4-(methylphosphinyl)-butanoate) to the phytotoxic L is described. Highly pure D-glufosinate was isolated in >98% enantiomeric excess from the racemate via fermentation with a strain of Escherichia coli expressing the PAT (L-glufosinate N-acetyl transferase) gene and purification of the unreacted D-enantiomer from the broth by ion exchange. A modified (F58K, M213S) form of the D-amino acid oxidase (DAAO) (EC 1.4.3.3) from Rhodosporidium toruloides was designed, tested in vitro and found to efficiently oxidize D-glufosinate to its 2-oxo derivative [2-oxo-4-(methylphosphinyl)-butanoic acid]. Tobacco (Nicotiana tabacum) plants were transformed to express this modified oxidase under control of the TAP1 tapetum-specific promoter. A number of the resultant transgenic lines exhibited complete male sterility that persisted for two or more weeks immediately following foliar treatment with 75 or 200 g/ha of D-glufosinate without exhibiting obvious phytotoxic symptoms or any measurable decline in female fertility. Similarly, plants containing the same construct and, additionally, a PAT gene expressed from a plastocyanin promoter exhibited significantly reduced male fertility and no reduction in female fertility following foliar application of racemic glufosinate. Thus, foliar application of d-glufosinate either purified or as the commercial herbicide, combined with anther expression of a modified DAAO promises to provide a cost-effective conditional chemical male sterility system with the characteristics necessary for practical F₁ hybrid seed production.
Localization of tissue inhibitor of metalloproteinases 1 (TIMP‐1) in human colorectal adenoma and adenocarcinoma (2004)

Tissue inhibitor of matrix metalloproteases 1 (TIMP-1) inhibits the proteolytic activity of matrix metalloproteases and hereby prevents cancer invasion. However, TIMP-1 also possesses other functions such as inhibition of apoptosis, induction of malignant transformation and stimulation of cell-growth. We have previously demonstrated that TIMP-1 is elevated in blood from colorectal cancer patients and that high TIMP-1 levels predict poor prognosis. To clarify the role of TIMP-1 in colorectal tumorigenesis, the expression pattern of TIMP-1 in benign and malignant colorectal tumors was studied. In all of 24 cases of colorectal adenocarcinoma TIMP-1 mRNA was detected by in situ hybridization. In all cases TIMP-1 expression was found in fibroblast-like cells located at the invasive front but was seen only sporadically in normal mucosa. No TIMP-1 mRNA was seen in any of the cases in benign or malignant epithelial cells, in vascular cells or smooth muscle cells. Comparison of sections processed for TIMP-1 in situ hybridization with sections immunohistochemically stained with antibodies against TIMP-1 showed good correlation between TIMP-1 mRNA and immunoreactivity. Combining TIMP-1 in situ hybridization with immunohistochemical staining for alpha-smooth muscle actin or CD68 showed TIMP-1 mRNA in myofibroblasts but not in macrophages. TIMP-1 mRNA was detected in 2 of 7 adenomatous polyps in the adenoma area: in both cases associated with focal stromal inflammation at the epithelial-stromal interface. In conclusion, TIMP-1 expression is a rare event in benign human colon tissue but is highly expressed by myofibroblasts in association with invading colon cancer cells.
Antialiasing through stochastic sampling (1985)

Stochastic sampling techniques , in particular Poisson and fittered sampling, are developed and analyzed. These approaches allow the construction of alias-free approximations to continuous functions using discrete calculations. Stochastic sampling scatters high frequency information into broadband noise rather than generating the false patterne produced by regular sampling. The type of randomness used in the sampling process controls the spectral character of the noise. The average sampling rate and the function being sampled determine the amount of noise that is produced. Stochastic sampling is applied adaptively so that a greater number of samples are taken where the function varies most. An estimate is used to determine how many samples to take over a given region. Noise reducing filters are used to increase the efficacy of a given sampling rate. The filter width is adaptively controlled to further improve performance. Stochastic sampling can be applied spatiotemporally as well as to other aspects of scene simulation. Ray tracing is one example of an image synthesis approach that can be antialiased by stochastic sampling.
Genome Screen for Asthma and Related Phenotypes in the French EGEA Study (2000)

A genome-wide search was conducted in 107 nuclear families with at least two siblings with asthma, as part of the French EGEA study. A two-stage analysis strategy was applied to the 107 families divided into two independent subsets of 46 and 61 families, where all regions detected in the first set of families were tested for replication in the second set. In addition, all regions reported by published genome scans in different populations were examined in the total sample. A total of 254 markers were typed in the first set of families and 70% of them in the second set. Linkage was investigated by model-free methods for asthma and four asthma-related phenotypes: bronchial responsiveness (BR), skin test response, total immunoglobulin E (IgE) levels, and eosinophil count. The two-stage analysis led to the detection of three regions: 11p13 for IgE, 12q24 for eosinophils, and 17q12-21 for asthma and skin tests. Among the regions reported by published genome screens, seven were found in the 107 French EGEA families: three being already detected by the two-stage analysis, 11p13 (p = 0.005), 12q24 (p = 0.0008), and 17q12-21 (p = 0.001), and four additional ones, 1p31 (p = 0.005) for asthma, 11q13 (p = 0.006) for IgE, 13q31 (p = 0.001) for eosinophils, and 19q13 (p = 0.02) for BR.