gebhart/patrepeval huggingface dataset:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks (2006)

The interpretation of large-scale protein network data depends on our ability to identify significant substructures in the data, a computationally intensive task. Here we adapt and extend efficient techniques for finding paths and trees in graphs to the problem of identifying pathways in protein interaction networks. We present linear-time algorithms for finding paths and trees in networks under several biologically motivated constraints. We apply our methodology to search for protein pathways in the yeast protein-protein interaction network. We demonstrate that our algorithm is capable of reconstructing known signaling pathways and identifying functionally enriched paths and trees in an unsupervised manner. The algorithm is very efficient, computing optimal paths of length 8 within minutes and paths of length 10 in about three hours.
On normality of Blaschke quotients (1988)

In this paper we give conditions on the zeros and poles of a Blaschke quotient in order to obtain a normal meromorphic function, extending the condition for normality given by Cima and Colwell to the case of zeros and poles forming interpolating sequences and of bounded multiplicities. It is also shown that a similar characterization does not apply in the case of unbounded multiplicities.
Just-in-case linking vs. just-in-time-linking—the Library Without Walls experience (1999)

No abstract available.
Analysis of B Cell Activation Requirements with TNP-Conjugated Polyacrylamide Beads (1979)

Abstract TNP-polyacrylamide beads of varying epitope density were used as antigens to stimulate normal adult spleen cells, neonatal spleen cells, and spleen cells from mice with the CBA/N immune defect. Lymphocytes from immune defective (CBA/N × DBA/2)F1 male mice or normal 2- to 3-week-old (C57BL/6 × DBA/2) F1 mice were unable to respond to TNP-polyacrylamide beads of low epitope density but responded quite well to high density TNP-polyacrylamide beads. Furthermore, immune defective F1 male spleen cells were shown to be unresponsive to TNP-Dextran yet mounted significant responses to TNP-Sephadex, an insoluble analog of TNP-Dextran. Use of an antiserum with anti-Lyb7.1 activity, which recognizes a mature subset of B cells, also pointed to qualitative differences in the stimulatory activities of highly substituted TNP-polyacrylamide beads and lightly substituted TNP-beads. This antiserum was able to inhibit responses to the low epitope TNP-polyacrylamide beads, which presumably activate a mature subset of B cells, but did not block responses to the highly conjugated TNP-beads, which appear to activate both immature B cells and mature B cells. In the course of these studies it became clear that TNP-polyacrylamide bead is not a truly thymus-independent (TI) antigen. Although it is able to stimulate significant responses in nude spleen cells, it is an ineffective immunogen when cultured with cells extensively depleted of T cells.
IL-15/IL-15Rα-mediated avidity maturation of memory CD8 + T cells (2004)

T cell avidity is critical to viral clearance, but mechanisms of CD8(+) T cell avidity maturation are poorly understood. Here, we find that IL-15 mediates two mechanisms of avidity maturation. (i) By selection at the population level, IL-15 promotes greater survival of high- compared with low-avidity cytotoxic T lymphocytes (CTLs). High-avidity CTLs express higher levels of IL-15Ralpha and persist longer by homeostatic proliferation. (ii) At the individual cell level, IL-15 induces higher levels of surface coreceptor CD8alphabeta, increasing functional avidity. IL-15 during priming selects or induces higher-avidity CTLs. Conversely, high-avidity CTLs are diminished in IL-15Ralpha knockout mice. These results provide an explanation of CD8+ T cell avidity maturation and may contribute to the design of novel vaccines.
A corpus analysis approach for automatic query expansion (1997)

Article Free Access Share on A corpus analysis approach for automatic query expansion Authors: Susan Gauch Electical Engineering and Computer Science, 415 Snow Hall, University of Kansas, Lawrence, KS Electical Engineering and Computer Science, 415 Snow Hall, University of Kansas, Lawrence, KSView Profile , Jianying Wang Electical Engineering and Computer Science, 415 Snow Hall, University of Kansas, Lawrence, KS Electical Engineering and Computer Science, 415 Snow Hall, University of Kansas, Lawrence, KSView Profile Authors Info & Claims CIKM '97: Proceedings of the sixth international conference on Information and knowledge managementJanuary 1997 Pages 278–284https://doi.org/10.1145/266714.266910Published:01 January 1997Publication History 17citation423DownloadsMetricsTotal Citations17Total Downloads423Last 12 Months11Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
In Vivo Circular RNA Expression by the Permuted Intron-Exon Method (2012)

Functional RNAs, e.g., aptamers (Lee et al., 2005; Que-Gewirth & Sullenger, 2007), ribozymes (Malhbacher et al., 2010), antisense oligonucleotides (Hnik et al., 2009), and double-stranded RNA (dsRNA) (Watts & Corey, 2010), hold promise for use as RNA drugs in the near future. However, the linear form of RNA without chemical modifications is rapidly degraded in both human serum and cell extracts due to endogenous nucleases. Therefore, it will likely be necessary to chemically modify these RNA drugs (Pestourie et al., 2005; Watts et al., 2008) to protect them from nuclease-dependent degradation. In fact, the recently developed aptamer drug pegaptanib sodium (Macugen®; Pfizer) for use against macular degradation consists of 2'-For 2'-OCH3-substituted nucleotides, thus preventing its rapid degradation in the ocular environment. Although at present it is the only commercially available RNA drug, we infer from the selling price of Macugen® that similar novel chemically modified RNA drugs are likely to be expensive because production of a chemically modified RNA molecule and scaling up the production yield of the RNA are expensive in principle. Therefore, the development of not only inexpensive but also durable RNA drugs will facilitate the widespread use of easily administered RNA drugs. To address the problems outlined above, our research group has considered in vivo circular RNA expression as a model for inexpensive RNA drug production because circular RNA molecules are resistant to exoribonucleases without any chemical modifications under cellular conditions. Therefore, the circular form of RNA would be a promising RNA drug candidate without requiring chemical modification.
[Effects of the calcium ion on the wound healing process]. (1987)

The present study was undertaken to elucidate the effect of calcium ion on the granulation tissue formation during wound healing. Male guinea pigs of Pilbright strain were chosen as the experimental animal. An appropriate open wound was aseptically made on the dorsum of the guinea pigs, which was then equipped with a sterile Teflon-cylinder. The amounts of granulation tissues developed within the cylinder were determined during 10 day period of the observation. In addition, various concentrations of CaCl2 were applied on the wound surface for up to 3 days after the wounding. Calmodulin contents in the granulation tissue were also determined using calmodulin-deficient phosphodiesterase prepared from bovine heart. Purified pig skin epidermal calmodulin was used as the standard. The results obtained were as follows: The amount of the granulation tissue increased in a stepwise manner during 3, 5, 7, and 10 days after the wounding. Calmodulin content in the granulation tissue was maximal on the day 3 after the wounding, waned on the day 5, and remained low on the days 7 and 10. A significant augmentation of the granulation tissue production as well as of calmodulin content was observed when CaCl2 was applied on the wound surface during 3 days after the wounding. These results suggest that calcium ion might have a significant role on granulation tissue development, possibly through the Ca++-calmodulin system, during early stages of wound healing process.
Folded Multilayer Microstrip Reflectarray With Shaped Pattern (2006)

A folded multilayer printed reflectarray with shaped pattern is demonstrated. The configuration consists of a multilayer twister reflectarray, a centered feed embedded in its structure and a polarizing grid, which acts as reflector and radome for each polarization, respectively. A design procedure, valid for obtaining any arbitrary shaped pattern, has been implemented. In order to achieve the pattern specifications along a frequency band, initially a multifrequency pattern synthesis method, which relies on a phase-only synthesis, is applied to obtain the required phase-shift on the reflectarray surface. Afterwards, each stacked patch is individually optimized to generate the required phase-shift previously synthesized. The method has been successfully applied to a LMDS base station antenna, characterized by a sectorial cosecant squared beam in the band 24.5-26.5 GHz. A breadboard consisting of a folded 3-layer circular reflectarray is presented. Measurements show a good concordance with theoretical patterns at 25 GHz, and good shaping of the beam along 24-26 GHz.
Gradient vector flow: a new external force for snakes (2002)

Snakes, or active contours, are used extensively in computer vision and image processing applications, particularly to locate object boundaries. Problems associated with initialization and poor convergence to concave boundaries, however, have limited their utility. This paper develops a new external force for active contours, largely solving both problems. This external force, which we call gradient vector flow (GVF) is computed as a diffusion of the gradient vectors of a gray-level or binary edge map derived from the image. The resultant field has a large capture range and forces active contours into concave regions. Examples on simulated images and one real image are presented.
The theory of latent vulnerability: Reconceptualizing the link between childhood maltreatment and psychiatric disorder (2015)

Maltreatment in childhood is associated with a significantly increased likelihood of psychiatric disorder that endures across the life span. If disorders emerge they tend to be more severe and less responsive to treatment. We introduce the concept of latent vulnerability as a way of conceptualizing the nature of this psychiatric risk. We argue that vulnerability to mental health problems can be understood as changes in a suite of neurocognitive systems that reflect adaptation or altered calibration to early neglectful or maltreating environments. Altered threat processing is presented as one exemplar candidate system. Heightened neurocognitive vigilance to threat is argued to reflect a calibration to an early at-risk environment that becomes maladaptive (and instantiates vulnerability) in the longer term. Other neurocognitive domains, including reward and memory processing, represent equally promising candidates for indexing latent vulnerability and warrant future enquiry. We suggest that the operationalization of latent vulnerability has the potential to guide a preventative psychiatry approach. Intervention currently occurs at two stages when maltreatment is confirmed: first, by addressing issues of risk; and second, by providing clinical intervention if a child meets criteria for psychiatric disorder. We argue that indexing latent vulnerability represents a third intervention opportunity, with the potential to target an indicated prevention approach for the most vulnerable children, offsetting risk trajectories before psychiatric disorders emerge.
Loss of CD4+ T Cell IL-6R Expression during Inflammation Underlines a Role for IL-6 Trans Signaling in the Local Maintenance of Th17 Cells (2010)

IL-6 responses are classically orchestrated via a membrane-bound IL-6R (CD126) alpha subunit (classical IL-6R signaling) or through a soluble form of this cognate receptor (IL-6 trans signaling). Appraisal of IL-6R expression on human and mouse T cells emphasized that IL-6R expression is closely linked with that of CCR7 and CD62L. In this regard, infiltrating effector T cells from clinical and experimental peritonitis episodes lose IL-6R expression, and anti-CD3/CD28 Ab costimulation of peripheral T cells in vitro leads to a downregulation in IL-6R expression. Consequently, IL-6 signaling through membrane-bound IL-6R seems to be limited to naive or central memory T cell populations. Loss of IL-6R expression by activated T cells further suggests that these effector cells might still retain IL-6 responsiveness via IL-6 trans signaling. Using IL-6R-deficient mice and recombinant tools that modulate the capacity of IL-6 to signal via its soluble receptor, we report that local control of IL-6 trans signaling regulates the effector characteristics of the T cell infiltrate and promotes the maintenance of IL-17A-secreting CD4(+) T cells. Therefore, we concluded that classical IL-6R signaling in naive or central memory CD4(+) T cells is required to steer their effector characteristics, whereas local regulation of soluble IL-6R activity might serve to maintain the cytokine profile of the Th cell infiltrate. Therefore, the activation status of a T cell population is linked with an alteration in IL-6 responsiveness.
Reviews: BDNF and Memory Formation and Storage (2007)

During the past decade, a large body of evidence has implicated BDNF in synaptic plasticity. In this review, we focus on the newer experiments that involve BDNF in different aspects of learning and memory processing-in particular, in memory persistence and storage.
TagSense (2011)

Mobile phones are becoming the convergent platform for personal sensing, computing, and communication. This paper attempts to exploit this convergence towards the problem of automatic image tagging. We envision TagSense, a mobile phone based collaborative system that senses the people, activity, and context in a picture, and merges them carefully to create tags on-the-fly. The main challenge pertains to discriminating phone users that are in the picture from those that are not. We deploy a prototype of TagSense on 8 Android phones, and demonstrate its effectiveness through 200 pictures, taken in various social settings. While research in face recognition continues to improve image tagging, TagSense is an attempt to embrace additional dimensions of sensing towards this end goal. Performance comparison with Apple iPhoto and Google Picasa shows that such an out-of-band approach is valuable, especially with increasing device density and greater sophistication in sensing/learning algorithms.
Interferon alpha-2a interactions on glass vial surfaces measured by atomic force microscopy. (2002)

Atomic force microscopy was used to study adsorption and adhesion peculiarities of interferon alpha-2a on glass and mica surfaces. The specific protein adsorption behavior as a function of the pH value was illustrated on mica by single molecule imaging, while adhesion forces between interferon molecules and inner surfaces of borosilicate glass vials were measured directly under aqueous buffer conditions by force microscopy. We found that the adhesion force on Schott FIOLAX Type I plus was reduced by 40% of the total adhesion force measured on Schott FIOLAX, a standard type I borosilicate glass quality. These results reflect the anticipated superiority of the special "Type I plus" coating over undesired protein adsorption to glass. In addition, this study gives insight into a new method to predict unintended protein adsorption to glass container walls and to characterize the adsorption process by force measurement.
The algR gene, which regulates mucoidy in Pseudomonas aeruginosa, belongs to a class of environmentally responsive genes (1989)

The Pseudomonas aeruginosa capsule, composed of polysaccharide alginate, is an important Pseudomonas virulence factor encountered primarily in cystic fibrosis. The regulatory algR gene positively controls transcription of a key alginate biosynthetic gene, algD. The algR gene was subcloned and sequenced by creating a set of nested deletions in M13 bacteriophage. DNA sequence analysis of algR revealed the homology of its gene product with a recently recognized class of environmentally responsive bacterial regulatory genes, including ompR, phoB, sfrA, ntrC, spoOA, dctD, and virG; these transcriptional activators control cellular reactions to osmotic pressure, phosphate limitations, or specific chemical compounds present in the medium or released from wounded host tissue. These findings indicate that novel conditions in lungs affected by cystic fibrosis may be participating in the control of mucoidy.
A note on the group lasso and a sparse group lasso (2010)

We consider the group lasso penalty for the linear model. We note that the standard algorithm for solving the problem assumes that the model matrices in each group are orthonormal. Here we consider a more general penalty that blends the lasso (L1) with the group lasso ("two-norm"). This penalty yields solutions that are sparse at both the group and individual feature levels. We derive an efficient algorithm for the resulting convex problem based on coordinate descent. This algorithm can also be used to solve the general form of the group lasso, with non-orthonormal model matrices.
Prominent roles of secondary anchor residues in peptide binding to HLA-A24 human class I molecules (1995)

The binding capacity of large sets of peptides corresponding to naturally occurring sequences and carrying previously defined A24-specific motifs was analyzed. It was found that only a minority (9-25%) of the motif-carrying peptides bound the relevant HLA-A molecule with good affinity (IC 50% < or = 50 nM), while the majority of them bound only weakly or not at all (IC 50% > or = 500 nM). By correlating the presence of specific residue types at each position along the peptide sequence with average binding affinity, the prominent influence of specific secondary interactions (secondary anchor residues) was revealed. Moreover, secondary interactions appeared to be size-dependent in that the specific effects detected differed in 9-mer and 10-mer peptide sets. Based on these observations, A24-specific refined motifs were also established for both 9-mer and 10-mer ligands, and their merit was verified by testing the binding capacity of independent sets of synthetic peptides. Such refined motifs should facilitate accurate prediction of potential A24-restricted peptide epitopes. It was also noted that certain crucial secondary interactions appear to be remarkably similar in the case of A24 and other HLA-A molecules previously analyzed (A*0201, A3, A11, and others). This may reflect contributions to binding affinity of relatively invariant residues located within the polymorphic pockets of the HLA binding groove.
Fast and efficient exact synthesis of single qubit unitaries generated by Clifford and T gates (2012)

In this paper, we show the equivalence of the set of unitaries computable by the circuits over the Clifford and T library and the set of unitaries over the ring $\mathbb{Z}[\frac{1}{\sqrt{2}},i]$, in the single-qubit case. We report an efficient synthesis algorithm, with an exact optimality guarantee on the number of Hadamard and T gates used. We conjecture that the equivalence of the sets of unitaries implementable by circuits over the Clifford and T library and unitaries over the ring $\mathbb{Z}[\frac{1}{\sqrt{2}},i]$ holds in the $n$-qubit case.
Effect of cellular differentiation on cytokine-induced expression of human immunodeficiency virus in chronically infected promonocytic cells: dissociation of cellular differentiation and viral expression (1995)

Cellular differentiation is thought to play an important role in the susceptibility of monocytic lineage cells to human immunodeficiency virus (HIV) infection as well as in their ability to support virus replication. In addition, virus replication in monocytes/macrophages has been demonstrated in vitro to be strongly modulated by several cytokines such as tumor necrosis factor alpha and granulocyte-macrophage colony-stimulating factor. The purpose of the present study was to investigate the interaction between cellular differentiation and cytokines in the regulation of HIV expression from chronically infected monocytic lineage cells. U1, a persistently HIV-infected promonocytic cell line, is characterized by low levels of virus expression which can be modulated by several cytokines. 1 alpha,-25-Dihydroxyvitamin D3 (Vit.D3), a well-known differentiating agent for myelomonocytic cells which has been previously reported to modulate HIV replication in other in vitro systems, induced maturation of U1 cells toward a macrophage-like phenotype, as demonstrated by the induction of the differentiation-associated cell surface markers CD14 and CD11b. Vit.D3-induced differentiation did not result in induction of HIV expression; however, when U1 cells were stimulated with tumor necrosis factor alpha in the presence of Vit.D3, a synergistic induction of cell differentiation and viral expression was demonstrated. In contrast, Vit.D3 suppressed the induction of HIV expression in U1 cells stimulated with gamma interferon, interleukin-6, and granulocyte-macrophage colony-stimulating factor, although synergy between Vit.D3 and these cytokines was observed in terms of cellular differentiation. These data suggest that differentiation of monocytic cells does not necessarily correlate with increased HIV expression.
Synthesis of new spiro compounds containing a carbamate group (2010)

1,3-Dipolar cycloaddition to methyl 4-[2-(2-oxo-2,3-dihydro-1H-indol-3-ylidene)-1-oxoethyl]-phenylcarbamate of diazomethane in chloroform-diethyl ether and of 3,4-dimethoxybenzonitrile oxide generated from the corresponding aldehyde oxime by the action of N-chlorobenzenesulfonamide sodium salt (Chloramine B) in boiling ethanol gave, respectively, methyl 4-(2-oxo-1′,5′-dihydro-1H-spiro[indole-3,4′-pyrazol]-3′-ylcarbonyl)phenylcarbamate and methyl 4-[3′-(3,4-dimethoxyphenyl)-2-oxo-1H,4′H-spiro[indole-3,5′-isoxazol]-4′-ylcarbonyl]phenylcarbamate. The condensation of methyl 4-[2-(2-oxo-2,3-dihydro-1H-indol-3-ylidene)-1-oxoethyl]phenylcarbamate with hydrazine hydrate in ethanol afforded methyl 4-(2-oxo-1,2,2′,4′-tetrahydrospiro[indole-3,3′-pyrazol]-5′-yl)phenylcarbamate.
Autoprocessing of the HIV‐1 protease using purified wild‐type and mutated fusion proteins expressed at high levels in Escherichia coli (1991)

Various constructs of the human immunodeficiency virus, type 1 (HIV-1) protease containing flanking Pol region sequences were expressed as fusion proteins with the maltose-binding protein of the malE gene of Escherichia coli. The full-length fusion proteins did not exhibit self-processing in E. coli, thereby allowing rapid purification by affinity chromatography on cross-linked amylose columns. Denaturation of the fusion protein in 5 M urea, followed by renaturation, resulted in efficient site-specific autoprocessing to release the 11-kDa protease. Rapid purification involving two column steps gave an HIV-1 protease preparations of greater than 95% purity (specific activity approximately 8500 pmol.min-1.micrograms protease-1) with an overall yield of about 1 mg/l culture. Incubation of an inactive mutant protease fusion protein with the purified wild-type protease resulted in specific trans cleavage and release of the mutant protease. Analysis of products of the HIV-1 fusion proteins containing mutations at either the N- or the C-terminal protease cleavage sites indicated that blocking one of the cleavage sites influences the cleavage at the non-mutated site. Such mutated full-length and truncated protease fusion proteins possess very low levels of proteolytic activity (approximately 5 pmol.min-1.micrograms protein-1).