gebhart/patrepeval huggingface dataset:
Ternary Copper Complexes for Photocleavage of DNA by Red Light:  Direct Evidence for Sulfur-to-Copper Charge Transfer and d−d Band Involvement (2003)

A new class of ternary copper(II) complexes of formulation [Cu(L(n)B](ClO(4)) (1-4), where HL(n) is a NSO-donor Schiff base (HL(1), HL(2)) and B is a NN-donor heterocyclic base viz. 1,10-phenanthroline (phen) and 2,9-dimethyl-1,10-phenanthroline (dmp), are prepared, structurally characterized, and their DNA binding and photocleavage activities studied in the presence of red light. Ternary complex [Cu(L(3))(phen)](ClO(4)) (5) containing an ONO-donor Schiff base and a binary complex [Cu(L(2))(2)] (6) are also prepared and structurally characterized for mechanistic investigations of the DNA cleavage reactions. While 1-4 have a square pyramidal (4 + 1) CuN(3)OS coordination geometry with the Schiff base bonded at the equatorial sites, 5 has a square pyramidal (4 + 1) geometry with CuN(3)O(2) coordination with the alcoholic oxygen at the axial site, and 6 has a square planar trans-CuN(2)O(2) geometry. Binding of the complexes 1-4 to calf thymus DNA shows the relative order: phen >> dmp. Mechanistic investigations using distamycin reveal minor groove binding for the complexes. The phen complexes containing the Schiff base with a thiomethyl or thiophenyl moiety show red light induced photocleavage. The dmp complexes are essentially photonuclease inactive. Complexes 5 and 6 are cleavage inactive under similar photolytic conditions. A 10 microM solution of 1 displays a 72% cleavage of SC DNA (0.5 microg) on an exposure of 30 min using a 603 nm Nd:YAG pulsed laser (60 mJ/P) in Tris-HCl buffer (pH 7.2). Significant cleavage of 1 is also observed at 694 nm using a Ruby laser. Complex 1 is cleavage inactive under argon or nitrogen atmosphere. It shows a more enhanced cleavage in pure oxygen than in air. Enhancement of cleavage in D(2)O and inhibition with sodium azide addition indicate the possibility of the formation of singlet oxygen as a reactive intermediate leading to DNA cleavage. The d-d band excitation with red light shows significant enhancement of cleavage yield. The results indicate that the phen ligand is necessary for DNA binding of the complex. Both the sulfur-to-copper charge transfer band and copper d-d band excitations helped the DNA cleavage. While the absorption of a red photon induces a metal d-d transition, excitation at shorter visible wavelengths leads to the sulfur-to-copper charge transfer band excitation at the initial step of photocleavage. The excitation energy is subsequently transferred to ground state oxygen molecules to produce singlet oxygen that cleaves the DNA.
Fabrication of periodically domain-inverted channel waveguides in lithium niobate for second harmonic generation (1989)

A method to produce periodically domain-inverted channel waveguides in LiNbO/sub 3/ is reported. With this type of waveguide, using quasi-phase matching (QPM), arbitrary wavelengths can be frequency doubled by choosing the appropriate period. It is concluded that, with improved fabrication methods, it will be possible to generate milliwatts of blue light with a diode laser as pump, which is of considerable interest.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cognitive dysfunction in HIV patients despite long-standing suppression of viremia (2010)

The prevalence of HANDs is high even in long-standing aviremic HIV-positive patients. However, HANDs without functional repercussion in daily life (asymptomatic neurocognitive impairment) is the most frequent subtype observed. In this population, the HIV dementia scale with a cutoff of 14 points or less seems to provide a useful tool to screen for the presence of HANDs.
Platelet Accumulation on Fibrin-coated Polyethylene: Role of Platelet Activation and Factor XIII (1995)

Platelet accumulation on small- and medium-calibre vascular grafts plays a significant role in graft occlusion. We examined platelet accumulation on the surface of fibrin-coated polyethylene tubing (internal diameter 0.17 cm) during 10 min flow (10 ml/min) at high wall shear rate (764 s-1). Washed platelets labelled with 51Cr were resuspended in Tyrode solution containing albumin, apyrase and red blood cells (hematocrit 40%). When the thrombin that was used to form the fibrin-coated surface was inactivated with FPRCH2Cl before perfusion of the tubes with the platelet: red blood cell suspension, the accumulation of platelets was 59,840 +/- 27,960 platelets per mm2, whereas accumulation on fibrin with residual active thrombin was 316,750 +/- 32,560 platelets per mm2 (n = 4). When the fibrin on the surface was cross-linked by including recombinant factor XIII (rFXIII) in the fibrinogen solution used to prepare the fibrin-coated surface, platelet accumulation, after thrombin neutralization, was reduced by the cross-linking from 46,974 +/- 9702 to 36,818 +/- 7964 platelets per mm2 (n = 12, p < 0.01). Platelet accumulation on tubes coated with D-dimer was ten times less than on tubes coated with D-domain; this finding also supports the observation that cross-linking of fibrin with the formation gamma-gamma dimers reduces platelet accumulation on the fibrin-coated surface. Thrombin-activated platelets themselves were shown to cross-link fibrin when they had adhered to it during perfusion, or in a static system in which thrombin was used to form clots from FXIII-free fibrinogen in the presence of platelets.(ABSTRACT TRUNCATED AT 250 WORDS)
Heat-Induced Aggregation of β-Lactoglobulin:  Role of the Free Thiol Group and Disulfide Bonds (1997)

The heat-induced aggregation of bovine β-lactoglobulin, dispersed in water at neutral pH and in different concentrations (10, 30, or 50 g of dry matter/L), was studied at 65 °C, and the results are related to a kinetic model. Native PAGE and SDS−PAGE analysis under nonreducing and reducing conditions showed that on heating disulfide-linked aggregates were formed and that the average size of these aggregates increased with increasing initial β-lactoglobulin concentration. In the presence of the thiol-blocking agent N-ethylmaleimide (NEM), at a molar ratio of NEM/β-lactoglobulin monomer of 1, all thiol groups were blocked and no disulfide-linked aggregates were formed, although with native PAGE high molecular mass noncovalently linked aggregates were observed. The formation of these aggregates accelerated with increasing NEM concentration until a molar ratio of NEM/β-lactoglobulin monomer of 1 was reached. In separate experiments we studied the effect of pH (in the range pH 6.0−8.0) on the aggregation of β-lactoglobulin and related this to the pH dependent reactivity of the thiol group. Keywords: β-Lactoglobulin; thermal treatment; denaturation; aggregation; thiol reactivity
Beta-casein gene promoter activity is regulated by the hormone-mediated relief of transcriptional repression and a mammary-gland-specific nuclear factor. (1991)

Transcription from the beta-casein milk protein gene promoter is induced by the synergistic action of glucocorticoid and prolactin hormones in the murine mammary epithelial cell line, HC11. We analyzed the binding of nuclear proteins to the promoter and determined their binding sites. Site-directed mutagenesis was used to determine the function of nuclear factor binding. During lactogenic hormone induction of HC11 cells, the binding of two nuclear factors increased. The binding of two other nuclear factors, present in uninduced cells, decreased. The basal activity of the promoter could be increased to and above the level of the induced wild-type promoter when the recognition sequences of the negatively regulated factors were mutated. This suggests that the beta-casein promoter is regulated by the relief of the repression of transcription. An essential tissue-specific factor was also found in nuclear extracts from the mammary glands of mice. Mutation of its recognition sequence in the beta-casein promoter led to the abolition of the induction of transcription by lactogenic hormones. The DNA sequences recognized by all five of these nuclear factors are conserved in the promoters of different casein genes from several species, confirming their importance in the regulation of milk protein gene transcription.
[Ambulatory abortion, its advantages and economic effectiveness]. (1992)

Presents data on abortions carried out by vacuum aspiration method in the earliest periods of unplanned pregnancy with the menses delay of up to 20 days in 622 women. The operation was performed in an outpatient setting. The incidence of immediate complications has made up 2.2%, late ones 4.13%; these values are much lower than after abortions during pregnancy weeks 6-12 (6.6 and 14.6%, respectively). The cost of such abortions, including the cost of treatment of late and immediate complications, makes up 9 rubles, whereas routine D&C costs 49 rubles. Vacuum aspiration abortion, carried out if menstrual bleeding is delayed by 16 to 20 days, is an effective, simple, and economic method of pregnancy discontinuation.
Regression methods in the comparison of accuracy (1982)

Monte Carlo simulation has been used to test the robustness of three methods of regression in the comparison of analytical accuracy. The methods used were simple linear regression, weighted linear regression and a new method based on maximum likelihood estimation. The new method is capable of unbiased estimation with different heteroscedastic variance of both the y-values and the x-values, and is the most generally useful. However, even simple linear regression can estimate linear biases accurately as long as elementary safeguards are applied. The simulations realistically covered a wide range of circumstances likely to be encountered in analytical practice.
Girls homozygous for an IL-2–inducible T cell kinase mutation that leads to protein deficiency develop fatal EBV-associated lymphoproliferation (2009)

The fatal immune dysregulation that sometimes follows EBV infection in boys has been linked to mutations in two X chromosome-encoded genes, SLAM-associated protein (SAP) and X-linked inhibitor of apoptosis (XIAP). In this study we describe 2 girls from a consanguineous Turkish family who died after developing severe immune dysregulation and therapy-resistant EBV-positive B cell proliferation following EBV infection. SNP array-based genome-wide linkage analysis revealed IL-2-inducible T cell kinase (ITK) as a candidate gene for this immunodeficiency syndrome. Both girls harbored a homozygous missense mutation that led to substitution of a highly conserved residue (R335W) in the SH2 domain of ITK. Characteristics of ITK deficiency in mouse models, such as absence of NKT cells and high levels of eomesodermin in CD8+ cells, were seen in either one or both of the girls. Two lines of evidence suggested that R335W caused instability of the ITK protein. First, in silico modeling of the mutant protein predicted destabilization of the SH2 domain. Additionally, Western blot analysis revealed that, unlike wild-type ITK, the R335W mutant was nearly undetectable when expressed in 293 T cells. Our results suggest that ITK deficiency causes what we believe to be a novel immunodeficiency syndrome that leads to a fatal inadequate immune response to EBV. Because ITK deficiency resembles EBV-associated lymphoproliferative disorders in boys, we suggest that this molecular cause should be considered during diagnosis and treatment.
The magical number seven, plus or minus two: Some limits on our capacity for processing information. (1956)

First, the span of absolute judgment and the span of immediate memory impose severe limitations on the amount of information that we are able to receive, process, and remember. By organizing the stimulus input simultaneously into several dimensions and successively into a sequence or chunks, we manage to break (or at least stretch) this informational bottleneck. Second, the process of recoding is a very important one in human psychology and deserves much more explicit attention than it has received. In particular, the kind of linguistic recoding that people do seems to me to be the very lifeblood of the thought processes. Recoding procedures are a constant concern to clinicians, social psychologists, linguists, and anthropologists and yet, probably because recoding is less accessible to experimental manipulation than nonsense syllables or T mazes, the traditional experimental psychologist has contributed little or nothing to their analysis. Nevertheless, experimental techniques can be used, methods of recoding can be specified, behavioral indicants can be found. And I anticipate that we will find a very orderly set of relations describing what now seems an uncharted wilderness of individual differences. Third, the concepts and measures provided by the theory of information provide a quantitative way of getting at some of these questions. The theory provides us with a yardstick for calibrating our stimulus materials and for measuring the performance of our subjects. In the interests of communication I have suppressed the technical details of information measurement and have tried to express the ideas in more familiar terms; I hope this paraphrase will not lead you to think they are not useful in research. Informational concepts have already proved valuable in the study of discrimination and of language; they promise a great deal in the study of learning and memory; and it has even been proposed that they can be useful in the study of concept formation. A lot of questions that seemed fruitless twenty or thirty years ago may now be worth another look. In fact, I feel that my story here must stop just as it begins to get really interesting. And finally, what about the magical number seven? What about the seven wonders of the world, the seven seas, the seven deadly sins, the seven daughters of Atlas in the Pleiades, the seven ages of man, the seven levels of hell, the seven primary colors, the seven notes of the musical scale, and the seven days of the week? What about the seven-point rating scale, the seven categories for absolute judgment, the seven objects in the span of attention, and the seven digits in the span of immediate memory? For the present I propose to withhold judgment. Perhaps there is something deep and profound behind all these sevens, something just calling out for us to discover it. But I suspect that it is only a pernicious, Pythagorean coincidence.
The Barley mlo-gene: an important powdery mildew resistance source (2000)

International audience
Structure-Function Analysis of Protease-activated Receptor 4 Tethered Ligand Peptides (2000)

Thrombin activates protease-activated receptors (PARs) by specific cleavage of their amino-terminal exodomains to unmask a tethered ligand that binds intramolecularly to the body of the receptor to effect transmembrane signaling. Peptides that mimic such ligands are valuable as agonists for probing PAR function, but the tethered ligand peptide for PAR4, GYPGKF, lacks potency and is of limited utility. In a structure-activity analysis of PAR4 peptides, AYPGKF was approximately 10-fold more potent than GYPGKF and, unlike GYPGKF, elicited PAR4-mediated responses comparable in magnitude to those elicited by thrombin. AYPGKF was relatively specific for PAR4 in part due to the tyrosine at position 2; substitution of phenylalanine or p-fluorophenylalanine at this position produced peptides that activated both PAR1 and PAR4. Because human platelets express both PAR1 and PAR4, it might be desirable to inhibit both receptors. Identifying a single agonist for both receptors raises the possibility that a single antagonist for both receptors might be developed. The AYPGKF peptide is a useful new tool for probing PAR4 function. For example, AYPGKF activated and desensitized PAR4 in platelets and, like thrombin, triggered phosphoinositide hydrolysis but not inhibition of adenylyl cyclase in PAR4-expressing cells. The latter shows that, unlike PAR1, PAR4 couples to G(q) and not G(i).
Highly Differentiated Motifs Responsible for Two Cytokine Activities of a Split Human tRNA Synthetase (1999)

While native human tyrosyl-tRNA synthetase (TyrRS) is inactive as a cell-signaling molecule, it can be split into two distinct cytokines. The enzyme is secreted under apoptotic conditions in culture where it is cleaved into an N-terminal fragment that harbors the catalytic site and into a C-domain fragment found only in the mammalian enzymes. The N-terminal fragment is an interleukin-8 (IL-8)-like cytokine, whereas the released C-domain is an endothelial-monocyte-activating polypeptide II (EMAP II)-like cytokine. Although the IL-8-like activity of the N-fragment depends on an ELR motif found in alpha-chemokines and conserved among mammalian TyrRSs, here we show that a similar (NYR) motif in the context of a lower eukaryote TyrRS does not confer the IL8-like activity. We also show that a heptapeptide from the C-domain has EMAP II-like chemotaxis activity for mononuclear phagocytes and polymorphonuclear leukocytes. Eukaryote proteins other than human TyrRS that have EMAP II-like domains have variants of the heptapeptide motif. Peptides based on these sequences are inactive as cytokines. Thus, the cytokine activities of split human TyrRS depend on highly differentiated motifs that are idiosyncratic to the mammalian system.
StixelNet: A Deep Convolutional Network for Obstacle Detection and Road Segmentation (2015)

General obstacle detection is a key enabler for obstacle avoidance in mobile robotics and autonomous driving. In this paper we address the task of detecting the closest obstacle in each direction from a driving vehicle. As opposed to existing methods based on 3D sensing we use a single color camera. The main novelty in our approach is the reduction of the task to a column-wise regression problem. The regression is then solved using a deep convolutional neural network (CNN). In addition, we introduce a new loss function based on a semi-discrete representation of the obstacle position probability to train the network. The network is trained using ground truth automatically generated from a laser-scanner point cloud. Using the KITTI dataset, we show that the our monocularbased approach outperforms existing camera-based methods including ones using stereo. We also apply the network on the related task of road segmentation achieving among the best results on the KITTI road segmentation challenge.
Answer mining from on-line documents (2001)

Mining the answer of a natural language open-domain question in a large collection of on-line documents is made possible by the recognition of the expected answer type in relevant text passages. If the technology of retrieving texts where the answer might be found is well developed, few studies have been devoted to the recognition of the answer type. This paper presents a unified model of answer types for open-domain Question/Answering that enables the discovery of exact answers. The evaluation of the model, performed on real-world questions, considers both the correctness and the coverage of the answer types as well as their contribution to answer precision.
Dynamic Function Placement in Active Storage Clusters (1999)

Abstract : Optimally partitioning application and file system functionality within a cluster of clients and servers is a difficult problem due to dynamic variations in application behavior, resource availability and workload mixes. This paper presents ABACUS, a run-time system that monitors and dynamically changes function placement for applications that manipulate large data sets. Several examples of data-intensive workloads are used to show the importance of proper function placement and its dependence on dynamic runtime characteristics, with performance differences frequently reaching 2-10X. We evaluate how well the ABACUS prototype adapts to run-time system behavior, including both long-term variation (e.g., filter selectivity) and short-term variation (e.g.,multi-phase applications and inter-application resource contention). Our experiments with ABACUS indicate that it is possible to adapt in all of these situations and that the adaptation converges most quickly in those cases where the performance impact is most significant.
The Intelligent vision sensor: Turning video into information (2007)

Video analytics for security and surveillance applications is becoming commonplace. Advances in algorithm robustness and low-cost video platforms have allowed analytics to become an ingredient for many different devices ranging from cameras to encoders to routers to storage. As algorithms become more refined, the analytics paradigm shifts from a human-support model to an automation model. In this context, ObjectVideo, the leader in intelligent video, has created a new concept in video analytics devices - the intelligent vision sensor (IVS). This device consists of a video imager and lens combined with an onboard processor and communication channel. This low-cost device turns video imagery into actionable information that can be used in building automation and business intelligence applications. This paper describes the technical and market drivers that facilitate the creation and adoption of the IVS device as well as a specific case study involving an application for heating, ventilation, and air conditioning (HVAC) and lighting control.
Derivation of a T cell hybridoma variant deprived of functional T cell receptor α and β chain transcripts reveals a nonfunctional α‐mRNA of BW5147 origin (1989)

We have isolated a variant of the DO-11.10.7 mouse T cell hybridoma which does not express functional T cell receptor alpha/beta chains. This variant, denoted 58 alpha-beta-, can be used as a recipient for T cell receptor alpha/beta gene transfer experiments to obtain cell lines which express only the products of the transfected alpha/beta genes at their surfaces. In the process of characterizing the defects affecting the 58 alpha-beta-T cell receptor genes, we have found that the parental BW5147 thymoma has undergone a previously unnoticed V alpha-J alpha rearrangement. This alpha rearrangement involves a V alpha pseudogene segment and accounts for the high level of alpha-mRNA transcripts present in the BW5147 alpha-beta- variant. Knowledge of the existence of this second, albeit nonfunctional, alpha-mRNA in BW5147 is of importance, since it could be, and actually already has been, mistakenly identified (due to partial nucleotide sequencing) in T hybrids as a functionally significant message donated by the normal T cell parent.
All in the family: Structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly (1998)

The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modern family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metal-binding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions.