gebhart/patrepeval huggingface dataset:
Quasi-inverses of schema mappings (2008)

Schema mappings are high-level specifications that describe the relationship between two database schemas. Two operators on schema mappings, namely the composition operator and the inverse operator, are regarded as especially important. Progress on the study of the inverse operator was not made until very recently, as even finding the exact semantics of this operator turned out to be a fairly delicate task. Furthermore, this notion is rather restrictive, since it is rare that a schema mapping possesses an inverse. In this article, we introduce and study the notion of a quasi-inverse of a schema mapping. This notion is a principled relaxation of the notion of an inverse of a schema mapping; intuitively, it is obtained from the notion of an inverse by not differentiating between instances that are equivalent for data-exchange purposes. For schema mappings specified by source-to-target tuple-generating dependencies (s-t tgds), we give a necessary and sufficient combinatorial condition for the existence of a quasi-inverse, and then use this condition to obtain both positive and negative results about the existence of quasi-inverses. In particular, we show that every LAV (local-as-view) schema mapping has a quasi-inverse, but that there are schema mappings specified by full s-t tgds that have no quasi-inverse. After this, we study the language needed to express quasi-inverses of schema mappings specified by s-t tgds, and we obtain a complete characterization. We also characterize the language needed to express inverses of schema mappings, and thereby solve a problem left open in the earlier study of the inverse operator. Finally, we show that quasi-inverses can be used in many cases to recover the data that was exported by the original schema mapping when performing data exchange.
Surface and polymer network stabilized reflective cholesteric liquid crystal displays (1995)

We report on the optical reflective properties of the planar texture of cholesteric liquid crystal displays. The cholesteric liquid crystal is made bistable by either dispersing a low concentration of polymer or by treating the cell substrate surfaces. We determine the role that the polymer network and surface treatment has on the reflective properties as a funciton of viewing angle using both collimated and diffuse illumination. Both the polymer network and surface treatment have the effect of distributing the orientation of the cholesteric helix axes about the cell normal. Theoretically we characterize these cells by this distribution.
Corticotropin Releasing Factor Binding Protein as a Novel Target to Restore Brain Homeostasis: Lessons Learned From Alcohol Use Disorder Research (2021)

Stress is well-known to contribute to the development of many psychiatric illnesses including alcohol and substance use disorder (AUD and SUD). The deleterious effects of stress have also been implicated in the acceleration of biological age, and age-related neurodegenerative disease. The physio-pathology of stress is regulated by the corticotropin-releasing factor (CRF) system, the upstream component of the hypothalamic-pituitary-adrenal (HPA) axis. Extensive literature has shown that dysregulation of the CRF neuroendocrine system contributes to escalation of alcohol consumption and, similarly, chronic alcohol consumption contributes to disruption of the stress system. The CRF system also represents the central switchboard for regulating homeostasis, and more recent studies have found that stress and aberrations in the CRF pathway are implicated in accelerated aging and age-related neurodegenerative disease. Corticotropin releasing factor binding protein (CRFBP) is a secreted glycoprotein distributed in peripheral tissues and in specific brain regions. It neutralizes the effects of CRF by sequestering free CRF, but may also possess excitatory function by interacting with CRF receptors. CRFBP's dual role in influencing CRF bioavailability and CRF receptor signaling has been shown to have a major part in the HPA axis response. Therefore, CRFBP may represent a valuable target to treat stress-related illness, including: development of novel medications to treat AUD and restore homeostasis in the aging brain. This narrative review focuses on molecular mechanisms related to the role of CRFBP in the progression of addictive and psychiatric disorders, biological aging, and age-related neurodegenerative disease. We provide an overview of recent studies investigating modulation of this pathway as a potential therapeutic target for AUD and age-related neurodegenerative disease.
Modality Conversion (2011)

Content adaptation currently appears to be the key solution to support the quality of service (QoS) for multimedia services over heterogeneous environments. In this chapter, we study modality conversion as an important adaptation method. We point out two main challenging issues of the problem of modality conversion: (1) the quantification of the content value (quality) when contents are drastically scaled and/or converted to other modalities and (2) the method to accurately decide the modality and content value for each object given that quantification. Accordingly, we will present in detail the solutions as well as the open questions to these two issues. Moreover, we discuss the benefits and obstacles as well as future trends of modality conversion in realizing the goal of universal multimedia access.
Making the hospital a safer place by sonochemical coating of all its textiles with antibacterial nanoparticles (2015)

The ability to scale-up the sonochemical coating of medical textiles with antibacterial nanoparticles is demonstrated in the current paper. A roll-to-roll pilot installation to coat textiles was built taking into consideration the requirements of the sonochemical process. A long-run experiment was conducted in which 2500 m of fabric were coated with antibacterial ZnO nanoparticles (NPs). The metal oxide NPs were deposited from an ethanol:water solution. In this continuous process a uniform concentration of coated NPs over the length/width of the fabric was achieved. The antibacterial efficiency of the sonochemically-coated textiles was validated in a hospital environment by a reduction in the occurrence of nosocomial infections. NP-coated bed sheets, patient gowns, pillow cover, and bed covers were used by 21 patients. For comparison 16 patients used regular textiles. The clinical data indicated the reduced occurrence of hospital-acquired infections when using the metal oxide NP-coated textiles. In order to reduce the cost of the coating process and considering safety issues during manufacturing, the solvent (ethanol:water) (9:1 v:v) used for the long-run experiment, was replaced by water. Although lesser amounts of ZnO NPs were deposited on the fabric in the water-based process the antibacterial activity of the textiles was preserved due to the smaller size of the particles.
The role of chemokines in the immunopathology of the liver (2000)

Chemokines are small protein inflammatory mediators that were classically known for their elicitation of inflammatory cells out of the vasculature. However, more contemporary studies show that these ubiquitous factors impinge on many facets of biology, including hematopoiesis, angiogenesis, and mitogeneis. The elucidation of mechanisms involved in the immunopathogenesis of liver disease has magnified the importance of chemokines in this organ. Accordingly, a number of in vitro and in vivo studies have highlighted the importance of chemokine biology in both acute and chronic liver disease, and a variety of liver diseases have been shown to involve chemokines and their receptors during the initiation and main tenance of liver pathology. A greater understanding of the role chemokines play during liver disease may permit the employment of therapies that target or enhance chemokines in the liver. This review will highlight the current clinical and experimental research in the immunopathogenesis of acute and chronic liver diseases.
Glyceraldehyde-3-phosphate dehydrogenase gene from Zymomonas mobilis: cloning, sequencing, and identification of promoter region (1987)

The gene encoding glyceraldehyde-3-phosphate dehydrogenase was isolated from a library of Zymomonas mobilis DNA fragments by complementing a deficient strain of Escherichia coli. It contained tandem promoters which were recognized by E. coli but appeared to function less efficiently than the enteric lac promoter in E. coli. The open reading frame for this gene encoded 337 amino acids with an aggregate molecular weight of 36,099 (including the N-terminal methionine). The primary amino acid sequence for this gene had considerable functional homology and amino acid identity with other eucaryotic and bacterial genes. Based on this comparison, the gap gene from Z. mobilis appeared to be most closely related to that of the thermophilic bacteria and to the chloroplast isozymes. Comparison of this gene with other glycolytic enzymes from Z. mobilis revealed a conserved pattern of codon bias and several common features of gene structure. A tentative transcriptional consensus sequence is proposed for Z. mobilis based on comparison of the five known promoters for three glycolytic enzymes.
Fetal Fibroblasts and Keratinocytes with Immunosuppressive Properties for Allogeneic Cell-Based Wound Therapy (2013)

Fetal skin heals rapidly without scar formation early in gestation, conferring to fetal skin cells a high and unique potential for tissue regeneration and scar management. In this study, we investigated the possibility of using fetal fibroblasts and keratinocytes to stimulate wound repair and regeneration for further allogeneic cell-based therapy development. From a single fetal skin sample, two clinical batches of keratinocytes and fibroblasts were manufactured and characterized. Tolerogenic properties of the fetal cells were investigated by allogeneic PBMC proliferation tests. In addition, the potential advantage of fibroblasts/keratinocytes co-application for wound healing stimulation has been examined in co-culture experiments with in vitro scratch assays and a multiplex cytokines array system. Based on keratin 14 and prolyl-4-hydroxylase expression analyses, purity of both clinical batches was found to be above 98% and neither melanocytes nor Langerhans cells could be detected. Both cell types demonstrated strong immunosuppressive properties as shown by the dramatic decrease in allogeneic PBMC proliferation when co-cultured with fibroblasts and/or keratinocytes. We further showed that the indoleamine 2,3 dioxygenase (IDO) activity is required for the immunoregulatory activity of fetal skin cells. Co-cultures experiments have also revealed that fibroblasts-keratinocytes interactions strongly enhanced fetal cells secretion of HGF, GM-CSF, IL-8 and to a lesser extent VEGF-A. Accordingly, in the in vitro scratch assays the fetal fibroblasts and keratinocytes co-culture accelerated the scratch closure compared to fibroblast or keratinocyte mono-cultures. In conclusion, our data suggest that the combination of fetal keratinocytes and fibroblasts could be of particular interest for the development of a new allogeneic skin substitute with immunomodulatory activity, acting as a reservoir for wound healing growth factors.
Two Supersonic Business Aircraft Conceptual Designs With and Without Sonic Boom Constraint (2005)

A pair of supersonic business jet conceptual designs has been developed to assess the impact of designing for reduced sonic boom. One aircraft was designed without a sonic boom constraint. The other was limited to an initial sonic boom overpressure of 0.4 lb/ft 2 . All other design requirements were the same. Sonic boom mitigation places a requirement on the buildup of lift and volume along the longitudinal axis of the aircraft, with any excess or shortfall adversely impacting the sonic boom. Methods were developed for incorporating this requirement into the conceptual design process. Both the method for incorporating the boom constraint in the design process and the result, a side-by-side comparison of one low-boom and one unconstrained aircraft with substantially identical performance in all other respects, are considered significant. The boom-constrained aircraft was approximately 25% longer with 18% higher takeoff gross weight than the unconstrained aircraft.
Heteroarylmethoxyphenylalkoxyiminoalkylcarboxylic Acids as Leukotriene Biosynthesis Inhibitors (2000)

A novel series of heteroarylmethoxyphenylalkoxyiminoalkylcarboxylic acids was studied as leukotriene biosynthesis inhibitors. A hypothesis of structure-activity optimization by insertion of an oxime moiety was investigated using REV-5901 as a starting point. A systematic structure-activity optimization showed that the spatial arrangement and stereochemistry of the oxime insertion unit proved to be important for inhibitory activity. The promising lead, S-(E)-11, inhibited LTB(4) biosynthesis in the intact human neutrophil with IC(50) of 8 nM and had superior oral activity in vivo, in a rat pleurisy model (ED(50) = 0.14 mg/kg) and rat anaphylaxis model (ED(50) = 0.13 mg/kg). In a model of lung inflammation, S-(E)-11 blocked LTE(4) biosynthesis (ED(50) of 0.1 mg/kg) and eosinophil influx (ED(50) of 0.2 mg/kg). S-(E)-11 (A-93178) was selected for further preclinical evaluation.
Rational Design of a Novel Fluorescent Biosensor for β-Lactam Antibiotics from a Class A β-Lactamase (2004)

A rational design strategy was used to construct a sensitive "turn-on" biosensor for beta-lactam antibiotics and beta-lactamase inhibitors from a class A beta-lactamase mutant with suppressed hydrolytic activity. A fluorescein molecule was attached to the 166 position on the Omega-loop of the E166C mutant close to the active site of the beta-lactamase. Upon binding with antibiotics or inhibitors, the flexibility of the Omega-loop allows the fluorescein molecule to move out from the active site and be more exposed to solvent. This process is accompanied by an increase in the fluorescence of the labeled enzyme. The fluorescence intensity of the biosensor increases with the concentration of antibiotics or inhibitors, which can detect penicillin G at concentrations as low as 50 nM in water. This approach opens a possibility for converting highly active and nonallosteric enzymes into substrate-binding proteins for biosensing purposes.
Computer-generated multiple-phase-level holograms using color printer techniques (1990)

Current techniques for constructing multiple-phase-level structures (e.g., phase holograms) use computer-generated masks to selectively etch a glass substrate, creating discrete phase levels based on varying glass thickness (i.e., kineform). This approach requires several procedural steps and expensive photolithographic equipment. We have developed a one-step technique using color-printer technology and photographic eqipment. Colors from the printer are mapped to discrete intensity levels on photographic emulsion, and bleaching the recorded film results in discrete phase levels. We have investigated the relationship between the optical density of colors generated by our printer and the corresponding phase changes after bleaching.
Adaptive Caching Networks with Optimality Guarantees (2016)

We study the problem of optimal content placement over a network of caches, a problem naturally arising in several networking applications, including ICNs, CDNs, and P2P systems. Given a demand of content request rates and paths followed, we wish to determine the content placement that maximizes the expected caching gain, i.e., the reduction of routing costs due to intermediate caching. The offline version of this problem is NP-hard and, in general, the demand and topology may be a priori unknown. Hence, a distributed, adaptive, constant approximation content placement algorithm is desired. We show that path replication, a simple algorithm frequently encountered in literature, can be arbitrarily suboptimal when combined with traditional eviction policies, like LRU, LFU, or FIFO. We propose a distributed, adaptive algorithm that performs stochastic gradient ascent on a concave relaxation of the expected caching gain, and constructs a probabilistic content placement within 1-1/e factor from the optimal, in expectation. Motivated by our analysis, we also propose a novel greedy eviction policy to be used with path replication, and show through numerical evaluations that both algorithms significantly outperform path replication with traditional eviction policies over a broad array of network topologies.
Stabilizing the HIV-1 Envelope Glycoprotein State 2A Conformation (2020)

The HIV-1 envelope glycoprotein (Env) trimer [(gp120/gp41)<sub>3</sub>] is a metastable complex expressed at the surface of viral particles and infected cells that samples different conformations. Before engaging CD4, Env adopts an antibody-resistant "closed" conformation (State 1). CD4 binding triggers an intermediate conformation (State 2) and then a more "open" conformation (State 3) that can be recognized by non-neutralizing antibodies (nnAbs) such as those that recognize the coreceptor binding site (CoRBS). Binding of antibodies to the CoRBS permits another family of nnAbs, the anti-cluster A family of Abs which target the gp120 inner domain, to bind and stabilize an asymmetric conformation (State 2A). Cells expressing Env in this conformation are susceptible to antibody-dependent cellular cytotoxicity (ADCC). This conformation can be stabilized by small-molecule CD4 mimetics (CD4mc) or soluble CD4 (sCD4) in combination with anti-CoRBS Ab and anti-cluster A antibodies. The precise stoichiometry of each component that permits this sequential opening of Env remains unknown. Here, we used a cell-based ELISA (CBE) assay to evaluate each component individually. In this assay we used a "trimer mixing" approach by combining wild-type (wt) subunits with subunits impaired for CD4 or CoRBS Ab binding. This enabled us to show that State 2A requires all three gp120 subunits to be bound by sCD4/CD4mc and anti-CoRBS Abs. Two of these subunits can then bind anti-cluster A Abs. Altogether, our data suggests how this antibody vulnerable Env conformation is stabilized.<b>Importance</b> Stabilization of HIV-1 Env State 2A has been shown to sensitize infected cells to ADCC. State 2A can be stabilized by a "cocktail" composed of CD4mc, anti-CoRBS and anti-cluster A Abs. We present evidence that optimal State 2A stabilization requires all three gp120 subunits to be bound by both CD4mc and anti-CoRBS Abs. Our study provides valuable information on how to stabilize this ADCC-vulnerable conformation. Strategies aimed at stabilizing State 2A might have therapeutic utility.
A Fast-Running, End-to-End Concussion Risk Model for Assessment of Complex Human Head Kinematics (2018)

An end-to-end, mechanism-based concussion risk model, linking head motion to axonal injury, has been demonstrated to predict concussion outcomes with greater sensitivity and specificity than external correlates such as peak head acceleration. The development of this model was driven by the need to more accurately translate head-worn sensor measurements into injury assessment in near-real time. The full end-to-end model is a detailed multi-scale model, composed of complex components (e.g., a human head finite element model), is computationally expensive, and requires specialized software. For practicality, this research-level model must be simplified into a standalone, fast-running algorithm that can be embedded on the microprocessor of a head-worn sensor. This article describes the development of a simplified, fast-running algorithm that delivers comparable results to those of the full end-to-end model. The dynamic axonal response of the human head finite element model to head motion is mathematically modeled using a lumped parameter system fitted to the finite element model response for a range of head motions. The other component models of the full end-to-end model were similarly reduced. For the same head kinematic scenarios, the probabilities of concussion obtained from the end-to-end model and from the simplified algorithm are compared well.
Quantitative analysis of focal adhesion dynamics using photonic resonator outcoupler microscopy (PROM) (2018)

Focal adhesions are critical cell membrane components that regulate adhesion and migration and have cluster dimensions that correlate closely with adhesion engagement and migration speed. We utilized a label-free approach for dynamic, long-term, quantitative imaging of cell-surface interactions called photonic resonator outcoupler microscopy (PROM) in which membrane-associated protein aggregates outcoupled photons from the resonant evanescent field of a photonic crystal biosensor, resulting in a highly localized reduction of the reflected light intensity. By mapping the changes in the resonant reflected peak intensity from the biosensor surface, we demonstrate the ability of PROM to detect focal adhesion dimensions. Similar spatial distributions can be observed between PROM images and fluorescence-labeled images of focal adhesion areas in dental epithelial stem cells. In particular, we demonstrate that cell-surface contacts and focal adhesion formation can be imaged by two orthogonal label-free modalities in PROM simultaneously, providing a general-purpose tool for kinetic, high axial-resolution monitoring of cell interactions with basement membranes.
Isolation of HLA locus-specific DNA probes from the 3'-untranslated region. (1984)

When human class I cDNA clones containing coding sequences are used to probe genomic DNA, 15-20 fragments, each containing a complete class I gene or pseudogene, are seen. Identification of which genomic DNA segments encode the HLA-A and -B antigens has to date required transfection of mouse L cells with cloned class I genes or analysis of HLA loss mutants. In this report we show that under high-stringency conditions, probes constructed from the 3'-untranslated region can be used to specifically identify the segments of DNA that encode the HLA-A and -B antigens in the human lymphoblastoid cell line 721. Examination of DNA from unrelated individuals indicates that these probes are locus specific and will permit identification of HLA-A and -B genes in the population.
ChemInform Abstract: Novel N‐[1‐(1‐Substituted 4‐Piperidinylmethyl)‐4‐piperidinyl]benzamides as Potent Colonic Prokinetic Agents. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The C-terminal antibody binding domain of<i>Candida albicans</i>mp58 represents a protective epitope during candidiasis (2004)

The 58-kDa surface mannoprotein of Candida albicans (mp58) elicits strong antibody responses during infection. Epitope mapping with sera from patients with candidiasis and control individuals indicated the presence of multiple IgG-reactive continuous epitopes on the protein, expanding both the amino- and carboxy-terminal domains and several internal regions. These immunoreactive regions were similar to the ones previously identified using sera from immunized animals. Two of the epitopic regions (including the C-terminal domain) showed increased reactivity with antibodies present in sera from patients with candidiasis as compared to control individuals. Patients who survived the infection displayed increased antibody reactivity towards the C-terminal epitope as compared to those succumbing to candidiasis. A monoclonal antibody directed towards this epitopic region conferred protection in serum therapy experiments in a murine model of hematogenously disseminated candidiasis. Together, these observations indicate the carboxy-terminal antibody binding domain of C. albicans mp58 represents a protective epitope during candidiasis.