gebhart/patrepeval huggingface dataset:
Rare Variants in Complex Traits: Novel Identification Strategies and the Role of de novo Mutations (2012)

Following the limited success of linkage and association studies aimed at identifying the genetic causes of common neurodevelopmental syndromes like autism and schizophrenia, complex traits such as these have recently been considered under the 'common disease-rare variant' hypothesis. Prior to this hypothesis, the study of candidate genes has enabled the discovery of rare variants in complex disorders, and in turn some of these variants have highlighted the genetic contribution of de novo variants. De novo variants belong to a subcategory of spontaneous rare variants that are largely associated with sporadic diseases, which include some complex psychiatric disorders where the affected individuals do not transmit the genetic defects they carry because of their reduced reproductive fitness. Interestingly, recent studies have demonstrated the rate of germline de novo mutations to be higher in individuals with complex psychiatric disorders by comparison to what is seen in unaffected control individuals; moreover, de novo mutations carried by affected individuals have generally been more deleterious than those observed in control individuals. Advanced sequencing technologies have recently enabled the undertaking of massive parallel sequencing projects that can cover the entire coding sequences (exome) or genome of several individuals at once. Such advances have thus fostered the emergence of novel genetic hypotheses and ideas to investigate disease-causative genetic variations. The genetic underpinnings of a number of sporadic complex diseases is now becoming partly explained and more major breakthroughs for complex traits genomics should be expected in the near future.
Diagnosis of moisture damage in asphalt pavements (2004)

One of the most common modes of premature failure of asphalt pavements is water damage. Moisture damage in hot-mix asphalt (HMA) pavements occurs when water infiltrates the pavement system, causing premature failure of hot-mix asphalt pavements, primarily through loss of adhesion between the asphalt binder and the aggregates. Loss of adhesion can lead to stripping of the asphalt film from the aggregate and raveling, where aggregates are dislodged from the pavement. The laboratory testing procedures currently available for testing HMA moisture susceptibility were primarily developed to determine the degree of resistance to moisture damage by a particular combination of asphalt and aggregate as well as compare mixes composed of different types and quantities of aggregate. These methods are all based on destructive testing. There is currently a need for innovative nondestructive testing technologies that can be used to identify and isolate the effects of water damage in mixtures. As a first step in the development of a non-destructive method to test HMA pavements, modal hammer tests were conducted on several test specimens of fine and coarse grained granite-based mixes commonly used by the Florida Department of Transportation (FDOT). The results of the testing indicate that there is a large frequency shift in the transfer function measurements for the damaged samples compared to the undamaged samples. The results imply that modal hammer testing may be used as a method to characterize the health of HMA pavements.
Multiplex glycan bead array for high throughput and high content analyses of glycan binding proteins (2018)

Glycan-binding proteins (GBPs) play critical roles in diverse cellular functions such as cell adhesion, signal transduction and immune response. Studies of the interaction between GBPs and glycans have been hampered by the availability of high throughput and high-content technologies. Here we report multiplex glycan bead array (MGBA) that allows simultaneous analyses of 384 samples and up to 500 glycans in a single assay. The specificity, sensitivity and reproducibility of MGBA are evaluated using 39 plant lectins, 13 recombinant anti-glycan antibodies, and mammalian GBPs. We demonstrate the utility of this platform by the analyses of natural anti-glycan IgM and IgG antibodies in 961 human serum samples and the discovery of anti-glycan antibody biomarkers for ovarian cancer. Our data indicate that the MGBA platform is particularly suited for large population-based studies that require the analyses of large numbers of samples and glycans.
Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS (2012)

A recently proposed quantum-chemical protocol for the description of the character of organic mixed-valence (MV) compounds, close from both sides to the localized/delocalized borderline, is evaluated and extended for a series of dinitroaryl radical anions 1-6. A combination of global hybrid functionals with exact-exchange admixtures of 35% (BLYP35) or 42% (BMK) with appropriate solvent modeling allows an essentially quantitative treatment of, for example, structural symmetry-breaking in Robin/Day class II systems, thermal electron transfer (ET) barriers, and intervalence charge-transfer (IV-CT) excitation energies, while covering also the delocalized class III cases. Global hybrid functionals with lower exact-exchange admixtures (e.g., B3LYP, M05, or M06) provide a too delocalized description, while functionals with higher exact-exchange admixtures (M05-2X, M06-2X) provide a too localized one. The B2PLYP double hybrid gives reasonable structures but far too small barriers in class II cases. The CAM-B3LYP range hybrid gives somewhat too high ET barriers and IV-CT energies, while the range hybrids ωB97X and LC-BLYP clearly exhibit too much exact exchange. Continuum solvent models describe the situation well in most aprotic solvents studied. The transition of 1,4-dinitrobenzene anion 1 from a class III behavior in aprotic solvents to a class II behavior in alcohols is not recovered by continuum solvent models. In contrast, it is treated faithfully by the novel direct conductor-like screening model for real solvents (D-COSMO-RS). The D-COSMO-RS approach, the TURBOMOLE implementation of which is reported, also describes accurately the increased ET barriers of class II systems 2 and 3 in alcohols as compared to aprotic solvents and can distinguish at least qualitatively between different aprotic solvents with identical or similar dielectric constants. The dominant role of the solvent environment for the ET character of these MV radical anions is emphasized, as in contrast to some previous computational suggestions essentially all of the present systems have delocalized class III character in the gas phase. The present approach allows accurate estimates from the gas phase to aprotic and protic solvent environments, without the need for explicit ab initio molecular dynamics simulations, and without artificial constraints.
Trans-Cinnamaldehyde Decreases Attachment and Invasion of Uropathogenic Escherichia Coli in Urinary Tract Epithelial Cells by Modulating Virulence Gene Expression (2011)

Trans-cinnamaldehyde may potentially be used as a safe, effective antimicrobial to control uropathogenic E. coli infection. Followup studies in animal models are warranted.
Hypomorphic Alleles RevealFCA-Independent Roles forFYin the Regulation ofFLOWERING LOCUS C (2011)

The autonomous floral promotion pathway plays a key role in the regulation of flowering in rapid-cycling Arabidopsis (Arabidopsis thaliana) by providing constitutive repression of the floral inhibitor FLOWERING LOCUS C (FLC). As a result, autonomous pathway mutants contain elevated levels of FLC and are late flowering. Winter annual Arabidopsis, in contrast, contain functional alleles of FRIGIDA (FRI), which acts epistatically to the autonomous pathway to up-regulate FLC and delay flowering. To further explore the relationship between FRI and the autonomous pathway, we placed autonomous pathway mutants in a FRI-containing background. Unexpectedly, we found that a hypomorphic allele of the autonomous pathway gene fy (fy null alleles are embryo lethal) displayed background-specific effects on FLC expression and flowering time; in a rapid-cycling background fy mutants contained elevated levels of FLC and were late flowering, whereas in a winter annual background fy decreased FLC levels and partially suppressed the late-flowering phenotype conferred by FRI. Because FY has been shown to have homology to polyadenylation factors, we examined polyadenylation site selection in FLC transcripts. In wild type, two polyadenylation sites were detected and used at similar levels. In fy mutant backgrounds, however, the ratio of products was shifted to favor the distally polyadenylated form. FY has previously been shown to physically interact with another member of the autonomous pathway, FCA. Interestingly, we found that fy can partially suppress FLC expression in an fca null background and promote proximal polyadenylation site selection usage in the absence of FCA. Taken together, these results indicate novel and FCA-independent roles for FY in the regulation of FLC.
Giant Cell Temporal Arteritis Associated with Overlying Basal Cell Carcinoma: Co-Incidence or Connection? (2012)

Giant cell arteritis is a granulomatous vasculitis of large and medium sized arteries manifesting as temporal arteritis and/or polymyalgia rheumatica. The histological assessment of temporal artery biopsies is frequently encountered in anatomical pathology and has important diagnostic consequences in patients clinically suspected of having giant cell arteritis. We present an intriguing case of giant cell arteritis associated with a Basal cell carcinoma and discuss the ongoing controversy pertaining to the association of giant cell arteritis/polymyalgia rheumatica with malignancy.
The inflammatory macrophage: a story of Jekyll and Hyde (2002)

Recent investigations have highlighted new roles for the macrophage (Mphi) in the biology of inflammation. Selective depletion of Mphis from inflamed sites has confirmed their predominant role in immune-mediated damage. The components of this injury have been dissected. Mphis mediate death of stromal, parenchymal and other immune cells by engaging the death programme, resulting in apoptosis. In addition, Mphis induce destruction of matrix and extracellular structures both directly and indirectly by inducing stromal cells to release matrix metalloproteinases. However, there is another side to the inflammatory Mphi. Evidence is provided that Mphis at the same sites possess the ability to aid cell proliferation, secrete and stabilize new matrix components and induce resident cells to secrete matrix components themselves. Mphi phagocytosis of apoptotic cells brings about a change from the cell-killing matrix-degrading cell to the matrix-generating cell-proliferating tissue-healing cell. Just as both Mphi types are necessary at the inflamed site, the right balance of these two populations is required for healing and resolution. Evidence of excessive inflammation as a manifestation of impaired phagocytosis of apoptotic cells emphasizes that defects in the transition from one Mphi type to another may account for the uncontrolled excessive inflammation seen in disease. Recent insights into the mechanisms by which apoptotic cells signal the change of function to the Mphi offer the prospect of novel targets for manipulation of Mphis in the inflamed tissue.
First step on the ladder? The varying roles and experiences of the support worker (2013)

Michelle Acum, John Maher &amp; Greg Stocks discuss their experiences working as support workers, including their reasons for taking on the role, details of work undertaken, the skills required to carry out the role, the most frustrating and enjoyable aspects and what they learnt.
Selection and identification of anaerobic lactobacilli producing inhibitory compounds against vaginal pathogens (2006)

Two strains of Lactobacillus crispatus (15L08 and 21L07) and one strain of Lactobacillus jensenii (5L08) were selected from amongst 100 isolates from the vaginas of healthy premenopausal women for properties relevant to mucosal colonization and the production of H2O2 and/or bacteriocin-like compound. All three strains self-aggregated and adhered to vaginal epithelial cells, displacing well-known vaginal pathogens, such as Gardnerella vaginalis and Candida albicans. Lactobacillus crispatus 15L08 was characterized as a potential H2O2 producer. A high level of bacteriocin-like compound was synthesized by L. jensenii 5L08, with a bactericidal mode of action for G. vaginalis, C. albicans and Escherichia coli. However, H2O2-dependent activity alone was not sufficient to inhibit the growth of C. albicans. Simultaneous actions of H2O2 and bacteriocin-like compound produced by lactobacilli may be important for antagonizing pathogenic bacteria. These strains of lactobacilli may be excellent candidates for eventual use as probiotics to restore the normal microbial communities in the vaginal ecosystem.
Twenty-five percent albumin prevents lung injury following shock/resuscitation (2003)

Resuscitation with 25% albumin attenuates lung injury in this rat model. The beneficial effect was due to reduced neutrophil sequestration. The antioxidant properties of the 25% albumin preparation appeared to be partially responsible for the effects observed. These studies suggest a novel role for 25% albumin as an anti-inflammatory agent in neutrophil-mediated diseases, such as acute respiratory distress syndrome.
IgG anti-DNA autoantibodies within an individual autoimmune mouse are the products of clonal selection. (1989)

Although mice from almost all inbred strains produce IgM anti-DNA antibody in response to B cell mitogens, only (NZB x NZW)F1 mice and mice from other strains that are genetically predisposed to autoimmunity spontaneously produce anti-DNA antibody of the IgG isotype. Because (NZB x NZW)F1 mice display marked B cell hyperactivity, anti-DNA antibody production in these mice has been thought to result from spontaneous, polyclonal B cell activation. Although this may be true for IgM anti-DNA antibodies, our results demonstrate that IgG anti-DNA antibodies are not polyclonal. Rather, IgG anti-DNA autoantibodies within an individual autoimmune mouse are oligoclonal and somatically mutated. These results demonstrate that IgG anti-DNA autoantibodies are the products of clonally selective B cell stimulation and exhibit the same characteristics as secondary immune antibodies to conventional immunogens: they are IgG, they are clonally restricted, and they are somatically mutated.
Structure, Reaction Enthalpies, Entropies, and Free Energies of Cation−Molecule Complexes. A Theoretical Study by Means of the ab Initio Complete Basis Set CBS-Q Method (1998)

Ab initio molecular orbital calculations at the CBS-Q level of theory have been performed for 72 complexes in order to determine the effects of molecular structure on gas-phase basicity toward H+, Li+, and Mg2+. It is shown that basicities toward metal cations Li+ and Mg2+ differ considerably from the corresponding gas-phase basicities toward H+. Calculated interaction energies vary as H+ ≫ Mg2+ > Li+. The relative basicities of the bases studied depend characteristically on type of cation and coordination site.
Perception-oriented Video Coding based on Image Analysis and Completion: A Review (2011)

Perception-oriented video coding based on image analysis and completion (IAC) has received increasing attention over recent years. Several approaches have been proposed that follow diverging strategies: from full compatibility to hybrid block transform coding to alternative codec designs. In this paper, we review the most significant issues in IAC coding and their relevance for future codec designs. The most promising pathways will be analyzed along with limitations and open issues. The challenges in IACbased video coding will be summarized using methods developed by the authors and others for block-based and region-based IAC coding.
Application of Sewage Sludge and Other Amendments to Coal Refuse Material: I. Effects on Chemical Composition (1989)

Abstract The effects of sewage sludge, lime, and gypsum on the chemical composition of coal refuse material were examined at a Fulton County, IL, land reclamation site. Treatments consisted of a control, 542 dry Mg ha −1 anaerobically digested sewage sludge, 89.6 Mg ha −1 lime, 112 Mg ha −1 gypsum, and combinations of these amendments. Analysis of coal refuse material (0–15 cm) from 1976 to 1981 showed that the sewage sludge + lime treatment was the most effective in maintaining the refuse pH, and in reducing water‐soluble Al and Fe, KCl extractable Al, and total acidity. Gypsum applications decreased the refuse pH and increased water‐soluble Al and Fe, KCl extractable Al, and total acidity. The effectiveness of treatments in reducing total acidity was sewage sludge + lime &gt; gypsum + sewage sludge + lime &gt; sewage sludge &gt; lime &gt; gypsum + sewage sludge &gt; control &gt; gypsum + lime &gt; gypsum. Concentrations of water‐soluble Ca, Mg, and Na reflected the additions of these cations made by various treatments and the contribution of these cations to refuse electrical conductivity (EC). Profile sampling (0–100 cm) in 1976 and 1981 showed a decline in pH, and an increase in water‐soluble Al and Fe and total acidity in 1981 samples from the sewage sludge and gypsum treatments. The changes in the sludge treatment indicate there was a solubilization of metals from the refuse material and sewage sludge with time, as the surface pH (0–15 cm) declined, and a subsequent increase in the total acidity from metals and acidic by‐products leached to the 15‐ to 100‐cm depths of the coal refuse material. In the gypsum treatment, the changes observed in the 1981 profile samples reflected the leaching of H 3 O + , metals, and acidic by‐products of pyrite oxidation produced by exchange with Ca from the gypsum amendment.
B Cell Activation State-Governed Formation of Germinal Centers following Viral Infection (2007)

Germinal centers are structures that promote humoral memory cell formation and affinity maturation, but the triggers for their development are not entirely clear. Activated extrafollicular B cells can form IgM-producing plasmablasts or enter a germinal center reaction and differentiate into memory or plasma cells, mostly of the IgG isotype. Vesicular stomatitis virus (VSV) induces both types of response, allowing events that promote each of these pathways to be studied. In this work, extrafollicular vs germinal center responses were examined at a cellular level, analyzing VSV-specific B cells in infected mice. We show that VSV-specific germinal centers are transiently formed when insufficient proportions of specific T cell help is available and that strong B cell activation in cells expressing high levels of the VSV-specific BCR promoted their differentiation into early blasts, whereas moderate stimulation of B cells or interaction with Th cells restricted extrafollicular responses and promoted germinal center formation.
Partitioning sequential circuits on dynamically reconfigurable FPGAs (1999)

A fundamental feature of Dynamically Reconfigurable FPGAs (DRFPGAs) is that the logic and interconnect are time-multiplexed. Thus, for a circuit to be implemented on a DRFPGA, it needs to be partitioned such that each subcircuit can be executed at a different time. In this paper, the partitioning of sequential circuits for execution on a DRFPGA is studied. To determine how to correctly partition a sequential circuit and what are the costs in doing so, we propose a new gate-level model that handles time-multiplexed computation. We also introduce an enchanced force directed scheduling (FDS) algorithm to partition sequential circuits that finds a correct partition with low logic and communication costs, under the assumption that maximum performance is desired. We use our algorithm to partition seven large ISCAS'89 sequential benchmark circuits. The experimental results show that the enhanced FDS reduces communication costs by 27.5 percent with only a 1.1 percent increase in the gate cost compared to traditional FDS.
Nature-inspired generation scheme for shell structures (2012)

Although less researched and put into practice in the building environment, pure plate structures are to be observed frequently in biological structures. The 3-plate principle which is common in the morphology and growth pattern of natural systems is also found to be of a structurally optimum content when considered from a plate point of view. This is for instance the case of the sea urchin’s plate skeleton morphology, which served as biological inspiration for the recently built ICD/ITKE Research Pavilion 2011 at the University of Stuttgart. The current paper will focus on the 3-plate principle and its mechanical features, also presenting study models to analyse the structural characteristics and advantages of the principle. Along with the theoretical background, the paper will introduce the structural concept of the pavilion, as well as the analysis methods used for its design and engineering.
Protocol Validation by Duologue-Matrix Analysis (1978)

A protocol is a set of rules which governs the interaction between processes. It is difficult to design protocols without errors because there are usually more interactions possible than anticipated. We are concerned with two-process protocols. A technique is described which identifies design errors in protocols. The technique is based on modeling a protocol as a pair of interacting graphs whereby interaction sequences are represented by path pairs (one path in each graph). The technique is currently limited to protocols that must revert to an initial or quiescent state after a finite number of interaction steps. The work represents a theory that can be automated on a digital computer.
Implementation of Multipath and Multiple Description Coding in OLSR (2009)

In this paper we discussed the application and the implementation of multipath routing and multiple description coding (MDC) extension of OLSR, called MP-OLSR. It is based on the link state algorithm and employs periodic exchange of messages to maintain topology information of the networks. In the mean time, it updates the routing table in an on-demand scheme and forwards the packets in multiple paths which have been determined at the source. If a link failure is detected, the algorithm recovers the route automatically. Concerning the instability of the wireless networks, the multiple description coding is used to improve reliability of the network transmission, and several methods are proposed to allocate the redundancy in different paths. The simulation in NS2 shows that the new protocol can effectively improve the performance of the networks. The implementation of MP-OLSR is also proposed in the end.