gebhart/patrepeval huggingface dataset:
Fast and Simple Relational Processing of Uncertain Data (2007)

This paper introduces U-relations, a succinct and purely relational representation system for uncertain databases. U-relations support attribute-level uncertainty using vertical partitioning. If we consider positive relational algebra extended by an operation for computing possible answers, a query on the logical level can be translated into, and evaluated as, a single relational algebra query on the U-relation representation. The translation scheme essentially preserves the size of the query in terms of number of operations and, in particular, number of joins. Standard techniques employed in off-the-shelf relational database management systems are effective for optimizing and processing queries on U-relations. In our experiments we show that query evaluation on U-relations scales to large amounts of data with high degrees of uncertainty.
The effect of linguistic constraints on the large scale organization of language (2011)

This paper studies the effect of linguistic constraints on the large scale organization of language. It describes the properties of linguistic networks built using texts of written language with the words randomized. These properties are compared to those obtained for a network built over the text in natural order. It is observed that the "random" networks too exhibit small-world and scale-free characteristics. They also show a high degree of clustering. This is indeed a surprising result - one that has not been addressed adequately in the literature. We hypothesize that many of the network statistics reported here studied are in fact functions of the distribution of the underlying data from which the network is built and may not be indicative of the nature of the concerned network.
Effects of Bending Excitation on the Reaction of Chlorine Atoms with Methane (2005)

Vibrierende Energie: Die Anregung der niederfrequenten CH4(ν4=1)-Deformationsschwingung vergrößert unerwartet den Querschnitt für die Reaktion mit Cl-Atomen um einen Faktor von zwei oder höher. Diese Verstärkung, die für Stoßenergien zwischen 0.12 und 0.26 eV konstant ist, deutet darauf hin, dass eine Scherbewegung, wie eine Streckbewegung auch, den Bruch der C-H-Bindung in dieser direkten Abstraktionsreaktion erleichtern kann (siehe Schema; Cl grün, C violett, H grau).
P143-M Microarray-Generated Phosphopeptide Selectivity Profiles for Fluorescent Conjugates of an Artificial Phosphomonoester-Binding Small Molecule; Implications for the Global Enrichment and Detection of Phosphopeptides and Phosphoproteins. (2007)

Reliable identification and characterization of protein kinase substrates is of paramount importance to deciphering cellular signaling pathways. Previously, an artificial phosphomonoester-binding molecule, 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-olato Zn(2) complex (a.k.a. Phos-tag) was shown to bind to phenylphosphate under physiological conditions with a K(d) of 25 nM. A fundamental challenge in chemical biology is efficiently performing comprehensive profiling of the activity of artificial chemical structures, such as the Phos-tag molecule, against the hundreds or even thousands of biological targets they could potentially interact with. A peptide microarray-based phosphorylation site screening assay was thus performed to determine the binding selectivity of fluorophore-conjugated Phos-tag molecule, based upon direct detection of binding through readout of fluorescent signal generated by the reporter group. Epitope mapping was performed on a comprehensive list of phosphorylation sites known to be expressed in the human proteome, including serine, threonine and tyrosine phosphorylated residues. The collected data was evaluated using a combination of different in-house software packages resulting in scores for each amino acid residue relative to the phosphorylation site. The study demonstrates that fluorophore-conjugated Phos-tag exhibits very broad substrate specificity and does not appear to depend upon a specific sequence surrounding the targeted phosphorylation site. This relatively low degree of sequence restriction at the phosphorylation recognition site suggests that Phos-tag is broadly suitable for universal enrichment and detection of phosphorylation sites on phosphoproteins and phosphopeptides. The fluorescent Phos-tag technology is easy to perform, cost effective and should allow rapid large-scale screening of protein and peptide phosphorylation using a variety of solid-phase assay formats.
Random Telegraph Noise-Induced Sensitivity of Data Retention to Cell Position in the Programmed Distribution of NAND Flash Memory Arrays (2015)

This letter highlights a random telegraph noise-induced sensitivity of the data retention threshold-voltage transient of nand Flash memory cells to their position in the programmed array distribution. This sensitivity appears with a reduction of the threshold-voltage loss of the cells in the lower part of the programmed distribution of the memory array and an increase of that of the cells in the upper part of the distribution. The experimental evidence is explained considering the impact of random telegraph noise on the programmed array distribution in the stretch of time in-between the program-and-verify operation and the first read operation used as reference for data retention assessment.
Federated XGBoost on Sample-Wise Non-IID Data (2022)

Federated Learning (FL) is a paradigm for jointly training machine learning algorithms in a decentralized manner which allows for parties to communicate with an aggregator to create and train a model, without exposing the underlying raw data distribution of the local parties involved in the training process. Most research in FL has been focused on Neural Network-based approaches, however Tree-Based methods, such as XGBoost, have been underexplored in Federated Learning due to the challenges in overcoming the iterative and additive characteristics of the algorithm. Decision tree-based models, in particular XGBoost, can handle non-IID data, which is significant for algorithms used in Federated Learning frameworks since the underlying characteristics of the data are decentralized and have risks of being non-IID by nature. In this paper, we focus on investigating the effects of how Federated XGBoost is impacted by non-IID distributions by performing experiments on various sample size-based data skew scenarios and how these models perform under various non-IID scenarios. We conduct a set of extensive experiments across multiple different datasets and different data skew partitions. Our experimental results demonstrate that despite the various partition ratios, the performance of the models stayed consistent and performed close to or equally well against models that were trained in a centralized manner.
Distinguishing between Hepatic Inflammation and Fibrosis with MR Elastography (2017)

Purpose To investigate the utility of magnetic resonance (MR) elastography-derived mechanical properties in the discrimination of hepatic inflammation and fibrosis in the early stages of chronic liver diseases. Materials and Methods All studies were approved by the institutional animal care and use committee. A total of 187 animals were studied, including 182 mice and five pigs. These animals represented five different liver diseases with a varying combination and extent of hepatic inflammation, fibrosis, congestion, and portal hypertension. Multifrequency three-dimensional MR elastography was performed, and shear stiffness, storage modulus, shear loss modulus, and damping ratio were calculated for all animals. Necroinflammation, fibrosis, and portal pressure were either histologically scored or biochemically and physically quantified in all animals. Two-sided Welch t tests were used to evaluate mean differences between disease and control groups. Spearman correlation analyses were used to evaluate the relationships between mechanical parameters and quantitative fibrosis extent (hydroxyproline concentration) and portal pressure. Results Liver stiffness and storage modulus increased with progressively developed fibrosis and portal hypertension (mean stiffness at 80 Hz and 48-week feeding, 0.51 kPa ± 0.12 in the steatohepatitis group vs 0.29 kPa ± 0.01 in the control group; P = .02). Damping ratio and shear loss modulus can be used to distinguish inflammation from fibrosis at early stages of disease, even before the development of histologically detectable necroinflammation and fibrosis (mean damping ratio at 80 Hz and 20-week feeding, 0.044 ± 0.012 in the steatohepatitis group vs 0.014 ± 0.008 in the control group; P < .001). Damping ratio and liver stiffness vary differently with respect to cause of portal hypertension (ie, congestion- or cirrhosis-induced hypertension). These differentiation abilities have frequency-dependent variations. Conclusion Liver stiffness and damping ratio measurements can extend hepatic MR elastography to potentially enable assessment of necroinflammatory, congestive, and fibrotic processes of chronic liver diseases. <sup>©</sup> RSNA, 2017 Online supplemental material is available for this article.
Evaporation‐Directed Crack‐Patterning of Metal–Organic Framework Colloidal Films and Their Application as Photonic Sensors (2017)

A straightforward crack-patterning method is reported allowing the direct formation of periodic cracks in metal-organic framework (MOF) nanoparticle films during dip-coating deposition. The crack propagation and periodicity can be easily tailored by controlling the evaporation front and the withdrawal speed. Several MOF-patterned films can be fabricated on large surfaces and on several substrates (flat, curved or flexible) including the inner surface of a tube, not achievable by other lithographic techniques. We demonstrate that the periodic cracked arrays diffract light and, due to the MOF sorption properties, photonic vapor sensors are fabricated. A new concept of "in-tube", MOF-based diffraction grating sensors is proposed with outstanding sensitivity that can be easily tuned "on-demand" as function of the desired detection range.
Expression and function of adhesion molecules on human hematopoietic stem cells: CD34+ LFA-1- cells are more primitive than CD34+ LFA-1+ cells (1992)

Advances in fluorescence-activated cell sorter technology have brought about multicolor analysis of cell phenotypes. To clarify the phenotypes of human hematopoietic stem cells (HSCs), we initially prepared novel antibodies against CD34 and labeled one of them (4A1) with allophycocyanin (APC). With this, we analyzed the phenotypes of CD34+ HSCs and showed that primitive HSCs or CD34+CD33- cells expressed adhesion molecules such as CD43, CD44, CD11a, CD11c, CD18, and leukocyte adhesion molecule (LAM-1). The more primitive hematopoietic cells or CD34+CD38- cells also expressed CD11a and CD18 with an incidence of 20% to 30%. To clarify the role of adhesion molecules in HSCs, we examined the colony forming capacity after long-term culture with allogeneic irradiated stromal layers. Among CD34+CD33- cells, CD18+ cells gave rise to colony-forming cells (CFCs) on stromal layers, but reached a maximum at week 2, after which the number of generated CFCs decreased. On the other hand, CD18- cells generated less CFCs than CD18+ cells at 2 to 3 weeks, but increased after 4 weeks of culture. When CD18 or CD11a antibody was added to a coculture system of CD34+CD33- cells with stromal layers, the number of generated CFCs decreased significantly compared with the no antibody control. Leukocyte function-associated antigen-1 (LFA-1) (CD11a/CD18) was expressed on some populations of hematopoietic cells and contributed to the proliferation by interacting with stromal cells. However, more primitive cells capable of reconstituting hematopoiesis did not express LFA-1. These data provide a rationale for the administration of anti- LFA-1 antibody after bone marrow transplantation for reducing the graft failure.
Supplementary Figure 5 from Cell Surface Delivery of TRAIL Strongly Augments the Tumoricidal Activity of T Cells (2023)

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Pharmacological activation of the ryanodine receptor in Jurkat T‐lymphocytes (1999)

1 Recently, we provided evidence for cyclic adenosine 5'-diphosphate-ribose, cADP-ribose, as a second messenger in Jurkat T-lymphocytes upon stimulation of the T-cell receptor/CD3- complex (Guse et al., 1999). cADP-ribose mobilizes Ca2+ from an intracellular Ca2+ store which is sensitive to caffeine and gated by the ryanodine receptor/Ca2+ release channel. In the present study we investigated the ability of the trypanocidal drug, suramin, to activate the ryanodine receptor of T-cells. Since suramin cannot permeate the plasma membrane, it was necessary to microinject the drug into Fura-2 loaded T-lymphocytes. 2 In a dose dependent manner suramin increased the intracellular Ca2+ concentration. The dose-response curve is very steep and calculates for an EC50 of 7. 6+/-2.9 mM suramin in the injection pipette. 3 Co-injection of the selective ryanodine receptor inhibitor ruthenium red completely abolished the suramin induced Ca2+ transient. This finding allows for the conclusion that the IP3-receptor sensitive Ca2+ pool is not the primary target of the suramin induced Ca2+ transient. 4 Furthermore, Ins(1,4,6)PS3, an antagonist of the InsP3-receptor could not suppress the suramin-induced Ca2+ signal. The suramin induced Ca2+ transients declined very slowly; however, in the presence of Ins(1,4,6)PS3 this decay was accelerated. In addition, suramin did not interact with the cADP-ribose binding site of the ryanodine receptor of T-cells. 5 In conclusion, suramin is found to be an agonist for the T-cell ryanodine receptor as previously found for the cardiac and skeletal muscle isoform. Therefore, suramin can be designated a universal ryanodine receptor agonist.
Draft Genome Sequence of Blautia luti DSM 14534 T , Isolated from Human Stool (2020)

Here, we report the draft sequence of <i>Blautia luti</i> strain DSM 14534<sup>T</sup>, originally isolated from human feces. This draft contains 74 contigs, comprising 3,718,760 bp with a G+C content of 42.87%. The annotated draft contains 3,338 coding sequences (CDSs) and 110 RNA genes.
APC/CTNNB1 (β‐catenin) pathway alterations in human prostate cancers (2002)

Genetic alterations serve as beacons for the involvement of specific pathways in tumorigenesis. It was previously shown that 5% of prostate tumors harbor CTNNB1 mutations, suggesting that this tumor type may involve a deregulated APC/CTNNB1 pathway. To explore this possibility further, we searched for mutations in genes implicated in this pathway in 22 samples that included cell lines, xenografts, and primary tumors. We identified seven alterations: two in CTNNB1, three in APC, and two in hTRCP1 (also known as BTRC) which controls the degradation of CTNNB1. Alterations in the CTNNB1 regulatory domain, APC, and hTRCP1 were mutually exclusive, consistent with their equivalent effects on CTNNB1 stability. These results suggest that CTNNB1 signaling plays a critical role in the development of a significant fraction of prostate cancers. Moreover, they provide the first evidence that hTRCP1 plays a role in human neoplasia.
Potential dual role of KGF/KGFR as a target option in novel therapeutic strategies for the treatment of cancers and mucosal damages (2012)

KGF/KGFR signaling can contribute to enhancing the malignant potential of epithelial cells and to promoting tumorigenesis. On the other hand, the therapeutic use of KGF in cancer patients provides epithelial protection, reducing chemotherapy side effects. FGFRs have become attractive antitumor targets and various inhibitors have been used to contrast tumor cell growth. The identification of KGFR-specific molecules might represent a promising therapeutic strategy that could increase the window of available agents and treatment methods.
Rationale of Extracorporeal Removal of Endotoxin in Sepsis: Theory, Timing and Technique (2010)

Several signs and symptoms in sepsis are due to the presence of endotoxin in the circulation. Both in animal and human models, there is an evident immunological response to the endotoxin insult. Furthermore, altered cardiovascular function, lung dysfunction and acute kidney injury are common in sepsis and endotoxemia. In these circumstances it would be extremely important to identify patients with sepsis in the early phases and to characterize the humoral alterations involved with it, including the identification and quantification of circulating endotoxin. Once this is obtained, it seems logical to try to remove as much of the circulating endotoxin as possible in order to mitigate the clinical effects of this condition. This can be achieved today with a very specific hemoperfusion process utilizing cartridges with immobilized polymixin B in an extracorporeal circuit. This approach seems to provide a significant removal of endotoxin with a significant reduction of its circulating levels. The clinical consequences of this approach can be summarized in a mitigation of the septic cascade in the early phases, with improvement of outcome. Recent clinical results seem to confirm these expectations showing a reduction of mortality in patients with early signs of abdominal sepsis due to recent surgery. This opens a new avenue for intervention in sepsis.
An alternative method for calculating the space-charge-limited current for a cylindrical diode (2004)

Summary form only given. Estimates of the space-charge-limited current density in cylindrical and spherical geometries are not readily available. The classic method for evaluating the limiting current between two coaxial electrodes was originally developed by Langmuir; the essence of the method is a series expansion of the solution as a power series in ln r/r/sub i/ where r/sub i/ is the inner (cathode) radius. This series converges slowly, a large number of terms must be evaluated for reasonable results, and it is not applicable when relativistic effects are significant. Direct numerical solution of the governing differential equation tends to give poor results; the differential equation is numerically "stiff." An alternative is to non-dimensionalize the governing differential equations, transform coordinates so that the solution is well-represented by low-order polynomials, and generate simple approximate solutions. An additional benefit of this alternative method is that a planar diode, an infinitesimally thin wire in a coaxial cylinder, and a point emitter in a concentric shell, can be shown to be special cases of the more general solution; these special cases are explicitly solved.
Effect of combined treatment with methylprednisolone and soluble Nogo‐66 receptor after rat spinal cord injury (2005)

Methylprednisolone (MP) is a synthetic glucocorticoid used for the treatment of spinal cord injury (SCI). Soluble Nogo-66 receptor (NgR) ectodomain is a novel experimental therapy for SCI that promotes axonal regeneration by blocking the growth inhibitory effects of myelin constituents in the adult central nervous system. To evaluate the potential complementarity of these mechanistically distinct pharmacological reagents we compared their effects alone and in combination after thoracic (T7) dorsal hemisection in the rat. Treatment with an ecto-domain of the rat NgR (27-310) fused to a rat IgG [NgR(310)ecto-Fc] (50 microm intrathecal, 0.25 microL/h for 28 days) or MP alone (30 mg/kg i.v., 0, 4 and 8 h postinjury) improved the rate and extent of functional recovery measured using Basso, Beattie, Bresnahan (BBB) scoring and footprint analysis. The effect of MP treatment on BBB score was apparent the day after SCI whereas the effect of NgR(310)ecto-Fc was not apparent until 2 weeks after SCI. NgR(310)ecto-Fc or MP treatment resulted in increased axonal sprouting and/or regeneration, quantified by counting biotin dextran amine-labeled corticospinal tract axons, and increased the number of axons contacting motor neurons in the ventral horn gray matter caudal to the lesion. Combined treatment with NgR(310)ecto-Fc and MP had a more pronounced effect on recovery of function and axonal growth compared with either treatment alone. The data demonstrate that NgR(310)ecto-Fc and MP act in a temporally and mechanistically distinct manner and suggest that they may have complementary effects.
A novel omni-directional perturbation platform (2004)

The study of human, upright-balance is often performed by perturbing a base on which a subject is standing. Once a perturbation is initiated, data describing a subject's ability to balance is recorded and analyzed. We introduce a novel perturbation device that can translate and rotate its base in any direction within a 2D plane. This robust perturbation envelope will expand researchers' abilities in the study of upright balance and balance recovery. The heart of the design is the use of four powered casters as the platform's transmission system. The casters' offset insures that the Jacobian matrix describing the system's planar motion is non-singular. A rapid embedded programming method is used to develop the control system. By controlling the orientation and speed of each caster, translation, rotation, or combined perturbations can be easily implemented.
Trajectories of Neurologic Recovery 12 Months After Hospitalization for COVID-19 (2022)

At 12 months after hospitalization for severe COVID-19, 87% of patients had ongoing abnormalities in functional, cognitive, or Neuro-QoL metrics and abnormal cognition persisted in 50% of patients without a history of dementia/cognitive abnormality. Only fatigue severity differed significantly between patients with or without neurologic complications during index hospitalization. However, significant improvements in cognitive (t-MoCA) and anxiety (Neuro-QoL) scores occurred in 56% and 45% of patients, respectively, between 6 and 12 months. These results may not be generalizable to those with mild or moderate COVID-19.
Star nanoparticles delivering HIV-1 peptide minimal immunogens elicit near-native envelope antibody responses in nonhuman primates (2019)

Peptide immunogens provide an approach to focus antibody responses to specific neutralizing sites on the HIV envelope protein (Env) trimer or on other pathogens. However, the physical characteristics of peptide immunogens can limit their pharmacokinetic and immunological properties. Here, we have designed synthetic "star" nanoparticles based on biocompatible N- [(2-hydroxypropyl)methacrylamide] (HPMA)-based polymer arms extending from a poly(amidoamine) (PAMAM) dendrimer core. In mice, these star nanoparticles trafficked to lymph nodes (LNs) by 4 hours following vaccination, where they were taken up by subcapsular macrophages and then resident dendritic cells (DCs). Immunogenicity optimization studies revealed a correlation of immunogen density with antibody titers. Furthermore, the co-delivery of Env variable loop 3 (V3) and T-helper peptides induced titers that were 2 logs higher than if the peptides were given in separate nanoparticles. Finally, we performed a nonhuman primate (NHP) study using a V3 glycopeptide minimal immunogen that was structurally optimized to be recognized by Env V3/glycan broadly neutralizing antibodies (bnAbs). When administered with a potent Toll-like receptor (TLR) 7/8 agonist adjuvant, these nanoparticles elicited high antibody binding titers to the V3 site. Similar to human V3/ glycan bnAbs, certain monoclonal antibodies (mAbs) elicited by this vaccine were glycan dependent or targeted the GDIR peptide motif. To improve affinity to native Env trimer affinity, nonhuman primates (NHPs) were boosted with various SOSIP Env proteins; however, significant neutralization was not observed. Taken together, this study provides a new