gebhart/patrepeval huggingface dataset:
Pseudoscorpion Wolbachia symbionts: Diversity and Evidence for a New Supergroup S (2020)

Abstract Background Wolbachia are the most widely spread endosymbiotic bacteria, present in a wide variety of insects and two families of nematodes, but as of now, relatively little genomic data has been available. The Wolbachia symbiont can be parasitic, as described for many arthropod systems, an obligate mutualist, as in filarial nematodes or a combination of both in some organisms. They are currently classified into 16 monophyletic lineage groups ("supergroups"). Although the nature of these symbioses remains largely unknown, expanded Wolbachia genomic data will contribute to understanding their diverse symbiotic mechanisms and evolution. Results This report focuses on Wolbachia infections in three pseudoscorpion species infected by two distinct groups of Wolbachia strains , based upon multi-locus phylogenies. Geogarypus minor harbours w Gmin and Chthonius ischnocheles harbours w Cisc, both closely related to supergroup H, while Atemnus politus harbours w Apol, a member of a novel supergroup S along with Wolbachia from the pseudoscorpion Cordylochernes scorpioides ( w Csco), most closely related to Wolbachia supergroups C and F. Using target enrichment by hybridization with Wolbachia -specific biotinylated probes to capture large fragments of Wolbachia DNA, we produced two draft genomes of w Apol. Annotation of w Apol highlights presence of a biotin operon, which is incomplete in many sequenced Wolbachia genomes. Conclusions The present study highlights at least two symbiont acquisition events among pseudoscorpion species. Phylogenomic analysis indicates that the Wolbachia from Atemnus politus ( w Apol), forms a separate supergroup ("S") with the Wolbachia from Cordylochernes scorpioides (w Csco). Interestingly, the biotin operon, present in w Apol, appears to have been horizontally transferred multiple times along Wolbachia evolutionary history.
Reduced graphene oxide supporting Ag meso-flowers and phenyl-modified graphitic carbon nitride as self-cleaning flexible SERS membrane for molecular trace-detection A Physicochemical and engineering aspects (2019)

There is an imperious demand on developing of self-cleaning surface enhanced Raman scattering (SERS) substrates, for eliminating traditional single-use substrates. Herein, ternary flexible membranes of reduced graphene oxide (r-GO) supporting Ag meso-flowers (Ag-MFs) and phenyl-modified graphitic carbon nitride nanosheets (PCNs) were fabricated for photocatalysis-driven self-cleaning SERS detection. In-situ growth of Ag-MFs with tunable morphology (such as coral-like, urchin-like, highly-branched, etc.) on r-GO surfaces provide abundant options for optimizing SERS detection limit, and thus, these PCNs/Ag-MFs@r-GO membranes exhibited strong SERS activity attributed to high density of intraparticle “hotspot” in Ag-MFs and preconcentration ability to probe molecules via π-π stacking. Among these membranes, the optimum PCNs/Ag-MFs@r-GO membrane shown a detection limit of 10−15 M for rhodamine 6G (R6G) molecules, and this membrane could effectively remove probe molecules due to the excellent photocatalytic activity. We used R6G or methylene blue (MB) molecules for investigating the self-cleaning repeatability and stability of this PCNs/Ag-MFs@r-GO membrane, and the signal intensity for SERS detection maintained a high degree of 95% after five cycle-runs. Besides, this PCNs/Ag-MFs@r-GO membrane can be used as a high-efficiency filter membrane for simultaneous detection and purification in wastewater treatment (10 mg/mL imidacloprid solution as the example).
Fluid motions in a peristaltic pump. (1966)

Massachusetts Institute of Technology. Dept. of Mechanical Engineering. Thesis. 1966. M.S.
Diffuse reflectance imaging for non-melanoma skin cancer detection using laser feedback interferometry (2016)

We propose a compact, self-aligned, low-cost, and versatile infrared diffuse-reflectance laser imaging system using a laser feedback interferometry technique with possible applications in in vivo biological tissue imaging and skin cancer detection. We examine the proposed technique experimentally using a three-layer agar skin phantom. A cylindrical region with a scattering rate lower than that of the surrounding normal tissue was used as a model for a non-melanoma skin tumour. The same structure was implemented in a Monte Carlo computational model. The experimental results agree well with the Monte Carlo simulations validating the theoretical basis of the technique. Results prove the applicability of the proposed technique for biological tissue imaging, with the capability of depth sectioning and a penetration depth of well over 1.2 mm into the skin phantom.
Maximal Deviations of Incomplete U-statistics with Applications to Empirical Risk Sampling (2013)

It is the goal of this paper to extend the Empirical Risk Minimization (ERM) paradigm, from a practical perspective, to the situation where a natural estimate of the risk is of the form of a K-sample U-statistics, as it is the case in the K-partite ranking problem for instance. Indeed, the numerical computation of the empirical risk is hardly feasible if not infeasible, even for moderate samples sizes. Precisely, it involves averaging O(n d1+...+d K) terms, when considering a U-statistic of degrees (d1,..., dK) based on samples of sizes proportional to n. We propose here to consider a drastically simpler Monte-Carlo version of the empirical risk based on O(n) terms solely, which can be viewed as an incomplete generalized U-statistic, and prove that, remarkably, the approximation stage does not damage the ERM procedure and yields a learning rate of order OP(1 / √ n). Beyond a theoretical analysis guaranteeing the validity of this approach, numerical experiments are displayed for illustrative purpose.
Human mast cells express stem cell factor (1998)

Stem cell factor (SCF) is a major cytokine regulator of mast cell growth and function. The present study demonstrates that human mast cells are able to produce SCF. Constitutive synthesis of SCF mRNA was seen in the mast cells isolated from human lung and skin by RT-PCR. This was confirmed by in situ hybridization in conjunctival mast cells of both tryptase-only (MCT) and tryptase/chymase (MCTC) subsets. SCF protein product was found in conjunctival MCT and MCTC mast cells by immunohistochemistry. Soluble SCF protein was detected in the culture supernatant of isolated lung mast cells by ELISA, and cross-linkage of IgE receptor (Fc epsilon-RI) on the lung mast cells in culture did not alter SCF mRNA expression, or the secreted soluble SCF protein. This was consistent with the finding that levels of SCF mRNA expression in conjunctival mast cells were similar between normal subjects and patients with seasonal allergic conjunctivitis (SAC). This study shows that human mast cells themselves are a cellular source of SCF, as well as being target cells for this growth factor. SCF may regulate mast cell growth and function via both paracrine and autocrine mechanisms. The production of SCF by mast cells may be regulated via mechanisms other than IgE receptor-mediated pathways.
Glycolytic Properties of High and Low Sarcoma-Producing Lines and Clones of Mouse Tissue-Culture Cells (1959)

Comparative anaerobic-glycolysis measurements were made of mouse sarcoma-producing cell lines, their clonal derivatives, and strains cultured from sarcomas produced by injection of these lines into mice of the original strain. These various sublines were all derived originally from one and the same cell cultured from normal subcutaneous connective adipose tissue. Sarcoma-producing cell lines of low tumor-producing potency had low glycolytic quotients (avg. QN2CO2, = 36–42), whereas lines of high sarcoma-producing capacity had high glycolytic quotients (avg. QN2CO2 = 93–110). One clone of intermediate glycolytic activity (avg. QN2CO2 = 58) displayed variable tumor latent periods. Tests were also made on two strains of fibroblasts recently isolated from subcutaneous adipose tissue of C3H mice. These recently isolated fibroblasts lacked the ability to produce tumors on reinjection into mice, and had relatively low glycolytic activities (avg. QN2CO2 = 33). Decreased sensitivity of glycolysis in vitro to inhibition by a specific anti-insulin (i.e., anti-hexokinase) inhibitor, a Podophyllum derivative, was associated with increased glycolytic and sarcoma-producing capacities. The possible role of the mitochondria as the loci, and hereditary carriers, of the glycolytic and other possible changes is considered.
Annotating the Little Prince with Chinese AMRs (2016)

Meaning Representation (AMR) is an annotation framework in which the meaning of a full sentence is represented as a rooted, acyclic, directed graph. In this paper, we describe a pilot project in which we develop specifications for the annotation of a Chinese AMR corpus: the Chinese translation of the Little Prince. The interagreement smatch score between the two annotators is 0.83. We also propose to integrate alignment into Chinese AMR annotation.
Diffractive- and Micro-structured Optics (2021)

Diffractive- and micro-structured optics technology provide new degrees of freedom for the design and optimization of optical systems. Using this technology one can create: large-aperture, lightweight optical elements; correct optical aberrations and achromatize optical systems; eliminate or reduce the need for exotic materials, such as flint glasses; combine multiple optical functions; and reduce significantly optical system weight, complexity and cost.
Inhibition of intestinal citrulline synthesis causes severe growth retardation in rats (1985)

delta-N-(phosphonacetyl)-L-ornithine (PALO) is a powerful and specific inhibitor of ornithine transcarbamylase (1), but it does not readily enter intact cells and therefore does not inhibit citrulline synthesis in intact liver or intestine. We have used the glycylglycine derivative of PALO (Gly-Gly-PALO) to evaluate the importance of intestinal citrulline synthesis in supplying arginine for growth. We have shown that the peptide derivative of PALO is selectively taken up by gut cells via the peptide permease and is released intracellularly as the free inhibitor. When administered in drinking water to 6-wk-old rat pups on an arginine-deficient diet, serum citrulline was reduced from 85 +/- 4.2 to 44 +/- 2.2 microM and arginine from 240.1 +/- 19.0 to 52.1 +/- 4.1 microM. Ornithine increased from 100 +/- 6.2 to 273.5 +/- 21.3 microM. Addition of 0.1 mM Gly-Gly-PALO to drinking water caused a rapid and complete inhibition of growth in rats on arginine-deficient diets, and this growth inhibition could be partially prevented by simultaneous administration of 1% (wt/wt) arginine to the diet and completely prevented with 1% (wt/wt) citrulline. The specificity of the effects of Gly-Gly-PALO on intestinal citrulline synthesis was shown by the inability of the drug to be taken up or to inhibit citrulline synthesis in isolated rat hepatocytes, and the oral administration of the drug had no effect on serum ammonia concentrations. The relative importance of endogenous synthesis of arginine compared with dietary arginine for growth was shown by the ability of Gly-Gly-PALO to inhibit the growth of rats maintained on standard laboratory chow containing normal levels of arginine.
Animal models of maple syrup urine disease (2009)

Maple syrup urine disease (MSUD) is an inherited aminoacidopathy resulting from dysfunction of the branched-chain keto acid dehydrogenase (BCKDH) complex. This disease is currently treated primarily by dietary restriction of branched-chain amino acids (BCAAs). However, dietary compliance is often challenging. Conversely, liver transplantation significantly improves outcomes, but donor organs are scarce and there are high costs and potential risks associated with this invasive procedure. Therefore, improved treatment options for MSUD are needed. Development of novel treatments could be facilitated by animal models that accurately mimic the human disease. Animal models provide a useful system in which to explore disease mechanisms and new preclinical therapies. Here we review MSUD and currently available animal models and their corresponding relevance to the human disorder. Using animal models to gain a more complete understanding of the pathophysiology behind the human disease may lead to new or improved therapies to treat or potentially cure the disorder.
Preparation of ZnxCd1-xS Nanocomposites in Polymer Matrices and Their Photophysical Properties (1998)

ZnS and ZnxCd1-xS nanocomposites were prepared in poly(methyl methacrylate) matrixes. By control of the amount of monomers in copolymerization, different Zn/Cd ratio samples were obtained. The solutions and films of these samples were characterized by absorption, fluorescence, and time-resolved spectroscopy. Continuous variation of the luminescence wavelength was observed by adjusting the molar ratio of Zn/Cd. The photophysical properties of these samples are discussed.
In Vivo Tibiofemoral Contact Kinematics and Contact Forces During Dynamic Weight-Bearing Activities Following Total Knee Arthroplasty (2008)

Accurate knowledge of in vivo articular contact kinematics and contact forces is required to quantitatively understand factors limiting life of total knee arthroplasty (TKA) implants, such as polyethylene component wear and implant loosening [1]. Determination of in vivo tibiofemoral contact forces has been a challenging issue in biomechanics. Historically, instrumented tibial implants have been used to measure tibiofemoral forces in vitro [2] and computational models involving inverse dynamic optimization have been used to estimate joint forces in vivo [3]. Recently, D’Lima et al. reported the first in vivo measurement of 6DOF tibiofemoral forces via an instrumented implant in a TKA patient [4]. However this technique does not provide a direct estimation of tibiofemoral contact forces in the medial and lateral compartments. Recently, a dual fluoroscopic imaging system has been used to accurately determine tibiofemoral contact locations on the medial and lateral tibial polyethylene surfaces [5]. The objective of this study was to combine the dual fluoroscope technique and the instrumented TKAs to determine the dynamic 3D articular contact kinematics and contact forces on the medial and lateral tibial polyethylene surfaces during functional activities.
Proceedings of the 16th international conference on World Wide Web (2007)

On behalf of the WWW2007 Program Committee, we are delighted to welcome you to WWW2007, the 16th conference in the World Wide Web conference series.

The number of submissions to the refereed papers track and their quality has grown over the years. This year we had a record 755 submissions, of which we accepted 111 papers (a 14.7% acceptance rate). In response to the growing interest from the research community, we added a fourth day to the refereed papers track program, which allowed us to accept approximately 20% more papers than previous years. Despite this increase, many good papers had to be turned away. The refereed papers track consists of thirteen research areas. This year, we introduced two new -- Web and and Web Data, which were formed by splitting the old XML and Web Services track into two new tracks. We also eliminated the Alternate papers tracks by folding those research areas into the regular refereed paper tracks. Thus, Technology for Developing Regions and Industrial Practice and Experience were regular refereed paper this year and submissions were subjected to the same process as other tracks. We are pleased to report that both sets of changes were successful--the new drew a healthy number of submissions and the quality of submissions to the new and the former alternate were comparable to the other tracks. The table below summarizes the number of submissions and the number of accepted papers in each track.

All papers underwent a rigorous review process by the technical program committee---each paper was reviewed by at least three reviewers, followed by an online discussion phase to reconcile conflicting opinions. Candidate accept, borderline and controversial papers were discussed at length at a two day program committee meeting, which was attended by all track and deputy chairs. Some track chairs attended the meeting via audio conferencing from a satellite California site. We are pleased with the final outcome and present to you a technical program comprising 111 papers, all of which are of the highest standard.
Omalizumab vs. placebo in the management of chronic idiopathic urticaria: a systematic review (2014)

CRD42014010029 (PROSPERO. International Prospective Register of Systematic Reviews).
Impact of Four Common Hydrogels on Amyloid-β (Aβ) Aggregation and Cytotoxicity: Implications for 3D Models of Alzheimer’s Disease (2020)

The physiochemical properties of hydrogels utilized in 3D culture can be used to modulate cell phenotype and morphology with a striking resemblance to cellular processes that occur <i>in vivo</i>. Indeed, research areas including regenerative medicine, tissue engineering, <i>in vitro</i> cancer models, and stem cell differentiation have readily utilized 3D biomaterials to investigate cell biological questions. However, cells are only one component of this biomimetic milieu. In many models of disease such as Alzheimer's disease (AD) that could benefit from the <i>in vivo</i>-like cell morphology associated with 3D culture, other aspects of the disease such as protein aggregation have yet to be methodically considered in this 3D context. A hallmark of AD is the accumulation of the peptide amyloid-β (Aβ), whose aggregation is associated with neurotoxicity. We have previously demonstrated the attenuation of Aβ cytotoxicity when cells were cultured within type I collagen hydrogels <i>versus</i> on 2D substrates. In this work, we investigated the extent to which this phenomenon is conserved when Aβ is confined within hydrogels of varying physiochemical properties, notably mesh size and bioactivity. We investigated the Aβ structure and aggregation kinetics in solution and hydrogels composed of type I collagen, agarose, hyaluronic acid, and polyethylene glycol using fluorescence correlation spectroscopy and thioflavin T assays. Our results reveal that all hydrogels tested were associated with enhanced Aβ aggregation and Aβ cytotoxicity attenuation. We suggest that confinement itself imparts a profound effect, possibly by stabilizing Aβ structures and shifting the aggregate equilibrium toward larger species. If this phenomenon of altered protein aggregation in 3D hydrogels can be generalized to other contexts including the <i>in vivo</i> environment, it may be necessary to reevaluate aspects of protein aggregation disease models used for drug discovery.
Hybrid Monoliths for Magnetically‐Driven Protein Separations (2014)

Monoliths represent powerful platforms for isolation of large molecules with high added value. This work presents a hybrid approach for antibody (Ab) capture and release. Using mostly natural polymers and clean processes, it is possible to create macroporous monoliths with well‐defined porous networks, tuneable mechanical properties, and easy functionalization with a biomimetic ligand specific for Ab. Magnetic nanoparticles (MNPs) are embedded on the monolith network to confer a controlled magnetic response that facilitates and accelerates Ab recovery in the elution step. The hybrid monolithic systems prepared with agarose or chitosan/poly(vinyl alcohol) (PVA) blends exhibit promising binding capacities of Abs directly from cell‐culture extracts (120 ± 10 mg Ab g −1 support) and controlled Ab magnetically‐assisted elution yielding 95 ± 2% recovery. Moreover, a selective capture of mAbs directly from cell culture extracts is achieved yielding a final mAb preparation with 96% of purity.
The MIMOME Channel (2007)

The MIMOME channel is a Gaussian wiretap channel in which the sender, receiver, and eavesdropper all have multiple antennas. We characterize the secrecy capacity as the saddle-value of a minimax problem. Among other implications, our result establishes that a Gaussian distribution maximizes the secrecy capacity characterization of Csisz{\'a}r and K{\o}rner when applied to the MIMOME channel. We also determine a necessary and sufficient condition for the secrecy capacity to be zero. Large antenna array analysis of this condition reveals several useful insights into the conditions under which secure communication is possible.
Cutaneous T‐cell lymphoma – Sézary syndrome in a Boxer (2015)

A 7-year-old male Boxer with a 3.5-year history of atopy and food hypersensitivity was presented with multiple poorly circumscribed nodules and maculae of the skin and tongue, and jaundiced mucosal membranes. Cytologic and histopathologic examination of the skin lesions revealed cutaneous epitheliotropic lymphoma. Cells were CD3(+) and CD8(+) in flow cytometry. The CBC showed a moderate leukocytosis with 16% atypical lymphocytes with irregularly cleaved nuclei. Flow cytometric phenotyping of peripheral blood showed an elevated proportion of the CD8(+) T-lymphocyte subpopulation, indicating a malignant population of T-cell origin, and the electropherogram of the PCR antigen receptor rearrangement produced a monoclonal peak for TCRγ. Liver enzyme activities were markedly increased and abdominal ultrasound examination showed increased echogenicity of the liver and enlarged abdominal lymph nodes. Fine-needle aspirates of the liver confirmed infiltration with lymphocytes exhibiting the same morphology as the cells detected in skin and peripheral blood. Treatment was induced with L-asparaginase, lomustine, and prednisone. Partial clinical remission of the skin and tongue lesions was achieved within 10 days, and hematologic abnormalities resolved. Despite further treatment with L-asparaginase and lomustine, the dog relapsed within one month and was euthanized. Presence of malignant lymphocytes in skin, peripheral blood, and liver indicate a rare variant of leukemic cutaneous T-cell lymphoma, equivalent of Sézary syndrome in a dog. This case report describes the use of flow cytometry as a complementary tool for lymphocyte characterization of skin lesions for the first time.
Analytical Solutions to the Unsteady Response of an Isolated Finite Span Swept Airfoil to an Incident Gust and Unsteady Response of a Rectilinear Swept Cascade to an Incident Gust Problems (2000)

The solution to the problem of unsteady response of an isolated finite span swept airfoil to an incident gust is most conveniently obtained by introducing an acoustic velocity potential and eliminating all primitive variables from the governing equations. The end result is the convected wave equation for the acoustic velocity potential, phi. For the unsteady response of a rectilinear swept cascade to an incident gust problem, the governing equation and the imposed boundary conditions are the same as those for the isolated airfoil problem.