gebhart/patrepeval huggingface dataset:
Efficient deanilidation of phosphoranilidates by the use of nitrites and acetic anhydride (1991)

Abstract Reagent systems of sodium– and tetrabutylammonium nitrite–acetic anhydride were proved to be extremely efficient for the deanilidation of nucleoside 3′‐phosphoranilidates, whose reactions were rapid with the former and instant with the latter. It was further found that the reagent system is applicable to oligonucleotide synthesis provided that the exocyclic amino groups of 2′‐deoxyadenosine, 2′‐deoxyguanosine, and 2′‐deoxycytidine were protected by succinylation.
Identification of candidate genes carrying polymorphisms associated with the risk of colorectal cancer by analyzing the colorectal mutome and microRNAome (2012)

The results support the study hypothesis and highlight the importance of SNPs within miRNA-dependent regulatory regions. Further studies on the role exerted by NUP210 and KIAA0182 in colorectal carcinogenesis are warranted.
Effect of Molecular Structure on the Adsorption of Protein on Surfaces with Grafted Polymers (2002)

The adsorption of proteins on surfaces with grafted polymers is studied using a molecular mean-field theory. The effects of changing the protein−surface interactions, the polymer−surface interactions, the polymer segment volume, and the type of possible protein conformations adsorbed are studied. The main results of these studies are for the equilibrium amount of protein adsorbed; however, the theory also enables the study of the conditions that determine the kinetics in the initial stages of the adsorption process. The amount of protein adsorbed on the surfaces with grafted polymers depends on the surface density of polymer, the protein−surface interaction, the polymer−surface interaction, the size of the polymer segments, and the ability of the proteins to undergo conformational changes upon adsorption. The proper choice of polymers used can lead to the specific adsorption of a given type of protein conformer. One of the main conclusions from this study is that protein adsorption is very sensitive to the details of the surface modifiers. For example, contrary to intuition, increasing the size of the polymer segments may result in an increase of the amount of protein adsorbed at fixed polymer surface coverage. The dependence of the adsorption of proteins on grafted polymer molecular weight depends on the interactions between the polymer and the surface. It is found that for model polymers mimicking poly(ethylene oxide), in terms of the monomer size and the bare ethylene oxide hydrophobic surface interactions, the adsorption of proteins is usually found to be at the crossover between two different regimes. The results presented here suggest what kind of polymers may be optimal for prevention of protein adsorption depending upon the type of surface.
Somatic therapies for treatment-resistant depression: ECT, TMS, VNS, DBS (2012)

The field of non-pharmacological therapies for treatment resistant depression (TRD) is rapidly evolving and new somatic therapies are valuable options for patients who have failed numerous other treatments. A major challenge for clinicians (and patients alike) is how to integrate the results from published clinical trials in the clinical decision-making process.We reviewed the literature for articles reporting results for clinical trials in particular efficacy data, contraindications and side effects of somatic therapies including electroconvulsive therapy (ECT), transcranial magnetic stimulation (TMS), vagal nerve stimulation (VNS) and deep brain stimulation (DBS). Each of these devices has an indication for patients with different level of treatment resistance, based on acuteness of illness, likelihood of response, costs and associated risks. ECT is widely available and its effects are relatively rapid in severe TRD, but its cognitive adverse effects may be cumbersome. TMS is safe and well tolerated, and it has been approved by FDA for adults who have failed to respond to one antidepressant, but its use in TRD is still controversial as it is not supported by rigorous double-blind randomized clinical trials. The options requiring surgical approach are VNS and DBS. VNS has been FDA-approved for TRD, however it is not indicated for management of acute illness. DBS for TRD is still an experimental area of investigation and double-blind clinical trials are underway.
Middle years teachers' conceptions and adaptive responses to student diversity in the culture of schooling (2014)

There is widespread agreement at the policy level that systems of education should be inclusive of an increasingly diverse student population; yet research indicates this to be a deficit area in teaching and learning practices. This research paper employs the sociocultural concept of 'funds of knowledge' to consider how teachers draw upon their unique experiences to frame student diversity, particularly related to student ability. We interview four teachers in middle years teaching roles and use content analysis to reveal the ways in which the teachers recognise and name student ability and how this impacts on their practices in relation to teaching and learning. Findings reveal that the teachers describe student ability in ways that reflect their funds of knowledge including aspects of their past, present and future notions of self. Two of the teachers drew upon institutional categories of student diversity that reflect a traditional approach to teaching and learning in order to describe their present practice and to envision the future - an approach to practice that they would have been enculturated into and which serves as their frame of reference. The other two teachers, both of whom are recently educated in the ways of their craft, constructed student diversity in terms of their own pedagogical practice. For them, practice draws on their recent university studies and on past experiences of self to envision a more egalitarian future for themselves and for their students. This research provides an insight into a promising future in addressing the challenge of enacting truly inclusive practices to meet the needs of our diverse student population. Furthermore, it reveals that teachers' funds of knowledge shape their understandings and practices in ways that can be either limiting or enabling, and that this range of diversity of teacher' views is currently being played out in classrooms.
Dorsal Root Ganglion Neurons Are Destroyed by Exposure in Utero to Maternal Antibody to Nerve Growth Factor (1980)

Rats and guinea pigs, when immunized with mouse nerve growth factor, produce antibodies that cross-react with their own nerve growth factor. The antibodies reach developing offspring of these animals both prenatally (rats and guinea pigs) and postnatally (rats). Depriving the fetus of nerve growth factor in this way results in the destruction of up to 85 percent of dorsal root ganglion neurons as well as destruction of sympathetic neurons. Sensory neurons of placodal origin in the nodose ganglion were not affected. These data demonstrate that dorsal root ganglion neurons go through a phase of nerve growth factor dependence in vivo.
Test requirements for embedded core-based systems and IEEE P1500 (2002)

Chips comprising reusable cores, i.e. pre-designed Intellectual Property (IP) blocks, have become an important part of IC-based system design. Using embedded cores enables the design of high-complexity system-chips with densities as high as millions of gates on a single die. The increase in using pre-designed IP cores in system-chips adds to the complexity of test. To test system-chips adequately, test solutions need to be incorporated into individual cores and then the tests from individual cores need to be scheduled and assembled into a chip level test. However with the increased usage of cores from multiple and diverse sources, it is essential to create standard mechanisms to make core test plug-and-play possible. This paper discusses in general the challenges in testing core-based system-chips and describes their corresponding test solutions. It concentrates on the common test requirements and introduces the on-going standardization efforts, specifically under IEEE P1500 Working Group, which is meant to standardize the interface between a core test and its host the System-on-Chip.
Shaping of ultrashort optical pulses by using an integrated acousto-optic tunable filter (1993)

Reshaping of ultrashort optical pulses at 1.53 μm by using an integrated acousto-optic tunable filter is reported. Control of the optical pulse shape is accomplished by adjusting the different radio-frequency electrical signals driving the acousto-optic filter. This is to our knowledge the first demonstration of ultrashort pulse shaping using an integrated-optic device and establishes a new application area for integrated wavelength-division-multiplexed devices, namely, for manipulation of coherent, ultrafast time-domain signals.
Autologous Bone Marrow Transplantation with Alkyl-Lysophospholipid-Purged Marrow (1993)

Autologous bone marrow transplantation (ABMT) appears to offer clinical benefit to leukemia patients, but the major reason for failure is relapse. This may be related to the presence of residual leukemic cells in the harvested marrow. To circumvent this problem, various procedures have been developed to purge ex vivo residual leukemic cells from the marrow. The alkyl-lysophospholipids are a new group of anticancer drugs that target membranes as their major site of action. They are unique in that they are relatively selectively toxic to neoplastic cells and spare normal marrow stem cells and progenitor cells. The most active compound is edelfosine. Twenty-nine patients with acute leukemia in second or subsequent remission or early relapse or in first remission, either with a history of treated extramedullary relapse, or requiring more than one induction program to achieve remission, underwent ablative therapy followed by infusion of autologous marrow which had been purged by a 4-hour exposure to edelfosine prior to cryopreservation. Thirty-one percent of the patients are alive and free of leukemia for a median of 630 days (range 185-1,613). These results in this high-risk group of patients warrant further investigation.
Visible luminescence from nanocrystalline silicon films produced by plasma enhanced chemical vapor deposition (1996)

Thin nanocrystalline silicon (nc-Si) films deposited by plasma enhanced chemical vapor deposition (PECVD) exhibited room-temperature photoluminescence in the visible range of the electromagnetic spectrum. High resolution transmission electron microscopy revealed that the films are made of Si crystals with dimensions 2–15 nm. The photoluminescence spectra of the nc-Si films were similar to the spectra observed from porous silicon produced by anodization and electrochemical dissolution of crystalline Si. This similarity suggests that the luminescence mechanism of nc-Si films is similar to the mechanism of light emission from porous silicon. The ability to manufacture luminescent Si films by methods which are compatible with the current Si based technology, such as PECVD, can provide new possibilities in the realization of optoelectronic devices.
Characterizing End-to-End Packet Delay and Loss in the Internet (1993)

We use the measured round trip delays of small UDP probe packets sent at regular time intervals to characterize the end-to-end packet delay and loss behavior in the Internet. By varying the interval between probe packets, it is possible to study the
Vascular endothelial growth factor selectively targets boronated dendrimers to tumor vasculature (2005)

Tumor neovasculature is a potential but, until very recently, unexplored target for boron neutron capture therapy (BNCT) of cancer. In the present report, we describe the construction of a vascular endothelial growth factor (VEGF)-containing bioconjugate that potentially could be used to target up-regulated VEGF receptors (VEGFR), which are overexpressed on tumor neovasculature. A fifth-generation polyamidoamine dendrimer containing 128 reactive amino groups was reacted with 105 to 110 decaborate molecules to produce a macromolecule with 1,050 to 1,100 boron atoms per dendrimer. This was conjugated to thiol groups of VEGF at a 4:1 molar ratio using the heterobifunctional reagent sulfo-LC-SPDP. In addition, the boronated dendrimer was tagged with a near-IR Cy5 dye to allow for near-IR fluorescent imaging of the bioconjugate in vitro and in vivo. As would be predicted, the resulting VEGF-BD/Cy5 bioconjugate was not cytotoxic to HEK293 cells engineered to express 2.5 x 10(6) VEGFR-2 per cell. Furthermore, it showed binding and activation of VEGFR-2 comparable with that of native VEGF. Internalization of VEGF-BD/Cy5 by PAE cells expressing 2.5 x 10(5) VEGFR-2 per cell was inhibited by excess VEGF, indicating a VEGFR-2-mediated mechanism of uptake. Near-IR fluorescent imaging of 4T1 mouse breast carcinoma revealed selective accumulation of VEGF-BD/Cy5, but not BD/Cy5, particularly at the tumor periphery where angiogenesis was most active. Accumulation of VEGF-BD/Cy5 in 4T1 breast carcinoma was diminished in mice pretreated with a toxin-VEGF fusion protein that selectively killed VEGFR-2-overexpressing endothelial cells. Our data lay the groundwork for future studies using the VEGF-BD/Cy5 bioconjugate as a targeting agent for BNCT of tumor neovasculature.
Reversible siRNA–polymer conjugates by RAFT polymerization (2008)

A straightforward synthetic method to prepare pyridyl disulfide end functionalized poly(PEG acrylate) by RAFT polymerization for efficient and reversible conjugation to siRNA is described.
Quantizing for minimum distortion (1960)

This paper discusses the problem of the minimization of the distortion of a signal by a quantizer when the number of output levels of the quantizer is fixed. The distortion is defined as the expected value of some function of the error between the input and the output of the quantizer. Equations are derived for the parameters of a quantizer with minimum distortion. The equations are not soluble without recourse to numerical methods, so an algorithm is developed to simplify their numerical solution. The case of an input signal with normally distributed amplitude and an expected squared error distortion measure is explicitly computed and values of the optimum quantizer parameters are tabulated. The optimization of a quantizer subject to the restriction that both input and output levels be equally spaced is also treated, and appropriate parameters are tabulated for the same case as above.
Immunocytokines and bispecific antibodies: two complementary strategies for the selective activation of immune cells at the tumor site (2016)

The activation of the immune system for a selective removal of tumor cells represents an attractive strategy for the treatment of metastatic malignancies, which cannot be cured by existing methodologies. In this review, we examine the design and therapeutic potential of immunocytokines and bispecific antibodies, two classes of bifunctional products which can selectively activate the immune system at the tumor site. Certain protein engineering aspects, such as the choice of the antibody format, are common to both classes of therapeutic agents and can have a profound impact on tumor homing performance in vivo of individual products. However, immunocytokines and bispecific antibodies display different mechanisms of action. Future research activities will reveal whether an additive of even synergistic benefit can be obtained from the judicious combination of these two types of biopharmaceutical agents.
The role of IgE in asthma (1998)

Asthma is a multifactorial and complex disease in which allergic factors and non-allergic triggers interact and result in bronchial obstruction and inflammation. Allergenic sensitization is important in the development of asthma and, although links between inhalant allergy and asthma have been known for many years, they have recently been re-emphasized. Indoor allergens are associated with asthma prevalence, severity and exacerbations whereas outdoor allergens such as pollens are associated with exacerbations. Moreover, there is a link between total IgE and asthma which appears to be independent of allergen sensitization. One of the typical aspects of airway inflammation of asthma is the infiltration of the airway wall by T helper type 2 (Th2) cells. These cells are attracted to inflammatory sites by adhesion molecules and chemokines among which CCR3 and CXCR4 receptors appear to be of importance. Differentiation of B cells into IgE-secreting plasma cells is a complex cascade of events in which cytokines play a crucial role. Both IL-4 and IL-13 are inducing IgE synthesis whereas IFN-gamma and IL-12 are blocking IgE synthesis. IgE production by B cells not only requires the presence of IL-4 or IL-13, but also a physical interaction between T and B cells, involving a number of surface and adhesion molecules such as CD40-CD40L and CD28/CD80. Production of TH2-cytokines is not restricted to T cells as basophils and mast cells can produce them indicating that these cells may be of importance in the synthesis of IgE.
A Novel Method to Calculate the G+C Content of Genomic DNA Sequences (2001)

The base composition of a DNA fragment or genome is usually measured by the proportion of A+T or G+C in the sequence. The G+C content along genomic sequences is usually calculated using an overlapping or non-overlapping sliding window method. The result and accuracy of such an approach depends on the size of the window and the moving distance adopted. In this paper, a novel windowless technique to calculate the G+C content of genomic sequences is proposed. By this method, the G+C content can be calculated at different "resolution". In an extreme case, the G+C content may be computed at a specific point, rather than in a window of finite size. This is particularly useful to analyze the fine variation of base composition along genomic sequences. As the first example, the variation of G+C content along each of 16 yeast chromosomes is analyzed. The G+C-rich regions with length larger than 5 kb sequences are detected and listed in details. It is found that each chromosome consists of several G+C-rich and G+C-poor regions alternatively, i.e., a mosaic structure. Another example is to analyze the G+C content for each of the two chromosomes of the Vibrio cholerae genome. Based on the variations of the G+C content in each chromosome, it is shown that some fragments in the Vibrio cholerae genome may have been transferred from other species. Especially, the position and size of the large integron island on the smaller chromosome was precisely predicted. This method would be a useful tool for analyzing genomic sequences.
Intelligent Transportation Systems and Truck Parking (2013)

The objective of this report is to provide background information and lay out the issues for prospective offerors responding to the solicitation in a Broad Agency Announcement seeking concept papers for a demonstration of a technology that conveys real-time information on parking availability for truckers on the road. The report addresses the following questions: (1) is there a shortage of parking? (2) is the truck parking shortage likely to worsen? (3) what are potential solutions? and (4) what can be done to better match supply and demand?
Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8) (1996)

The genome of the Kaposi sarcoma-associated herpesvirus (KSHV or HHV8) was mapped with cosmid and phage genomic libraries from the BC-1 cell line. Its nucleotide sequence was determined except for a 3-kb region at the right end of the genome that was refractory to cloning. The BC-1 KSHV genome consists of a 140.5-kb-long unique coding region flanked by multiple G + C-rich 801-bp terminal repeat sequences. A genomic duplication that apparently arose in the parental tumor is present in this cell culture-derived strain. At least 81 ORFs, including 66 with homology to herpesvirus saimiri ORFs, and 5 internal repeat regions are present in the long unique region. The virus encodes homologs to complement-binding proteins, three cytokines (two macrophage inflammatory proteins and interleukin 6), dihydrofolate reductase, bcl-2, interferon regulatory factors, interleukin 8 receptor, neural cell adhesion molecule-like adhesin, and a D-type cyclin, as well as viral structural and metabolic proteins. Terminal repeat analysis of virus DNA from a KS lesion suggests a monoclonal expansion of KSHV in the KS tumor.
Structured importance sampling of environment maps (2003)

We introduce structured importance sampling, a new technique for efficiently rendering scenes illuminated by distant natural illumination given in an environment map. Our method handles occlusion, high-frequency lighting, and is significantly faster than alternative methods based on Monte Carlo sampling. We achieve this speedup as a result of several ideas. First, we present a new metric for stratifying and sampling an environment map taking into account both the illumination intensity as well as the expected variance due to occlusion within the scene. We then present a novel hierarchical stratification algorithm that uses our metric to automatically stratify the environment map into regular strata. This approach enables a number of rendering optimizations, such as pre-integrating the illumination within each stratum to eliminate noise at the cost of adding bias, and sorting the strata to reduce the number of sample rays. We have rendered several scenes illuminated by natural lighting, and our results indicate that structured importance sampling is better than the best previous Monte Carlo techniques, requiring one to two orders of magnitude fewer samples for the same image quality.
Probiotic Encapsulation Technology: From Microencapsulation to Release into the Gut (2012)

Probiotic encapsulation technology (PET) has the potential to protect microorgansisms and to deliver them into the gut. Because of the promising preclinical and clinical results, probiotics have been incorporated into a range of products. However, there are still many challenges to overcome with respect to the microencapsulation process and the conditions prevailing in the gut. This paper reviews the methodological approach of probiotics encapsulation including biomaterials selection, choice of appropriate technology, in vitro release studies of encapsulated probiotics, and highlights the challenges to be overcome in this area.
CENTRAL NERVOUS SYSTEM ANGIITIS. (2000)

This book carries the air of a labour of love. I warmed to it from the moment I read the first paragraph. It is such an unexpected pleasure to meet (in print, anway) someone who shares the same irritants—the `widespread (and it's the same this side of the Atlantic too, I regret to say, Dr Schmidley), groundless belief' in the value of lupus vasculitis as a common pathological substrate for CNS systemic lupus erythematosus, and in angiography as a useful …
Weak-localization effect in superconductors from radiation damage (2000)

Large reductions of the superconducting transition temperature ${T}_{c}$ and the accompanying loss of the thermal electrical resistivity (electron-phonon interaction) due to radiation damage have been observed for several $A15$ compounds, Chevrel phase and ternary superconductors, and ${\mathrm{NbSe}}_{2}$ in the high-fluence regime. We examine these behaviors based on a recent theory of the weak localization effect in superconductors. We find a good fitting to the experimental data. In particular, the weak localization correction to the phonon-mediated interaction is derived from the density correlation function. It is shown that weak localization has a strong influence on both the phonon-mediated interaction and the electron-phonon interaction, which leads to the universal correlation of ${T}_{c}$ and the resistance ratio.