gebhart/patrepeval huggingface dataset:
INTRAVITREAL BEVACIZUMAB FOR THE MANAGEMENT OF CHOROIDAL NEOVASCULARIZATION IN PSEUDOXANTHOMA ELASTICUM (2007)

These short-term results support the use of intravitreal bevacizumab for the management of CNV in patients with PXE. Continued experience with intravitreal bevacizumab in this population will help establish its longer-term efficacy and better define the potential need for serial injections to maintain these results.
Mismatch Extension Ability of Yeast and Human DNA Polymerase η (2001)

DNA polymerase eta (Poleta) functions in error-free replication of UV-damaged DNA, and in vitro it efficiently bypasses a cis-syn T-T dimer by incorporating two adenines opposite the lesion. Steady state kinetic studies have shown that both yeast and human Poleta are low-fidelity enzymes, and they misincorporate nucleotides with a frequency of 10(-2)-10(-3) on both undamaged and T-T dimer-containing DNA templates. To better understand the role of Poleta in error-free translesion DNA synthesis, here we examine the ability of Poleta to extend from base mismatches. We find that both yeast and human Poleta extend from mismatched base pairs with a frequency of approximately 10(-3) relative to matched base pairs. In the absence of efficient extension of mismatched primer termini, the ensuing dissociation of Poleta from DNA may favor the excision of mismatched nucleotides by a proofreading exonuclease. Thus, we expect DNA synthesis by Poleta to be more accurate than that predicted from the fidelity of nucleotide incorporation alone.
The effect of northern fowl mite (Ornithonyssus sylviarum) infestation on hen physiology, physical condition, and egg quality (2016)

The northern fowl mite (NFM), Ornithonyssus sylviarum, is the most common ectoparasite of laying hens in North America. Infestation can cause a reduction in egg production, egg weights, and feed conversion efficiency. However, there is a lack of information on the effects of NFM on hen physiology, physical condition, and egg quality. Singly caged beak-trimmed White Leghorn hens (N = 32) were infested with mites at 25 wk of age. The condition of each hen was assessed at wk 0 (infestation) and wk 5 and 7 post-infestation to determine comb temperatures and feather, skin, and comb condition. Heterophil-lymphocyte (H/L) ratios and body weight (BW) were evaluated at wk 0 and wk 1, 3, 5, and 7 post-infestation. Egg weight, egg specific gravity, yolk color, Haugh unit (HU), and eggshell thickness were determined prior to infestation (wk −1) and at 1, 3, 5, and 7 wk post-infestation. The H/L ratio (P < 0.0001), HU (P < 0.0001), and egg specific gravity (P = 0.001) were lowest, and the egg yolk color was lightest (P = 0.087) at wk 5, the peak of infestation. At wk 5 and 7, more than 65% of the hens had red skin and more than 75% had scabs on the vent; in addition more than 84% had grey-black vent feathers. There were no effects of infestation on comb color, comb temperature, feather cover, BW, or eggshell thickness. It was concluded that infestation with NFM has negative effects on interior egg quality and hen integument. A decrease in H/L ratio was also observed at the peak of infestation. However, the effects of NFM on the immune system are unclear, and H/L ratio might not be a good stress measure in hens highly infested with NFM.
Hybrid Collaborative Filtering with Autoencoders (2016)

Collaborative Filtering aims at exploiting the feedback of users to provide personalised recommendations. Such algorithms look for latent variables in a large sparse matrix of ratings. They can be enhanced by adding side information to tackle the well-known cold start problem. While Neu-ral Networks have tremendous success in image and speech recognition, they have received less attention in Collaborative Filtering. This is all the more surprising that Neural Networks are able to discover latent variables in large and heterogeneous datasets. In this paper, we introduce a Collaborative Filtering Neural network architecture aka CFN which computes a non-linear Matrix Factorization from sparse rating inputs and side information. We show experimentally on the MovieLens and Douban dataset that CFN outper-forms the state of the art and benefits from side information. We provide an implementation of the algorithm as a reusable plugin for Torch, a popular Neural Network framework.
CCL2/CCR2 Regulates the Tumor Microenvironment in HER-2/neu-Driven Mammary Carcinomas in Mice (2016)

Chronic inflammation is a hallmark of cancer. Inflammatory chemokines, such as C-C chemokine ligand 2 (CCL2), are often present in tumors but their roles in cancer initiation and maintenance are not clear. Here we report that CCL2 promotes mammary carcinoma development in a clinically relevant murine model of breast cancer. Targeted disruption of Ccl2 slowed the growth of activated Her2/neu-driven mammary tumors and prolonged host survival. Disruption of Ccl2 was associated with a decrease in the development and mobilization of endothelial precursor cells (EPCs) which can contribute to tumor neovascularization. In contrast, disruption of Ccr2, which encodes CCL2's sole signaling receptor, accelerated tumor development, shortened host survival, and mobilized EPCs. However, pharmacological inhibition of CCR2 phenocopied Ccl2 disruption rather than Ccr2 disruption, suggesting that the Ccr2-/- phenotype is a consequence of unanticipated alterations not linked to intact CCL2/CCR2 signaling. Consistent with this explanation, Ccr2-/- monocytes are more divergent from wild type monocytes than Ccl2-/- monocytes in their expression of genes involved in key developmental and functional pathways. Taken together, our data suggest a tumor-promoting role for CCL2 acting through CCR2 on the tumor microenvironment and support the targeting of this chemokine/receptor pair in breast cancer.
One-Electron Reduction and Oxidation Studies of the Radiation Sensitizer Gadolinium(III) Texaphyrin (PCI-0120) and Other Water Soluble Metallotexaphyrins (1999)

The radiation sensitizer gadolinium(III) texaphyrin 2 (XYTRIN; PCI-0120; Gd−Tex2+) and several other water soluble metallotexaphyrin complexes were prepared and studied using pulse radiolysis. All of the metallotexaphyrins were found to react with solvated electrons and hydroxyl radicals, yielding the corresponding one-electron reduced and oxidized metallotexaphyrins, respectively. The rates of the reduction processes range from 3.7 × 1010 to 6.8 × 1010 M-1 s-1 (±10%), while those involving oxidation range from 2.5 × 109 to 7.4 × 109 M-1 s-1 (±10%). The spectral characteristics of the transformed metallotexaphyrins produced by these reactions, e.g., a broad absorption band with a λmax centered around 830 nm, are consistent with ligand-centered redox processes. Reaction of the metallotexaphyrins with solvated electrons affords species which exhibit metal dependent behavior. In the absence of hydroxyl radicals, the decay of the reduced metallotexaphyrins produced by reaction with electrons involves an initial protonation event followed by either a dimerization process or a disproportionation step. These latter transformations are followed by a second protonation event.
Evaluation of the efficacy of a dill extract in vitro and in vivo (2010)

Lysyl oxidase-like (LOXL) is an extracellular enzyme that catalyses the cross-linking between microfibrils and tropoelastin (TE), thereby ensuring elastic fibre functionality. With ageing, LOXL expression decreases, thus participating in the loss of skin elasticity. In a previous study, we showed that a dill seed extract [INCI name: Peucedanum graveolens (Dill) extract] could increase LOXL expression in cultured dermal fibroblasts. Besides, we showed a good correlation between the measurements of skin elasticity obtained in vitro and in vivo using a fully automated bio-tribometer designed to measure the biomechanical properties of soft and complex materials like skin. The aim of this study was to evaluate the ability of the dill extract to improve skin elasticity in vitro and in vivo using different models. Using the bio-tribometer, we first showed that the lateral elasticity of dermis equivalents (DEs) treated with the dill extract at 1% was significantly increased by +29% (P < 0.01) when compared to untreated DEs. In vivo, skin firmness and elastic recovery measured using cutometry methods were also significantly improved compared to placebo in volunteers treated for 56 days with a formula containing 1% of dill extract. Moreover, the clinical evaluation evidenced significant improvements in 'skin elasticity' compared to placebo. A majority of subjects treated with the dill extract also noted significant improvements in skin elasticity, firmness and slackness of the jaw line. Finally, mean wrinkle area and length were also significantly reduced compared to placebo after 84 days as measured using silicone replicas taken from the crow's feet. In summary, this study showed that the dill extract could improve elasticity of DEs in vitro as well as skin biomechanical properties and appearance in vivo. It also highlights the relevance of using the bio-tribometer as an exploratory tool for the measurement of skin elasticity in vitro.
A Novel Class of in Vivo Active Anticancer Agents:  Achiralseco-Amino- andseco-Hydroxycyclopropylbenz[e]indolone (seco-CBI) Analogues of the Duocarmycins and CC-1065 (2005)

One achiral seco-hydroxycyclopropylbenz[e]indolone (seco-CBI) (12) and seven achiral seco-amino-CBI (11a-g) analogues of CC-1065 and the duocarmycins were designed, synthesized and evaluated for their DNA-binding and anticancer properties. These compounds contain a core 2-chloroethylnaphthalene structure and they do not have a stereocenter. From thermal cleavage gel analyses, compounds 11a-g and 12 demonstrated similar covalent sequence specificity to adozelesin 3 and the racemic seco-CBI-TMI 4 for binding to the 5'-AAAAA(865)-3' site. Continuous exposure of human (K562) and murine (B16, L1210 and P815) cancer cell lines to the compounds demonstrated their significant cytotoxicity, with IC50 values in the sub-micromolar range. Generally, a good leaving group on the ethyl moiety and a free amino or hydroxyl group on the naphthyl moiety are essential for activity. According to NCI's cytotoxicity screen, compounds 11a and 12 were active against human cancer cell lines derived from lung, colon, melanoma, renal system, and breast. At the respective doses of 15 and 20 mg/kg (administered via an ip route), compounds 11a and 12 inhibited the growth of murine B16-F0 melanoma in C57BL/6 mice, with minimal toxicity, and 11a gave a significant anticancer effect. The in vivo anticancer activity of compound 11a was confirmed in a human tumor xenograft study (advanced stage SC-OVCAR-3 ovarian cancer growing in scid mice). Finally, compound 11a was not toxic to murine bone marrow cell growth in culture at a dose that was toxic for the previously reported compound 4.
Prediction of similar transforming regions in simian virus 40 large T, adenovirus E1A, and myc oncoproteins (1988)

Regions containing similar elements of primary and predicted secondary structure were identified in simian virus 40 large T, adenovirus E1A, c-myc and v-myc proteins by a computer program with a set of highly specific, complex pattern descriptors. In all cases these regions were localized in domains of the respective proteins known to be required for transforming activity. We suggest that these apparently structurally similar regions may mediate a common biological function.
Debugging with reverse watchpoint (2003)

Many programmers have had to deal with an overwritten variable resulting for example from an aliasing problem. The culprit is obviously the last write-access to that memory location before the manifestation of the bug. The usual technique for removing such bugs starts with the debugger by (1) finding the last write and (2) moving the control point of execution back to that time by re-executing the program from the beginning. We call the feature to implement this process "reverse watchpoint" and believe automating it is important. In this paper we propose a new concept, "position ", that is, a point in the program execution trace, as needed for step (2) above. The position enables debuggers to automate the control of program execution to support common debugging activities. We have implemented position in Java with a bytecode transformer. Measurements show that position can be provided with an acceptable amount of overhead.
Preoperative training modifies radial maze performance in rats with ischemic hippocampal injury. (1989)

Rats exposed to 30 minutes of four-vessel occlusion reliably develop severe bilateral CA1 hippocampal injury; under certain conditions of radial maze training, such rats perform the reference memory component as well as controls yet perform the working memory component worse than controls. Reference memory is thought to depend on invariable and working memory on variable spatial information. We assessed the effect of training before ischemia. In Experiment 1, rats trained for 36 trials on 12-arm radial mazes before ischemia demonstrated a persistent impairment on the working memory task but eventually performed the reference memory task comparable to controls. Ischemic rats made more working memory errors as the number of choices increased. This pattern of working memory errors was similar to that in controls except, as expected, ischemic rats made many more errors. In Experiment 2, training for 80 trials before ischemia in rats decreased the severity of both the working and the reference memory impairment. Ischemia did not affect motor behavior in either experiment. These results characterize the working memory deficit in ischemic rats and demonstrate the importance of experimental factors, particularly in the design of treatment strategies to reduce functional impairments caused by ischemia.
Germanium-Assisted Direct Growth of Graphene on Arbitrary Dielectric Substrates for Heating Devices (2017)

Direct growth of graphene on dielectric substrates is a prerequisite to the development of graphene-based electronic and optoelectronic devices. However, the current graphene synthesis methods on dielectric substrates always involve a metal contamination problem, and the direct production of graphene patterns still remains unattainable and challenging. Herein, a semiconducting, germanium (Ge)-assisted, chemical vapor deposition approach is proposed to produce monolayer graphene directly on arbitrary dielectric substrates. By the prepatterning of a catalytic Ge layer, the graphene with desired pattern can be achieved conveniently and readily. Due to the catalysis of Ge, monolayer graphene is able to form on Ge-covered dielectric substrates including SiO<sub>2</sub> /Si, quartz glass, and sapphire substrates. Optimization of the process parameters leads to complete sublimation of the catalytic Ge layer during or immediately after formation of the monolayer graphene, enabling direct deposition of large-area and continuous graphene on dielectric substrates. The large-area, highly conductive graphene synthesized on a transparent dielectric substrate using the proposed approach has exhibited a wide range of applications, including in both defogger and thermochromic displays, as already successfully demonstrated here.
Control of a Living Radical Polymerization of Methacrylates by Light (2012)

On–off: A living radical polymerization procedure, which utilizes ppm levels of an iridium-based photoredox catalyst, affords control over chain growth through mediation by visible light (see scheme; Pn=polymer chain, X=halogen, M=monomer). This process can be activated and deactivated by light, enables control over the molecular weight and molecular weight distributions, and tolerates different functional groups. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
UDP-GlcNAc transport across the Golgi membrane: electroneutral exchange for dianionic UMP (1990)

We have examined the coupling and charge stoichiometry for UDP-GlcNAc transport into Golgi-enriched vesicles from rat liver. In the absence of added energy sources, these Golgi vesicles concentrate UDP-GlcNAc at least 20-fold, presumably by exchange with endogenous nucleotides. Under the conditions used, extravesicular degradation of UDP-GlcNAc has been eliminated, and less than 15% of the internalized radioactivity becomes associated with endogenous macromolecules. Of the remaining intravesicular label, 85% remains unmetabolized UDP-[3H]GlcNAc, and approximately 15% is hydrolyzed to [3H]GlcNAc-1-phosphate. Efflux of accumulated UDP-[3H]GlcNAc is induced by addition of UMP, UDP, or UDP-galactose to the external medium. Permeabilization of Golgi vesicles causes a rapid and nearly complete loss of internal UDP-[3H]GlcNAc, indicating that the results reflect transport and not binding. Moreover, transport of UDP-[3H]GlcNAc into these Golgi vesicles was stimulated up to 5-fold by mechanically preloading vesicles with either UDP-GlcNAc or UMP. The response of UMP/UMP exchange and UMP/UDP-GlcNAc exchange to alterations in intravesicular and extravesicular pH suggests that UDP-GlcNAc enters the Golgi apparatus in electroneutral exchange with the dianionic form of UMP.
Synthesis of nitropolychlorinated dibenzo-p-dioxins (NPCDDs) and their photochemical reaction with nucleophiles (1995)

A series of nitropolychlorodibenzo-p-dioxins (NPCDDs) was synthesized by condensation between catechols and 2,6-dinitrohalobenzene derivatives. In the presence of sodium ethoxide in anhydrous ethanol, these underwent photochemical S N 2Ar* substitutions meta to the nitro group in high chemical yield and moderate quantum yield. Both ring-opening and chloride replacement reactions were observed. The reactions involved the triplet excited state of the NPCDD, and showed a linear relationship between Φ −1 and [nucleophile] −1 . Analogous reactions with KCN in methanol showed similar behaviour, but the products could not be isolated. Keywords: photosubstitution, S N 2Ar*, dibenzo-p-dioxins.
Activation of Neutrophils and Inhibition of the Proinflammatory Cytokine Response by Endogenous Granulocyte Colony‐Stimulating Factor in Murine Pneumococcal Pneumonia (2004)

Granulocyte colony-stimulating factor (G-CSF) is considered to improve host defense during infection, via increased recruitment of and enhanced performance of neutrophils and subsequent inhibition of potentially harmful proinflammatory mediators. The present study sought to determine the role of endogenous G-CSF in host defense against pneumococcal pneumonia. Patients with unilateral community-acquired pneumonia demonstrated elevated concentrations of G-CSF in bronchoalveolar lavage fluid obtained from the infected, but not from the contralateral, site. Treatment of mice with pneumococcal pneumonia with an anti-G-CSF antibody reduced neutrophil counts in lung tissue and diminished CD11b expression on pulmonary neutrophils but increased the lung concentrations of tumor necrosis factor- alpha, interleukin-1 beta, and cytokine-induced neutrophil chemoattractant. Treatment with anti-G-CSF did not influence the outgrowth of pneumococci in lungs, the dissemination of the infection, or survival in murine pneumonia. During pneumococcal pneumonia, G-CSF is produced locally at the site of the infection, where it exerts both pro- and anti-inflammatory effects.
Influence of age and maternal antibodies on antibody responses of neonatal piglets vaccinated against Mycoplasma hyopneumoniae (2004)

Objective: To assess the relative importance of age and maternal antibodies on antibody responses of neonatal piglets to a commercial Mycoplasma hyopneumoniae vaccine. Methods: Piglets from 20 sows in each of two commercial swine operations (with serological evidence of M hyopneumoniae exposure) were vaccinated once at 2, 3, or 4 weeks of age with an M hyopneumoniae bacterin, or were nonvaccinated controls. Serum IgG antibodies were assayed by ELISA, using surface antigens of M hyopneumoniae, in serum samples collected from pigs in the first week of life and at prevaccination, 3 weeks postvaccination, and 2.5 months of age. Sows were vaccinated against M hyopneumoniae in Herd B, but not in Herd A. Results: In Herd A, piglets had moderate titers of maternal antibodies. Vaccinated pigs had significantly higher antibody responses than nonvaccinates. Higher prevaccination titers were associated with lower responses. Age at vaccination was not associated with response to vaccination. In Herd B, piglets had high titers of maternal antibodies. Antibody titers of vaccinated pigs did not decline as rapidly as those of nonvaccinated pigs, and vaccinates had higher titers at 2.5 months of age. Implications: Titer of maternal antibodies, but not age (ie, immaturity of immune function), is a major concern when piglets are vaccinated against M hyopneumoniae. Vaccination of pigs as young as 2 weeks of age may induce active antibody responses in the presence of moderate titers of maternal antibodies. Caution should be used in extrapolating these findings to other vaccines and vaccination protocols
1310nm silicon evanescent laser (2007)

We report the first 1310 nm hybrid laser on a silicon substrate. This laser operates continuous wave (C.W.) up to 105 degrees C. The room temperature threshold current of this laser is 30 mA, and the maximum single sided fiber-coupled output power is 5.5 mW.
Regulation of idiotope expression. IV. Genetic linkage of two D region-dependent T15 idiotopes to the IgH allotype. (1989)

The idiotopic (Id) repertoire of antibody response to phosphocholine was studied in mouse strains with different IgH allotypes. The T15 idiotype-bearing (T15+) serum antibody and antibody plaque-forming cells (PFC) were characterized with four monoclonal anti-Id that recognize distinct Id determinants on T15+ antibody encoded by VH-1 (of the S107 gene family), DH FL16.1, JH-1 and Vk22 germ-line genes. We have previously shown that expression of the Id designated AB1-2 and B36-82 depends on the third hypervariable loop (D region), whereas the other Id, MaId5-4 and B24-44, are influenced by VH structures outside of the D region. All four Id were expressed in the PC-response of all mouse strains tested, except the Ighj strains (C3H/HeJ, CBA/H-T6, PL/j), where the D region-dependent Id, AB1-2 and B36-82, were absent. The other Id, however, were normally expressed on individual PFC as well as the serum antibody of the Ighj strains. Expression of AB1-2 and B36-82 on 50% of PFC occurred in (BALB/c-Igha x C3H/HeJ-Ighj)F1 mice. The absence of Id correlated with a unique RFLP of the S107 gene family in Ighj strains. Finally, Id expression segregated with the appropriate RFLP pattern in individual (BALB/c x C3H/HeJ)F2 mice. These data demonstrate a selective genetic linkage of discrete T15 Id determinants, AB1-2 and B36-82 with the Igh allotype. By comparing these results with the available Ig sequences, we suggest that the Ighj allotype may be associated with an allelic form of the DH-FL16.1 segment which with VH-1, JH-1, and the Vk 22 code for the phosphocholine-specific antibody in the mouse.
On the Introduction of a Trifluoromethyl Substituent in the Epothilone Setting:  Chemical Issues Related to Ring Forming Olefin Metathesis and Earliest Biological Findings (2002)

The disclosure herein describes the synthesis of 10,11-dehydro-13,14-desoxy-27-trifluoro-[17]epothilone B via a stereoselective ring-closing metathesis and provides early biological evaluation data pertinent to this compound. [reaction: see text]